@article {pmid41062579,
year = {2025},
author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J},
title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35107},
pmid = {41062579},
issn = {2045-2322},
support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; },
mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Microbiota ; },
abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.},
}

China
*Museums
*Air Microbiology
*Bacteria/genetics/classification/isolation & purification/drug effects
Microbiota

@article {pmid41062543,
year = {2025},
author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L},
title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35039},
pmid = {41062543},
issn = {2045-2322},
mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; },
abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.},
}

Humans
*Bile Acids and Salts/blood
*Gastrointestinal Microbiome
*Crohn Disease/blood/microbiology
*Colitis, Ulcerative/blood/microbiology
Female
Male
Adult
Biomarkers/blood
Middle Aged
*Inflammation/blood
Case-Control Studies
Feces/microbiology

@article {pmid41062510,
year = {2025},
author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X},
title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8934},
pmid = {41062510},
issn = {2041-1723},
support = {R15LM013460//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; },
abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.},
}

*Deep Learning
*Proteomics/methods
*Peptides/analysis
Humans
Gastrointestinal Microbiome
Neural Networks, Computer
Databases, Protein
Metagenome

@article {pmid41062486,
year = {2025},
author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B},
title = {Node role of wild boars in virus circulation among wildlife and domestic animals.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8938},
pmid = {41062486},
issn = {2041-1723},
mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; },
abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.},
}

Animals
*Sus scrofa/virology
*Animals, Wild/virology
Swine/virology
*Animals, Domestic/virology
China/epidemiology
Disease Reservoirs/virology
Virome/genetics
Humans
*Viruses/genetics/classification/isolation & purification
*Swine Diseases/virology
Zoonoses/virology
Phylogeny

@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129125},
doi = {10.1128/spectrum.01291-25},
pmid = {41059690},
issn = {2165-0497},
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}

@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.

METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by α-diversity, β-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.

RESULTS: Overall, no significant differences in viral and bacterial α- or β-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.

CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}

Humans
*Respiratory Tract Infections/virology/microbiology/complications
*Metagenomics
Male
Middle Aged
Female
Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Virome
Bronchoalveolar Lavage Fluid/virology/microbiology
Microbiota
Aged
*Respiratory Insufficiency/virology/microbiology
Adult

@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
doi = {10.1098/rsif.2025.0183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigación/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}

*Models, Biological
*Ecosystem
Bayes Theorem
*Microbiota
Humans

@article {pmid40985550,
year = {2025},
author = {He, Y and Baltar, F and Wang, Y},
title = {Seasonal variability in community structure and metabolism of active deep-sea microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf214},
pmid = {40985550},
issn = {1751-7370},
support = {ZDSYS20230626091459009//Shenzhen Key Laboratory of Advanced Technology for Marine Ecology/ ; //National Natural Science Foundation of China/ ; },
mesh = {*Seasons ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; China ; *Microbiota ; Archaea/classification/metabolism/genetics ; Metagenome ; },
abstract = {Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA degradation and microbial community shifts. Here, we employed an in situ DNA/RNA co-extraction device to collect 18 time-series nucleic acid samples during winter and summer in the South China Sea, minimizing sampling perturbation for metatranscriptome and metagenome analyses. Between the two seasons, the prokaryotic microbiota showed seasonal variations in species composition. Burkholderiales dominated in summer, whereas Pseudomonadales, Bacillales, and Rhodobacterales were enriched in winter. However, the dominant transcriptionally active taxa affiliated with Nitrososphaerales, MGIII, SAR324, UBA11654, Marinisomatales, and Poseidoniales remained largely stable across seasons. Among eukaryotes, Ciliophora were the most active, whereas Retaria were abundant but inactive. Despite the stable active prokaryotic community, metabolic profiles differed significantly between seasons. In the winter, autotrophic microorganisms, particularly Nitrososphaerales, exhibited higher CO2 fixation activity via the 3HP/4HB cycle, accompanied by enhanced ammonia oxidation for energy generation. In addition, CO oxidation activity was also elevated. In the summer, the primary source of energy originated from heterotrophic microorganisms capable of utilizing fatty acids, benzoate, and H2, likely relying on anaerobic respiration within organic particles. This may relate to nutrient source variations as reflected by the different levels of microbial network complexity between the two seasons. Altogether, our in situ metatranscriptomes revealed the metabolic activities and adaptations of active microbial groups across seasons, providing a basis for identifying the microbial contributors to elemental cycles in the deep ocean.},
}

*Seasons
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
China
*Microbiota
Archaea/classification/metabolism/genetics
Metagenome

@article {pmid40972887,
year = {2025},
author = {Hitch, TCA and Bosch, J and Bolsega, S and Deschamps, C and Etienne-Mesmin, L and Treichel, N and Blanquet-Diot, S and Ocvirk, S and Basic, M and Clavel, T},
title = {Function-based selection of synthetic communities enables mechanistic microbiome studies.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf209},
pmid = {40972887},
issn = {1751-7370},
support = {CA23110//European Union, COST action INFOGUT/ ; 513892404//German Research Foundation/ ; 460129525//German Research Foundation/ ; NFDI4Microbiota//German Research Foundation/ ; 403224013//German Research Foundation/ ; SFB1382//German Research Foundation/ ; 395357507//German Research Foundation/ ; SFB1371//German Research Foundation/ ; 01KA2103//German Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Mice ; Humans ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; *Host Microbial Interactions ; Metagenome ; Germ-Free Life ; *Gastrointestinal Microbiome ; Colitis/microbiology ; },
abstract = {Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.},
}

Animals
Mice
Humans
*Microbiota
Inflammatory Bowel Diseases/microbiology
*Host Microbial Interactions
Metagenome
Germ-Free Life
*Gastrointestinal Microbiome
Colitis/microbiology

@article {pmid40956094,
year = {2025},
author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA},
title = {Profiling bile acids in the stools of humans and animal models of cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0145125},
pmid = {40956094},
issn = {2165-0497},
support = {ES 033988-01A1/NH/NIH HHS/United States ; 05912G223//Cystic Fibrosis Foundation/ ; T32HL134598/NH/NIH HHS/United States ; R01AI164772, U01AI163063, P30DK117469/NH/NIH HHS/United States ; P20-GM130454/NH/NIH HHS/United States ; },
mesh = {*Cystic Fibrosis/microbiology/metabolism ; Animals ; *Bile Acids and Salts/metabolism/analysis ; *Feces/chemistry/microbiology ; Humans ; Mice ; Disease Models, Animal ; Ferrets ; Male ; Gastrointestinal Microbiome ; Female ; Child ; Bacteria/classification/genetics/metabolism/isolation & purification ; Child, Preschool ; Adolescent ; },
abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with aberrant bile acid (BA) metabolism. As little is known about BA in children with CF (cwCF), we performed both comprehensive (n = 89) and focused (n = 21) BA profiling in stool of children with or without CF. Our results reveal select BA species and metabolites are significantly different between cwCF and nonCF controls. Focused BA profiling revealed a significant increase in total BA levels and selected changes in a subset of BA classes for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in this small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroidetes (lower in cwCF) phylum are consistent with prior reports. A trend was noted toward reduced abundance of bsh gene families, a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Observed modest changes in both BAs and microbial BA metabolism-related gene abundances may suggest a possible combination of defects in host and microbial BA metabolic pathways in cwCF. Fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, and while the ferret model reproduced significant differences between CF and nonCF animals, the nonCF animals showed higher levels of BA (opposite of what is observed in humans), indicating that neither model recapitulated BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF and highlight limitations of CF animal models for BA functional studies.

IMPORTANCE: Changes in the abundance and/or composition of intestinal BAs may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for cwCF. Matched metagenomic analysis suggests possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.},
}

*Cystic Fibrosis/microbiology/metabolism
Animals
*Bile Acids and Salts/metabolism/analysis
*Feces/chemistry/microbiology
Humans
Mice
Disease Models, Animal
Ferrets
Male
Gastrointestinal Microbiome
Female
Child
Bacteria/classification/genetics/metabolism/isolation & purification
Child, Preschool
Adolescent

@article {pmid40914155,
year = {2025},
author = {Muñoz, VR and Moreau, F and Soto, M and Watanabe, Y and Pham, LD and Zhong, J and Zimmerman, S and Brandao, BB and Girdhar, K and Avila, J and Pan, H and Dreyfuss, JM and Mi, MY and Gerszten, RE and Altindis, E and Kostic, A and Clish, CB and Kahn, CR},
title = {Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.},
journal = {Cell metabolism},
volume = {37},
number = {10},
pages = {2048-2065.e6},
doi = {10.1016/j.cmet.2025.08.005},
pmid = {40914155},
issn = {1932-7420},
mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; Diet, High-Fat/adverse effects ; Male ; Humans ; *Portal Vein/metabolism ; Gluconeogenesis ; Hepatocytes/metabolism/drug effects ; Vancomycin/pharmacology ; Liver/metabolism ; Obesity/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Diet and obesity contribute to insulin resistance and type 2 diabetes, in part via the gut microbiome. To explore the role of gut-derived metabolites in this process, we assessed portal/peripheral blood metabolites in mice with different risks of obesity/diabetes, challenged with a high-fat diet (HFD) + antibiotics. In diabetes/obesity-prone C57BL/6J mice, 111 metabolites were portally enriched and 74 were peripherally enriched, many of which differed in metabolic-syndrome-resistant 129S1/129S6 mice. Vancomycin treatment of HFD-fed C57BL/6J mice modified the microbiome and the portal/peripheral ratio of many metabolites, including upregulating tricarboxylic acid (TCA) cycle-related metabolites, like mesaconate, in portal blood. Treatment of isolated hepatocytes with mesaconate, itaconate, or citraconate improved insulin signaling and transcriptionally regulated genes involved in gluconeogenesis, fatty acid oxidation, and lipogenesis in vitro and in vivo. In humans, citraconate levels are inversely correlated with plasma glucose. Thus, portal versus peripheral metabolites play important roles in mediating effects of the microbiome on hepatic metabolism and the pathogenesis of HFD-related insulin resistance.},
}

Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Mice
Diet, High-Fat/adverse effects
Male
Humans
*Portal Vein/metabolism
Gluconeogenesis
Hepatocytes/metabolism/drug effects
Vancomycin/pharmacology
Liver/metabolism
Obesity/metabolism
Diabetes Mellitus, Type 2/metabolism
Anti-Bacterial Agents/pharmacology

@article {pmid40862625,
year = {2025},
author = {Ao, J and Tang, X and Li, Z and Tang, Z},
title = {Shrub encroachment alters microbial community composition and soil carbon and nitrogen cycling functional genes in northern peatlands.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0054225},
pmid = {40862625},
issn = {2165-0497},
support = {2023YFF1304604-3//National Key Research and Development Program of China/ ; XZ202401ZY0110//Key R&D Program of Tibet Autonomous Region, China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; Wetlands ; *Microbiota/genetics ; Fungi/genetics/classification/metabolism/isolation & purification ; Carbon Cycle/genetics ; Nitrogen Fixation/genetics ; Ecosystem ; },
abstract = {Changes in vegetation, such as shrub encroachment in grassland and wetland ecosystems, significantly influence soil microbial communities and biogeochemical processes. However, the specific impact of shrub encroachment on peatland ecosystems remains poorly understood. This study used a "space-for-time" approach, collecting soil samples from three encroachment stages-uninvaded, shrub invasion, and shrub invasion expansion-at two depths (0-30 cm and 30-60 cm). Metagenomic sequencing was used to assess the microbial community composition and functional gene dynamics. Shrub encroachment significantly alters soil physicochemical properties, nutrient availability, and microbial communities. Alpha diversity of bacteria and fungi was influenced by shrub encroachment and depth, whereas beta diversity varied mainly with depth. Functional carbon fixation genes (korA and pps) increased during shrub encroachment, while methane oxidation (hdrA2) and carbon degradation genes (GH31 and GH51) decreased before increasing. In addition, functional genes linked to nitrogen cycling (nifD, nifH, amoA, and amoC) declined, indicating a reduction in nitrogen fixation and nitrification pathways. Correlation and Mantel tests revealed that the total soil carbon content was the primary driver of these functional changes. These findings highlight the dynamic microbial responses to shrub encroachment and offer insights into the soil carbon and nitrogen-cycling mechanisms in peatlands.IMPORTANCEShrub encroachment is transforming peatlands and altering their ecological and biogeochemical functions. This study provides critical insights into how shrub invasion affects microbial communities and functional genes responsible for carbon and nitrogen cycling in peatland soils. By revealing the underlying genetic mechanisms, this study enhances our understanding of the consequences of vegetation shifts on ecosystem processes. These findings are essential for predicting and managing peatland responses to environmental changes, helping to preserve their role as vital carbon and nutrient reservoirs.},
}

*Soil Microbiology
*Carbon/metabolism/analysis
*Soil/chemistry
*Bacteria/genetics/classification/metabolism/isolation & purification
*Nitrogen Cycle/genetics
Nitrogen/metabolism
Wetlands
*Microbiota/genetics
Fungi/genetics/classification/metabolism/isolation & purification
Carbon Cycle/genetics
Nitrogen Fixation/genetics
Ecosystem

@article {pmid40833093,
year = {2025},
author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R},
title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0311924},
pmid = {40833093},
issn = {2165-0497},
mesh = {*Metagenomics/methods/standards ; Humans ; *High-Throughput Nucleotide Sequencing/methods/standards ; *DNA Contamination ; *Microbiota/genetics ; Workflow ; *DNA, Bacterial/genetics/isolation & purification ; Indicators and Reagents ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.},
}

*Metagenomics/methods/standards
Humans
*High-Throughput Nucleotide Sequencing/methods/standards
*DNA Contamination
*Microbiota/genetics
Workflow
*DNA, Bacterial/genetics/isolation & purification
Indicators and Reagents
Bacteria/genetics/classification/isolation & purification

@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
doi = {10.1371/journal.pone.0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}

Humans
Male
Female
*Dysbiosis/microbiology
*Ischemic Attack, Transient/microbiology
*Microbiota/genetics
Middle Aged
Case-Control Studies
Aged
*Ischemic Stroke/microbiology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Saliva/microbiology
Bacteria/genetics/classification
*Mouth/microbiology

@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
doi = {10.1371/journal.pone.0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).

METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.

RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p = 0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p = 0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p = 0.056 and 1.11 [0.58, 1.64] unadjusted p= < .001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p = 0.001 for each 10% increase in virome score).

CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}

Humans
*Cystic Fibrosis/microbiology/complications
*Microbiota
Male
Female
Adult
Sputum/microbiology
*Diabetes Mellitus/microbiology/etiology
Glucose Tolerance Test
Young Adult
Lung/microbiology
Respiratory Function Tests
Pseudomonas aeruginosa

@article {pmid40919785,
year = {2025},
author = {Zou, Y-y and Yu, B-j and He, C and Ding, L and Xu, X and Wan, J-h and Lei, Y-p and Huang, X and Xiong, H-f and He, W-h and Luo, L-y and Xia, L and Lv, N-h and Zhu, Y},
title = {Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0129925},
doi = {10.1128/spectrum.01299-25},
pmid = {40919785},
issn = {2165-0497},
support = {No.82370661//National Natural Science Foundation of China/ ; YFYKCTDPY202202//Science and Technology Innovation Team Cultivation Project of the First Affiliated Hospital of Nanchang University/ ; },
mesh = {Animals ; *Rifaximin ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; Humans ; Disease Models, Animal ; Female ; *Pancreatitis/drug therapy/microbiology/pathology ; Middle Aged ; *Inflammation/drug therapy ; Adult ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; },
abstract = {UNLABELLED: Severe acute pancreatitis (SAP) is characterized by systemic inflammation and intestinal barrier dysfunction and is often associated with gut microbiota dysbiosis. Rifaximin, a gut-specific non-absorbable antibiotic, is known to modulate the gut microbiota. Here, we investigated rifaximin's effects and mechanisms in SAP using murine models and a single-center, open-label, randomized controlled trial (Chinese Clinical Trial Registry: ChiCTR2100049794). In mice, rifaximin attenuated pancreatic injury and systemic inflammation and altered gut microbiota composition by decreasing mucin-degrading genera such as Akkermansia (P < 0.05). These protective effects persisted in antibiotic-treated and germ-free mice, suggesting mechanisms not solely dependent on gut microbiota modulation. In patients with predicted SAP (n = 60), rifaximin significantly reduced systemic inflammation compared with controls. WBC decreased from a median of 11.50 × 10[9]/L (IQR 8.76-15.68) to 8.49 × 10[9]/L (6.93-10.20; P = 0.04) and TNF-α from 15.05 pg/mL (12.73-19.75) to 11.00 pg/mL (8.74-15.40; P = 0.009). However, the incidence of culture-confirmed infection did not differ between the rifaximin and control groups (13.3% vs. 13.3%; RR, 1.00; 95% CI, 0.28-3.63). Adverse events were comparable between groups. Metagenomic analyses revealed suppression of mucin-degrading bacteria (e.g., Akkermansia, Bacteroides fragilis, and Hungatella hathewayi) (P < 0.05) and reductions in mucin-degrading carbohydrate-active enzymes, including sialidases and fucosidases. In conclusion, among patients with predicted SAP, rifaximin did not reduce culture-confirmed infectious complications within 90 days after randomization compared with standard care, despite significant improvements in systemic inflammatory markers and selected fecal microbiome features. Larger randomized controlled trials are warranted to validate these findings.

IMPORTANCE: Although rifaximin has been used to target gut-derived inflammation in other contexts, its role in SAP remains largely unexplored. In this study, rifaximin treatment was associated with reduced pancreatic injury and systemic inflammation in both murine models and patients with predicted SAP. Treatment also led to changes in gut microbial composition, notably a decrease in mucin-degrading taxa. Importantly, similar protective effects were also observed in antibiotic-treated and germ-free mice, indicating that rifaximin may act via microbiota-dependent and host-directed pathways. These findings offer novel insights into the gut-pancreas axis and suggest that rifaximin holds therapeutic potential by modulating gut microbial composition and host inflammatory responses in SAP.},
}

Animals
*Rifaximin
*Gastrointestinal Microbiome/drug effects
Mice
Male
Humans
Disease Models, Animal
Female
*Pancreatitis/drug therapy/microbiology/pathology
Middle Aged
*Inflammation/drug therapy
Adult
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Mice, Inbred C57BL
Dysbiosis/drug therapy

@article {pmid40915262,
year = {2025},
author = {Liu, S and Feng, K and Zhang, D and Liu, Y and Wang, J and Lu, B and Xing, D},
title = {Self-regulating adaptability of biofilm microbiomes enhances manganese and ammonia removal in microbial electrochemical filters under dioxane exposure.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139776},
doi = {10.1016/j.jhazmat.2025.139776},
pmid = {40915262},
issn = {1873-3336},
mesh = {*Biofilms ; *Ammonia/metabolism ; *Microbiota ; *Manganese/metabolism ; *Dioxanes ; *Water Pollutants, Chemical/metabolism ; Filtration ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Electrochemical Techniques ; Water Purification/methods ; },
abstract = {Understanding the stability and assemblage of biofilm microbiomes under oligotrophic conditions is critical for improving groundwater bioremediation. In this study, a novel microbial electrochemical filter (MEF) was developed to explore the impact of weak electrical stimulation on functional adaptability of biofilms under oligotrophic and 1,4-dioxane exposure conditions. Under 20 mg/L 1,4-dioxane stress, the MEF achieved 94.72 % manganese removal and 27.27 % ammonia nitrogen removal, while the conventional biofilter exhibited 88.76 % manganese removal with negligible ammonia nitrogen removal. Metagenomics analyses revealed that dominant populations in the MEF included Nitrospira, Bradyrhizobium, and Nitrosomonas, with relative abundance of 6.23 -10.78 %, 5.81 -6.15 %, and 1.62 -5.58 %, respectively. Weak electrical stimulation enriched the manganese oxidation-associated genes cotA, mnxG, and mcoA, whose total relative abundances being 6.3 times that of the conventional biofilter before dioxane exposure and 2.0 times after exposure. Genes encoding ammonia monooxygenase (amoABC), hydroxylamine dehydrogenase (hao) increased by 2.4- and 1.9-fold, respectively, compared to the conventional biofilter. Additionally, genes involved in the reductive tricarboxylic acid cycle and nitrogen fixation were twice as abundant in the MEF than in the conventional biofilter, suggesting enhanced nutrients availability for heterotrophic bacteria during start-up. These findings demonstrated that weak electrical stimulation effectively regulated biofilm microbiomes and enhance pollutant removal in MEF under oligotrophic conditions.},
}

*Biofilms
*Ammonia/metabolism
*Microbiota
*Manganese/metabolism
*Dioxanes
*Water Pollutants, Chemical/metabolism
Filtration
Biodegradation, Environmental
Bacteria/genetics/metabolism
Electrochemical Techniques
Water Purification/methods

@article {pmid40910779,
year = {2025},
author = {Hanawa, S and Son, A and Kato, T and Matsuo, Y and Omae, T and Omori, Y and Yoshikawa, K and Yamanegi, K and Hirota, K and Ohno, H and Ogura, H and Ishido, S and Noguchi, K and Kishimoto, H},
title = {Identification of beneficial symbiont candidates in commensalism as potential oral gatekeepers.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0158825},
doi = {10.1128/spectrum.01588-25},
pmid = {40910779},
issn = {2165-0497},
support = {JP23H05357//Japan Society for the Promotion of Science/ ; JP22K09106//Japan Society for the Promotion of Science/ ; //Hyogo College of Medicine/ ; },
mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; Microbiota ; Male ; Female ; *Mouth Neoplasms/microbiology ; Middle Aged ; Probiotics ; *Bacteria/classification/genetics/isolation & purification ; Adult ; RNA, Ribosomal, 16S/genetics ; Healthy Volunteers ; Aged ; Dysbiosis/microbiology ; },
abstract = {The basis of the development of oral cancer has been reported to be inflammation (e.g., periodontitis) caused by dysbiosis of the oral microbiota (i.e., a decrease in beneficial oral symbionts). Since a decrease in beneficial symbionts is connected to oral cancer, restoring these bacteria may help prevent it. Based on this, oral probiotics using beneficial oral symbionts are under development. Therefore, it is necessary to understand how beneficial oral symbionts are maintained in a healthy oral cavity. We evaluated a cohort consisting of 42 healthy volunteers and 39 oral cancer patients via 16S metagenomic analysis. Beneficial symbiont candidates were mined by comparing the oral microbiota of healthy volunteers with that of oral cancer patients, and the interaction mode among the beneficial symbiont candidates was further examined. Cancer patients exhibited decreased relative abundance of the genera Rothia and Streptococcus. In addition, both bacterial genera further decreased in advanced cancer, highlighting them as beneficial candidates. Furthermore, these two bacterial genera demonstrated a positive correlation in terms of relative abundance. Rothia dentocariosa isolated from a representative healthy volunteer was suggested to support the survival of Streptococcus salivarius through possible syntrophic interaction. Thus, we report a potential syntrophic interaction between Streptococcus spp. and Rothia spp. as a possible mechanism underlying oral health maintenance. Given that S. salivarius is currently employed as an oral probiotic, our findings provide insights into the development of probiotics for oral cancer.IMPORTANCEPathobiont candidates associated with oral cancer are currently being thoroughly investigated. However, it is not clear which bacteria and how their interactions contribute to preventing the development of oral cancer. In this report, we demonstrate for the first time the presence of a potential syntrophic interaction between Rothia spp. and Streptococcus spp., both of which were identified as beneficial symbiont candidates in the oral cavity.},
}

Humans
*Symbiosis
*Mouth/microbiology
Microbiota
Male
Female
*Mouth Neoplasms/microbiology
Middle Aged
Probiotics
*Bacteria/classification/genetics/isolation & purification
Adult
RNA, Ribosomal, 16S/genetics
Healthy Volunteers
Aged
Dysbiosis/microbiology

@article {pmid40886530,
year = {2025},
author = {Miao, L and Ma, T and Qi, J and Deng, Y and Hong, Y and Gong, X and Zang, H and Cheng, Y and Li, C},
title = {Deciphering intrakingdom synergism in 17β-estradiol degradation through DNA-SIP coupled metagenomics: Metabolic cooperation and niche partitioning in bioaugmented soil microbiomes.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139709},
doi = {10.1016/j.jhazmat.2025.139709},
pmid = {40886530},
issn = {1873-3336},
mesh = {Metagenomics ; *Soil Microbiology ; Biodegradation, Environmental ; *Estradiol/metabolism ; *Microbiota ; Rhodococcus/metabolism/genetics ; *Soil Pollutants/metabolism ; Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; },
abstract = {17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310-1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter, Mycobacterium, Rhodococcus, Sphingomonas, and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole timeflight mass spectrometry (HPLCQTOFMS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track [13]C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.},
}

Metagenomics
*Soil Microbiology
Biodegradation, Environmental
*Estradiol/metabolism
*Microbiota
Rhodococcus/metabolism/genetics
*Soil Pollutants/metabolism
Microbial Consortia
RNA, Ribosomal, 16S/genetics

@article {pmid40882374,
year = {2025},
author = {Chen, Y and Zhang, Y and Li, J and Li, Y and Chen, Z and Qin, J and Deng, Z and Wang, X},
title = {Fe(Ⅱ)-mediated detoxification mitigates low-dose rare earth elements-induced stress on anammox consortia for mining tailwater treatment.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139681},
doi = {10.1016/j.jhazmat.2025.139681},
pmid = {40882374},
issn = {1873-3336},
mesh = {Mining ; *Metals, Rare Earth/toxicity ; *Water Pollutants, Chemical/toxicity/metabolism ; Bioreactors ; *Microbial Consortia/drug effects ; Wastewater ; *Ferrous Compounds/chemistry ; Biodegradation, Environmental ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; Water Purification/methods ; *Iron ; },
abstract = {Rare earth mining activities cause severe nitrogen pollution in watersheds, yet the residual hazardous rare earth elements (REEs) toxicity in tailings wastewater challenges biological nitrogen removal technology. This work demonstrated that introducing low-dose Fe(II) into partial denitrification/anammox (PD/A) system significantly alleviated REEs-induced stress on anammox consortia via detoxification and physical barrier reinforcement. The PD/A bioreactor with 15 mg/L Fe(II) (R1) was compared against a control without Fe(II) for real rare earth tailings wastewater treatment. Metagenomic analysis identified 1.14-fold upregulation of hydrazine (N2H4) dehydrogenase alongside substantial 5.82-fold downregulation of N2H4 synthase in R1, indicating a critical metabolic reconfiguration that expedited the degradation of toxic intermediates and alleviated REEs-mediated cytotoxicity. Electrons with lower redox potential released from N2H4 oxidation were more effectively utilized for carbon fixation, as evidenced by the upregulated electron transport complexes and Wood-Ljungdahl pathway. Concurrent biosynthetic modulation stimulated lipopolysaccharide production (module M00063) and carbohydrate storage (module M00064), collectively reinforcing microbial stress resilience through both defensive metabolites (lipopolysaccharides and trehalose) and hydrophobicity-driven aggregation. Moreover, modified 2-P logistic modeling confirmed elevated REEs inhibition thresholds under Fe(II) mediation. This study reveals the defense mechanism of Fe(II)-enhanced anammox consortia against REEs stress, providing new insights for sustainable bioremediation in rare earth mining areas.},
}

Mining
*Metals, Rare Earth/toxicity
*Water Pollutants, Chemical/toxicity/metabolism
Bioreactors
*Microbial Consortia/drug effects
Wastewater
*Ferrous Compounds/chemistry
Biodegradation, Environmental
Waste Disposal, Fluid/methods
Oxidation-Reduction
Water Purification/methods
*Iron

@article {pmid40865218,
year = {2025},
author = {Yang, H and Fu, H and Zhao, Y and Li, R and Cao, M and Liu, Y and Ni, Y and Song, W and Liang, Y and Cai, P and Chang, W and Tao, F and Wang, H and Liu, K},
title = {Antibiotic resistance genes in multi-matrices of Chaohu Lake: Spatiotemporal variation and correlation with pesticides and PPCPs.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139604},
doi = {10.1016/j.jhazmat.2025.139604},
pmid = {40865218},
issn = {1873-3336},
mesh = {*Lakes/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; *Pesticides/analysis ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; *Genes, Bacterial ; Geologic Sediments/microbiology ; Animals ; Pharmaceutical Preparations/analysis ; Microbiota ; Spatio-Temporal Analysis ; Fishes ; China ; },
abstract = {This study explored the spatiotemporal distributions of microorganisms and antibiotic resistance genes (ARGs) in the surface water, sediments, and fish intestinal contents (IC) of Chaohu Lake, and further revealed the pharmaceuticals and personal care products (PPCPs), pesticides in lake water and their relationships with ARGs. 53 types of pesticides and 25 types of PPCPs were identified in the river-lake system basin, with the highest concentrations observed for tebuconazole (1142.36 ng/L) and amantadine (851.41 ng/L). Higher concentrations of these target contaminants were detected in the western part of the lake and during the wet season. No significant east-west differences in ARGs and microbiota across the three environmental matrices were found, whereas seasonal variations impacted lake water and IC more profoundly than sediments. Significant correlations between microbiota and ARGs in the lake water and IC, while those in sediments showed weaker associations. Co-occurrence network analysis showed, among three environmental media, β-lactam and multidrug-resistant genes were widespread found, and Proteobacteria were identified as a stable host. Non-antibiotic pollutants, such as amantadine and terbuthylazine, displayed significant positive correlations with ARGs, similar to sulfamethoxazole and clindamycin. Our findings highlight the important roles of seasonal hydrological changes and non-antibiotic pollutants in the dissemination of ARGs.},
}

*Lakes/microbiology/chemistry
*Water Pollutants, Chemical/analysis
*Pesticides/analysis
*Drug Resistance, Microbial/genetics
Environmental Monitoring
*Genes, Bacterial
Geologic Sediments/microbiology
Animals
Pharmaceutical Preparations/analysis
Microbiota
Spatio-Temporal Analysis
Fishes
China

@article {pmid40824084,
year = {2025},
author = {Li, J and Liang, L and Ye, J and Miao, Y and Zhao, K and Tian, Y and Li, X and Li, X and Chen, X and Wen, B and He, Y and Chen, B and Qin, L and Wang, Y and Fu, X},
title = {Gastric microbiota transplantation enhanced the eradication of refractory Helicobacter pylori infection by modulating the gastric microbiota: a pilot study.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0326324},
doi = {10.1128/spectrum.03263-24},
pmid = {40824084},
issn = {2165-0497},
support = {2024ZYD0144 and 24ZYZYTS0389//Central Government-Directed Project for Local Science and Technology Development/ ; 24WXXT05//Health Commission of Sichuan Province/ ; },
mesh = {Humans ; *Helicobacter Infections/therapy/microbiology ; Pilot Projects ; *Helicobacter pylori ; Male ; Middle Aged ; Female ; Adult ; Gastric Mucosa/microbiology ; *Gastrointestinal Microbiome ; Gastritis, Atrophic/therapy/microbiology ; *Stomach/microbiology ; Aged ; Dysbiosis/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {UNLABELLED: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. In this study, we investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. We performed a metagenomic analysis of the microecological systems across different regions of the stomach, including the gastric fluid (GF), the gastric mucus layer (GML), and the gastric mucosa (GM). We initiated a clinical GMT intervention by transplanting microbial communities from healthy individuals' GML into patients exhibiting refractory H. pylori infection and chronic atrophic gastritis. Our findings demonstrated significant disparities in species richness among the GF, GML, and GM, with the GML exhibiting the highest diversity of unique microbial genera. H. pylori infection primarily influenced the relative species abundance within the GML community, without altering its fundamental composition. Clinically, GMT was well-tolerated by all recipients and showed substantial synergistic efficacy against refractory H. pylori infection, achieving a 100% eradication rate in all patients, and significantly alleviating symptoms in individuals with H. pylori-positive atrophic gastritis (P < 0.05). Compared with the gastric microbiota of H. pylori-negative patients, the gastric microbiota of H. pylori-positive patients treated with GMT exhibited closer alignment with those of healthy donors. In conclusion, GMT utilizing GML enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis through modulating the gastric microbiota.

IMPORTANCE: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. We investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. GMT significantly enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis. GMT demonstrated improvements in the cure rate of refractory H. pylori infection, potentially offering a new clinical treatment approach. This finding provides new insights and a potential therapeutic direction for treating dysbiosis related chronic gastric diseases.},
}

Humans
*Helicobacter Infections/therapy/microbiology
Pilot Projects
*Helicobacter pylori
Male
Middle Aged
Female
Adult
Gastric Mucosa/microbiology
*Gastrointestinal Microbiome
Gastritis, Atrophic/therapy/microbiology
*Stomach/microbiology
Aged
Dysbiosis/therapy/microbiology
Anti-Bacterial Agents/therapeutic use

@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}

Humans
*Skin/radiation effects/microbiology/metabolism
Animals
Mice
Microbiota/radiation effects
Bioengineering
Cell Proliferation/radiation effects
Dose-Response Relationship, Radiation

@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Hippocampus/metabolism/pathology/immunology
Mice
Pregnancy
Fecal Microbiota Transplantation
*Depression/microbiology/metabolism
*Dysbiosis/microbiology/complications
Humans
Lipopolysaccharides/blood
Germ-Free Life
*Neuroinflammatory Diseases/metabolism/microbiology
Microglia
*Pregnancy Complications/microbiology
Disease Models, Animal
Behavior, Animal
Interleukin-6/metabolism
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
doi = {10.1073/pnas.2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}

Animals
*Methane/metabolism/biosynthesis
*Fermentation/drug effects
*Rumen/microbiology/metabolism
Cattle
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Animal Feed
*Ruminants/microbiology/metabolism
Microbiota/drug effects
Fatty Acids, Volatile/metabolism

@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation & purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}

Humans
*Mucormycosis/diagnosis/microbiology/drug therapy
*Mucorales/genetics/isolation & purification/classification
Male
Female
Middle Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Aged
Adult
ROC Curve
Antifungal Agents/therapeutic use
Microbiota

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}

New York City
*Metagenome
*Parks, Recreational
Metagenomics
Humans
*Seawater/microbiology
Microbiota/genetics
*Water Microbiology

@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70054},
doi = {10.1111/1755-0998.70054},
pmid = {41048034},
issn = {1755-0998},
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}

@article {pmid40966609,
year = {2025},
author = {Wu, L and Bao, D and Liao, H and Yan, M and Ge, Y and Han, Z and Xia, X},
title = {Pore-scale mass transfer heterogeneity shapes nutrient accessibility and functional assembly in porous microbial ecosystems.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf205},
pmid = {40966609},
issn = {1751-7370},
support = {2023YFF1103701//National Key Research and Development Program of China/ ; },
mesh = {*Ecosystem ; *Microbiota ; Porosity ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenomics ; Soil Microbiology ; Amino Acids/metabolism ; Biomass ; },
abstract = {Porous ecosystems represent ubiquitous microbial habitats across natural settings including soil, gut tract, and food matrices, where microscale spatial architecture critically shapes microbial colonization and interactions. Yet, the mechanisms of how pore-scale physical constraints influence microbial community assembly and metabolic performance remain poorly understood. Here, we employed a microfluidic platform with tunable inter-pillar spacings, coupled with a multi-omics approach including in situ imaging, exometabolomics, metagenomics, and metatranscriptomics, to investigate how pore-size modulates microbial community dynamics. Comparing representative small (50 μm) and large (150 μm) pore-sizes, we found that larger pore-sizes promoted greater biomass accumulation and significantly enhanced exometabolite production, particularly of amino acids. Microscopy and quantitative assays revealed that 150 μm pores facilitated more efficient substrate degradation, especially of carbohydrates. Taxonomic profiling showed that increasing pore-size reduced community evenness while enhancing richness, selectively enriching carbohydrate-degrading and amino acid-producing taxa, and promoting more complex, positively correlated co-occurrence networks. Metatranscriptomic analysis further demonstrated that larger pore-size significantly upregulated key functional genes involved in substrate degradation, amino acid biosynthesis, and stress response pathways. Fluorescent tracer assays revealed pronounced mass transfer heterogeneity, where smaller pores exhibited prolonged solute persistence and steeper chemical gradients, ultimately restricting substrate availability and microbial activity. Collectively, our results reveal that alleviation of microscale spatial constraints enhances nutrient accessibility, metabolic function, and community organization in porous ecosystems, underscoring the pivotal role of physical microstructure in regulating both the taxonomic composition and functional capacity of microbial ecosystems.},
}

*Ecosystem
*Microbiota
Porosity
*Nutrients/metabolism
*Bacteria/metabolism/genetics/classification
Metagenomics
Soil Microbiology
Amino Acids/metabolism
Biomass

@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {49},
number = {8},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
mesh = {Humans ; *Appendicitis/microbiology/diagnosis/surgery ; Prospective Studies ; Male ; Adult ; Female ; *Rectum/microbiology ; *Microbiota ; Middle Aged ; Appendectomy ; Cohort Studies ; Aged ; Young Adult ; },
abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).},
}

Humans
*Appendicitis/microbiology/diagnosis/surgery
Prospective Studies
Male
Adult
Female
*Rectum/microbiology
*Microbiota
Middle Aged
Appendectomy
Cohort Studies
Aged
Young Adult

@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}

*Bioreactors/microbiology
Anaerobiosis
*Sewage/microbiology
Methane/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Temperature
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics

@article {pmid41044404,
year = {2025},
author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL},
title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34482},
pmid = {41044404},
issn = {2045-2322},
abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.},
}

@article {pmid41044010,
year = {2025},
author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L},
title = {The untapped potential of short-read sequencing in biodiversity research.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.09.001},
pmid = {41044010},
issn = {0168-9525},
abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.},
}

@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}

*Ice Cover/microbiology/virology
*Bacteria/genetics/virology/classification
*Microbiota/genetics
*Viruses/genetics/classification/isolation & purification
Switzerland
Metagenomics/methods
Ecosystem
Host Specificity

@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Soil Microbiology
Metagenomics
*Amorphophallus/microbiology
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification

@article {pmid41039256,
year = {2025},
author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y},
title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {607},
pmid = {41039256},
issn = {1471-2180},
support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Metagenomics ; },
abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.},
}

*Soil Microbiology
*Phosphorus/metabolism
China
Soil/chemistry
Grassland
*Carbon/metabolism
Desert Climate
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Microbiota
Metagenomics

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

Animals
Larva/microbiology/growth & development
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Metagenome
*Diptera/microbiology/growth & development
Animal Feed/analysis
RNA, Ribosomal, 16S/genetics
Metagenomics
Diet
Phylogeny
Chickens

@article {pmid41039197,
year = {2025},
author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI},
title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {601},
pmid = {41039197},
issn = {1471-2180},
support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; },
mesh = {*Soil Microbiology ; South Africa ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Metagenomics ; *Microbiota ; *Fabaceae/growth & development/microbiology ; Agriculture ; Farmers ; Biodiversity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tropical Climate ; Vigna/growth & development ; },
abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.

RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.

CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.},
}

*Soil Microbiology
South Africa
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
Metagenomics
*Microbiota
*Fabaceae/growth & development/microbiology
Agriculture
Farmers
Biodiversity
Phylogeny
RNA, Ribosomal, 16S/genetics
Tropical Climate
Vigna/growth & development

@article {pmid41037127,
year = {2025},
author = {Arunrat, N and Mhuantong, W and Sereenonchai, S},
title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {102},
pmid = {41037127},
issn = {1432-184X},
support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; },
mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; },
abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.},
}

*Soil Microbiology
Thailand
*Bacteria/classification/genetics/metabolism/isolation & purification
Soil/chemistry
*Microbiota
Nitrogen/metabolism
Nitrification
*Agriculture/methods
Nitrogen Fixation
Nitrogen Cycle

@article {pmid41036626,
year = {2025},
author = {Xia, Y and Liang, L and Wang, X and Chen, Z and Liu, J and Yang, Y and Xie, H and Ding, Z and Huang, X and Long, S and Wang, Z and Xu, X and Ding, C and Chen, Q and Feng, Q},
title = {MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.},
journal = {Nucleic acids research},
volume = {53},
number = {18},
pages = {},
doi = {10.1093/nar/gkaf954},
pmid = {41036626},
issn = {1362-4962},
support = {2022YFA1304100//National Key R&D Program of China/ ; 82 270 980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; 82 202 539//National Natural Science Foundation of China/ ; 2023ZD0501406//National Science and Technology Major Program/ ; 2019//National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; #202412A001//horizontal cooperation project with Shenzhen 01 Life Institute/ ; #202112E401//horizontal cooperation project with Shenzhen 01 Life Institute/ ; },
mesh = {*Metagenomics/methods ; Workflow ; *Software ; *Metagenome/genetics ; *Microbiota/genetics ; Humans ; },
abstract = {Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.},
}

*Metagenomics/methods
Workflow
*Software
*Metagenome/genetics
*Microbiota/genetics
Humans

@article {pmid41035224,
year = {2025},
author = {Farini, A and Strati, F and Molinaro, M and Mostosi, D and Saccone, S and Tripodi, L and Troisi, J and Landolfi, A and Amoroso, C and Cassani, B and Blanco-Míguez, A and Leonetti, E and Bazzani, D and Bolzan, M and Fortunato, F and Caprioli, F and Facciotti, F and Torrente, Y},
title = {Immunoproteasome Inhibition Positively Impacts the Gut-Muscle Axis in Duchenne Muscular Dystrophy.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {16},
number = {5},
pages = {e70054},
doi = {10.1002/jcsm.70054},
pmid = {41035224},
issn = {2190-6009},
support = {M6/C2_CALL 2022//PNRR/ ; FRRB-2022//Unmet Medical Needs, Fondazione Regionale per la Ricerca Biomedica/ ; GJC21084//Cariplo Telethon Alliance GJC2021-2022/ ; //NextGenerationEU/ ; //MUR/ ; PR-0394//Gruppo familiari beta-sarcoglicanopatie/ ; PNC-E3-2022-23683266-CUP: C43C22001630001//Hub Life Science-Diagnostica Avanzata/ ; //Associazione Centro Dino Ferrari/ ; },
mesh = {Animals ; *Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Proteasome Inhibitors/pharmacology/therapeutic use ; *Muscle, Skeletal/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred mdx ; Male ; *Proteasome Endopeptidase Complex/metabolism ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Duchenne Muscular Dystrophy (DMD) features immune-muscle crosstalk, where muscle fibre degeneration enhances pro-inflammatory macrophage infiltration, worsening inflammation and impairing regeneration.

METHODS: We investigated the impact of immunoproteasome (IP) inhibition on the gut-muscle axis in mdx mice, a well-established model of DMD. We employed microbiota perturbation models, including broad-spectrum antibiotic treatment (ABX) and faecal microbiota transplantation (FMT) from IP-inhibited mdx mice. IP inhibition effects were assessed by analysing gut microbiota composition, intestinal inflammation, muscle integrity and associated metabolic and inflammatory pathways.

RESULTS: IP inhibitor ONX-0914 significantly impacted the intestinal inflammatory microenvironment and gut microbiota of mdx mice. ONX-0914 treatment increased gastrointestinal transit (increased wet/dry faecal weights, p = 0.0486 and p = 0.0112, respectively) and partially restored intestinal barrier integrity (reduced FITC-dextran leakage, p = 0.0449). JAM-A was significantly upregulated (p < 0.0001). Colonic CD206+ M2 macrophages increased, while CD68 + M1 cells partially decreased. ONX-0914 downregulated IP isoforms in macrophages (PSMB8: p = 0.0022; PSMB9: p = 0.0186) as well as FOXO-1 (p = 0.0380) and TNF-α (p = 0.0487). Antibiotic-induced microbiota depletion abrogated these effects. Metagenomic analysis revealed significant differences in microbiota composition between C57Bl controls and mdx mice (PERMANOVA p < 0.001), with ONX-0914 inducing enrichment of stachyose degradation pathways. Metabolomic analysis showed enrichment of bacterial metabolites, fatty acid and sugar metabolism pathways, with increased glutathione, galactose, glycerol, glyceraldehyde and TCA cycle intermediates. ONX-0914 improved mitochondrial activity in skeletal muscle, as increased expression of ETC complexes (mdx vs. mdx+ONX: Complex II, p = 0.0338; Complex IV, p = 0.0023) and TCA enzymes (mdx vs. FTMmdx+ONX: IDH p = 0.0258; FH p = 0.0366). This led to a shift towards oxidative muscle fibres and improved muscle morphology (increased fibre size, p < 0.0001 mdx vs. mdx+ONX and mdx vs. FTMmdx+ONX). Muscle performance was enhanced with reduced CPK levels (p = 0.0015 mdx vs. mdx+ONX) and fibrosis (decreased TGFβ: mdx vs. mdx+ONX, p = 0.0248; mdx vs. FTMmdx+ONX, p = 0.0279). ONX-0914 reduced CD68+ (mdx vs. mdx+ONX, p = 0.0024; mdx vs. FTMmdx+ONX, p < 0.0001) and increased CD206+ (mdx vs. FTMmdx+ONX: p = 0.0083) macrophages in muscle, downregulated inflammatory genes (mdx vs. mdx+ONX: ccl2 p = 0.0327, vcam-1p = 0.0378) and reduced pro-inflammatory proteins (MCP1, mdx vs. mdx+ONX, p = 0.0442). Inflammatory cytokines and endothelial vessel density in ONX-0914 treated mdx were restored to wild type mice. These data demonstrate that ONX-0914 enhances muscle function through microbiota-dependent mechanisms.

CONCLUSIONS: Our study advances the understanding of the role of dysbiosis in DMD disease and identifies IP inhibition as a potential therapeutic strategy to modulate the dystrophic gut-muscle axis, offering new perspectives for microbiota-targeted therapies.},
}

Animals
*Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology
Mice
Gastrointestinal Microbiome/drug effects
*Proteasome Inhibitors/pharmacology/therapeutic use
*Muscle, Skeletal/drug effects/metabolism
Disease Models, Animal
Mice, Inbred mdx
Male
*Proteasome Endopeptidase Complex/metabolism
Mice, Inbred C57BL

@article {pmid41034963,
year = {2025},
author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL},
title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {199},
pmid = {41034963},
issn = {2049-2618},
support = {Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; DBI 20222070//National Science Foundation/ ; 1K08ES034821-01A1/NH/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.

RESULTS: In relation to urine sample volume, ≥ 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.

CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.},
}

*Metagenomics/methods
Animals
Dogs
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Humans
Metagenome
*Microbiota/genetics
DNA, Bacterial/genetics
*Urinary Tract/microbiology
*Urine/microbiology
Gastrointestinal Microbiome/genetics

@article {pmid41006832,
year = {2025},
author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ},
title = {A roadmap for equitable reuse of public microbiome data.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2384-2395},
pmid = {41006832},
issn = {2058-5276},
support = {CTC 1439/2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; MO3498/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OCE-2049445//National Science Foundation (NSF)/ ; },
mesh = {*Microbiota/genetics ; *Information Dissemination/methods ; Humans ; },
abstract = {Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates that the data creators prefer to be contacted before data reuse, and simultaneously provides data consumers with a mechanism to get in touch with the data creators. The DRI aims to facilitate and foster collaborations, and serve as a guideline that can be expanded to other data types.},
}

*Microbiota/genetics
*Information Dissemination/methods
Humans

@article {pmid40987851,
year = {2025},
author = {Du, LF and Shi, W and Cui, XM and Fan, H and Jiang, JF and Bian, C and Ye, RZ and Wang, Q and Zhang, MZ and Yuan, TT and Xia, LY and Ruan, XD and Chang, QC and Du, CH and Que, TC and Wang, X and Han, XH and Yang, TC and Jiang, BG and Chen, JY and Wang, XR and Tan, LF and Liu, YW and Deng, LL and Liu, Y and Zhu, Y and Pan, YS and Wang, N and Lin, ZT and Li, LF and Li, C and Shen, SJ and Liu, YT and Tian, D and Han, XY and Wang, J and Wang, YF and Gao, WY and Li, YY and Xiong, T and Wang, TH and Shi, XY and Zhu, DY and Zhu, JG and Wang, CC and Shi, WQ and Zhan, L and Liu, ZH and Feng, D and Zhao, L and Sun, Y and , and Wang, J and Jia, N and Zhao, F and Cao, WC},
title = {Genome-resolved metagenomics reveals microbiome diversity across 48 tick species.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2631-2645},
pmid = {40987851},
issn = {2058-5276},
support = {2019YFC1200501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025009//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Ticks/microbiology/classification/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; China ; Symbiosis ; Tick-Borne Diseases ; Genome-Wide Association Study ; Host Microbial Interactions/genetics ; Host-Pathogen Interactions/genetics ; },
abstract = {Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host-microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.},
}

Animals
*Metagenomics/methods
*Ticks/microbiology/classification/genetics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*Genome, Bacterial
Phylogeny
China
Symbiosis
Tick-Borne Diseases
Genome-Wide Association Study
Host Microbial Interactions/genetics
Host-Pathogen Interactions/genetics

@article {pmid40935925,
year = {2025},
author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y},
title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2396-2411},
pmid = {40935925},
issn = {2058-5276},
support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Phenazines/metabolism/pharmacology ; Rhizosphere ; *Microbiota/drug effects ; Bacillus subtilis/drug effects/genetics/enzymology ; *DNA Topoisomerase IV/metabolism/antagonists & inhibitors/genetics ; Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; *Bacteria/genetics/classification/metabolism/drug effects ; Fusarium/drug effects ; Pseudomonas/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Genome, Bacterial ; DNA Damage/drug effects ; Metagenomics ; },
abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.},
}

*Phenazines/metabolism/pharmacology
Rhizosphere
*Microbiota/drug effects
Bacillus subtilis/drug effects/genetics/enzymology
*DNA Topoisomerase IV/metabolism/antagonists & inhibitors/genetics
Plant Diseases/microbiology/prevention & control
Soil Microbiology
*Bacteria/genetics/classification/metabolism/drug effects
Fusarium/drug effects
Pseudomonas/metabolism/genetics
Bacterial Proteins/metabolism/genetics
Genome, Bacterial
DNA Damage/drug effects
Metagenomics

@article {pmid40921745,
year = {2025},
author = {Zhang, X and Li, Y and Qin, Y and Liao, Z and Deng, C and Chen, Y and Li, Y and Qian, H and He, Y and Chen, S and Shi, G and Liu, Y},
title = {Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren's disease.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2591-2602},
pmid = {40921745},
issn = {2058-5276},
support = {82471833//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101841//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171779//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82371802//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023J06055//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; 2022XMSLCYX01//Xiamen Municipal Bureau of Science and Technology (Xiamen Science and Technology Bureau)/ ; },
mesh = {*Capsid Proteins/immunology/genetics ; *Sjogren's Syndrome/immunology/virology ; Humans ; *Autoantigens/immunology ; *Molecular Mimicry/immunology ; Animals ; Mice ; Female ; *Autoimmunity ; Saliva/virology ; Autoantibodies/immunology/blood ; Middle Aged ; Male ; Adult ; Virome ; },
abstract = {Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren's disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion of Siphoviridae bacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry.},
}

*Capsid Proteins/immunology/genetics
*Sjogren's Syndrome/immunology/virology
Humans
*Autoantigens/immunology
*Molecular Mimicry/immunology
Animals
Mice
Female
*Autoimmunity
Saliva/virology
Autoantibodies/immunology/blood
Middle Aged
Male
Adult
Virome

@article {pmid40819273,
year = {2025},
author = {Puranik, S and Mekali, J and Damodaram, KJP},
title = {Seed Biopriming From Basics to Omics: Relieving Plants From Biotic Stress Through the Microbial Way.},
journal = {Journal of basic microbiology},
volume = {65},
number = {10},
pages = {e70083},
doi = {10.1002/jobm.70083},
pmid = {40819273},
issn = {1521-4028},
mesh = {*Seeds/microbiology/growth & development ; *Stress, Physiological ; *Crops, Agricultural/microbiology/growth & development ; Plant Diseases/prevention & control/microbiology ; Rhizosphere ; Animals ; Metabolomics ; Proteomics ; Microbiota ; Plant Development ; *Agricultural Inoculants/physiology ; Metagenomics ; Plant Growth Regulators/metabolism ; },
abstract = {From seed to harvest, cultivated crops face numerous biotic stresses, including insects, nematodes, and diseases, which significantly hinder their growth and vigor, resulting in substantial crop losses. In contrast to use of toxic agrochemicals, seed biopriming with microbial inoculants has emerged as an effective and eco-friendly alternative against pathogens and pests. Seed biopriming involves coating seeds with beneficial microorganisms that enhance protection and immunity against a variety of harmful pests and pathogens. These microbial agents colonize the seeds and establish themselves in the rhizosphere, reducing the impact of biotic stresses while fostering a healthier environment for plant growth. They are known to exhibit several mechanisms against pathogens and pests, like production of cell wall degrading enzymes, antibiosis, competition, induced systemic resistance, chelation of iron etc. Additionally, these microorganisms regulate phytohormone levels, further optimizing the physiological and metabolic characteristics of plants. This approach not only promotes robust plant growth but also enhances tolerance to deleterious bacteria, fungi, nematodes and arthropods, ensuring healthier crops. These interactions can further be well studied and expressed by using different omics approaches like metagenomics (of seed microbiome), proteomics, transcriptomics, metabolomics and differential gene expression. This review highlights the role and benefits of seed biopriming as a sustainable strategy to manage biotic stresses effectively, and the importance of omics for better understanding of complex processes during such interactions, contributing to resilient agricultural production systems and environmental sustainability.},
}

*Seeds/microbiology/growth & development
*Stress, Physiological
*Crops, Agricultural/microbiology/growth & development
Plant Diseases/prevention & control/microbiology
Rhizosphere
Animals
Metabolomics
Proteomics
Microbiota
Plant Development
*Agricultural Inoculants/physiology
Metagenomics
Plant Growth Regulators/metabolism

@article {pmid41030387,
year = {2025},
author = {Zheng-Qiang, L and Jun, L and Rui, A and Rui, L and Wei, D and Ping, M and Xu, Y and Rong, S and Xiao-Yan, Y and Wen, X},
title = {A probiotic for preventing microplastic toxicity: Clostridium dalinum mitigates microplastic-induced damage via microbiota-metabolism-barrier interactions.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101200},
pmid = {41030387},
issn = {2665-9271},
abstract = {Microplastics (MPs) are widely distributed and accumulated in the environment, making it nearly impossible for humans to avoid ingestion. Their toxicity can cause serious health damage and pose a threat to human health. In this context, developing strategies to prevent and restore toxic damage from their ingestion is extremely urgent. This study comprehensively employs various techniques, including metagenomics and metabolomics, to explore the pre-protective and restorative effects of Clostridium dalinum, a potential probiotic with excellent antioxidant and anti-inflammatory capabilities, on damage induced by exposure to polystyrene microplastics (PS-MPs) in mice. The results show that exposure to PS-MPs leads to significant intestinal damage in mice; preemptive intake of C. dalinum for pre-protection, or post-exposure intake of C. dalinum for restorative treatment, both significantly reduced the damage caused by MPs exposure, as evidenced by changes in intestinal length (PS-MPs exposure vs C. dalinum pre-protection vs C. dalinum restoration vs control = 36.55 vs 39.94 vs 40.12 vs 41.05 cm), barrier protein content (27.12 % vs 97.28 % vs 97.73 % vs 100.00 %), and inflammation levels (284.56 % vs 101.05 % vs 98.17 % vs 100.00 %). Mechanistically, the pre-protective and restorative effects of C. dalinum both rely on upregulating the expression of barrier proteins such as ZO-1 and Occludin and inhibiting the TLR4/NF-κB inflammatory signaling pathway. Meanwhile, the two intervention modes also exhibit specific mechanisms: in the pre-protection mode, C. dalinum enhances lipid metabolic balance and antioxidant reserves by pre-activating the PPARγ/GPR43 pathway, and enriches the ABC transporters pathway to promote toxin efflux capacity, thereby preventing PS-MPs-induced damage; in the restoration mode, C. dalinum repairs intestinal damage by enriching the beneficial bacterium Lachnospiraceae NK4A136 and inhibiting the pro-inflammatory bacterium Desulfovibrio, and regulating intestinal metabolites. In summary, this study is the first to confirm that C. dalinum can effectively prevent and restore intestinal damage caused by PS-MPs exposure through the synergistic pathway of "microbiota-metabolism-barrier". Importantly, this study is the first to reveal the potential and unique mechanisms of probiotics in preventing and restoring MPs exposure toxicity, providing a theoretical basis for the future development of probiotic-based defense strategies.},
}

@article {pmid41029845,
year = {2025},
author = {Rey-Velasco, X and Auladell, A and Deulofeu-Capo, O and Lundin, D and Pinhassi, J and Ferrera, I and Sánchez, O and Gasol, JM},
title = {Decoding the genetic drivers of marine bacterial blooms through comparative genomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {198},
pmid = {41029845},
issn = {2049-2618},
support = {PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; PID2021-125469NB-C31//Ministerio de Ciencia e Innovación/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; SPIP2020-02595//Ministerio para la Transición Ecológica y el Reto Demográfico/ ; FPU20/01625//Ministerio de Universidades/ ; },
mesh = {*Bacteria/genetics/classification/growth & development/isolation & purification ; *Genome, Bacterial ; *Seawater/microbiology ; *Genomics/methods ; *Microbiota/genetics ; Phytoplankton ; Metagenome ; Eutrophication ; Metagenomics/methods ; },
abstract = {BACKGROUND: While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as "bloomers," have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.

RESULTS: We tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.

CONCLUSIONS: In this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.},
}

*Bacteria/genetics/classification/growth & development/isolation & purification
*Genome, Bacterial
*Seawater/microbiology
*Genomics/methods
*Microbiota/genetics
Phytoplankton
Metagenome
Eutrophication
Metagenomics/methods

@article {pmid41029787,
year = {2025},
author = {Lemieux, É and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, É and Fournaise, S and Vincent, AT},
title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {402},
pmid = {41029787},
issn = {1756-0500},
support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; },
abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.

RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both α- and β-diversity between sample types (digesta, feces) than between treatments. β-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. β-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Swine/microbiology
*Bacteriophages/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Feces/microbiology/virology
Cross-Over Studies

@article {pmid41028378,
year = {2026},
author = {Sahil, R and Jain, M},
title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2977},
number = {},
pages = {181-196},
pmid = {41028378},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; },
abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.},
}

*Microbiota/genetics
*Metagenomics/methods
*Fabaceae/microbiology/genetics
*Computational Biology/methods
Data Analysis
Metagenome
Multiomics

@article {pmid40958146,
year = {2025},
author = {Yang, Q and Liu, J and Lyu, S and Li, S and Han, Q and Ma, C and Du, Z and Zhang, T},
title = {Ovalbumin Peptides Restore Intestinal Barrier Integrity via Gut-Liver Axis Modulation of Bile Salt Hydrolase and Bile Acids Crosstalk.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {39},
pages = {24741-24752},
doi = {10.1021/acs.jafc.5c07236},
pmid = {40958146},
issn = {1520-5118},
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Ovalbumin/chemistry/administration & dosage ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Male ; *Amidohydrolases/metabolism/genetics ; Humans ; *Intestinal Mucosa/metabolism/drug effects ; *Peptides/administration & dosage/chemistry ; *Colitis/metabolism/drug therapy/microbiology/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fibroblast Growth Factors/metabolism/genetics ; *Inflammatory Bowel Diseases/metabolism/drug therapy/microbiology/genetics ; Mucin-2/genetics/metabolism ; Tumor Necrosis Factor-alpha/genetics/metabolism ; },
abstract = {Inflammatory bowel disease (IBD) is characterized by intestinal barrier dysfunction and bile acid (BA) dysmetabolism. BA metabolism was a pivotal regulator in the "gut-liver axis" to maintain intestinal homeostasis. Ovalbumin-derived peptides (OVA-Ps) exhibit potential in barrier repair; however, their systemic mechanisms within the microbiota-BA-host network remain underexplored. This study investigates the therapeutic potential of the oligomer OVA-P in a DSS-induced colitis mouse model. OVA-P administration significantly alleviated colitis symptoms, restored colon length, reduced pro-inflammatory cytokines (tumor necrosis factor-α), and enhanced antioxidant markers (SOD). Mechanistically, the OVA-P reshaped gut microbiota composition, suppressed bile salt hydrolase (BSH), and elevated conjugated BAs (e.g., taurocholic acid) levels. These changes activated the farnesoid X receptor (FXR) pathway, upregulating tight junction protein (ZO-1), and mucin (MUC-2) expression, thereby restoring intestinal barrier integrity. Metabolomic and metagenomic analyses confirmed the OVA-P-mediated modulation of the gut-liver axis through FXR-SHP/FGF15 signaling, highlighting its role in maintaining BA homeostasis. These findings provide insights into the use of OVA-P as a dietary intervention for IBD by targeting microbiota-BA-FXR interactions, offering a foundation for high-value egg protein applications in functional foods.},
}

Animals
*Bile Acids and Salts/metabolism
Mice
Gastrointestinal Microbiome/drug effects
*Ovalbumin/chemistry/administration & dosage
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Male
*Amidohydrolases/metabolism/genetics
Humans
*Intestinal Mucosa/metabolism/drug effects
*Peptides/administration & dosage/chemistry
*Colitis/metabolism/drug therapy/microbiology/genetics
Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Fibroblast Growth Factors/metabolism/genetics
*Inflammatory Bowel Diseases/metabolism/drug therapy/microbiology/genetics
Mucin-2/genetics/metabolism
Tumor Necrosis Factor-alpha/genetics/metabolism

@article {pmid40925130,
year = {2025},
author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ},
title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {9},
pages = {103659},
doi = {10.1016/j.jpet.2025.103659},
pmid = {40925130},
issn = {1521-0103},
mesh = {*Lupus Erythematosus, Systemic/microbiology/immunology/therapy/drug therapy ; Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation/methods ; Dysbiosis/immunology ; },
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.},
}

*Lupus Erythematosus, Systemic/microbiology/immunology/therapy/drug therapy
Humans
*Gastrointestinal Microbiome/drug effects/immunology
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation/methods
Dysbiosis/immunology

@article {pmid40794770,
year = {2025},
author = {Chia, M and Pop, M and Salzberg, SL and Nagarajan, N},
title = {Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.},
journal = {Cancer research},
volume = {85},
number = {19},
pages = {3584-3595},
pmid = {40794770},
issn = {1538-7445},
support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; OFYIRG21nov-0024//National Medical Research Council (NMRC)/ ; R35-GM130151//National Institute of General Medical Sciences (NIGMS)/ ; R01-HG006677//National Human Genome Research Institute (NHGRI)/ ; NRFI09-0015//National Research Foundation Singapore (NRF)/ ; },
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; },
abstract = {The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research holds promise for identifying noninvasive biomarkers and possibly new paradigms for cancer treatment. In this review, we explore the key computational challenges and opportunities in analyzing cancer-associated microbiomes (in tumor/normal tissues and other body sites, e.g., gut, oral, and skin), focusing on sequencing-driven strategies and associated considerations for taxonomic and functional characterization. The discussion covers the strengths and limitations of current analysis tools for identifying contamination, determining compositional bias, and resolving species and strains, as well as the statistical, metabolic, and network inferences that are essential to uncover host-microbiome interactions. Several key considerations are required to guide the choice of databases used for metagenomic analysis in such studies. Recent advances in spatial and single-cell technologies have provided insights into cancer-associated microbiomes, and Artificial Intelligence-driven protein function prediction might enable rapid advances in this field. Finally, we provide a perspective on how the field can evolve to manage the ever-growing size of datasets and generate robust and testable hypotheses. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .},
}

Humans
*Neoplasms/microbiology
*Microbiota
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods

@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}

Animals
*Gastrointestinal Microbiome
*Bacteriophages/genetics/classification/physiology/isolation & purification
*Bacteria/classification/genetics/isolation & purification/virology
*Ecosystem
RNA, Ribosomal, 16S/genetics
*Antelopes/microbiology/virology
Metagenome
Feces/microbiology

@article {pmid41026152,
year = {2025},
author = {Nassirnia, S and Scherz, V and Greub, G and Caruana, G and Taffé, P and Jaton, K and Papis, S and Posfay-Barbe, KM and Mornand, A and Rochat-Guignard, I and Bertelli, C and Asner, SA},
title = {Concordance between upper and lower airway microbiota in children with cystic fibrosis.},
journal = {Journal of medical microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002079},
pmid = {41026152},
issn = {1473-5644},
mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Adolescent ; Longitudinal Studies ; *Respiratory System/microbiology ; Metagenomics ; Infant ; },
abstract = {Introduction. Sputum is the most used sample type to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate.Hypothesis. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.Aim. We aimed to compare bacterial community diversity and composition between sputum and throat swabs in the full cohort and in patients with paired samples from the same visit.Methodology. The prospective longitudinal multicentre MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.Results. Sputum and throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen's kappa: 0.6). Differences in bacterial abundance were observed (P=0.001), but not presence/absence (P=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swab microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (adjusted Rand index=0.08 and 0.10). The average beta-diversity distances between samples collected from the same visit were shorter (0.505±0.056 95% confidence interval), compared with sputum (0.695±0.017) or throat swab (0.704±0.045) from the same patient collected during different visits.Conclusion. Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.},
}

Humans
*Cystic Fibrosis/microbiology
*Sputum/microbiology
*Microbiota
Child
*Pharynx/microbiology
Male
Female
*Bacteria/classification/genetics/isolation & purification
Prospective Studies
RNA, Ribosomal, 16S/genetics
Child, Preschool
Adolescent
Longitudinal Studies
*Respiratory System/microbiology
Metagenomics
Infant

@article {pmid40940575,
year = {2025},
author = {Abenaim, L and Mercati, D and Mandoli, A and Carpentier, J and Noël, G and Conti, B and Caparros Megido, R and Dallai, R},
title = {Exploring the plastivorous activity of Hermetia illucens (Diptera Stratiomyidae) larvae.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {36},
pages = {21649-21665},
pmid = {40940575},
issn = {1614-7499},
mesh = {Animals ; Larva ; *Diptera ; Biodegradation, Environmental ; Gastrointestinal Microbiome ; },
abstract = {Hermetia illucens (Diptera Stratiomyidae), also known as Black Soldier Fly (BSF), is one of the insect species most investigated for biodegradation ability in its larvae. H. illucens larvae can biodegrade organic waste but also contaminants like pesticides, antibiotics, and mycotoxins. This study wants to investigate the ability of these larvae to degrade polystyrene (PS). Experiments evaluated the growth performance, survival rates, intestinal and intracellular morphological alterations, degradation by-product formation and intestinal microbiota alterations of larvae fed a PS-enriched diet. Despite the addition of PS microparticles, no significant differences in growth or survival were observed compared to the standard diet (p > 0.05). Confocal Laser Scanning Microscopy and Transmission Electron Microscopy confirmed the presence of PS microparticles in the larval gut, with potential signs of biodegradation. Metabolomic analyses identified styrene in the gut after 1 and 3 days of PS feeding, but its occurrence was likely due to thermal depolymerisation of the PS microparticles under GC-MS conditions. Metagenomic analysis revealed significant shifts in the intestinal microbiota. Notably, an enrichment of Corynebacterium, known for its role in aerobic PS degradation, and the abundance increase of other genera (Enterococcus, Enterobacteriaceae, Enterobacter, and Escherichia-Shigella) associated with synthetic polymer metabolism was observed. These results confirm the potential of BSF larvae to manage plastic waste through the interaction between their gut microbiota and synthetic materials. This study provides a foundation for future research focusing on isolating bacterial communities and enzymatic processes involved in polymer degradation, aiming to develop sustainable strategies for plastic waste management.},
}

Animals
Larva
*Diptera
Biodegradation, Environmental
Gastrointestinal Microbiome

@article {pmid40037519,
year = {2025},
author = {Jawale, N and Shenberger, JS and Rodriguez, RJ and Shetty, AK and Garg, PM},
title = {The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis.},
journal = {American journal of perinatology},
volume = {42},
number = {14},
pages = {1836-1845},
pmid = {40037519},
issn = {1098-8785},
support = {U54 GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428//NIGMS of the NIH/ ; },
mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/virology ; Infant, Newborn ; *Gastrointestinal Microbiome ; Infant, Premature ; Dysbiosis/microbiology ; Bacteriophages ; *Infant, Premature, Diseases/microbiology ; Mycobiome ; Virome ; Virus Diseases/complications ; },
abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..},
}

Humans
*Enterocolitis, Necrotizing/microbiology/virology
Infant, Newborn
*Gastrointestinal Microbiome
Infant, Premature
Dysbiosis/microbiology
Bacteriophages
*Infant, Premature, Diseases/microbiology
Mycobiome
Virome
Virus Diseases/complications

@article {pmid41025248,
year = {2025},
author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK},
title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {9},
pages = {e2507003},
doi = {10.71150/jm.2507003},
pmid = {41025248},
issn = {1976-3794},
support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.},
}

Animals
*Microbiota/genetics
*DNA, Bacterial/isolation & purification/genetics
*Aquatic Organisms/microbiology
*Bacteria/genetics/isolation & purification/classification
*Porifera/microbiology
Symbiosis
Republic of Korea
*Invertebrates/microbiology
Anthozoa/microbiology
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction

@article {pmid41024767,
year = {2025},
author = {Ezzat, WM},
title = {Machine learning as an artificial intelligence application in management of chronic hepatitis B virus infection.},
journal = {World journal of gastroenterology},
volume = {31},
number = {35},
pages = {109776},
doi = {10.3748/wjg.v31.i35.109776},
pmid = {41024767},
issn = {2219-2840},
mesh = {Humans ; *Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Hepatitis B virus/pathogenicity ; Algorithms ; Artificial Intelligence ; Antiviral Agents/therapeutic use ; Supervised Machine Learning ; },
abstract = {Let's review the role of gut microbiota in pathogenesis of chronic hepatitis B infection as addressed in by Zhu et al. Zhu et al used high-throughput technology to characterize the microbial ecosystems, which led to an explosion of various types of molecular profiling data, such as metagenomics, metatranscriptomics, and metabolomics. To analyze such data, machine learning (ML) algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and, particularly, for generating models that can accurately predict phenotypes. Strong evidence suggests that such gut microbiome-based stratification could guide customized interventions to benefit human health. Supervised learning includes designing an algorithm to fix a pre-identified problem. To get an answer, ML software must access data that have been nominated. On the other hand, unsupervised learning does not address any pre-defined problems. Bias should be eliminated as much as possible. In unsupervised learning, an ML algorithm works to identify data patterns without any prior operator input. This can subsequently lead to elements being identified that could not be conceived by the operator. At the intersection between supervised and unsupervised learning is semi-supervised ML. Semi-supervised learning includes using a partially labeled data set. The ML algorithm utilizes unsupervised learning to label data (that has not yet been labelled) by drawing findings from the labeled data. Then, supervised techniques can be used to solve defined problems involving the labeled data. Reinforcement learning, which is similar to supervised learning in the meaning, is goal-oriented. Reinforcement learning does not need labeled data, instead, it is provided with a set of regulations on a problem. An algorithm will carry out operations to try to answer questions involving the problem. Based on obtained data of gut microbiota, various therapeutic modalities can be applied: Prebiotics, probiotics, postbiotics, engineered bacteria, bacteriophage, and novel microbe-materials therapeutic system and fecal transplantation. In conclusion, ML is an artificial intelligence application that helps in providing new perspectives on tailored therapy. Furthermore, assessing the impact of gut microbiota modification is a critical step in advanced liver disease management. These new artificial intelligence techniques although promising, still require further analysis and validation in future studies.},
}

Humans
*Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology
*Machine Learning
*Gastrointestinal Microbiome
*Hepatitis B virus/pathogenicity
Algorithms
Artificial Intelligence
Antiviral Agents/therapeutic use
Supervised Machine Learning

@article {pmid41024212,
year = {2025},
author = {Wang, Y and Gong, L and Dong, D and Li, X},
title = {Metagenomic binning reveals community and functional characteristics of sulfur- and methane-oxidizing bacteria in cold seep sponge ground.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {122},
pmid = {41024212},
issn = {2524-6372},
support = {KEXUE2020GZ01//The Senior User Project of R/V Kexue/ ; 42176114//The National Natural Science Foundation of China/ ; ZR2023MD100//Natural Science Foundation of Shandong Province/ ; },
abstract = {BACKGROUND: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.

RESULTS: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.

CONCLUSIONS: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.},
}

@article {pmid41023790,
year = {2025},
author = {Cao, L and Sun, H and Wang, Y and Wei, Z and Zhang, J and Wang, Y and Yan, J and Zhu, Y and Cheng, N and He, S and Liu, X and Li, T and Wang, M and Li, E},
title = {Comparative analysis of metagenomics between high- and medium-temperature daqu, and microbial succession in Jiang-Nong Jianxiang Baijiu fermentation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {852},
pmid = {41023790},
issn = {1471-2164},
mesh = {*Fermentation ; *Metagenomics/methods ; *Alcoholic Beverages/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Temperature ; Phylogeny ; },
abstract = {BACKGROUND: The mixture of high-temperature Daqu and medium-temperature Daqu can be used to produce Chinese Jiang-Nong Jianxiang Baijiu. This study used metagenomic sequencing and physicochemical analysis to investigate the microbial community and functionality of high-temperature Daqu and medium-temperature Daqu. In addition, exploring the changes of microbial communities during the Jiang-Nong Jianxiang Baijiu fermentation process.

RESULTS: The results showed that Lichtheimia ramose and Saccharopolyspora rectivirgula were the significantly different species in high-temperature Daqu. However, Paecilomyces variotii, Aspergillus chevalieri, and Rasamsonia emersonii were the significantly different species in medium-temperature Daqu. The medium-temperature Daqu had higher saccharifying power (101.20 ± 1.85 U/g) than high-temperature Daqu (60.00 ± 0.58 U/g). And the protease activity of high-temperature Daqu (62.47 ± 5.84 U/mg) was significantly higher than medium-temperature Daqu (36.10 ± 1.13 U/mg). The community structure analysis results of the stack fermentation stage showed that the mixture of high-temperature Daqu and medium-temperature Daqu inherited the community advantages of both high-temperature Daqu and medium-temperature Daqu. With Jiang-Nong Jianxiang Baijiu fermentation, the significantly different species changed from Pichia sp., Acetobacter sp., and Lactobacillus sp. to Pediococcus sp., Lactobacillus sp., Lentilactobacillus sp., Saccharomyces sp., Thermoactinomyces sp., and Saccharopolyspora sp., implying the importance of acid-resistant and ethanol-resistant microorganisms for the production of flavor substances in the late Baijiu fermentation.

CONCLUSIONS: Our research revealed the difference in microbial communities between high-temperature Daqu and medium-temperature Daqu, and demonstrated the shifts and functionality of microbiota during Jiang-Nong Jianxiang Baijiu fermentation. This study provides a theoretical reference for utilizing core synergistic microbiota and their functional traits in Baijiu fermentation starters to improve Baijiu quality.},
}

*Fermentation
*Metagenomics/methods
*Alcoholic Beverages/microbiology
*Microbiota
*Bacteria/genetics/classification
Temperature
Phylogeny

@article {pmid41023192,
year = {2025},
author = {Vishal, V and Thakur, P and Tigga, SS and Lal, S},
title = {A metagenomic assessment of overburden dump of coal mine soil bacterial consortium from Jharkhand, India.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1161},
pmid = {41023192},
issn = {1573-2959},
mesh = {*Soil Microbiology ; India ; *Bacteria/classification/genetics ; *Coal Mining ; *Environmental Monitoring ; *Soil Pollutants/analysis ; Metagenomics ; Soil/chemistry ; *Microbial Consortia ; Biodegradation, Environmental ; RNA, Ribosomal, 16S ; Coal ; },
abstract = {Overburden dump (OBD) of coal mine waste soils is arguably a major source of heavy metals and metalloids, leading to both public health and ecological consequences. This study employed hypervariable V3-V4 region of 1.5 kbp 16S rDNA gene-based amplicon metagenomic sequencing to analyze unexplored bacterial diversity and its phenotypical and hypothetical functions, emphasizing the significance of these studies for assessing the potential of bioremediation. Triplicate coal OBD soil samples were collected from the coal dumping yard of Sarubera Colliery from Atna-Chainpur and agricultural soils from Ramgarh Cantonment, Jharkhand. There were 30 phyla And 320 operational taxonomic units (OTUs) recorded in coal OBD soil, while agricultural soil had 26 phyla And 240 OTUs. Proteobacteria were the predominant phylum in both environments. Firmicutes, Actinobacteria, and Bacteroidetes were the most prevalent phyla in the coal OBD soil, whereas Acidobacteria, Planctomycetes, and Nitrospirae were most frequently found in agricultural soil. Alphaproteobacteria and Gammaproteobacteria was the most abundant classes, and whereas the mesophilic Acinetobacter were the most abundant genus detected in coal OBD soil. The PICRUSt2 pipeline predicted hypothetical functional categories, identifying 2404 EC numbers, 7813 KO terms, And 442 MetaCyc pathways. The most enriched categories were RNA polymerase sigma-70 factor, ABC transporters, And 3-oxoacyl-[acyl-carrier-protein] reductase, aerobic respiration pathways, and pyruvate fermentation biosynthesis pathways. Taxonomy-to-phenotypic mapping was used to record phenotypic categories like oxygen requirement, temperature range, energy sources, biotic relationships, and Gram stain nature between the two habitats. The presence of nitrogen-fixing and phosphate-solubilizing bacteria in coal OBD soil offers their key roles of biodegrading polycyclic aromatic hydrocarbons (PAHs), speeding mineralization, and ameliorating environmental issues that threaten plant viability.},
}

*Soil Microbiology
India
*Bacteria/classification/genetics
*Coal Mining
*Environmental Monitoring
*Soil Pollutants/analysis
Metagenomics
Soil/chemistry
*Microbial Consortia
Biodegradation, Environmental
RNA, Ribosomal, 16S
Coal

@article {pmid41022942,
year = {2025},
author = {Halifu, S and Deng, X and Yang, L and Qian, L and Yang, L},
title = {Metagenomic analysis of pathogenicity of puccinia xanthii on invasive plant xanthium italicum.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33530},
pmid = {41022942},
issn = {2045-2322},
support = {KX031042//PhD research startup foundation of Shihezi University/ ; KX6107//a program of Shihezi University/ ; },
mesh = {*Plant Diseases/microbiology ; Plant Leaves/microbiology ; *Xanthium/microbiology ; *Metagenomics/methods ; *Puccinia/genetics/pathogenicity ; Introduced Species ; Photosynthesis ; China ; },
abstract = {Biological invasion refers to the establishment and proliferation of non-indigenous species in previously unoccupied areas, where they form wild populations. Xanthium italicum, an invasive species in Xinjiang, China, negatively affects local ecosystems, agriculture, and animal husbandry. In this study, we investigated the pathogenicity of Puccinia xanthii on the leaves of X. italicum by exploring the morphological characteristics of the pathogenic fungi, leaf enzyme activity measurement, photosynthesis measurement, and metagenomic sequencing. This study showed that P. xanthii infects the leaves of X. italicum, significantly reducing the activities of lyase, oxidoreductase, and antioxidant enzymes, including phenylalanine ammonia-lyase (PAL), superoxide dismutase (SOD), polyphenol oxidase (PPO), and catalase (CAT), as well as impairing photosynthesis. Furthermore, metagenomic analysis indicated that P. xanthii infection reduced the homogeneity and richness of phyllosphere microorganisms and increased the abundance of P. xanthii in the phyllosphere. Functional analysis also revealed that P. xanthii infection altered the diversity of microbial functions and eventually led to the development of disease symptoms and the demise of leaves through activated oxidative phosphorylation.},
}

*Plant Diseases/microbiology
Plant Leaves/microbiology
*Xanthium/microbiology
*Metagenomics/methods
*Puccinia/genetics/pathogenicity
Introduced Species
Photosynthesis
China

@article {pmid41022706,
year = {2025},
author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE},
title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8559},
pmid = {41022706},
issn = {2041-1723},
support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; },
mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; },
abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.},
}

Phylogeny
*Haptophyta/genetics/classification/metabolism
Phylogeography
Gene Transfer, Horizontal
Metagenome
Oceans and Seas
Genome
Genomics

@article {pmid41021050,
year = {2025},
author = {Kishk, M and Rahmeh, R and Asiri, F and Karam, H and Al-Muhanna, K and Hejji, AB and Shajan, A and Al-Salem, SM},
title = {Substrate-specific microbial community shifts during mesophilic biodegradation of polymers in compost amended soil.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {93},
pmid = {41021050},
issn = {1572-9729},
support = {FB187K//Kuwait Institute for Scientific Research/ ; },
mesh = {Biodegradation, Environmental ; *Soil Microbiology ; *Soil/chemistry ; *Polymers/metabolism ; *Composting ; *Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Fungi/metabolism/genetics/classification ; Starch/metabolism ; },
abstract = {Plastics are widely utilized across various industries, but their persistent accumulation in the environment has become a major ecological concern. Biodegradable alternatives offer a potential solution to plastic pollution; however, their degradation behavior under environmentally relevant conditions remains underexplored. This study evaluates the aerobic biodegradation of four polymer materials: starch, commercial thermoplastic starch of polyester origin (TPS1), linear low-density polyethylene (LLDPE), and a co-polyester thermoplastic starch (TPS2), over 180 days at 25 °C in a compost-soil matrix using the testing protocols of ASTM D5988-18 for carbon dioxide (CO2) evolution. Microbial community dynamics were profiled using 16S rRNA and ITS2 amplicon sequencing. TPS2 reached complete mineralization (~ 100%) in 28 days, followed by starch at 71.1% by day 180. TPS1 showed partial mineralization of 38.6%, while LLDPE showed minimal mineralization (21.9%) as expected. Alpha diversity revealed higher bacterial richness in starch treatments and a marked reduction in fungal diversity in TPS1 and LLDPE. Differential abundance testing revealed significant microbial shifts between treatments. Linear discriminant analysis Effect Size (LEfSe) identified polymer-specific microbial biomarkers, including Paenibacillus and Botryotrichum for starch, Acrophialophora and Mycothermus for TPS2, and the Mycobacterium for LLDPE. Subgroup 10 Acidobacteria was uniquely enriched in TPS2-treated samples. These taxa reflect substrate-driven microbial selection. Coupling CO2 mineralization with microbial profiling offers a practical framework to evaluate polymer biodegradability and guide the design of soil-degradable bioplastics. Overall, these findings demonstrate that polymer composition significantly influences microbial community structure and mineralization performance under mesophilic conditions.},
}

Biodegradation, Environmental
*Soil Microbiology
*Soil/chemistry
*Polymers/metabolism
*Composting
*Bacteria/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics
*Microbiota
Fungi/metabolism/genetics/classification
Starch/metabolism

@article {pmid41017911,
year = {2025},
author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J},
title = {Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1649384},
pmid = {41017911},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Premature ; India/epidemiology ; Infant, Newborn ; *Enterocolitis, Necrotizing/microbiology/epidemiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Enterobacteriaceae/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is an inflammatory bowel disease that primarily affects preterm infants. Predisposing risk factors for NEC include prematurity, formula feeding, anemia, and sepsis. To date, no studies have investigated the gut microbiota of preterm infants with NEC in India.

METHOD: In the current study, shotgun metagenomic sequencing was performed on fecal samples from premature infants with NEC and healthy preterm infants (n = 24). Sequencing was conducted using the NovaSeq X Plus platform, generating 2 × 150 bp paired-end reads. The infants were matched based on gestational age and postnatal age.

RESULT: The median time to NEC diagnosis was 9 days (range: 1-30 days). Taxonomic analysis revealed a high prevalence of Enterobacteriaceae at the family level, with the genera Klebsiella and Escherichia particularly prominent in neonates with NEC. No statistically significant differences in alpha or beta diversity were observed between stool samples from infants with and without NEC. Linear regression analysis demonstrated that Enterobacteriaceae were significantly more abundant in stool samples from infants with NEC than without NEC (q < 0.05). Differential abundance analysis using Linear Discriminant Analysis Effect Size (LEfSe) identified Klebsiella pneumoniae and Escherichia coli as enriched in the gut microbiota of preterm infants with NEC. Functional analysis revealed an increase in genes associated with lipopolysaccharide (LPS) O-antigen, the type IV secretion system (T4SS), the L-rhamnose pathway, quorum sensing, and iron transporters, including ABC transporters, in stool samples from infants with NEC.

CONCLUSION: The high prevalence of Enterobacteriaceae and enrichment of LPS O-antigen and T4SS genes may be associated with NEC in Indian preterm infants.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant, Premature
India/epidemiology
Infant, Newborn
*Enterocolitis, Necrotizing/microbiology/epidemiology
Feces/microbiology
*Metagenomics/methods
Male
Female
Enterobacteriaceae/genetics/isolation & purification/classification

@article {pmid41017909,
year = {2025},
author = {Maan, S and Batra, K and Rajendhran, J and Joseph, R and Singh, VK and Chaudhary, D and Sindhu, S and Kadian, V and Kumar, A and Maan, NS and Mor, S},
title = {Exploring viral diversity in diarrheic porcine feces: a metagenomic analysis from an Indian swine farm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1653342},
pmid = {41017909},
issn = {2235-2988},
mesh = {Animals ; Swine ; *Feces/virology ; *Swine Diseases/virology/epidemiology ; *Metagenomics ; India/epidemiology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Diarrhea/veterinary/virology ; Farms ; Genome, Viral ; Virome ; *Virus Diseases/veterinary/virology ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Pig husbandry is a vital sector in India, providing nutritional security and employment for marginalized communities. Pigs are advantageous due to high reproduction rates and fecundity, shorter generation intervals, and efficient feed conversion, requiring minimal housing. However, the swine industry encounters significant disease challenges, particularly viral gastroenteritis, which poses serious public health risks, especially in developing countries. Pigs serve as natural reservoirs and amplifiers for numerous viruses with zoonotic potential, making disease surveillance essential.

MATERIALS: In this study, we conducted a metagenomic analysis of 15 fecal samples from diarrheic pigs on a farm in India, marking the first exploration of the fecal virome diversity in this region. Our next-generation sequencing approach has enabled the unbiased detection of multiple viral agents in the porcine fecal samples, detecting both known and novel viral agents without prior target knowledge.

RESULTS: The key and novel viruses obtained in our study were porcine circovirus, porcine parvovirus 7, porcine mamastrovirus 3, porcine sapelovirus A, and porcine enterovirus G. This work resulted in the generation of full genomes for multiple porcine viruses, including Circovirus, Enterovirus, Sapelovirus, and Mamastrovirus, along with partial genomes of Parvovirus, Picobirnavirus, Porcine stool-associated RNA virus (Porcine Posavirus), Kobuvirus, and Rotavirus, all subjected to phylogenetic analysis.

CONCLUSION: Our survey indicates frequent co-infections with diverse viruses, creating conducive environments for viral recombination and reassortment. Continuous surveillance of viral pathogens in animal populations is essential for understanding the dynamics of both known and novel viruses and for detecting emerging pathogens, along with their zoonotic and pathogenic potential.},
}

Animals
Swine
*Feces/virology
*Swine Diseases/virology/epidemiology
*Metagenomics
India/epidemiology
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Diarrhea/veterinary/virology
Farms
Genome, Viral
Virome
*Virus Diseases/veterinary/virology
High-Throughput Nucleotide Sequencing

@article {pmid41015602,
year = {2025},
author = {Nazrin, MRR and Pavan, JS and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Kamil, D and Subramanian, S},
title = {Host-Driven Functional Divergence in Gut Microbiota of Honeybees Apis cerana and Apis mellifera: Implications for Pollination, Nutrition, and Sustainable Apiculture.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {531},
pmid = {41015602},
issn = {1432-0991},
mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Pollination ; },
abstract = {Honeybees are indispensable in sustaining natural ecosystems and global crop production by pollinating key food crops. Understanding their gut microbiota is crucial for insights into their health, nutrition, and behavior, with broader ecological and agricultural relevance. This study compares the gut microbiota of Apis cerana and Apis mellifera, focusing on bacterial composition, diversity, and functional roles. Using culture-dependent and metagenomic methods, core bacteria such as Lactobacillus, Fructobacillus, Gilliamella apicola, Bartonella apis, and Snodgrassella alvi were identified, linked to carbohydrate and nitrogen metabolism, immune modulation, and polysaccharide degradation. A. mellifera exhibited greater microbial and functional diversity, reflected in higher Shannon (1.22 vs. 1.08) and Simpson (0.675 vs. 0.655) indices. Strong intraspecies correlations and weaker interspecies correlations (Pearson's r = 0.6486) indicated distinct microbial profiles, supported by PCA (75.3% variation) and Adonis test (P = 0.04, R[2] = 0.723). Functional analysis via MG-RAST and UniFrac-based PCoA showed species-specific differences in key metabolic pathways. Enzymatic profiling revealed Fructobacillus fructosus with high invertase activity (7.31 ± 0.30) and Apilactobacillus apinorum with strong pectinolytic activity (4.707 ± 0.36), enhancing honeybee nutrition. These findings have significant implications for pollination efficiency, probiotic development, and sustainable apiculture, ultimately supporting conservation strategies and the resilience of honeybee populations.},
}

Bees/microbiology/physiology
Animals
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Pollination

@article {pmid41013611,
year = {2025},
author = {Kazarina, A and Sarkar, S and Adams, B and Vogt, B and Rodela, L and Pogranichny, S and Powell, S and Wiechman, H and Heeren, L and Reese, N and Thompson, D and Ran, Q and Hartung, E and Akhunova, A and Akhunov, E and Johnson, L and Jumpponen, A and Lee, STM},
title = {Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {310},
pmid = {41013611},
issn = {1474-760X},
support = {2020-67019-3180//National Institute of Food and Agriculture/ ; 2238633//National Science Foundation CAREER Award/ ; OIA-1656006//National Science Foundation Award/ ; INV-004430/GATES/Gates Foundation/United States ; },
mesh = {*Rhizosphere ; *Stress, Physiological ; *Plant Roots/microbiology/metabolism ; *Droughts ; Soil Microbiology ; *Microbiota ; },
abstract = {BACKGROUND: Plants have evolved alongside microbes, enabling plants to better cope with abiotic and biotic stress. Interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants exhibit a "home field advantage" by preferentially recruiting microbes unique to their native environments, likely through mutual recognition and selective recruitment mechanisms.

RESULTS: Using gene- and genome-centric approaches, we assess the functional potential of root-associated microbes and profile their host metabolites to uncover the metabolic outputs potentially regulating host‒microbe interactions in Andropogon gerardii. We find that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine is highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses.

CONCLUSIONS: This study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance their ability to thrive in stressful environments. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture when coping with climate change.},
}

*Rhizosphere
*Stress, Physiological
*Plant Roots/microbiology/metabolism
*Droughts
Soil Microbiology
*Microbiota

@article {pmid41013568,
year = {2025},
author = {Lei, Y and Zheng, Y and Yan, Y and Zhang, K and Sun, X and Yang, B and Ge, L and Meng, Z and Cao, X and Zhang, X and Yan, X and Xu, Y and Zhang, T and Shi, J and Chen, S and Qiu, Q and Chen, Y and Deng, L and Li, Z and Wang, X and Zhang, K},
title = {Deciphering functional landscapes of rumen microbiota unveils the role of Prevotella bryantii in milk fat synthesis in goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {311},
pmid = {41013568},
issn = {1474-760X},
support = {2022YFD1300203//the National Key Research and Development Program of China/ ; 2022ZD04014//the Biological Breeding-Major Projects/ ; CARS-39-03//the China Agricultural Research System/ ; 32402785//the National Natural Science Foundation of China/ ; 2024PT-ZCK-71-3//the Key Research and Development Program of Shaanxi Province/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Milk/metabolism ; *Prevotella/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Lactation ; *Microbiota ; Lipid Metabolism ; Niacinamide/metabolism ; },
abstract = {BACKGROUND: The rumen microbiome is critical for regulating milk synthesis in dairy livestock, yet the molecular mechanisms linking microbial functions to host lipid metabolism remain poorly understood. While host genetics and microbial composition have been studied, integrative analyses of the rumen-blood-mammary gland axis remain lacking.

RESULTS: Here, we present the goat rumen microbial reference gene catalog and 5514 metagenome-assembled genomes (MAGs) from 160 multi-breed rumen samples. Integrating this resource with lactation data from 177 Saanen dairy goats, we identify Prevotella spp. as keystone taxa driving concurrent increases in milk yield and fat percentage. Functional and metabolomic profiling reveals that Prevotella bryantii B14 synthesizes nicotinate, which is converted to nicotinamide in circulation. Using in vitro and in vivo models, we demonstrate that nicotinamide activates the mTORC1 pathway in mammary epithelial cells via GPR109A, which upregulates transcription factors SREBP and PPAR-γ and the downstream lipogenic genes FASN, ACCα, and SCD1 to promote milk fat synthesis. In contrast, the relative deficiency of P. bryantii B14 and the associated reduction in nicotinamide levels in the rumen of poor lactating dairy goats may represent a significant contributor to impaired lactation performance. Additionally, the enhanced hydrogenotrophic methanogenesis activity may also adversely affect their lactation phenotype.

CONCLUSIONS: Our study establishes a causal link between rumen microbial metabolism and mammary lipid synthesis mediated by nicotinamide-mTORC1 signaling and identifies Prevotella abundance as a biomarker for precision breeding. These findings advance the understanding of microbiome-host crosstalk in lactation and provide actionable strategies for enhancing dairy productivity through microbiota-targeted interventions.},
}

Animals
*Rumen/microbiology/metabolism
*Goats/microbiology
*Milk/metabolism
*Prevotella/genetics/metabolism
Female
*Gastrointestinal Microbiome
Lactation
*Microbiota
Lipid Metabolism
Niacinamide/metabolism

@article {pmid41012703,
year = {2025},
author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP},
title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.},
journal = {Viruses},
volume = {17},
number = {9},
pages = {},
pmid = {41012703},
issn = {1999-4915},
support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; },
abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.

METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.

RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.

CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.},
}

*Genome, Viral
*Plant Viruses/genetics/physiology
Host Specificity
Metagenomics
Plant Diseases/virology
Plants/virology

@article {pmid41012679,
year = {2025},
author = {Hernández, LHA and da Silva, FS and da Paz, TYB and Dias, DD and de Barros, BCV and Nunes, BTD and Casseb, LMN and da Silva, SP and da Costa Vasconcelos, PF and Cruz, ACR},
title = {Virome Analysis of Small Mammals from the Brazilian Amazon.},
journal = {Viruses},
volume = {17},
number = {9},
pages = {},
pmid = {41012679},
issn = {1999-4915},
support = {3286/2013//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 88887.636166/2021-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 310295/2021-1//National Council for Scientific and Technological Development/ ; 406490/2023-6//National Council for Scientific and Technological Development/ ; 314522/2021-2//National Council for Scientific and Technological Development/ ; 406360/2022-7//Instituto Nacional de Ciência e Tecnologia em Viroses Emergentes e Reemergentes/ ; },
mesh = {Animals ; Brazil ; *Virome ; *Chiroptera/virology ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Opossums/virology ; *Rodentia/virology ; Animals, Wild/virology ; *Mammals/virology ; },
abstract = {The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health.},
}

Animals
Brazil
*Virome
*Chiroptera/virology
*Viruses/genetics/classification/isolation & purification
Genome, Viral
Phylogeny
High-Throughput Nucleotide Sequencing
*Opossums/virology
*Rodentia/virology
Animals, Wild/virology
*Mammals/virology

@article {pmid41011853,
year = {2025},
author = {Saylam, E and Özden, Ö and Yerlikaya, FH and Sivrikaya, A and Yormaz, S and Arslan, U and Topkafa, M and Maçin, S},
title = {Investigation of Intestinal Microbiota and Short-Chain Fatty Acids in Colorectal Cancer and Detection of Biomarkers.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
pmid = {41011853},
issn = {2076-0817},
support = {22401140//Selçuk University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/diagnosis/pathology/metabolism ; Male ; Female ; *Fatty Acids, Volatile/metabolism/analysis ; Middle Aged ; Feces/microbiology/chemistry ; Haptoglobins ; Aged ; Protein Precursors ; Acute-Phase Proteins/analysis ; Cholera Toxin/blood ; *Biomarkers, Tumor ; Carrier Proteins/blood ; Membrane Glycoproteins/blood ; Biomarkers ; Bacteria/classification/genetics/isolation & purification ; Adult ; },
abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide and a significant global health issue. The human gut microbiota, a complex ecosystem hosting numerous microorganisms such as bacteria, viruses, fungi, and protozoa, plays a crucial role. Increasing evidence indicates that gut microbiota is involved in CRC pathogenesis. In this study, the gut microbiota profiles, short-chain fatty acids, zonulin, and lipopolysaccharide-binding protein levels of newly diagnosed CRC patients were analyzed along with healthy controls to elucidate the relationship between CRC and the gut microbiota. The study included 16 newly diagnosed CRC patients and 16 healthy individuals. For microbiota analysis, DNA isolation from stool samples was performed using the Quick-DNA™ Fecal/Soil Microbe Miniprep Kit followed by sequencing using the MinION device. Data processing was conducted using Guppy software (version 6.5.7) and the Python (3.12) programming language. ELISA kits from Elabscience were utilized for analyzing LBP and zonulin serum levels. Fecal short-chain fatty acids were analyzed using GC-MS/MS equipped with a flame ionization detector and DB-FFAP column. Microbial alpha diversity, assessed using Shannon and Simpson indices, was found to be lower in CRC patients compared to healthy controls (p = 0.045, 0.017). Significant differences in microbial beta diversity were observed between the two groups (p = 0.004). At the phylum level, Bacteroidota was found to be decreased in CRC patients (p = 0.027). Potential biomarker candidates identified included Enterococcus faecium, Ruminococcus bicirculans, Enterococcus gilvus, Enterococcus casseliflavus, Segatella oris, and Akkermansia muciniphila. Serum zonulin levels were higher in CRC patients (CRC = 70.1 ± 26.14, Control = 53.93 ± 17.33, p = 0.048). There is a significant relationship between gut microbiota and CRC. A multifactorial evaluation of this relationship could shed light on potential biomarker identification and the development of new treatment options for CRC.},
}

Humans
*Gastrointestinal Microbiome
*Colorectal Neoplasms/microbiology/diagnosis/pathology/metabolism
Male
Female
*Fatty Acids, Volatile/metabolism/analysis
Middle Aged
Feces/microbiology/chemistry
Haptoglobins
Aged
Protein Precursors
Acute-Phase Proteins/analysis
Cholera Toxin/blood
*Biomarkers, Tumor
Carrier Proteins/blood
Membrane Glycoproteins/blood
Biomarkers
Bacteria/classification/genetics/isolation & purification
Adult

@article {pmid41011835,
year = {2025},
author = {Ezzat, A and Abd El Wahed, A and Ceruti, A and El Asely, AM and Khalifa, MS and Winters, AD and Truyen, U and Shaheen, AA and Faisal, M},
title = {Exploring the Virome of Nile Tilapia (Oreochromis niloticus) Using Metagenomic Analysis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
pmid = {41011835},
issn = {2076-0817},
mesh = {Animals ; *Cichlids/virology ; *Virome/genetics ; *Metagenomics/methods ; Phylogeny ; *Fish Diseases/virology ; *Viruses/genetics/classification/isolation & purification ; Egypt ; DNA Viruses/genetics/classification/isolation & purification ; Metagenome ; },
abstract = {Nile tilapia (Oreochromis niloticus) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is scarce information on the biology and epidemiology of these viruses. This exploratory metagenomic study used Oxford Nanopore Technology (ONT) sequencing to profile the virome compositions of both wild and farmed Nile tilapia across five regions in Egypt. The Nile tilapia virome was dominated by two double-stranded DNA bacteriophages, Muvirus mu and M. sfmu, which constituted 79.8% of the detected sequences. Eukaryotic viruses, including members of the families Amnoonviridae, Peribunyaviridae, and Baculoviridae, were also identified. Two giant DNA viruses known to infect Acanthamoeba spp., Mollivirus sp., and Pandoravirus sp. were identified in the spleen virome of tilapia from a single sampling site. The diversity analysis showed no significant differences among tissue types or sampling sites. Phylogenetic analyses were performed on a single virus detected of potential pathogenicity, an amnoonvirus. The analyses demonstrated that the detected virus is a member of the family Amnoonviridae and placed it alongside members of the Tilapinevirus genus. The virus, however, was distinct from the other two members in the genus: T. tilapae and T. poikilos. This study underscores the usefulness of ONT in providing a foundational understanding of the Nile tilapia virome.},
}

Animals
*Cichlids/virology
*Virome/genetics
*Metagenomics/methods
Phylogeny
*Fish Diseases/virology
*Viruses/genetics/classification/isolation & purification
Egypt
DNA Viruses/genetics/classification/isolation & purification
Metagenome

@article {pmid41010985,
year = {2025},
author = {Petrelli, F and Ghidini, A and Dottorini, L and Ghidini, M and Zaniboni, A and Tomasello, G},
title = {Clinical Evidence for Microbiome-Based Strategies in Cancer Immunotherapy: A State-of-the-Art Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {9},
pages = {},
pmid = {41010985},
issn = {1648-9144},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immunotherapy/methods ; *Neoplasms/therapy ; Immune Checkpoint Inhibitors/therapeutic use ; Probiotics/therapeutic use ; },
abstract = {The gut microbiome has emerged as a critical determinant of immune-checkpoint inhibitor (ICI) efficacy. A narrative review of 95 clinical studies (2015-2025) shows that patients with greater gut microbial diversity and relative enrichment of commensals such as Akkermansia, Ruminococcus, and other short-chain fatty acid producers experience longer progression-free and overall survival, particularly in melanoma and non-small-cell lung cancer. Broad-spectrum antibiotics given within 30 days of ICI initiation and over-the-counter mixed probiotics consistently correlate with poorer outcomes. Early phase I/II trials of responder-derived fecal microbiota transplantation in ICI-refractory melanoma achieved objective response rates of 20-40%, while pilot high-fiber or plant-forward dietary interventions improved immunologic surrogates such as CD8[+] tumor infiltration. Machine-learning classifiers that integrate 16S or metagenomic profiles predict ICI response with an area under the ROC curve of 0.83-0.92. Methodological heterogeneity across sampling, sequencing, and clinical endpoints remains a barrier, underscoring the need for standardization and larger, well-powered trials.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Immunotherapy/methods
*Neoplasms/therapy
Immune Checkpoint Inhibitors/therapeutic use
Probiotics/therapeutic use

@article {pmid41010544,
year = {2025},
author = {Liu, Y and Kuang, W and Li, M and Wang, Z and Liu, Y and Zhao, M and Huan, H and Yang, Y},
title = {Cholesterol-Lowering Mechanism of Lactobacillus Bile Salt Hydrolase Through Regulation of Bifidobacterium pseudolongum in the Gut Microbiota.},
journal = {Nutrients},
volume = {17},
number = {18},
pages = {},
pmid = {41010544},
issn = {2072-6643},
support = {2024YFF0619500; no. BK20231280; CX(22)2019//National Key Research and Development Program of China; Natural Science Foundation of Jiangsu; Jiangsu Agriculture Science and Technology Innovation Fund/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Amidohydrolases/metabolism/pharmacology ; *Cholesterol/blood ; Mice ; Male ; *Bifidobacterium/growth & development/drug effects/metabolism ; *Lactobacillus/enzymology ; *Hypercholesterolemia/blood/microbiology ; Cholesterol 7-alpha-Hydroxylase/metabolism ; Fibroblast Growth Factors/metabolism ; Mice, Inbred C57BL ; *Anticholesteremic Agents/pharmacology ; Bile Acids and Salts/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Probiotics ; },
abstract = {Background: Cardiovascular diseases (CVDs) represent a major global health burden, and cholesterol reduction is a key strategy for their prevention and management. This study investigated the mechanism by which bile salt hydrolase (BSH) from Lactobacilli reduces cholesterol levels by modulating the growth of Bifidobacterium pseudolongum. Methods: The BSH-recombinant strain YB334 was administered to high-cholesterol-diet mice, and the cholesterol-lowering function of the strain was evaluated by assessing serum cholesterol parameters, including total cholesterol (TC), low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Metagenomic sequencing was used to analyze the gut microbiota, leading to the screening and acquisition of the "responsive" strains affected by BSH. Subsequent investigations were conducted into their cholesterol-lowering effects and mechanisms of action. Results: Oral administration of the BSH-recombinant strain YB334 can effectively reduce serum cholesterol levels in hypercholesterolemic mice while simultaneously leading to a significant increase in the abundance of B. pseudolongum within the gut microbiota. In vitro experiments indicated that this increased abundance might be closely associated with the strain's high tolerance to CA, the catalytic product of the BSH enzyme. The BPL-4 strain, obtained through screening, demonstrated cholesterol-lowering efficacy. Mechanistically, BPL-4 altered bile acid pool composition and modulated the farnesoid X receptor (FXR) signaling axis: it suppressed ileal FXR-fibroblast growth factor 15 (FGF15) expression, thereby de-repressing hepatic cholesterol 7α-hydroxylase (CYP7A1) and accelerating cholesterol catabolism into bile acids. Conclusions: This study provides the first evidence that BSH from lactobacilli can shape the signature gut microbiota by modulating bile acid metabolism via the FXR-CYP7A1 axis, thereby demonstrating a mechanism for its cholesterol-lowering effects.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Amidohydrolases/metabolism/pharmacology
*Cholesterol/blood
Mice
Male
*Bifidobacterium/growth & development/drug effects/metabolism
*Lactobacillus/enzymology
*Hypercholesterolemia/blood/microbiology
Cholesterol 7-alpha-Hydroxylase/metabolism
Fibroblast Growth Factors/metabolism
Mice, Inbred C57BL
*Anticholesteremic Agents/pharmacology
Bile Acids and Salts/metabolism
Receptors, Cytoplasmic and Nuclear/metabolism
Probiotics

@article {pmid41009770,
year = {2025},
author = {Pita-Galeana, MA and Ruhle, M and López-Vázquez, L and de Anda-Jáuregui, G and Hernández-Lemus, E},
title = {Computational Metagenomics: State of the Art.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
pmid = {41009770},
issn = {1422-0067},
mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Machine Learning ; Metagenome ; },
abstract = {Computational metagenomics has revolutionized our understanding of the human microbiome, enabling the characterization of microbial diversity, the prediction of functional capabilities, and the identification of associations with human health outcomes. This review provides a concise yet comprehensive overview of state-of-the-art computational approaches in metagenomics, alongside widely used methods and tools employed in amplicon-based metagenomics. It is intended as an introductory resource for new researchers, outlining key methodologies, challenges, and future directions in the field. We discuss recent advances in bioinformatics pipelines, machine learning (ML) models, and integrative frameworks that are transforming our understanding of the microbiome's role in health and disease. By addressing current limitations and proposing innovative solutions, this review aims to outline a roadmap for future research and clinical translation in computational metagenomics.},
}

*Metagenomics/methods
Humans
*Microbiota/genetics
*Computational Biology/methods
Machine Learning
Metagenome

@article {pmid41007466,
year = {2025},
author = {Godoy-Vitorino, F},
title = {Strengthening Integrative Microbiome Research Through Regional Leadership.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {9},
pages = {},
pmid = {41007466},
issn = {1660-4601},
support = {1P20GM156713-01/GM/NIGMS NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; 2U54MD007600//Center for Collaborative Research in Minority Health and Health Disparities/ ; },
mesh = {*Microbiota ; Puerto Rico ; Leadership ; Humans ; Metagenomics ; Research/organization & administration ; },
abstract = {Microbiome science has revolutionized modern biology, shifting the focus from pathogens to the essential roles of beneficial microbes in health, metabolism, and ecosystems. Advances in genomic technologies like metagenomics have rapidly expanded our understanding of microbial diversity and function. Despite this progress, global microbiome research remains concentrated in high-resource regions, limiting diverse perspectives and opportunities in places like the Caribbean. This communication discusses the establishment of the first Center for Microbiome Sciences in Puerto Rico, which addresses this gap by providing local researchers with access to advanced tools, training, and infrastructure through broader collaboration. Novelty, services, and ideas on the integration of activities among local centers for the scientific improvement of the region are addressed. Additionally, how the center is poised to contribute to improving public and environmental health is also highlighted.},
}

*Microbiota
Puerto Rico
Leadership
Humans
Metagenomics
Research/organization & administration

@article {pmid41006795,
year = {2025},
author = {Aoyagi, LN and Wang, Y and Ohbayashi, T and Hirono, Y and Hayatsu, M and Tago, K},
title = {Diversity and characterization of the ammonia-oxidizing bacteria responsible for nitrification in tea field soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33221},
pmid = {41006795},
issn = {2045-2322},
support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; 16K14874//MEXT KAKENHI/ ; 19H01156//MEXT KAKENHI/ ; 28004A//Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries, and Food Industry/ ; },
mesh = {*Nitrification ; *Ammonia/metabolism ; *Soil Microbiology ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil/chemistry ; Archaea/metabolism/genetics/classification ; Phylogeny ; *Tea/microbiology ; Biodiversity ; },
abstract = {Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and comammox Nitrospira have been considered to coexist in acidic soils, oxidizing ammonia within their respective niches. However, their relative contributions to soil nitrification, as well as their properties and ecological roles in acidic soils, remain poorly understood. This study focused on AOB in acidic tea field soils, investigating their ecology and physiology through metagenomic analysis and the genomic and physiological characterization of AOB isolates. β-AOB were significantly more abundant than γ-AOB and AOA in soil layers with the highest potential for nitrification activity, indicating that β-AOB play a key role in acidic tea soil. Diversity analysis of this dominant group identified Nitrosospira as the major genus present in tea fields, and four pure strains representing some of the main operational taxonomic units in this environment were isolated. Physiological and genetic characterization of these isolates revealed some distinct traits compared to other species of the genus and closely related taxa, suggesting adaptations that may contribute to niche differentiation and survival in acidic soils. These findings provide new insights into the ecological role of β-AOB in acidic soils and may inform strategies to manage soil nitrification and reduce nitrogen loss in agricultural ecosystems.},
}

*Nitrification
*Ammonia/metabolism
*Soil Microbiology
Oxidation-Reduction
*Bacteria/metabolism/genetics/classification/isolation & purification
Soil/chemistry
Archaea/metabolism/genetics/classification
Phylogeny
*Tea/microbiology
Biodiversity

@article {pmid41006325,
year = {2025},
author = {Zhang, L and Zhou, DD and Feng, J and Liao, ZJ and Shu, XL and Yang, RM and Gao, YC and Zhou, HH and Zhang, W and Zou, Y and Liu, R},
title = {Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {188},
pmid = {41006325},
issn = {2055-5008},
support = {2021YFA1301200//the National Key Research and Development Program/ ; No. 82474022, 31801121, 82373961//the National Scientific Foundation of China/ ; 2022RC1022//the Hunan Provincial Science and Technology Innovation Plan Project/ ; },
mesh = {*Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Fungi/classification/genetics/isolation & purification ; Animals ; Mice ; Feces/microbiology ; Cohort Studies ; *Neoplasms/drug therapy/microbiology ; },
abstract = {Gut microbiota influence on the effectiveness of immune checkpoint inhibitors (ICIs), but research on fungi-an essential component of the microbiome-has been limited. This multi-cohort meta-analysis of 976 fecal metagenomes across 8 cohorts, representing melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC), identified fungal species associated with ICI efficacy. In melanoma, Rhizophagus irregularis and Debaryomyces hansenii were correlated with poor responses, whereas Aspergillus avenaceus was associated with great efficacy. In NSCLC, an increased abundance of Aspergillus pseudonomiae was associated with a favorable prognosis. Stronger bacterial-fungal interactions were observed in responders. The presence of certain fungi in fungal enterotypes, like Aspergillus or Saccharomyces, was linked to better efficacy to ICIs. Mouse models revealed Debaryomyces hansenii impaired ICI efficacy by reducing CD8+ T cells. Our findings highlight specific fungal signatures that may inform strategies to enhance ICI efficacy and encourage further research on microbial impacts on treatment outcomes.},
}

*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Humans
*Gastrointestinal Microbiome/drug effects
*Fungi/classification/genetics/isolation & purification
Animals
Mice
Feces/microbiology
Cohort Studies
*Neoplasms/drug therapy/microbiology

@article {pmid41005935,
year = {2026},
author = {Yang, W and Xin, X and Cao, X},
title = {Impacts of trace ofloxacin on autotrophic denitrification process driven by pyrite/sulfur: Performance, microbial community evolution and metagenomic analysis.},
journal = {Journal of environmental sciences (China)},
volume = {159},
number = {},
pages = {775-784},
doi = {10.1016/j.jes.2025.03.062},
pmid = {41005935},
issn = {1001-0742},
mesh = {*Denitrification/drug effects ; Autotrophic Processes ; *Water Pollutants, Chemical/toxicity/analysis ; Sulfides/chemistry ; *Ofloxacin/toxicity/analysis ; Sulfur/chemistry ; Iron/chemistry ; Metagenomics ; *Microbiota/drug effects ; Anti-Bacterial Agents/toxicity ; Bioreactors ; },
abstract = {In this work, ofloxacin (OFL), a kind of frequently detected antibiotic in groundwater, was selected to explore its impact (at ng/L-µg/L-level) on denitrification performance in an autotrophic denitrification system driven by pyrite/sulfur (FeS2/S[0]). Results showed that OFL restrained nitrate removal efficiency, and the inhibition degree was positively related to the concentration of OFL. After being exposed to increased OFL (200 ng/L-100 µg/L) for 69 days, higher inhibition of electron transport activity (ETSA), enzyme activities of nitrate reductase (NAR), and nitrite reductase (NIR) were acquired. Meanwhile, the extracellular protein (PN) content of sludge samples was remarkably stimulated by OFL to resist the augmented toxicity. OFL contributed to increased microbial diversity and sulfur/sulfide oxidation functional genes in ng/L-level bioreactors, whereas led to a decline in µg/L level experiments. With OFL at concentrations of 200 ng/L and 100 µg/L, the whole expression of 10 key denitrification functional genes was depressed, and the higher the OFL concentration, the lower the expression level. However, no significant proliferation of antibiotic resistance genes (ARGs) either in 200 ng/L-OFL or 100 µg/L-OFL groups was observed. Two-factor correlation analysis results indicated that Thiobacillus, Anaerolineae, Anaerolineales, and Nitrospirae might be the main hosts of existing ARGs in this system.},
}

*Denitrification/drug effects
Autotrophic Processes
*Water Pollutants, Chemical/toxicity/analysis
Sulfides/chemistry
*Ofloxacin/toxicity/analysis
Sulfur/chemistry
Iron/chemistry
Metagenomics
*Microbiota/drug effects
Anti-Bacterial Agents/toxicity
Bioreactors

@article {pmid41005808,
year = {2025},
author = {Purcell, M and Ackland, J and Staples, KJ and Freeman, A and Wilkinson, TMA},
title = {The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {34},
number = {177},
pages = {},
pmid = {41005808},
issn = {1600-0617},
mesh = {Humans ; *Virome ; *Viruses/genetics/pathogenicity/immunology ; Host-Pathogen Interactions ; *Microbiota ; *Respiratory System/virology ; *Respiratory Tract Infections/virology ; Metagenomics ; *Respiratory Tract Diseases/virology/diagnosis ; Animals ; },
abstract = {The human respiratory tract virome is an underexplored component of the microbiome that includes eukaryotic viruses, bacteriophages and archaeal viruses. The respiratory virome represents a dynamic and heterogeneous ecosystem, shaped by host, environmental and microbial factors. Advances in metagenomic sequencing have expanded our understanding of virome composition, dynamics and potential roles in health and disease. Despite increasing interest, virome research remains fragmented and often secondary to bacteriome studies. Challenges in study design, genomic characterisation and interpretation limit consistent conclusions. This review summarises current knowledge of the respiratory virome in health and across acute and chronic respiratory diseases, including acute respiratory infection, asthma, COPD, cystic fibrosis and bronchiectasis. While each condition is distinct, they share features of airway inflammation and immune dysregulation where the virome may act as a modifier or marker. Across these syndromes, emerging evidence highlights the consistent detection of respiratory viruses including potential commensals, such as Anelloviridae, and the often-overlooked role of bacteriophages. We also discuss the concept of viral dark matter, where large proportions of sequence data remain unclassified, potentially representing novel viral taxa. Technical and conceptual challenges are evaluated, alongside recent methodological innovations such as meta-transcriptomics and viral enrichment protocols. We outline how standardised, multi-omic and longitudinal approaches are urgently needed to clarify the virome's functional role, interactions with immunity and microbial communities and its utility as a biomarker or therapeutic target.},
}

Humans
*Virome
*Viruses/genetics/pathogenicity/immunology
Host-Pathogen Interactions
*Microbiota
*Respiratory System/virology
*Respiratory Tract Infections/virology
Metagenomics
*Respiratory Tract Diseases/virology/diagnosis
Animals

@article {pmid40999698,
year = {2025},
author = {Elliott, L and Coissac, E},
title = {Can Amplicon Sequencing Be Replaced by Metagenomics for Biodiversity Inventories?.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70047},
doi = {10.1111/1755-0998.70047},
pmid = {40999698},
issn = {1755-0998},
support = {819192//European Research Council (ERC)/ ; },
}

@article {pmid40998902,
year = {2025},
author = {Satpathy, SS and Pradhan, D},
title = {Unveiling community structure, antimicrobial resistance, and virulence factor of a wastewater sample of dairy farm located in mayurbhanj, odisha, India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32919},
pmid = {40998902},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; India ; *Virulence Factors/genetics ; *Dairying ; *Bacteria/genetics/drug effects/pathogenicity/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Farms ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Water Microbiology ; },
abstract = {Nutrient-rich dairy wastewater (DWW) is an excellent growing medium for microbes. Their antimicrobial resistance (AMR) genes and pathogenic roles remain in the DWW and even multiply in environmental settings, in contrast to many chemical toxins that break down over time. Necessary steps and standardized techniques for tracking AMR in DWW samples are desperately needed. In this context, a DWW sample was evaluated to assess the necessity of remediation and develop a suitable treatment technique. Physicochemical characterizations of the sample showed an elevated level of pollutants like proteins, fats, and carbohydrates that led to the water pollution and microbial diversity (e.g., 36 phyla, 72 classes, 111 orders, 168 families, 275 genera, and 347 species). The Shannon and Simpson indices showed that the DWW sample had a high level of microbial diversity of a few species. The gene ontology (GO) analysis revealed the functional categories with 2795 genes belonging to 11 virulence categories. Most of the identified AMR genes belonged to beta-lactamase, and the majority of them were linked to Escherichia coli, Mycobacterium tuberculosis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, etc. The major bacterial phyla carrying AMR genes included Firmicutes (36%), Proteobacteria (31%), Actinobacteria (21%), and Bacteroidetes (5%).},
}

*Wastewater/microbiology
India
*Virulence Factors/genetics
*Dairying
*Bacteria/genetics/drug effects/pathogenicity/isolation & purification
*Drug Resistance, Bacterial/genetics
Farms
Animals
Anti-Bacterial Agents/pharmacology
*Microbiota
Water Microbiology

@article {pmid40996787,
year = {2025},
author = {Bergner, L and Catalano, S and Nichols, J and Da Silva Felipe, A and Cao, X and Mair, D and Nankasi, A and Arinaitwe, M and Mubangizi, A and Pybus, OG and Standley, C and Faust, CL and Raghwani, J},
title = {Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001513},
pmid = {40996787},
issn = {2057-5858},
mesh = {Animals ; *Viral Load ; *Metagenomics/methods ; Feces/virology ; *Animals, Wild/virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics/classification/isolation & purification ; RNA Viruses/genetics/isolation & purification ; DNA Viruses/genetics/isolation & purification ; Rodentia/virology ; },
abstract = {Metagenomics is a powerful tool for characterizing viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causative agents of emerging outbreaks with unknown aetiology. Additionally, metagenomic data contain valuable information about the amount of virus present within samples (i.e. viral load), which can provide insights into transmission potential, time since infection and, in turn, epidemic trajectories. However, before we can effectively use metagenomic data to inform transmission, we need to understand the general relationship between sequencing outputs and viral load. Here, using a commercially available probe panel targeting a wide diversity of viruses, we investigated the detection and recovery of virus genomes by spiking known concentrations of DNA and RNA viruses into wild rodent faecal samples. In total, 15 experimental replicates were sequenced with target enrichment sequencing and compared to shotgun sequencing of the same background samples. Target-enriched sequencing recovered all spike-in viruses at every concentration (10[2], 10[3] and 10[5]±1 log genome copies) and showed a log-linear relationship between spike-in concentration and mean read depth. Background viruses (including Kobuvirus and Cardiovirus) were recovered consistently across all biological and technical replicates and by shotgun sequencing, but genome coverage was variable between virus genera and likely reflected the composition of the target enrichment probe panel. Overall, our study highlights the strengths and weaknesses of using commercially available panels to quantify and characterize wildlife viromes and underscores the importance of probe panel design for accurately interpreting coverage and read depth. To advance the use of metagenomics for understanding virus transmission, further research will be needed to elucidate how sequencing strategy (e.g. library depth and pooling), virome composition and probe design influence viral read counts and genome coverage.},
}

Animals
*Viral Load
*Metagenomics/methods
Feces/virology
*Animals, Wild/virology
Genome, Viral
High-Throughput Nucleotide Sequencing/methods
*Viruses/genetics/classification/isolation & purification
RNA Viruses/genetics/isolation & purification
DNA Viruses/genetics/isolation & purification
Rodentia/virology

@article {pmid40996703,
year = {2025},
author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE},
title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
pmid = {40996703},
issn = {1758-0463},
support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; },
mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; },
abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.},
}

*Microbiota/genetics
Humans
*Databases, Genetic
Data Curation
Metadata
Animals
Metagenomics

@article {pmid40995781,
year = {2025},
author = {Hensen, T and Thiele, I},
title = {Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2554195},
pmid = {40995781},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/metabolism/blood ; Male ; Female ; Biomarkers/blood/metabolism ; Middle Aged ; Aged ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics ; Leucine/metabolism/blood ; },
abstract = {Human gut microbiota have been implicated in metabolic disruptions in Parkinson's disease (PD). However, the underlying mechanisms linking gut microbiota to these disease-related metabolic changes remain largely unknown. In this study, we applied constraint-based metabolic modeling to identify potential causal links between compositional shifts in gut microbiota in PD and metabolic blood markers of PD. We personalized in silico whole-body metabolic models with gut metagenomics of 435 PD patients and 219 healthy controls and profiled in silico gut microbiome influences on 116 blood metabolites with replicated associations with PD diagnosis. Our analysis identified a reduced capacity of the PD host-microbiome co-metabolism to produce L-leucine and leucylleucine in blood. These metabolic predictions were traced back to lower L-leucine production of Roseburia intestinalis and higher L-leucine consumption by Methanobrevibacter smithii in PD microbiomes. We further predicted reduced host-microbiome production capacities of butyrate, myristic acid, and pantothenate in the blood of PD patients and linked these associations to reduced relative abundances of Faecalibacterium prausnitzii. Finally, lower nicotinic acid production capacities were predicted in PD patients, which were associated with increased relative abundances and increased nicotinic acid consumption of Ruthenibacterium lactatiformans in PD. In conclusion, we predicted that the gut microbiome can drive altered blood levels of six metabolites in PD and identified candidate microbial species that may influence these metabolic alterations. These findings may facilitate the development of novel therapies targeting the gut-brain axis in PD.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/microbiology/metabolism/blood
Male
Female
Biomarkers/blood/metabolism
Middle Aged
Aged
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics
Leucine/metabolism/blood

@article {pmid40995227,
year = {2025},
author = {Lee, SH and Kim, EB and Park, SC and Nam, SJ and Cho, H and Jeon, HJ and Lee, SP},
title = {Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1651316},
pmid = {40995227},
issn = {2235-2988},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Body Mass Index ; Female ; Male ; Middle Aged ; Obesity/microbiology ; *Gastrointestinal Microbiome/genetics ; Adult ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; DNA, Ribosomal/chemistry/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Overweight/microbiology ; Metagenomics ; Phylogeny ; },
abstract = {INTRODUCTION: Obesity is a multifactorial condition influenced by various factors, including the gut microbiota. However, the relationship between the gastric microbiota and obesity remains poorly understood. This study aimed to investigate the composition of gastric microbiota, excluding Helicobacter pylori, in relation to body mass index (BMI) and metabolic indicators.

METHODS: Thirty participants undergoing health checkups were classified into three groups-normal weight (BMI 18.5-22.9), overweight (BMI 23.0-24.9), and obese (BMI ≥25.0)-with ten individuals per group. Those with H. pylori infection, atrophic gastritis, or intestinal metaplasia were excluded. Gastric microbiota from four antral biopsies per subject were analyzed using 16S rRNA sequencing and functional profiling by metagenomic prediction.

RESULTS AND DISCUSSION: Alpha diversity (Gini-Simpson index) was significantly lower in the combined overweight/obese group than that in the normal group (P=0.049). Beta diversity analysis revealed clear group separation (Bray-Curtis, P=0.005; unweighted UniFrac, P=0.004). Significant species differences between the groups were observed; specifically, the abundances of Muribaculum gordoncarteri, Turicibacter bilis, and Duncaniella dubosii, were significantly reduced in the overweight/obese group. Functional predictions showed differential enrichment of pathways related to fatty acid, amino acid, vitamin, and carbohydrate metabolism across BMI categories. These findings suggest that alterations in the gastric microbiota may be linked to obesity and metabolic dysregulation.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Body Mass Index
Female
Male
Middle Aged
Obesity/microbiology
*Gastrointestinal Microbiome/genetics
Adult
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA
DNA, Ribosomal/chemistry/genetics
*Bacteria/classification/genetics/isolation & purification
*Stomach/microbiology
Overweight/microbiology
Metagenomics
Phylogeny

@article {pmid40993967,
year = {2025},
author = {Bibbò, S and Ahlström, G and Pes, GM and Graham, DY and Engstrand, L and Merola, E and Dore, MP},
title = {Resilience of the Gut Microbiome to Short Proton Pump Inhibitor Therapy With or Without High-Dosage L. reuteri in H. pylori-Infected Adults.},
journal = {Helicobacter},
volume = {30},
number = {5},
pages = {e70064},
pmid = {40993967},
issn = {1523-5378},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Limosilactobacillus reuteri/physiology/growth & development ; *Helicobacter Infections/drug therapy/microbiology ; *Proton Pump Inhibitors/therapeutic use/administration & dosage ; Female ; Male ; Middle Aged ; Double-Blind Method ; Adult ; Pantoprazole/therapeutic use ; *Probiotics/administration & dosage ; Helicobacter pylori/drug effects ; Feces/microbiology ; Aged ; },
abstract = {BACKGROUND: Helicobacter pylori eradication therapy typically consists of a combination of antibiotics and an antisecretory drug. Probiotics may be added to reduce side effects and possibly improve outcomes.

MATERIALS AND METHODS: We conducted a double-blind, randomized trial of pantoprazole plus either Lactobacillus reuteri (Gastrus) (high dose) or a matching placebo to assess the impact on the gut microbiota of H. pylori-positive adults. Fecal samples were collected at baseline and after one and 2 months for shotgun metagenomic sequencing.

RESULTS: A total of 26 patients were recruited and completed therapy. L. reuteri was only detected in the group that received supplemental L. reuteri and only at the 1-month post-treatment interval. L. reuteri failed to colonize for long-term the gut, and challenge with L. reuteri failed to alter alpha-diversity (Shannon index) or beta-diversity (community ordination) metrics at any time point. Machine learning (PLS-DA) analysis identified the presence of L. reuteri as the most distinguishing feature at 1 month. No other taxa showed a significant difference between groups.

CONCLUSION: Short-term administration of pantoprazole and L. reuteri had no lasting effects on gut microbial composition. While L. reuteri transiently bloomed during supplementation, the overall gut microbiota showed resilience, returning to baseline shortly after therapy.

TRIAL REGISTRATION: Identifier: NCT03404440.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Limosilactobacillus reuteri/physiology/growth & development
*Helicobacter Infections/drug therapy/microbiology
*Proton Pump Inhibitors/therapeutic use/administration & dosage
Female
Male
Middle Aged
Double-Blind Method
Adult
Pantoprazole/therapeutic use
*Probiotics/administration & dosage
Helicobacter pylori/drug effects
Feces/microbiology
Aged

@article {pmid40993109,
year = {2025},
author = {Zeng, Y and Zhong, X and Chai, L and Zhang, X and Lu, Z and Liu, G and Tu, T and Lu, L and Zhang, R and Yu, H and Zhang, S and Wang, S and Shen, C and Shi, J and Xu, Z},
title = {Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {186},
pmid = {40993109},
issn = {2055-5008},
support = {32201993//National Natural Science Foundation of China/ ; 31901658//National Natural Science Foundation of China/ ; 2024T170375//China Postdoctoral Science Foundation/ ; },
mesh = {*Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbial Consortia ; Ecosystem ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Fermentation ; Phylogeny ; },
abstract = {Elucidating the temporal dynamics of complex microbial consortia is crucial for engineering robust microbiome. We investigated prokaryotic evolution in pit mud, a centuries-old engineered environment used in Chinese liquor fermentation. Metagenomic analysis of 120 pit mud samples across different ages revealed a transition from generalist-dominated to specialist-enriched communities. This shift was characterized by decreased hydrolytic potential and increased organic acid metabolism, with key taxonomic changes including declines in Proteiniphilum and Petrimonas, and increases in Methanobacterium and Caproicibacter. The mature specialist community accelerates the short-chain organic acids turnover through syntrophic fatty acid oxidation, methanogenesis, and carbon chain elongation, maintaining ecosystem stability. While nutrient availability primarily shapes early stages community interactions, environmental stress becomes a dominant factor in mature systems. These insights into long-term prokaryotic adaptation provide a foundation for the rational design of resilient, functionally optimized microbial communities for biotechnological applications.},
}

*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbial Consortia
Ecosystem
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics
Fermentation
Phylogeny

@article {pmid40989903,
year = {2025},
author = {Malygina, EV and Potapova, NA and Imidoeva, NA and Vavilina, TN and Belyshenko, AY and Morgunova, MM and Dmitrieva, ME and Shelkovnikova, VN and Vlasova, AA and Lipatova, OE and Zhilenkov, VM and Batalova, AA and Stoyanova, EE and Axenov-Gribanov, DV},
title = {Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20037},
pmid = {40989903},
issn = {2167-8359},
mesh = {Russia ; *Microbiota ; *Ascomycota/genetics/classification/isolation & purification ; Symbiosis ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; Mycorrhizae/genetics ; },
abstract = {The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving controlled cultivation. This study aimed to characterize the microbial communities within the surface and gleba of truffle ascomata using 16S and 18S rRNA gene sequencing and identify the taxonomic composition and ecological roles of these microbiota. Specimens of Tuber magnatum (white truffle) and Tuber macrosporum (smooth black truffle) were collected, with T. magnatum representing the first documented discovery of this species in Russia. Metabarcoding profiling identified both species-specific and shared microbial taxa, with the yeast-like fungus Geotrichum spp. emerging as a core symbiont in both truffle species. Its consistent detection in surface and gleba tissues suggests a critical role in mycorrhizal establishment and spore dispersal, potentially mediated by sulfur volatiles that attract mycophagous fauna. In T. magnatum, the bacterial community was dominated by Proteobacteria, particularly Alphaproteobacteria and Gammaproteobacteria, with the nitrogen-fixing genus Bradyrhizobium being especially abundant. The truffle microbiota predominantly comprised soil-derived microorganisms (e.g., nitrogen-fixing Rhizobiaceae spp., phenol-degrading Mycoplana spp.) and plant-associated symbionts (e.g., ectomycorrhizal Sebacina spp.), implicating these communities in nutrient cycling, xenobiotic degradation, and host plant interactions. By elucidating the taxonomic and functional profiles of truffle-associated microbiota, this study provides foundational insights into their ecological contributions. Chemical differences align with tissue-specific microbial communities, suggesting microenvironmental specialization in bioactive compound synthesis. These findings advance efforts to replicate critical symbiotic interactions in vitro, a prerequisite for developing sustainable cultivation protocols for T. magnatum and T. macrosporum under controlled conditions.},
}

Russia
*Microbiota
*Ascomycota/genetics/classification/isolation & purification
Symbiosis
Soil Microbiology
RNA, Ribosomal, 16S/genetics
RNA, Ribosomal, 18S/genetics
Phylogeny
Mycorrhizae/genetics

@article {pmid40988537,
year = {2025},
author = {Tsamadou, V and Ohlsson, JA and Schnürer, A},
title = {Converge or Diverge? Exploring the Fate of Taxonomically Different Anaerobic Digestion Communities Under Uniform Growth Conditions.},
journal = {Microbial biotechnology},
volume = {18},
number = {9},
pages = {e70233},
pmid = {40988537},
issn = {1751-7915},
support = {310432//Energimyndigheten/ ; //Swedish Research Council (VR). The grant agreement corresponds to the Swedish Research Council./ ; //Sveriges Lantbruksuniversitet/Swedish University of Agricultural Sciencesarch Council through grant agreement no. 2022-06725/ ; },
mesh = {Anaerobiosis ; Culture Media/chemistry ; *Bacteria/classification/genetics/metabolism/growth & development ; Sewage/microbiology ; Ammonia/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bioreactors/microbiology ; Biofuels ; DNA, Ribosomal/chemistry/genetics ; *Biota ; Sequence Analysis, DNA ; Metagenomics ; },
abstract = {Biogas inocula with distinct taxonomic compositions often converge to similar communities when fed the same substrate, indicating strong substrate-driven deterministic assembly. Nevertheless, stochastic processes have also been suggested as a critical element for microbial assembly in biogas systems. To date, assembly processes have mainly been investigated with undefined, non-sterile substrates, making it difficult to exclude the influence of external microorganisms. The aim of the present study was to investigate whether three taxonomically distinct anaerobic digestion (AD) communities would converge when exposed to uniform growth conditions during semi-continuous operation with a sterilised defined medium. The inocula originated from mesophilic processes using different substrates (food waste, sludge, and manure) and total ammonia levels (0.5-7.2 g/L). The medium was formulated to support all four main metabolic steps of AD: hydrolysis, fermentation, anaerobic oxidation, and methanogenesis. Taxonomic, phylogenetic, and functional analyses conducted via 16S and metagenomic sequencing showed that the substrate had no deterministic effect on microbial community taxonomic composition. Instead, the final community structure was dictated primarily by the initial inoculum, regardless of changes in substrate composition or ammonia levels. Despite taxonomic divergence, broad-level functionality and operational performance remained similar between communities.},
}

Anaerobiosis
Culture Media/chemistry
*Bacteria/classification/genetics/metabolism/growth & development
Sewage/microbiology
Ammonia/metabolism
RNA, Ribosomal, 16S/genetics
Phylogeny
Bioreactors/microbiology
Biofuels
DNA, Ribosomal/chemistry/genetics
*Biota
Sequence Analysis, DNA
Metagenomics

@article {pmid40983948,
year = {2025},
author = {Zafeiropoulos, H and Delopoulos, EIM and Erega, A and Schneider, A and Geirnaert, A and Morris, J and Faust, K},
title = {microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {292},
pmid = {40983948},
issn = {1474-760X},
support = {101000309//Horizon 2020/ ; 101000309//Horizon 2020/ ; 9017//EMBO Scientific Exchange Grant/ ; },
mesh = {*Software ; *Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Metagenome ; Databases, Genetic ; *Microbiota ; },
abstract = {Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 annotated representative genomes. microbetag can be applied to custom (metagenome-assembled) genomes via its stand-alone version. MGG, a Cytoscape app designed to support microbetag, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.},
}

*Software
*Metabolic Networks and Pathways
Molecular Sequence Annotation
Metagenome
Databases, Genetic
*Microbiota

@article {pmid40982389,
year = {2025},
author = {Pizzini, JD and Midani, FS and Britton, RA},
title = {Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA).},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {223},
pages = {},
doi = {10.3791/68788},
pmid = {40982389},
issn = {1940-087X},
mesh = {*Bioreactors/microbiology ; *Microbiota/physiology ; Humans ; },
abstract = {The human microbiome comprises diverse and dynamic microbial communities that play essential roles in host health. Understanding these communities and their responses to environmental factors is critical for advancing microbiome-based therapeutics. Traditional in vitro models for cultivating human-derived microbiota often lack scalability and require extensive technical expertise, limiting their accessibility and throughput. To address these limitations, we developed the Minibioreactor Array (MBRA) system -- a modular, single-stage, continuous-flow platform for high-throughput cultivation of microbial communities. This system enables parallel cultivation of up to 48 distinct microbial communities, supporting experimental flexibility while maintaining the stable growth of complex ecosystems. This protocol provides detailed guidance on MBRA fabrication, assembly, sterilization, and operation. The system's modular design allows for easy integration into anaerobic chambers and supports customization for a wide range of experimental applications. It has been used to study microbial responses to antibiotics, dietary compounds, and pathogen invasion, and to screen for pathogen-resistant communities. With its accessibility, scalability, and reproducibility, the MBRA represents a powerful model system for investigating microbial interactions and advancing microbiome research.},
}

*Bioreactors/microbiology
*Microbiota/physiology
Humans

@article {pmid40982108,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Demonstrated role of sulfate-reducing bacterial consortia in anaerobic paracetamol biodegradation.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {91},
pmid = {40982108},
issn = {1572-9729},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST) PURSE Grant, New Delhi, India/ ; },
mesh = {*Acetaminophen/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Sulfates/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics/classification ; *Water Pollutants, Chemical/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The escalating global production and usage of paracetamol (C8H9NO2), a widely administered analgesic and antipyretic pharmaceutical, has led to its ubiquitous presence in environmental matrices, including surface waters, municipal wastewater, and even potable water sources. Owing to its persistence and bioaccumulative potential, paracetamol poses a significant ecotoxicological threat, particularly through trophic transfer in aquatic ecosystems. Conventional wastewater treatment methods often fall short in completely eliminating such micropollutants. In this context, bioremediation offers a promising, sustainable, and cost-effective alternative for pharmaceutical remediation. This study investigates the anaerobic degradation potential of two sulfate-reducing bacterial consortia, designated Consortium I and Consortium II, isolated from Okhla landfill leachate and enriched with distinct Postgate media formulations. Paracetamol was introduced at varying concentrations (50-500 mg/L), with and without supplementation of an auxiliary carbon source, sodium lactate. Metagenomic profiling via 16S rRNA sequencing revealed that Consortium I was primarily composed of Clostridium (40.1%) and Acidipropionibacterium (31.2%), whereas Consortium II exhibited a dominant presence of Clostridium (80.3%) and Bacillus (7.99%). Consortium II exhibited superior degradation kinetics, achieving complete removal of 500 mg/L paracetamol in 48 h under lactate-free conditions. Conversely, the presence of sodium lactate significantly attenuated degradation efficiency, suggesting substrate competition and metabolic preference. Gas chromatography-mass spectrometry (GC-MS) identified 4-aminophenol and hydroquinone as transient intermediates, supporting a proposed anaerobic degradation pathway for paracetamol. These findings underscore the potential of native sulfate reducing bacterial consortia in the bioremediation of contaminants and provide mechanistic insight into anaerobic paracetamol degradation, offering a viable strategy for enhanced treatment efficacy of contaminated waste streams.},
}

*Acetaminophen/metabolism
Biodegradation, Environmental
*Microbial Consortia
*Sulfates/metabolism
Anaerobiosis
*Bacteria/metabolism/genetics/classification
*Water Pollutants, Chemical/metabolism
RNA, Ribosomal, 16S/genetics