@article {pmid41804674,
year = {2026},
author = {Liu, D and Luo, M and Li, M and Chen, C and Chen, S and Wu, Y and Zhang, G and Gao, Y and Hong, Y and Zhou, Q and Li, X and Zhou, S and Wu, Y and Zhao, Y and Zhang, Y and Yin, J},
title = {Dynamic interaction between Escherichia coli enterotoxins and bacteriocins.},
journal = {The FEBS journal},
volume = {293},
number = {16},
pages = {4860-4881},
pmid = {41804674},
issn = {1742-4658},
support = {2023YFD1401400//the National Key R&D Program of China/ ; 32471200//the National Natural Science Foundation of China/ ; kq2208167//the Natural Science Foundation of Changsha/ ; xjt [2021] 346//the postgraduate joint training base project in Hunan Province/ ; 2023JJ10029//the Natural Science Foundation for Distinguished Young Scholars of Hunan Province/ ; },
mesh = {Animals ; *Enterotoxins/metabolism/genetics ; *Enterotoxigenic Escherichia coli/metabolism/genetics/pathogenicity ; *Bacteriocins/metabolism/genetics ; Mice ; *Escherichia coli Proteins/metabolism/genetics ; Colicins/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; *Bacterial Toxins/metabolism/genetics ; Signal Transduction ; Swine ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Coculture Techniques ; },
abstract = {The intestinal microbiota constitutes a crucial defense barrier against pathogenic invasion; however, the molecular mechanisms enabling pathogens to evade or modulate this defense remain poorly understood. Here, we established a coculture model combining the commensal Escherichia coli Y18J, isolated from the piglet gut, and the enterotoxigenic E. coli (ETEC) strain W25K to investigate microbe-pathogen interactions. Our findings reveal a bidirectional regulatory mechanism between Y18J and W25K mediated by bacteriocin and toxin signaling. Colicin B/M produced by Y18J upregulates the expression of heat-stable enterotoxin (ST) in W25K during the early phase of coculture, while ST suppresses colicin B/M synthesis in Y18J. At later stages, colicin B/M stimulates heat-labile enterotoxin (LT) expression, which in turn enhances colicin B/M production. Notably, LT markedly reduces intestinal colonization of W25K(ST[-]LT[+]) in murine hosts. Leveraging metagenomic and bioinformatic analyses, we further identified a Ligilactobacillus strain within the murine gut microbiota capable of producing multiple bacteriocins that effectively inhibit W25K colonization. Transcriptomic profiling of Y18J revealed glutamine synthetase as a pivotal regulator of colicin B/M-mediated antagonism. Mechanistic investigations demonstrated that ST suppresses colicin B/M expression through the cGMP signaling pathway, whereas LT enhances it via the cAMP signaling pathway. Collectively, these findings uncover a dual regulatory mechanism through which bacterial enterotoxins modulate probiotic antimicrobial activity, providing new insights into the molecular dialog between commensal and pathogenic bacteria. This study establishes a conceptual framework for developing microbiota-based strategies to prevent and control enteric infections.},
}

Animals
*Enterotoxins/metabolism/genetics
*Enterotoxigenic Escherichia coli/metabolism/genetics/pathogenicity
*Bacteriocins/metabolism/genetics
Mice
*Escherichia coli Proteins/metabolism/genetics
Colicins/genetics/metabolism
Gastrointestinal Microbiome/genetics
*Bacterial Toxins/metabolism/genetics
Signal Transduction
Swine
Escherichia coli/metabolism
Gene Expression Regulation, Bacterial
Coculture Techniques

@article {pmid42168845,
year = {2026},
author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P},
title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42168845},
issn = {1471-2180},
support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/metabolism/blood ; Biomarkers/blood ; Multiomics ; Metabolomics/methods ; Female ; *Gastrointestinal Microbiome ; Male ; Feces/microbiology ; Aged ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Dysbiosis/microbiology ; Metagenomics/methods ; },
abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.},
}

Humans
*Parkinson Disease/microbiology/metabolism/blood
Biomarkers/blood
Multiomics
Metabolomics/methods
Female
*Gastrointestinal Microbiome
Male
Feces/microbiology
Aged
Middle Aged
*Bacteria/classification/genetics/isolation & purification/metabolism
Dysbiosis/microbiology
Metagenomics/methods

@article {pmid42270686,
year = {2026},
author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ},
title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42270686},
issn = {2045-2322},
mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; Metagenome ; *Sequence Analysis, DNA/methods ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; DNA, Bacterial/genetics ; *Bacteria/genetics/classification ; },
abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.},
}

*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing
Metagenome
*Sequence Analysis, DNA/methods
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Reproducibility of Results
DNA, Bacterial/genetics
*Bacteria/genetics/classification

@article {pmid42271421,
year = {2026},
author = {Stanford, J and Supple, H and Collins, CE and Clarke, ED},
title = {Associations between diet, metabolome, gut microbiota and blood pressure in Australian adults.},
journal = {Nutrition journal},
volume = {25},
number = {1},
pages = {},
pmid = {42271421},
issn = {1475-2891},
mesh = {Humans ; Female ; Male ; *Blood Pressure/physiology ; Australia ; Adult ; Cross-Sectional Studies ; *Metabolome ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Diet ; Cross-Over Studies ; Nuts ; Hypertension ; Feces/microbiology ; Biomarkers/blood/urine ; },
abstract = {PURPOSE: Early metabolomic and microbial markers of blood pressure (BP) dysregulation may be detectable before clinical hypertension develops. This exploratory study aimed to examine associations among dietary intake, BP, metabolomic profiles (plasma and urine), and gut microbiota composition. A secondary aim was to assess whether circulating metabolites mediate relationships between significant dietary factors and BP.

METHOD: This was a cross-sectional analysis of baseline data from a randomised cross-over trial. Usual dietary intake was assessed using the Australian Eating Survey (AES)[®] - Heart version Food Frequency Questionnaire. In-clinic BP measurements were measured and participants provided plasma, urine, and stool samples. Plasma and urine were analysed via untargeted metabolomics. Stool samples were collected for shotgun metagenomic sequencing, though metagenomic data was not included in this analysis. Associations between BP, individual metabolites, microbial taxa, and alpha diversity were assessed using linear regression with false discovery rate (FDR) correction. Causal mediation analysis was performed using nonparametric bootstrapping.

RESULT: Thirty-four Australian adults (mean age: 38.4 ± 18.1 years; 52.9% female) had complete data at baseline. Nut intake (servings/day and % energy) was the only dietary factor significantly associated with systolic BP (SBP), with higher intake linked to a 1.13 mmHg reduction. Twenty-nine plasma lipid metabolites were significantly associated with SBP after FDR correction. Of these, nine lipid-related metabolites, particularly 1,2-dilinoleoyl-GPC (18:2/18:2) and 1-linoleoyl-GPC (18:2), were observed to partially mediate the nut-SBP relationship. No urinary metabolites or microbial taxa were significantly associated with BP.

CONCLUSIONS: In this exploratory cross-sectional study, specific lipid metabolites were associated with SBP and partly accounted for the nut-SBP association. These hypothesis-generating findings suggest potential biomarkers of nut intake and BP regulation, warranting confirmation in larger longitudinal, interventional, and mechanistic studies.

TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (Registration number ACTRN12622001321730, Registration date 12/10/2022).},
}

Humans
Female
Male
*Blood Pressure/physiology
Australia
Adult
Cross-Sectional Studies
*Metabolome
*Gastrointestinal Microbiome/physiology
Middle Aged
*Diet
Cross-Over Studies
Nuts
Hypertension
Feces/microbiology
Biomarkers/blood/urine

@article {pmid42283827,
year = {2026},
author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K},
title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42283827},
issn = {1432-184X},
support = {No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; Forests ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Introduced Species ; *Impatiens/microbiology/growth & development ; *Microbiota ; Poland ; Metagenomics ; Biodiversity ; },
abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.},
}

*Rhizosphere
*Soil Microbiology
Forests
*Bacteria/classification/genetics/isolation & purification/metabolism
Introduced Species
*Impatiens/microbiology/growth & development
*Microbiota
Poland
Metagenomics
Biodiversity

@article {pmid42285959,
year = {2026},
author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X},
title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42285959},
issn = {2158-3188},
mesh = {Humans ; Female ; Male ; Prospective Studies ; Aged ; *Gastrointestinal Microbiome/physiology ; *Cardiac Surgical Procedures/adverse effects ; Multiomics ; *Postoperative Complications/metabolism/microbiology ; Middle Aged ; *Amino Acids, Branched-Chain/metabolism ; Feces/microbiology ; *Delirium/metabolism/microbiology ; Preoperative Period ; Metabolomics ; },
abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.},
}

Humans
Female
Male
Prospective Studies
Aged
*Gastrointestinal Microbiome/physiology
*Cardiac Surgical Procedures/adverse effects
Multiomics
*Postoperative Complications/metabolism/microbiology
Middle Aged
*Amino Acids, Branched-Chain/metabolism
Feces/microbiology
*Delirium/metabolism/microbiology
Preoperative Period
Metabolomics

@article {pmid42286497,
year = {2026},
author = {Gao, X and Sanui, A and Rasmika Dewi, DAP and Lucaci, AG and Mason, CE and Suzuki, H},
title = {Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42286497},
issn = {2730-6844},
support = {U54AG089334//National Institute for Health and Care Research/ ; JPMJCR20H1//JST CREST/ ; 20K10436//JSPS KAKENHI/ ; JAHMEC.G-02, 2022//Japan Architectural Health, Management and Education Center Research grant/ ; },
mesh = {*Microbiota ; Tokyo ; Shotgun Sequencing ; *Metagenomics ; Humans ; *Railroads ; *Metagenome ; },
abstract = {OBJECTIVES: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide "Urban Microbiomes in Japan" project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments.

DATA DESCRIPTION: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 × 150 bp paired-end reads.},
}

*Microbiota
Tokyo
Shotgun Sequencing
*Metagenomics
Humans
*Railroads
*Metagenome

@article {pmid42429762,
year = {2026},
author = {Putman, T and Abdel-Hamid, AM and Galbraith, E and Schimmel, P and Kim, H and Yasuma, T and Alhawsawi, MAB and Boateng, KA and Holmes, J and Duersteler, M and D'Alessandro-Gabazza, CN and Fujimoto, H and Kobayashi, T and Walden, KKO and Rendon, G and Fields, CJ and Zuckermann, FA and Mackie, RI and Son, S and Leistikow, KR and Gabazza, EC and King, MR and Cann, I},
title = {A Bacillus-based direct-fed microbial mixture remodels the gut microbiome to augment the respiratory health of Salmonella-infected pigs.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {8},
pages = {e0097226},
pmid = {42429762},
issn = {1098-5336},
support = {MDG Project fund 547965//Microbial Discovery Group/ ; 2017-67015-26629//U.S. Department of Agriculture/ ; },
mesh = {Animals ; Swine ; *Salmonella Infections, Animal/microbiology/therapy ; *Bacillus/physiology ; *Gastrointestinal Microbiome/drug effects ; *Porcine Reproductive and Respiratory Syndrome/microbiology ; Lung/pathology/microbiology ; Animal Feed/analysis ; *Swine Diseases/microbiology ; Porcine respiratory and reproductive syndrome virus/physiology ; *Probiotics/administration & dosage ; },
abstract = {Commercial pork production is practiced worldwide and represents a major source of protein for global populations. Pigs, however, are plagued by various diseases that affect their productivity. A common practice is to administer antibiotics in the feed to reduce infections and promote growth. However, antibiotic utilization in pig production has been identified as a source of spread of antibiotic resistance genes, prompting the need for antibiotic alternatives in swine production. Salmonella enterica serotype Choleraesuis and porcine reproductive and respiratory syndrome virus (PRRSV) are two disease agents with a significant impact on the pork industry. In this study, we designed experiments to test the hypothesis that a Bacillus-based direct-fed microbial (DFM) cocktail will alleviate the impact of Salmonella infection alone or in combination with PRRSV. Both single and dual infections resulted in shifts in the cecal microbiota from that of the Control group, with administration of the DFM dampening this effect, especially in the Salmonella-infected group. In the absence of the DFM, the infected pigs exhibited gross changes in the lungs, including tissue hepatization. Significantly, the DFM application suppressed the lesions in the lungs of Salmonella-only infected pigs. Using metagenome-assembled genomes, we found that DFM administration to Salmonella-only infected pigs led to cecal microbiota enriched in the potential to produce immune-stimulating short-chain fatty acids and naturally occurring antimicrobials, including peptides. The putative antimicrobial peptides derived from this study, upon biochemical characterization, could lead to their application as novel antimicrobials in animal agriculture and health.IMPORTANCEAntibiotics, as feed additives, have been integral to commercial pork production. Their use, however, has fostered the spread of antibiotic resistance genes in the environment. In this study, we explored the use of a mixture of naturally occurring bacteria, comprising species of the genus Bacillus, as an alternative to antibiotics in the pig diet. The bacterial mixture reversed disease lesions in the lungs of pigs infected with Salmonella enterica serotype Choleraesuis, a bacterium that causes severe disease in commercial pigs. Our findings suggest that applying the bacterial mixture to the Salmonella-infected pigs shifts the microbes in the gut to a community that is endowed with antimicrobials that mitigate the effects of Salmonella infection. We present data showing the novelty of putative antimicrobials discovered in the present study and postulate that their characterization will yield new antimicrobials that can be used in different sectors of animal production and health. PRRSV was included in the study to model a common bacterial-viral co-infection in swine, as it exacerbates disease severity. This design allowed assessment of whether Bacillus-based DFM could improve outcomes along the gut-lung axis under realistic co-infection conditions.},
}

Animals
Swine
*Salmonella Infections, Animal/microbiology/therapy
*Bacillus/physiology
*Gastrointestinal Microbiome/drug effects
*Porcine Reproductive and Respiratory Syndrome/microbiology
Lung/pathology/microbiology
Animal Feed/analysis
*Swine Diseases/microbiology
Porcine respiratory and reproductive syndrome virus/physiology
*Probiotics/administration & dosage

@article {pmid42461036,
year = {2026},
author = {Munford, KE and Grégoire, DS and Hug, LA},
title = {Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {8},
pages = {e0031126},
pmid = {42461036},
issn = {1098-5336},
support = {Tier II//Canada Research Chairs/ ; ER19-15-228//Ontario Early Research Award/ ; 2016-03686//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Waste Disposal Facilities ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Solid Waste/analysis ; *Microbiota ; Metals/metabolism/analysis ; Water Pollutants, Chemical/analysis ; Metagenome ; },
abstract = {Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership, and metal cycling across a landfill's lifespan has not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing Older (aged 31-39 years) and Newer (aged 3-20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals-all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemical data from the time of filling to the present and microbial membership data across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual model for understanding this critical, final stage in a landfill's life cycle.IMPORTANCEAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond ~20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership, and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension-a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer term.},
}

*Waste Disposal Facilities
*Bacteria/genetics/metabolism/classification/isolation & purification
*Solid Waste/analysis
*Microbiota
Metals/metabolism/analysis
Water Pollutants, Chemical/analysis
Metagenome

@article {pmid42474201,
year = {2026},
author = {Palmer, B and Couradeau, EM and Johansen, JR and Kurbessoian, T and Carranza, JO and Stajich, JE and Ward, R and Pietrasiak, N},
title = {Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {8},
pages = {e0104326},
pmid = {42474201},
issn = {1098-5336},
support = {DEB-0842702//National Science Foundation/ ; DEB-841734//National Science Foundation/ ; DEB-9870201//National Science Foundation/ ; CA-R-PPA-5062-H//USDA National Institute of Food and Agriculture and Hatch Appropriations/ ; JOTR-2006-SCI-0018//National Park Service and Bureau of Land Management/ ; MOJA-2008-SCI-0024//National Park Service and Bureau of Land Management/ ; MOJA-2009-SCI-0039//National Park Service and Bureau of Land Management/ ; PEN04949//USDA National Institute of Food and Agriculture and Hatch Appropriations/ ; UT-06-032-12-P//National Park Service and Bureau of Land Management/ ; },
mesh = {*Cyanobacteria/genetics/classification/physiology/metabolism ; *Microbiota ; Metagenome ; *Soil Microbiology ; Phylogeny ; Metagenomics ; },
abstract = {The cyanosphere is composed of non-cyanobacterial microorganisms living within the exopolysaccharide sheath of cyanobacteria, interacting with the cyanobacterial hosts and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres can help predict the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity and functions within the cyanosphere remains limited. Here, we used metagenomic sequencing to reconstruct 415 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 terrestrial cyanobacteria cultures, representing 12 cyanobacterial orders. Our findings showed that the composition of cyanosphere microbial communities was significantly shaped by environmental factors such as habitat of host origin, including precipitation and temperature. Three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, suggesting a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, an anaerobic process that retains nitrogen in the host-cyanosphere system in contrast to denitrification. While nitrogen fixation was more common in the cyanobacteria, 15 cyanospheres also contained nitrogen fixation genes, including in hosts that were nitrogen fixation capable themselves. The cyanosphere also contained genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities.IMPORTANCEOur study identifies members of an understudied and under-valued microbial community, the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a novel approach to studying the cyanosphere, providing insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.},
}

*Cyanobacteria/genetics/classification/physiology/metabolism
*Microbiota
Metagenome
*Soil Microbiology
Phylogeny
Metagenomics

@article {pmid42496154,
year = {2026},
author = {Zhang, J and Cai, L and Wang, L and Zhang, L and Meng, N and Chen, A and Ma, Q},
title = {Marine antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one disrupts sediment microbiome structure and function: insights from absolute quantification and enzyme activity dynamics.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {8},
pages = {e0081926},
pmid = {42496154},
issn = {1098-5336},
support = {2025-MSLH-076//Liaoning Provincial Science and Technology Joint Program Project/ ; KF2026005//Key Laboratory of Biotechnology and Bioresources Utilization/ ; },
mesh = {*Geologic Sediments/microbiology ; *Disinfectants/pharmacology ; *Thiazoles/pharmacology/toxicity ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/analysis/genetics ; *Bacteria/drug effects/enzymology/genetics/classification ; },
abstract = {The organic booster biocide DCOIT (4,5-dichloro-2-n-octyl-4-isothiazolin-3-one) is widely used in marine antifouling systems, yet its ecological impacts on sediment microbiomes remain poorly understood. Here, we integrated absolute quantitative 16S rRNA gene sequencing, metagenomics, and enzyme activity assays to examine microbial responses to DCOIT exposure (0-50 μg/g sediment) over 30 days. DCOIT induced oxidative stress and bioenergetic impairment, accompanied by reduced microbial activity and inhibition of key enzyme-mediated processes involved in organic matter turnover and nitrogen transformation. Absolute quantification revealed a compensatory increase in total microbial abundance by Day 30, despite persistent diversity loss and community restructuring. Metagenomic analysis showed that DCOIT disturbed functional potentials related to carbon and nitrogen cycling. Kordiimonas, Aliikangiella, and Neptuniibacter emerged as potential contributors to nitrogen transformation, whereas Marinobacter was more closely associated with potential DCOIT transformation. DCOIT exposure also enriched adaptive traits, including chemotaxis, motility, quorum sensing, and biofilm regulation, and was accompanied by increased multidrug efflux systems and heavy metal resistance determinants. Our findings provide novel insights into the ecotoxicological risks of isothiazolinone biocides and highlight the potential for DCOIT to undermine sediment ecosystem functions and microbial habitat health. Given its extensive application, this study emphasizes the need to consider the microbial ecological consequences of DCOIT accumulation in seafloor environments.IMPORTANCEDCOIT is widely used in marine antifouling coatings and can accumulate in benthic sediments, yet its effects on sediment microbiomes remain poorly defined. This study shows that DCOIT disrupts microbial energy status, enzyme activities, community structure, and nitrogen-cycling functions while selecting for adaptive traits and resistance-related determinants. By integrating absolute quantification, metagenomics, and enzyme assays, our work demonstrates that DCOIT poses microbial ecological risks beyond toxicity to macroorganisms and should be considered in assessments of antifouling biocides.},
}

*Geologic Sediments/microbiology
*Disinfectants/pharmacology
*Thiazoles/pharmacology/toxicity
*Microbiota/drug effects
RNA, Ribosomal, 16S/analysis/genetics
*Bacteria/drug effects/enzymology/genetics/classification

@article {pmid42589241,
year = {2026},
author = {Wang, Q and Wang, BY and Wilus, D and Xie, H},
title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
pmid = {42589241},
issn = {1422-0067},
support = {R16GM149359/GM/NIGMS NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; R16 GM149359/GM/NIGMS NIH HHS/United States ; U01 DE033241/DE/NIDCR NIH HHS/United States ; UG3 HG013248/HG/NHGRI NIH HHS/United States ; U54MD007586/MD/NIMHD NIH HHS/United States ; },
mesh = {Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; Female ; Male ; Adult ; Middle Aged ; *Periodontitis/microbiology/therapy ; Metagenome ; Dental Scaling ; Root Planing ; Metagenomics/methods ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced probing depth, clinical attachment level, bleeding on probing, and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of the microbial community. Established periodontal pathogens, including Porphyromonas gingivalis, as well as the emerging pathogens Escherichia coli and Burkholderia multivorans, decreased following treatment. Tannerella forsythia also showed a marked reduction after treatment, although this decrease was not significant after false discovery rate (FDR) correction. In contrast, health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus, increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified significant treatment-associated differences in carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.},
}

Humans
*Dental Plaque/microbiology
*Microbiota/genetics
Female
Male
Adult
Middle Aged
*Periodontitis/microbiology/therapy
Metagenome
Dental Scaling
Root Planing
Metagenomics/methods

@article {pmid42589351,
year = {2026},
author = {Shen, H and Huang, S and Wang, Z and Zhou, S and Huang, L and Zhang, H and Han, Y and Jiang, J and Guo, H},
title = {Glycyrrhizic Acid Alleviates Atherosclerosis in ApoE[-/-] Mice via Microbial Indole-3-Lactic Acid-Mediated AhR-p65 Interaction in the Endothelium.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
pmid = {42589351},
issn = {1422-0067},
support = {No. 3332025150//Fundamental Research Funds for the Central Universities/ ; No. 2025-I2M-KJ-016//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Animals ; *Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology ; Mice ; *Glycyrrhizic Acid/pharmacology/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism ; Male ; *Transcription Factor RelA/metabolism ; *Apolipoproteins E/deficiency/genetics ; Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Humans ; Fecal Microbiota Transplantation ; Endothelium, Vascular/metabolism/drug effects ; Mice, Knockout ; },
abstract = {Glycyrrhizic acid (GL), a natural triterpenoid glycoside extracted from the "medicine food homology" herb Glycyrrhiza glabra L., exhibits potent anti-atherosclerotic effects; yet its underlying mechanisms remain unclear due to its poor oral bioavailability. The gut microbiota plays a pivotal role in the development of atherosclerosis (AS). In this study, the microbiota-dependent anti-AS effects of GL were evaluated in high-fat diet (HFD)-fed ApoE[-/-] mice using antibiotic depletion and fecal microbiota transplantation (FMT). Integrated metagenomic and metabolomic analyses were performed to identify the key bioactive microbial metabolite. Further in vivo and in vitro experiments, including co-immunoprecipitation and dual-luciferase reporter assays, were utilized to elucidate the underlying molecular mechanisms. It was demonstrated that oral administration of GL alleviated AS in a microbiota-dependent manner by reversing gut dysbiosis, improving intestinal barrier function, and reducing pro-inflammatory lipopolysaccharide (LPS) levels. GL shifted intestinal tryptophan metabolism toward bacterial-derived indole-3-lactic acid (ILA) production, suppressing LPS-induced vascular endothelial adhesion dysfunction by activating the aryl hydrocarbon receptor (AhR). Mechanistically, ILA-activated AhR interacted with the NF-κB subunit p65 in the cytoplasm, effectively preventing the nuclear translocation of p65 and suppressing the promoter activities of adhesion molecules (VCAM1 and ICAM1), resulting in the amelioration of HFD-induced AS. These findings elucidate the microbiota-dependent mechanism of orally administered GL against AS, and highlight the therapeutic potential of targeting the ILA-AhR-p65 axis in the vascular endothelium as a strategy for AS.},
}

Animals
*Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology
Mice
*Glycyrrhizic Acid/pharmacology/therapeutic use
*Receptors, Aryl Hydrocarbon/metabolism
*Indoles/metabolism
Male
*Transcription Factor RelA/metabolism
*Apolipoproteins E/deficiency/genetics
Gastrointestinal Microbiome/drug effects
Diet, High-Fat/adverse effects
Mice, Inbred C57BL
Humans
Fecal Microbiota Transplantation
Endothelium, Vascular/metabolism/drug effects
Mice, Knockout

@article {pmid42589527,
year = {2026},
author = {Coppini, M and Mauceri, R and Vacca, D and Bertolazzi, G and Caponio, VCA and Rodolico, V and Belmonte, B and Campisi, G},
title = {Longitudinal Exploratory Analysis of Salivary Microbiota Profiles in Patients with Oral Squamous Cell Carcinoma Before and After Surgery: A Pilot Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
pmid = {42589527},
issn = {1422-0067},
mesh = {Humans ; *Saliva/microbiology ; Pilot Projects ; *Mouth Neoplasms/microbiology/surgery ; Female ; Male ; *Microbiota ; *Carcinoma, Squamous Cell/surgery/microbiology ; Middle Aged ; Aged ; Longitudinal Studies ; Metagenomics/methods ; Bacteria/genetics/classification ; Adult ; Metagenome ; },
abstract = {Salivary microbiome profiling may represent a promising non-invasive approach for characterizing OSCC-associated microbial patterns and longitudinal microbiome dynamics during patient management. This exploratory pilot study aimed to longitudinally assess salivary microbiota profiles in patients with oral squamous cell carcinoma (OSCC) before and after tumor resection using Oxford Nanopore Technology. Unstimulated saliva samples were collected from 16 patients with OSCC at two time points (before and after tumor resection) and from 10 OSCC-free reference subjects. Microbial DNA was extracted using the QIAamp DNA Blood Kit (QIAGEN GmbH, Hilden, Germany) and subjected to long read metagenomic sequencing using the Oxford Nanopore MinION platform (v. 20.06.4, Oxford Nanopore Technologies, Oxford, UK). Taxonomic profiling was performed to longitudinally characterize salivary microbiota composition within patients and to provide descriptive comparisons with the OSCC-free reference cohort. Longitudinal analysis identified differences in salivary microbiota profiles between pre- and post-resection samples. Before surgery, an increased relative abundance of Neisseria subflava and Leptotrichia buccalis was observed. Post-surgical samples showed higher levels of Glaesserella parasuis, Streptomyces anulatus, and Lactobacillus species. Distinct microbial patterns were also descriptively observed between OSCC patients and OSCC-free controls, suggesting disease-associated dysbiosis. This exploratory longitudinal pilot study suggests differences in salivary microbiota profiles between samples collected before and after tumor resection in patients with OSCC, including changes in taxonomic composition and reduced alpha diversity. Given the limited sample size and the potential influence of unmeasured perioperative factors, these findings should be considered hypothesis-generating. Larger, well-controlled longitudinal studies incorporating standardized oral health assessment and detailed perioperative metadata are required to clarify the biological and clinical relevance of these observations.},
}

Humans
*Saliva/microbiology
Pilot Projects
*Mouth Neoplasms/microbiology/surgery
Female
Male
*Microbiota
*Carcinoma, Squamous Cell/surgery/microbiology
Middle Aged
Aged
Longitudinal Studies
Metagenomics/methods
Bacteria/genetics/classification
Adult
Metagenome

@article {pmid42589672,
year = {2026},
author = {Zeng, C and Chen, J and Yong, X and Xie, Y},
title = {Convergent Gut Microbiome Remodeling Across Ischemic Stroke, Myocardial Infarction, and Longevity Reveals a Shared Ecological Signature of Aging and Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
pmid = {42589672},
issn = {1422-0067},
support = {cstc2021jcyj-msxmx0848//Natural Science Foundation of Chongqing/ ; BSKJ2022006//Bishan District Science and Technology Bureau/ ; 81773954//National Natural Science Foundation of China (NSFC)/ ; 202310617015//National College Student Innovation and Entrepreneurship Program/ ; X2024160170123, X2026106170029//Chongqing College Students' Innovation and Entrepreneurship Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Aging ; *Myocardial Infarction/microbiology ; *Longevity ; *Ischemic Stroke/microbiology ; Male ; Female ; Aged ; Dysbiosis/microbiology ; },
abstract = {Gut microbiota dysbiosis has been associated with ischemic stroke (IS), myocardial infarction (MI), and aging, but whether these contexts share reproducible microbial features remains unclear. We conducted an exploratory and hypothesis-generating descriptive study of genus-level microbiota patterns across an internal IS cohort and publicly available external IS, MI, and age-stratified or longevity-associated datasets. Analyses were performed within predefined age strata and interpreted cautiously because of the small internal cohort, cross-cohort heterogeneity, and the absence of direct metabolite, intestinal barrier, inflammatory, or microbial activity measurements. No taxon in the internal cohort remained statistically significant after false-discovery-rate correction; therefore, all taxonomic observations were treated as descriptive. Candidate overlapping features included repeated detection of Escherichia-Shigella and Klebsiella and non-uniform patterns among genera previously associated with short-chain fatty acid metabolism, including Faecalibacterium, Blautia, and Roseburia. Lachnoclostridium and Bacteroides showed opposite abundance gradients in selected cross-dataset comparisons. These observations suggest possible ecological overlap across ischemic disease and age-associated microbiome contexts, but they do not establish causality, disease-specific biomarkers, or shared microbial function. The mechanistic models discussed in this manuscript are literature-informed hypotheses based on exploratory compositional data and require future validation in larger, harmonized longitudinal cohorts using metagenomic, metabolomic, clinical, and experimental measurements.},
}

Humans
*Gastrointestinal Microbiome
*Aging
*Myocardial Infarction/microbiology
*Longevity
*Ischemic Stroke/microbiology
Male
Female
Aged
Dysbiosis/microbiology

@article {pmid42593705,
year = {2026},
author = {Wei, W and Zhou, L and Huang, Y and Lu, Z and Zhang, R and Zeng, M and Wang, X},
title = {Association Between Gut Microbiota Dysbiosis and Bilirubin Metabolism Dysregulation in Children with Heart Failure.},
journal = {Journal of cardiovascular translational research},
volume = {19},
number = {1},
pages = {},
pmid = {42593705},
issn = {1937-5395},
mesh = {Humans ; *Heart Failure/microbiology/diagnosis/blood ; *Bilirubin/blood ; *Dysbiosis ; *Gastrointestinal Microbiome ; Female ; Child, Preschool ; Male ; Child ; Case-Control Studies ; Biomarkers/blood ; Feces/microbiology ; Age Factors ; Metabolomics ; Infant ; Ribotyping ; Clostridium/genetics ; Adolescent ; Eubacteriales ; },
abstract = {Patients with heart failure (HF) demonstrate dysregulation in bilirubin metabolism. The specific characteristics of intestinal bilirubin metabolism in HF remain unclear. This study involved metagenomic sequencing and metabolomic profiling of fecal samples from 45 children with HF and 32 healthy children. Serum total bilirubin levels were 11.3umol/L, 19.4umol/L and 5.0umol/L in HF New York Heart Association (NYHA) I-II, NYHA III-IV and control group (p < 0.001), and the median gut microbiome health index (GMHI) were - 0.78, -1.53 and 0.09 in each (p < 0.001). The abundance of 2 bacteria species containing bilirubin reductase, Ruminococcus gnavus (p = 0.028) and Clostridium sp.M62/1 (p = 0.002) significantly decreased in NYHA III-IV group. The gut downstream bilirubin products, urobilinogen and stercobilin were decreased in the HF group; while the upstream bilirubin products, unconjugated and conjugated bilirubin increased. Dysbiosis of the gut microbiome and the decrease of bilirubin reductase containing bacteria in pediatric HF patients related to a reduction in gut bilirubin metabolism.},
}

Humans
*Heart Failure/microbiology/diagnosis/blood
*Bilirubin/blood
*Dysbiosis
*Gastrointestinal Microbiome
Female
Child, Preschool
Male
Child
Case-Control Studies
Biomarkers/blood
Feces/microbiology
Age Factors
Metabolomics
Infant
Ribotyping
Clostridium/genetics
Adolescent
Eubacteriales

@article {pmid42594433,
year = {2026},
author = {Fan, Y and Wei, Q and Zhang, P and Zou, L and Aisikaier, A and Ma, X and Dai, Z and Tian, Y and Li, Y and Wang, F and Yang, S and Cao, W},
title = {Hydrological regime modulates nitrogen retention-removal shifts in a glacier-oasis alpine river by restructuring multi-trophic interactions and microbial assembly.},
journal = {Journal of environmental management},
volume = {415},
number = {},
pages = {130604},
doi = {10.1016/j.jenvman.2026.130604},
pmid = {42594433},
issn = {1095-8630},
abstract = {Nitrogen (N) cycling in glacier-oasis alpine rivers exhibits distinct spatiotemporal patterns driven by multi-trophic community interactions. This study integrated 16S/18S rRNA sequencing with metagenomic analysis to investigate N-transformation dynamics across trophic levels and their response to varying hydrological regimes. The α-diversity of multi-trophic communities exhibited trophic-level-specific longitudinal patterns, with bacteria and algae generally showing higher diversity in the oasis reach (OR), whereas protozoans and metazoans were more diverse in the glacial reach (GR). In the OR, the species turnover of microeukaryotes exceeded 40%, and the pooled OR-irrigation channel reach (ICR) group exhibited 9.1-22.6-fold greater network complexity than the GR. The abundances of functional genes associated with nitrification and denitrification were 12.3-13.8 and 4.7-9.6 times higher in the OR than in the GR, respectively; N fixation potential was 2.4-14.1 times greater and bacterial α-diversity was 0.94-1.42 times higher in the OR than in the GR. Notably, only during the dry season did the GR exhibit 63-84% higher nitrate assimilation than the OR. Path analysis revealed that algae-protozoan symbiosis promoted N assimilation and retention (β = 0.87), whereas bacterial communities enhanced dissimilatory nitrate reduction and denitrification, facilitating N removal (β > 0.66). In contrast, metazoan predation (β = -0.78) and dissolved oxygen (β = -0.24) suppressed denitrification. The differentiation of N-cycling functions was governed by high α- and β-diversity within microbial communities. Heterogeneous selection and dispersal limitation during community assembly, acting through cross-trophic cascading effects, collectively balanced N retention against removal and ultimately determined the fate of N in the river ecosystem. Climate change may redistribute N-cycling hotspots along alpine rivers by altering hydrological regimes and riverine gradients, potentially increasing eutrophication risk by reducing N removal and enhancing N retention.},
}

@article {pmid42185302,
year = {2026},
author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R},
title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42185302},
issn = {2055-5008},
support = {2020/06077-9//São Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//São Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; },
mesh = {*Triticum/microbiology/growth & development ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; *Disease Resistance ; Rhizosphere ; Plant Roots/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.},
}

*Triticum/microbiology/growth & development
*Soil Microbiology
*Plant Diseases/microbiology/prevention & control
*Microbiota
*Disease Resistance
Rhizosphere
Plant Roots/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid42376710,
year = {2026},
author = {Arguelles, EDLR and Mugikura, K and Sato, S},
title = {Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin.},
journal = {Journal of phycology},
volume = {62},
number = {4},
pages = {1221-1239},
doi = {10.1111/jpy.70195},
pmid = {42376710},
issn = {1529-8817},
support = {21A402//Japan Society for the Promotion of Science/ ; 23K05398//Japan Society for the Promotion of Science/ ; 26K01814//Japan Society for the Promotion of Science/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {*Diatoms/physiology ; *Microbiota ; *Biofilms/growth & development ; *Zeatin/metabolism ; *Introduced Species ; *Rivers/microbiology ; Japan ; Bacteria/metabolism ; Eutrophication ; },
abstract = {The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.},
}

*Diatoms/physiology
*Microbiota
*Biofilms/growth & development
*Zeatin/metabolism
*Introduced Species
*Rivers/microbiology
Japan
Bacteria/metabolism
Eutrophication

@article {pmid42429677,
year = {2026},
author = {Sarkar, M and Maddheshiya, A and Tailor, P and Nath, S and Makkar, N and , and Misra, S and Desiraju, BK and Wadhwa, N and Bhatnagar, S and Kshetrapal, P and Mukherjee, S},
title = {Longitudinal shifts in oral microbiome composition and metabolic pathways associated with preterm birth.},
journal = {mSystems},
volume = {11},
number = {8},
pages = {e0018426},
doi = {10.1128/msystems.00184-26},
pmid = {42429677},
issn = {2379-5077},
support = {BT/PR34219/MED/97/463/2019//Department of Biotechnology, Ministry of Science and Technology, India/ ; 60108//BRIC-NIBMG Intramural funding/ ; },
mesh = {Humans ; Female ; *Premature Birth/microbiology/metabolism ; *Microbiota/genetics ; Pregnancy ; *Metabolic Networks and Pathways ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Adult ; Longitudinal Studies ; Saliva/microbiology ; },
abstract = {Oral dysbiosis in pregnant women with oral diseases has been associated with adverse pregnancy outcomes. However, the inter-individual variability in oral microbiome composition of pregnant women without any oral disease, and its role in preterm birth, has not been studied yet. Here, we have collected saliva from 20 term birth (TB) and 20 preterm birth (PTB) delivering women without any self-reported oral disease at three trimesters (n = 120). Microbial DNA was subjected to 16S rRNA gene sequencing for taxonomic classification, and microbial pathways were investigated by PICRUSt2. In a subset of samples, shotgun metagenomic sequencing was done to identify microbial species, their gene families, and their pathways. TB and PTB women were distributed into three distinct oral community types (OCTs). Haemophilus parainfluenzae and Rothia mucilaginosa were associated with TB and PTB, respectively. The chorismate biosynthesis pathway, essential for folic acid biosynthesis, was significantly enriched in TB, whereas the enterobactin biosynthesis pathway that produces iron chelators (siderophores) was significantly enriched in PTB. The heterolactic fermentation pathway that reduces oral pH was enriched in PTB. Our data suggest that oral microbiome changes might have an impact on birth outcomes in women even without any history of self-reported oral disease during the pregnancy period.IMPORTANCEThe importance of this study lies in demonstrating that compositional and functional shifts in the oral microbiome are associated with pregnancy outcomes. Using a longitudinal design across three trimesters in an Indian cohort, we show that pregnant women segregate into distinct oral community types with consistent associations to term birth (TB) and preterm birth (PTB). Importantly, the TB-associated microbiome was enriched in taxa and pathways linked to vitamin and amino acid biosynthesis, including chorismate and threonine metabolism, which are critical for fetal growth. In contrast, PTB was associated with pathways related to iron scavenging and acidification of the oral environment, suggesting a metabolically stressed and dysbiotic state. These findings highlight the oral microbiome as a previously underappreciated, modifiable factor in pregnancy outcomes and underscore its potential relevance for early risk stratification and preventive strategies against PTB.},
}

Humans
Female
*Premature Birth/microbiology/metabolism
*Microbiota/genetics
Pregnancy
*Metabolic Networks and Pathways
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Adult
Longitudinal Studies
Saliva/microbiology

@article {pmid42523106,
year = {2026},
author = {Xu, S and Yang, L and Gao, J and Shi, Y and Tang, X and Cai, H and Yang, L and Han, Y and Lin, L and Meng, R and Sun, J and Guan, W-j and Tang, T and Shu, W and Cao, C and Zheng, X-y and Wang, Z and Yi, X},
title = {The associations of human genetic variations with airway microbiome, environmental exposures, and respiratory health.},
journal = {mSystems},
volume = {11},
number = {8},
pages = {e0044226},
doi = {10.1128/msystems.00442-26},
pmid = {42523106},
issn = {2379-5077},
support = {2022YFA1304300//National Key Research and Development Program of China/ ; 82495200, 82495201, 32170109, 32470094, 82404335, 32400372//National Natural Science Foundation of China/ ; 2024ZD0528400, 2025ZD0549003//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; GZNL2023A02001//Major Project of Guangzhou National Laboratory/ ; 2023A1515012367, 2023A1515012328//GuangDong Basic and Applied Basic Research Foundation/ ; 0820250237//Guangdong Special Support Program/ ; SKLRD-OP-202507//Open Project of Sate Key Laboratory of Respiratory Disease/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Environmental Exposure/adverse effects ; *Genetic Variation ; Female ; Male ; *Respiratory System/microbiology ; Air Pollutants/adverse effects ; Polymorphism, Single Nucleotide ; Middle Aged ; Sputum/microbiology ; Pulmonary Disease, Chronic Obstructive/genetics/microbiology ; },
abstract = {UNLABELLED: The intricate interactions between environmental exposures, the respiratory microbiome, and host genetic variations remain inadequately understood in the context of respiratory health. This study utilized sputum metagenomic data from 1,651 individuals in our previous cohort to elucidate these associations. Mendelian randomization indicated that air pollutants (e.g., SO2, CO, and PM2.5) were associated with lung function, which is potentially mediated by microbes, such as Actinomyces, Haemophilus influenzae, and Veillonella spp. Several genetic loci associated with respiratory microbiome variation were found to be linked to genotype-dependent associations between environmental exposures and lung function. For bacteria, the MEOX1 locus (rs1973191819) was associated with lower Filifactor alocis abundance under air pollutant exposure. The FAM110D (1:26157175) and USP36 (rs1343834070) loci showed associations with higher levels of certain pathogenic taxa (e.g., Ralstonia pickettii, Neisseria) and lower levels of the commensal Oribacterium, increasing chronic obstructive pulmonary disease (COPD) risk. For fungi, DNAJC18 and CCDC57 loci exhibited associations with Candida and Penicillium abundance, respectively. These genotype-dependent associations between the microbiome and environmental exposures provide insights into airway dysbiosis and susceptibility to respiratory diseases.

IMPORTANCE: This study reveals why individuals exposed to identical air pollution exhibit varying degrees of respiratory severity, pointing to a critical missing link: our genetics. While pollution is a known disease trigger, our findings demonstrate that host genetic variation actively regulates and shapes the respiratory microbiome under environmental stress. By mapping specific genetic loci to pollutant-driven bacterial shifts, this work elucidates how host genetics filters environmental risks to govern microbial homeostasis. These results underscore the necessity of incorporating host-microbiome genetic regulation into environmental health research. Ultimately, this study shifts the paradigm toward personalized medicine, enabling the early identification of at-risk individuals and the development of targeted, microbiome-informed interventions.},
}

Humans
*Microbiota/genetics
*Environmental Exposure/adverse effects
*Genetic Variation
Female
Male
*Respiratory System/microbiology
Air Pollutants/adverse effects
Polymorphism, Single Nucleotide
Middle Aged
Sputum/microbiology
Pulmonary Disease, Chronic Obstructive/genetics/microbiology

@article {pmid42532286,
year = {2026},
author = {Zhang, Y and Hu, L and Ding, X and Liu, L and Xue, L and Miao, L},
title = {Investigating gut microbiota and their metabolites as biomarkers for tacrolimus pharmacokinetic variability.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {225},
number = {},
pages = {107626},
doi = {10.1016/j.ejps.2026.107626},
pmid = {42532286},
issn = {1879-0720},
mesh = {*Tacrolimus/pharmacokinetics ; *Immunosuppressive Agents/pharmacokinetics ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; Humans ; Kidney Transplantation ; Biomarkers/metabolism ; Male ; Female ; },
abstract = {Tacrolimus (TAC), a cornerstone immunosuppressant in transplantation, presents a clinical challenge due to its narrow therapeutic index and substantial interindividual pharmacokinetic (PK) variability. This exploratory study investigated the association between gut microbiota composition, short-chain fatty acid (SCFA) metabolites, and TAC PK variability during the early post-kidney transplantation period. Based on prediction errors derived from a previously established population PK model, 36 transplant recipients were stratified into positive (n = 17) and negative (n = 19) deviation groups. Metagenomic sequencing and targeted SCFA metabolomic analysis of fecal samples revealed that the negative deviation group exhibited significantly reduced gut microbial diversity and altered community structure. Among 142 differentially abundant taxa, 10 microbial features, including Enterococcaceae - associated taxa, showed discriminative potential between the two PK phenotypes (AUC > 0.7), with three Enterococcus species (E. durans, E. faecium, and E. hirae) showing particularly robust signals (Cohen's d > 1.0 and power > 80%). Functional analysis suggested downregulation of butyrate biosynthesis pathways in the negative deviation group, which was consistent with significantly lower fecal butyrate and total SCFA concentrations. These hypothesis-generating findings suggest that gut microbiota and SCFAs are associated with TAC PK phenotypes, but independent validation in larger cohorts is required before clinical translation.},
}

*Tacrolimus/pharmacokinetics
*Immunosuppressive Agents/pharmacokinetics
Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome
Feces/microbiology/chemistry
Humans
Kidney Transplantation
Biomarkers/metabolism
Male
Female

@article {pmid42579339,
year = {2026},
author = {Douwes, H and Dutkiewicz, Z and Rinke, C},
title = {Predicting the plastic biodegradation potential within microbial lineages and across global ecosystems.},
journal = {Microbial genomics},
volume = {12},
number = {8},
pages = {},
pmid = {42579339},
issn = {2057-5858},
mesh = {*Plastics/metabolism ; *Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism/enzymology ; Metagenome ; *Archaea/genetics/classification/metabolism/enzymology ; Ecosystem ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Hidden Markov Models ; },
abstract = {Plastic waste pollution is a global issue that threatens biodiversity and human health. Current plastic waste management practices are not sufficient to keep up with increasing plastic production rates. Microorganisms have the capacity to degrade different types of bio-based and synthetic plastics through enzymatic reactions, offering an alternative solution to traditional plastic recycling techniques. A limited number of plastic-degrading enzymes have been identified, sequenced and characterized; however, studies exploring the distribution of homologues of these enzymes across habitats and microbial taxa have remained scarce. Here, we applied analytical techniques to search for genes encoding potential plastic-degrading enzymes in environmental metagenome datasets and genomes of the Genome Taxonomy Database (GTDB) to explore the geographic and taxonomic distribution patterns of plastic-degrading microorganisms. Hidden Markov Models (HMMs) were constructed from amino acid sequences of known, experimentally verified and putative plastic-degrading enzymes. The HMMs were applied to landfill, soil, river, lake and ocean metagenomes and all archaeal and bacterial genomes in the GTDB. An abundance of hits was discovered across aquatic and terrestrial metagenomes with the majority occurring in polluted rivers, polar oceans and deep ocean samples. GTDB hits were mainly consistent with known plastic-degrading microbial lineages, while also revealing potential plastic-degrading archaeal taxa. The results of this study may be able to assist in the discovery of novel plastic-degrading enzymes for application in plastic waste biodegradation solutions.},
}

*Plastics/metabolism
*Biodegradation, Environmental
*Bacteria/genetics/classification/metabolism/enzymology
Metagenome
*Archaea/genetics/classification/metabolism/enzymology
Ecosystem
Phylogeny
Metagenomics
Genome, Bacterial
Hidden Markov Models

@article {pmid42583788,
year = {2026},
author = {Han, L and Wu, X and Gong, B and Li, X and Li, X and Wang, Z},
title = {A Two-Sample Mendelian Randomisation Analysis of the Oral Microbiome and Oral/Oropharyngeal/Tongue Cancers.},
journal = {Oral health & preventive dentistry},
volume = {24},
number = {},
pages = {613-621},
pmid = {42583788},
issn = {1757-9996},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Tongue Neoplasms/microbiology ; *Oropharyngeal Neoplasms/microbiology ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Mouth Neoplasms/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Tongue/microbiology ; },
abstract = {OBJECTIVE: To assess the potential causal relationships of the oral microbiome with the risks of oral cancer, oropharyngeal cancer, and tongue cancer using two-sample Mendelian randomisation (MR) analysis, while distinguishing these from reverse causal effects of the cancers on microbial abundance.

METHODS AND MATERIALS: Using single-nucleotide polymorphisms as instrumental variables, we applied the MR inverse-variance-weighted approach to evaluate the effects of the dorsal-tongue and salivary microbiomes on oral, oropharyngeal, and tongue cancers. Analyses were conducted with the R package TwoSampleMR, leveraging genome-wide association study (GWAS) summary statistics from CNGBdb, the FinnGen consortium, and other sources. Sensitivity, heterogeneity, and pleiotropy assessments were performed. Additionally, reverse MR sensitivity analyses were conducted to explore the possible causal influence of cancers on the oral microbiota.

RESULTS: Using a single nucleotide polymorphism (SNP) significance threshold of p 5 × 10-6, our large-scale MR study revealed genetically supported causal relationships between microbial taxa derived from saliva and the tongue and the risk of oral, oropharyngeal, and tongue cancers. Integrating these results, we found that both 's Veillonella_rogosae_mgs_2008' and 's unclassified_mgs_1048' conferred a reduced risk of oropharyngeal and tongue cancers. Sensitivity analyses based on heterogeneity tests and pleiotropy evaluations further corroborated the robustness of our findings, lending additional credibility to the conclusions.

CONCLUSION: This study leveraged large-scale publicly available genetic data and identified significant causal relationships between the oral microbiota and cancers of the oral cavity, oropharynx, and tongue. Reverse MR analyses indicated that oral and tongue cancers may in turn alter the abundance of specific oral microbes, suggesting a potential bidirectional causal loop. Future work should integrate metagenomic data to further validate these microbiota-cancer associations.},
}

Humans
*Mendelian Randomization Analysis
*Microbiota/genetics
*Tongue Neoplasms/microbiology
*Oropharyngeal Neoplasms/microbiology
Polymorphism, Single Nucleotide
Genome-Wide Association Study
*Mouth Neoplasms/microbiology
Saliva/microbiology
*Mouth/microbiology
Tongue/microbiology

@article {pmid42584931,
year = {2026},
author = {Kaszecki, E and Azimychetabi, Z and Emery, RJN and Saville, BJ},
title = {Integrated transcriptomic and hormonomic insights into cadmium tolerance of a Euglena mutabilis fungal-algal-bacterial consortium.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
pmid = {42584931},
issn = {1465-2080},
mesh = {*Cadmium/metabolism/toxicity ; *Transcriptome ; *Euglena/genetics/metabolism/drug effects ; *Microbial Consortia/genetics ; *Fungi/genetics/metabolism ; Gene Expression Profiling ; *Bacteria/genetics/metabolism/classification ; Chloroplasts/metabolism ; },
abstract = {Acidic, metal-contaminated environments harbour specialized microbial consortia adapted to extreme stress. We examined an environmental Euglena mutabilis culture naturally associated with Talaromyces and Acidiphilium acidophilum and exposed it to cadmium (Cd). Integrated transcriptomic, hormonal, structural and taxonomic analyses revealed a coordinated Cd-tolerance strategy. RNA sequencing showed differential regulation of metal transporters consistent with a shift from Cd uptake to intracellular sequestration. Transmission electron microscopy confirmed Cd compartmentalization within chloroplasts and increased paramylon granules. Cd exposure suppressed light-harvesting complex genes and formate/nitrite transporters while maintaining core photosynthetic function. Hormone profiling indicated strong repression of bioactive auxin and cytokinin (CK) free bases, alongside accumulation of CK nucleotides and downregulation of CK biosynthetic and activation genes. Metagenomics revealed Cd-driven enrichment of Talaromyces and Acidiphilium, implicating them in detoxification and stress support. Together, these responses highlight early Cd uptake followed by chloroplast-based detoxification, metabolic buffering via paramylon, hormonal downregulation of growth and community-mediated resilience.},
}

*Cadmium/metabolism/toxicity
*Transcriptome
*Euglena/genetics/metabolism/drug effects
*Microbial Consortia/genetics
*Fungi/genetics/metabolism
Gene Expression Profiling
*Bacteria/genetics/metabolism/classification
Chloroplasts/metabolism

@article {pmid42587419,
year = {2026},
author = {Chang, H and Yang, Y and Zhang, P and Lei, Z and Zhang, Y and Li, S and Wang, L and Wang, Y and Jiang, J and Li, L and Shi, H and Shi, A},
title = {Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {9},
pages = {e70836},
pmid = {42587419},
issn = {1478-3231},
support = {2025JC-YBQN-1179//Natural Science Basic Research Program of Shaanxi Province/ ; 2025SCIPT-63//Scientific Research Supporting Fund of the Second Affiliated Hospital of Xi'an Jiaotong University/ ; },
mesh = {Humans ; *Liver Cirrhosis/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/genetics ; Case-Control Studies ; Metagenome ; Metagenomics ; Male ; },
abstract = {BACKGROUND: The gut microbiota contributes to liver cirrhosis (LC), yet the gut virome and its cross-kingdom ecology with bacteria are less well defined.

METHODS: To characterize LC-associated virome alterations and assess their clinical relevance, we reanalyzed publicly available faecal metagenomes from patients with LC and healthy controls. After quality control and removal of human reads, sequences were mapped to the Chinese Gut Viral Catalogue at 95% nucleotide similarity, viral operational taxonomic units (vOTUs) were annotated using the latest ICTV framework, and viral functions were inferred by KEGG annotation. Differential vOTUs and bacterial species, virus-bacteria networks and random forest classifiers were constructed with internal and external validation.

RESULTS: LC showed reduced viral richness and Shannon diversity, and a distinct Bray-Curtis separation from controls. Ten viral families and 473 vOTUs differed between groups (59 LC-enriched). KEGG-based profiling highlighted functional shifts in LC-enriched viruses, including increased K01185 (lysozyme) and K02172 (blaR1). Virus-bacteria networks were markedly sparser in LC than in controls (130 vs. 509 significant correlations). A virome-based random forest model distinguished patients from controls with high accuracy in internal (optimal AUC = 0.911) and external (optimal AUC = 0.773) validation cohorts, and the model combining viral and bacterial features achieved similarly robust performance.

CONCLUSIONS: LC is associated with disrupted gut viral-bacterial ecology, and virome features show promise as non-invasive biomarkers, warranting longitudinal and mechanistic follow-up.},
}

Humans
*Liver Cirrhosis/microbiology/virology
*Virome
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/genetics
Case-Control Studies
Metagenome
Metagenomics
Male

@article {pmid42588064,
year = {2026},
author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA},
title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.},
journal = {Nutrients},
volume = {18},
number = {15},
pages = {},
pmid = {42588064},
issn = {2072-6643},
support = {E022 Program Recursos Fiscales para la Investigación//Instituto Nacional de Pediatria/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration & dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration & dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; },
abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.},
}

Humans
*Autism Spectrum Disorder/microbiology/therapy
Male
*Gastrointestinal Microbiome/genetics
Female
Mexico
Longitudinal Studies
*Synbiotics/administration & dosage
Child
Feces/microbiology
Child, Preschool
Probiotics/administration & dosage
Dietary Supplements
Treatment Outcome
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology

@article {pmid42530375,
year = {2026},
author = {Wang, Z and Gao, Q and Li, S and Fang, Z and Hu, L and Li, R and Zeng, Z and Liu, Y and Li, C and Chen, H},
title = {Epigallocatechin gallate inhibits high-fat/choline diet-induced trimethylamine production via regulation of intestinal Serratia and Lactobacillus communities.},
journal = {Food & function},
volume = {17},
number = {16},
pages = {7400-7414},
doi = {10.1039/d6fo02528e},
pmid = {42530375},
issn = {2042-650X},
mesh = {Animals ; *Catechin/analogs & derivatives/pharmacology ; *Methylamines/metabolism ; *Choline/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; Male ; *Lactobacillus/drug effects/metabolism ; Intestines/microbiology ; Mice, Inbred C57BL ; },
abstract = {High-fat/choline diets can induce the production of the enterogenous metabolite trimethylamine-N-oxide (TMAO). TMAO is synthesized from its precursor trimethylamine (TMA), which is generated via choline cleavage catalyzed by choline trimethylamine-lyase/choline TMA-lyase-activating enzyme (CutC/D) expressed by gut microbes; subsequently, TMA is oxidized to TMAO by flavin-containing monooxygenase 3 (FMO3) in the liver. While epigallocatechin gallate (EGCG) is well recognized for its gut microbiota-remodeling capacity, how it modulates TMA/TMAO metabolism through this pathway, along with the time-dependent effectiveness of EGCG intervention, remains to be elucidated. We conducted animal experiments to evaluate the inhibitory effect of time-dependent EGCG intervention on TMA/TMAO production induced by high-fat/choline diets in mice. We further identified gut bacterial strains associated with TMA levels using metagenomics and machine learning techniques, and verified the underlying mechanisms through in vitro anaerobic culture and molecular simulations. Results demonstrated EGCG significantly reduced TMA/TMAO levels in mice by regulating the choline-CutC/D-FMO3 axis. Specifically, Serratia exhibited a positive correlation with CutC enzyme activity, while Lactobacillus showed a negative correlation with TMA levels. Mechanistically, EGCG exerted a direct bacteriostatic effect on Serratia marcescens by disrupting its cell membrane structure and inhibiting its CutC enzyme activity. Meanwhile, EGCG significantly enriched Lactobacillus johnsonii, with the abundance of this strain peaking after long-term intervention. Although Lactobacillus johnsonii does not directly degrade TMA, it indirectly reduces TMA levels by inhibiting the growth of Serratia marcescens. Long-term continuous supplementation with EGCG yielded the optimal inhibitory effect on TMA/TMAO production. Hence, EGCG exerts its function primarily through a dual mechanism: directly inhibiting the growth and CutC enzyme activity of the TMA-producing bacterium Serratia marcescens, and indirectly antagonizing Serratia marcescens by promoting the proliferation of the beneficial bacterium Lactobacillus johnsonii. This study provides novel theoretical insights into the mechanism by which EGCG alleviates TMA/TMAO metabolic disorders induced by high-fat/choline diets via gut microbiota modulation.},
}

Animals
*Catechin/analogs & derivatives/pharmacology
*Methylamines/metabolism
*Choline/adverse effects
Mice
*Gastrointestinal Microbiome/drug effects
*Diet, High-Fat/adverse effects
Male
*Lactobacillus/drug effects/metabolism
Intestines/microbiology
Mice, Inbred C57BL

@article {pmid42571835,
year = {2026},
author = {Wang, G and Li, J and Wang, D and Chen, SS and Zheng, G and Zhou, S and Wang, T and Zhou, Y},
title = {Microbial community structure, function and environmental drivers of the urban soil plastisphere in a typical megacity, China.},
journal = {Environmental research},
volume = {306},
number = {Pt 4},
pages = {125432},
doi = {10.1016/j.envres.2026.125432},
pmid = {42571835},
issn = {1096-0953},
mesh = {China ; *Soil Microbiology ; Fungi/genetics ; *Soil Pollutants/analysis ; Cities ; *Environmental Monitoring ; Bacteria/genetics/classification ; *Microbiota ; Soil/chemistry ; *Microplastics/analysis ; },
abstract = {The plastisphere in urban soils remains poorly understood despite its potential ecological significance. Here, 42 samples, including 21 soil samples and 21 plastisphere samples, were collected from seven functional zones in Nanjing, and metagenomic sequencing, bioinformatics, and quantitative modeling with multisource geographic and soil data were employed to investigate the community structure, function and environmental drivers of the soil plastisphere in this typical megacity, China. Fungi, particularly Ascomycota and the genus Fusarium (LDA score = 4.73), exhibited stronger selective enrichment in the plastisphere than bacteria did, with this pattern being consistent across all functional zones, suggesting that the intrinsic properties of microplastics (MPs) govern taxonomic assembly. Plastisphere co-occurrence networks were simpler, more modular, and less robust than soil networks were, indicating that the structurally vulnerable microbial community was shaped predominantly by stochastic assembly (R[2] > 0.2). Functional analysis further revealed significant alterations in the characteristics of denitrification genes (napA, norB, and narH/narY/nxrB), suggesting modified nitrogen cycling potential. Critically, pollutants, especially MPs themselves, partially overrode geospatial and edaphic factors as direct drivers of plastisphere communities, representing fundamental decoupling from the natural environmental matrix governing bulk soil. Pollutants strongly negatively affected fungal compositions and networks in the plastisphere, amplifying the ecological hazards of coexisting contaminants. These findings revealed that MP pollution modified microbial community assembly in urban soils, creating a decoupled, pollutant-driven microbial system. Integrating these effects into urban environmental risk assessments is therefore urgently needed.},
}

China
*Soil Microbiology
Fungi/genetics
*Soil Pollutants/analysis
Cities
*Environmental Monitoring
Bacteria/genetics/classification
*Microbiota
Soil/chemistry
*Microplastics/analysis

@article {pmid42577578,
year = {2026},
author = {Song, Y and Zhang, X and Wang, H and Wang, Y and Zhang, S and Li, Y and Cui, X and Li, X and Li, Y and Wang, J and Su, J and Zheng, Y and Gai, W and Liu, W},
title = {Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799148},
pmid = {42577578},
issn = {2235-2988},
mesh = {Humans ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Microbiota ; *Endosonography/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; *Neoplasms/complications/drug therapy ; Bacteria/classification/genetics/isolation & purification ; Bronchoscopy ; Aged, 80 and over ; Adult ; Sepsis ; },
abstract = {INTRODUCTION: Patients treated with systemic anti-tumor therapies are more likely to develop pulmonary infections due to weakened immune systems. This study aims to evaluate the clinical application of radial endobronchial ultrasound (R-EBUS) combined with metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infections among patients undergoing systemic anti-tumor therapy.

METHODS: This study is a single-center retrospective analysis that includes 84 patients with pulmonary infections following systemic anti-tumor therapy. Patients were stratified into sepsis (SOFA score ≥2, n=32) and non-sepsis (SOFA score <2, n=52) groups based on Sepsis-3.0 criteria. BALF samples were subjected to both mNGS and conventional microbiological tests (CMT). Pathogen profiles, diagnostic performance, clinical impact on antimicrobial therapy, and microbiome diversity were analyzed.

RESULTS: mNGS demonstrated a significantly higher positive detection rate than CMT (95.24% vs. 30.95%, P < 0.001). mNGS identified a broader spectrum of pathogens, including bacteria, fungi, and viruses, and detected mixed infections more frequently than CMT. The clinical impact of mNGS was positive in 84.52% of cases, primarily by initiating targeted therapy or confirming empirical treatment. Microbiome analysis revealed significantly lower alpha diversity (Shannon, ACE, Chao1 indices) in the severe group compared to the non-severe group.

DISCUSSION: EBUS-guided mNGS of BALF was associated with improved pathogen detection in malignancy patients with pulmonary infections, leading to a high rate of beneficial antimicrobial adjustments. Distinct microbial signatures are associated with infection severity, suggesting potential diagnostic and therapeutic implications.},
}

Humans
Female
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Male
Retrospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Aged
Microbiota
*Endosonography/methods
*Respiratory Tract Infections/diagnosis/microbiology
*Neoplasms/complications/drug therapy
Bacteria/classification/genetics/isolation & purification
Bronchoscopy
Aged, 80 and over
Adult
Sepsis

@article {pmid42577830,
year = {2026},
author = {Martínez-Cuesta, R and Hoess, R and Geist, J and Schloter, M and Schulz, S},
title = {The larval gut as a mirror: bacterial community composition and functional potential of mayfly larvae reflect site and seasonality differences.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag192},
pmid = {42577830},
issn = {2730-6151},
abstract = {Land use intensification is a major driver of biodiversity loss across ecosystems, yet its consequences for host-associated microbiomes in freshwater food webs remain poorly understood. In this case study, we used the gut microbiome of mayfly larvae (Ephemera danica) as a sensitive biological interface to assess how site-specific adjacent land use types shape microbial community composition and functions in stream ecosystems. Larvae were sampled in summer and autumn from sites adjacent to forest, extensive grassland, and intensive agriculture along the Otterbach stream (Bavarian Forest, Germany). Combining 16S ribosomal RNA (rRNA) amplicon sequencing with long-read metagenomics, we show that site-specific land use, in interaction with seasonality, significantly restructures larval gut bacterial communities without affecting alpha diversity. Rather than introducing distinct agriculturally derived taxa, agricultural land use acted as a selective environmental filter, enriching bacterial groups with specific functional traits. Taxa enriched in the sites adjacent to agricultural sites harboured genes involved in complex carbon and xenobiotic degradation, short-chain fatty acid production, efflux pumps, and stress response. These functional signatures were further supported by 14 metagenome-assembled genomes linked to these enriched taxa. Together, our results reveal that site in combination with seasonality not only reshaped bacterial community composition without affecting alpha diversity but also triggered shifts in the abundance of genes involved in microbial-host interactions and degradation pathways in E. danica larvae. This study also highlights the larval gut microbiome as a sensitive indicator of environmental change, suggesting that environmental microbial shifts may have cascading consequences for freshwater trophic interactions and ecosystem functioning.},
}

@article {pmid42249286,
year = {2026},
author = {Qiu, X and Li, W and Zhang, M and Lei, S and Chen, H and Wang, X and Miao, Y and Yu, Z and Wu, Y and Hou, Z},
title = {The impact of hydrogen sulfide on gut microbiota of diabetic mice with lower limb arterial ischemia.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42249286},
issn = {1471-2180},
support = {H2020206490//Natural Science Foundation of Hebei Province/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; H2024206134//Key Project of Natural Science Foundation of Hebei Province (Class A)/ ; },
mesh = {Animals ; *Hydrogen Sulfide/pharmacology/administration & dosage/blood ; *Ischemia/microbiology/drug therapy ; Mice, Inbred C57BL ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Hindlimb/blood supply ; *Diabetes Mellitus, Experimental/complications/microbiology ; Muscle, Skeletal/drug effects/pathology/blood supply ; Bacteria/classification/genetics/drug effects/isolation & purification ; Disease Models, Animal ; Feces/microbiology ; Blood Glucose ; },
abstract = {BACKGROUND: The prevalence of hindlimb ischemia (HLI) associated with diabetes mellitus (DM) is high. However, its prevention and treatment face significant challenges. This study explored the effects of hydrogen sulfide (H2S) intervention in mice with DM and HLI, while concurrently investigating its regulatory effects on gut microbial homeostasis.

METHODS: The diabetic model in C57BL/6J mice was established through intraperitoneal injection of streptozotocin. The HLI model was created by ligating and severing the femoral artery, with subsequent initiation of a 21-day exogenous H2S intervention. Fecal samples from the mice were collected at four time points: before model establishment, 3 days after successful induction of the diabetes model, 3 days after establishment of the HLI model, and after 21 days of H2S intervention for metagenomic analysis. Body weight, blood glucose levels, and hindlimb blood flow in the mice were monitored. Additionally, functional assessment and histopathological examination of the ischemic skeletal muscle were performed to evaluate contractile and morphological properties.

RESULTS: H2S administration significantly enhanced hindlimb blood perfusion and restored plasma H2S concentrations in diabetic mice with HLI, concurrently improving both function and morphological integrity of the ischemic skeletal muscle. Bacterial abundance at the phylum level showed changes over the course of the experiment, particularly in Bacteroidetes and Firmicutes. In the DM + HLI group, the Firmicutes-to-Bacteroidetes ratio was significantly elevated; however, H2S treatment downregulated this alteration. H2S intervention modulated the abundance of various bacterial species, increasing Lactobacillus murinus and Faecalibacterium prausnitzii, while simultaneously downregulating inflammation-related bacteria such as Ruminococcus sp. JE7A12. Microbial network analysis revealed that the DM + HLI and H2S groups had lower network complexity than the control group. Furthermore, functional metagenomic profiling identified 28 differentially expressed genes, which were annotated to 8 primary and 30 secondary KEGG pathways, with 6 genes specifically enriched in carbohydrate metabolism pathways.

CONCLUSION: Exogenous H2S administration improved hindlimb blood perfusion, restored contractile function, and preserved morphological integrity of ischemic skeletal muscle in diabetic mice with HLI. Concurrently, H2S treatment altered the abundance of gut microbiota, improving microbial balance. Targeting the gut microbiota via H₂S suggests a potential translational avenue that warrants causal investigation for the treatment of diabetic limb ischemia. Further studies are warranted to establish causal relationships and elucidate the underlying mechanisms linking H2S, gut microbiota, and vascular recovery.},
}

Animals
*Hydrogen Sulfide/pharmacology/administration & dosage/blood
*Ischemia/microbiology/drug therapy
Mice, Inbred C57BL
Mice
*Gastrointestinal Microbiome/drug effects
Male
*Hindlimb/blood supply
*Diabetes Mellitus, Experimental/complications/microbiology
Muscle, Skeletal/drug effects/pathology/blood supply
Bacteria/classification/genetics/drug effects/isolation & purification
Disease Models, Animal
Feces/microbiology
Blood Glucose

@article {pmid42252423,
year = {2026},
author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ},
title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42252423},
issn = {1471-2180},
support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Química Valaner-MGI Mexico/ ; },
mesh = {Fermentation ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Alcoholic Beverages/microbiology ; Microbiota ; *Microbial Consortia ; Metagenomics/methods ; },
abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.},
}

Fermentation
*Bacteria/classification/metabolism/genetics/isolation & purification
*Alcoholic Beverages/microbiology
Microbiota
*Microbial Consortia
Metagenomics/methods

@article {pmid42378973,
year = {2026},
author = {Min, H and Wang, Y and Wang, Q and Zhang, J and Lin, L and Li, X and Li, B},
title = {Cefpirome biodegradation by enriched bacterial consortia and isolated strain Bosea sp. MYQ: Novel insights on biodegradation pathway and bacterial interaction patterns.},
journal = {Water research},
volume = {304},
number = {},
pages = {126351},
doi = {10.1016/j.watres.2026.126351},
pmid = {42378973},
issn = {1879-2448},
mesh = {Biodegradation, Environmental ; Cefpirome/metabolism ; *Cephalosporins/metabolism ; *Microbial Consortia ; Bacteria/metabolism ; },
abstract = {Deciphering the metabolic fate of cefpirome is essential for designing more efficient biodegradation strategies. In this study, we integrated second- and third-generation metagenomic sequencing with high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (HPLC-QTOF-MS) to unravel cefpirome biodegradation by a long-term enriched bacterial consortium and its key isolate Bosea sp. MYQ. Five biodegradation products were detected and mapped onto three cooperative pathways. Among them, four products involved in Pathways 2 and 3 were first identified in cefpirome biodegradation. Genome-scale metabolic modeling and genome-resolved metagenomics jointly revealed a pollutant-degrading network coordinated by two keystone donors, MAG2 (Variovorax) and MAG3 (Bosea sp. MYQ). They were primarily responsible for β-lactam ring-opening and the formation of downstream products, while exporting diverse metabolic intermediates to sustain pathway continuity through cross-feeding. Notably, MAG3 (Bosea sp. MYQ) encodes per-1 and bla, which likely contribute critically to cefpirome degradation by underpinning key β-lactam transformation steps. Complementary functions were provided by auxiliary and rare members, particularly MAG4 (Hyphomicrobium), MAG7 (Pandoraea), MAG10 (Methyloversatilis), and MAG21 (Phenylobacterium). These findings expand the repertoire of cefpirome-degrading microorganisms, reveal previously unrecognized biodegradation pathways, and clarify the microbial interaction network underpinning fourth-generation cephalosporin removal.},
}

Biodegradation, Environmental
Cefpirome/metabolism
*Cephalosporins/metabolism
*Microbial Consortia
Bacteria/metabolism

@article {pmid42576510,
year = {2026},
author = {Nio, SA and Mantilen Ludong, DP},
title = {Water Deficit During the Vegetative Stage Alters the Structure of Root-Associated Microbial Communities in Local North Sulawesi Rice.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {29},
number = {5},
pages = {243-250},
doi = {10.3923/pjbs.2026.243.250},
pmid = {42576510},
issn = {1812-5735},
mesh = {*Oryza/microbiology/growth & development/metabolism ; *Plant Roots/microbiology ; Droughts ; Water/metabolism ; *Microbiota/physiology ; Indonesia ; Rhizosphere ; },
abstract = {Background and Objective: Changes in rhizosphere microbial populations have been reported in response to drought, temperature fluctuations, CO2 levels and other environmental factors. However, the structure of the root-associated microbes in local North Sulawesi rice using a metagenomic approach has not yet been investigated. This study examined the microbial community structure in local North Sulawesi rice (cv. Superwin) under drought (water deficit) conditions compared to well-watered conditions at the vegetative phase. Materials and Methods: Rice plants were grown in polybags filled with a 5:1:1 mixture of garden soil, compost and rice husks and were allowed to grow until the four-fully-expanded leaf stage. They were then subjected to two treatments for 14 days: well-watered conditions (irrigated to 100% field capacity) and water deficit conditions (0% field capacity). Root samples were collected for next-generation sequencing analysis to assess molecular response of Superwin rice to water deficit. Results: During drought, several root-associated microbes were more prevalent, including Nitrospirota at the phylum level, Rubrobacteria at the class level, Micrococcales at the order level, Gaiellaceae at the family level, Gaiella at the genus level and Gaiella occulta at the species level. Conclusion: Root-associated microbes, including taxa Nitrospirota, Rubrobacteria, Micrococcales, Gaiellaceae, Gaiella and Gaiella occulta, have a higher relative abundance in rice plants under water deficit. Gaiella occulta serves as sensitive indicator of water deficit in North Sulawesi local rice, i.e. Superwin.},
}

*Oryza/microbiology/growth & development/metabolism
*Plant Roots/microbiology
Droughts
Water/metabolism
*Microbiota/physiology
Indonesia
Rhizosphere

@article {pmid42265587,
year = {2026},
author = {Liang, X and Li, J and Liu, P and Lai, Z and Huang, S and Xie, F and Jin, W and Mao, S},
title = {Rumen ecological distribution of Pichia yeasts and their effects on rumen fermentation and microbial community.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42265587},
issn = {1471-2180},
support = {32272896//The National Natural Science Foundation of China/ ; 32361143788//The National Natural Science Foundation of China/ ; QTPY2026017//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Rumen/microbiology ; Fermentation ; *Pichia/classification/metabolism/genetics/isolation & purification/physiology ; Cattle ; Animal Feed/microbiology/analysis ; *Microbiota ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Yeast supplementation has been widely studied to enhance rumen fermentation and feed efficiency, yet developing efficient yeasts adapted to the rumen environment remains a challenge. In this study, two rumen-derived Pichia strains (Pichia membranifaciens M12 and Pichia kudriavzevii Y4) were evaluated using in vitro rumen fermentation experiments, including a control and three supplementation groups (2 × 10[5], 2 × 10[6], and 2 × 10[7] CFU/mL) for each strain. Results indicated that the two strains did not affect pH but significantly reduced concentrations of ammonium nitrogen (NH3-N) and microbial crude protein (MCP). At 24 h, NH3-N decreased by up to 13.3% and MCP by 18.5%, while at 48 h, NH3-N showed a reduction of up to 22.0% and MCP decreased by up to 5.7%. P. membranifaciens significantly increased the concentration of total volatile fatty acids by 15.4% and elevated the proportions of acetate and propionate at 48 h. Microbial community analysis revealed that these shifts in fermentation parameters were associated with an altered bacterial community structure. Specifically, P. membranifaciens enriched cellulolytic bacteria (Ruminococcus), while reducing amylolytic and proteolytic taxa (Prevotella), and promoted the propionate‑producer (Succiniclasticum). These findings suggested that P. membranifaciens has the potential to influence rumen microbiota. Further examination of the in vivo prevalence of Pichia yeasts species via ITS (n = 72; average parity 2.8 ± 1.1) revealed a lower prevalence and relative abundance for P. membranifaciens compared to P. kudriavzevii. Metagenomic analysis (n = 8; average parity 2.7 ± 0.9) detected both species at low abundances. Overall, this study indicated that rumen-derived Pichia yeasts have the capacity to modulate rumen fermentation, with P. membranifaciens warranting further in vivo evaluation.},
}

Animals
*Rumen/microbiology
Fermentation
*Pichia/classification/metabolism/genetics/isolation & purification/physiology
Cattle
Animal Feed/microbiology/analysis
*Microbiota
Fatty Acids, Volatile/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid42316154,
year = {2026},
author = {Seo, E and Kim, SH and Kwak, MJ and Hwang, JK and Mustafa, G and Chang, YS and Hoh, JK and Jeon, BH and Park, HK and Kim, Y},
title = {Gut dysbiosis associated with neonatal respiratory distress syndrome and biological plausibility of disease-specific probiotic intervention: a translational study.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42316154},
issn = {1479-5876},
support = {202400000002957//College of Medicine, Hanyang University/ ; RS-2023-00255939//Korea Institute of Energy Technology Evaluation and Planning/ ; NSIT; RS-2025-16068814//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/pharmacology ; *Dysbiosis/microbiology/complications ; Animals ; *Respiratory Distress Syndrome, Newborn/microbiology/complications ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; *Translational Research, Biomedical ; Female ; Male ; Feces/microbiology ; Mice ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND: Neonatal respiratory distress syndrome (RDS) is among the most prevalent morbidities in late preterm and term infants. Although the gut-lung axis has been implicated in neonatal respiratory disease, the relationship between RDS and early gut microbiome composition remains poorly characterized. This study aimed to characterize gut microbiome alterations associated with RDS and surfactant replacement therapy (SRT), and to evaluate the biological plausibility of a disease-specific probiotic intervention.

METHODS: Two complementary cohorts were prospectively enrolled. In the clinical observational cohort (n = 45), fecal samples collected within 48 h of birth were analyzed by Nanopore 16S rRNA sequencing across three groups: infants without RDS (control group, n = 25), infants with RDS who did not receive SRT (RDS(S-) group, n = 7), and infants with RDS who received SRT (RDS(S+) group, n = 13). In the probiotic discovery cohort (n = 40), gut microbiota of infants without RDS (CON group, n = 17) and infants with RDS (RDS group, n = 23) were characterized by metagenomic sequencing and culturomics. Candidate probiotic strains were evaluated in a fermenter for intestinal microbiota model (FIMM) and a fecal microbiota transplantation (FMT) mouse model.

RESULTS: The RDS(S-) group exhibited depletion of beneficial taxa including Bifidobacterium and Lacticaseibacillus and enrichment of opportunistic pathogens including Enterococcus and Staphylococcus. Following SRT, gut microbial profiles partially shifted toward those of the control group. Limosilactobacillus fermentum SLAM_LAF05 and Bifidobacterium longum SLAM_BIL02 were identified as CON-enriched candidate probiotic strains through direct microbiome comparison and selected based on superior acid and bile tolerance and adhesion capacity. In the FIMM model, probiotic supplementation increased microbial diversity and suppressed opportunistic pathogens. In the FMT mouse model, probiotic supplementation was associated with upregulation of ZO-1, MUC2, and Reg3g, reduction of fecal calprotectin, and restoration of serum IgG levels.

CONCLUSIONS: This study provides an early translational characterization of RDS-associated gut dysbiosis and its partial resolution following SRT, and establishes proof-of-concept for a disease-specific probiotic approach. These findings offer a new perspective on the interplay between gut microbial dynamics and the early postnatal respiratory course, and provide a basis for future investigations into microbiota-targeted strategies in neonates with RDS.},
}

Humans
*Probiotics/therapeutic use/pharmacology
*Dysbiosis/microbiology/complications
Animals
*Respiratory Distress Syndrome, Newborn/microbiology/complications
Infant, Newborn
*Gastrointestinal Microbiome/drug effects
*Translational Research, Biomedical
Female
Male
Feces/microbiology
Mice
Fecal Microbiota Transplantation

@article {pmid42572222,
year = {2026},
author = {Kirilina, IV and Roumiantsev, SA and Gaponov, AM and Savchyk, DV and Khusnutdinova, DR and Grigoryeva, TV and Teplyakova, ED and Shestopalov, AV},
title = {[The contribution of the intestinal microbiome to the formation of the general profile of bacterial DNA in the blood of obese children].},
journal = {Voprosy pitaniia},
volume = {95},
number = {3},
pages = {107-116},
doi = {10.33029/0042-8833-2026-95-3-107-116},
pmid = {42572222},
issn = {0042-8833},
support = {//The research was carried out under the contract no. 0373100122119000041 within the project "Creation of a bank of biosamples of blood serum and feces from healthy donors and patients with obesity, metabolic syndrome, type 2 diabetes mellitus, and impaired mucosal barrier of the gastrointestinal tract, in order to identify candidate species nonspecific mediators of the quorum sensing microbiota systems of human, which modulate the endocrine and metabolic function of adipose tissue"/ ; },
mesh = {Humans ; Child ; *DNA, Bacterial/blood ; Cross-Sectional Studies ; Feces/microbiology ; Adolescent ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Pediatric Obesity/microbiology/blood ; Lipid Metabolism ; Carbohydrate Metabolism ; Obesity/microbiology/blood ; *Gastrointestinal Microbiome ; },
abstract = {UNLABELLED: Obesity is a multifactorial disease. The gut microbiome disturbances play a significant role in the development of obesity, but emerging data point to a blood microbiome and its association with obesity and other pathologies. Bacterial DNA in the blood represents a pathogen-associated molecular pattern capable of activating the immune system and thereby triggering a cascade of inflammatory responses. The question remains open as to where the bacterial DNA originates, which biotopes shape it, and what role the gut microbiome plays in forming the pool of bacterial DNA in blood. The aim of the study was to compare the bacterial DNA profiles of feces and blood in obese children, to establish relationships between bacterial DNA in blood and feces, and with carbohydrate and lipid metabolism parameters.

MATERIAL AND METHODS: This single-center, cross-sectional study included children and adolescents aged 10 to 18 years with varying degrees of alimentary-constitutional obesity (n=79) and without obesity (n=84). The taxonomic profile of bacterial DNA in blood and feces was analyzed using metagenomic sequencing. Bacterial DNA was isolated from blood and stool samples, and the v3-v4 variable region of the 16S rRNA gene was sequenced. To identify the relationship between bacterial DNA in blood and feces and lipid and carbohydrate metabolism parameters [glucose, total cholesterol, high-density lipoprotein and low-density lipoprotein (LDL)], Spearman's correlation coefficients were calculated.

RESULTS: When comparing bacterial DNA from blood and feces, obese children more often isolated DNA from the families Lactobacillaceae (p=0.043), Porphyromonadaceae (p=0.022), Ruminococcaceae (p=0.065) and less often from Prevotellaceae (p=0.028) and Coriobacteriaceae (p=0.085) compared to children and adolescents without obesity. In obese children, the contribution of intestinal taxa (Lachnospiraceae, Ruminococcaceae, Bacteroidaceae) to the formation of the bacterial DNA profile of the blood was significantly reduced, but the contribution of extraintestinal biotopes (skin, soil and water) was more diverse. Positive associations were found between bacterial DNA of fecal Ruminococcaceae taxa and the level of total cholesterol (ρ=0.347, p=0.002) and LDL (ρ=0.313, p=0.005) and of fecal Coriobacteriaceae and these lipid metabolism parameters (ρ=0.304, p=0.007 and ρ=0.317, p=0.005) in obese children. No positive associations were found between fecal and blood taxa and glucose level.

CONCLUSION: In obese and non-obese children and adolescents, the general profile of bacterial blood DNA is formed by both intestinal and extra-intestinal biotopes. However, in obese children, taxa from extra-intestinal biotopes predominate in the formation of the blood microbiome, which is confirmed by analyzing the proximity of the taxonomic composition of bacterial DNA in blood and feces based on beta diversity indices. The relationship of taxa with blood cholesterol and LDL levels can be considered as a target for microbiota modification and thus reducing the risks of metabolic complications in obesity.},
}

Humans
Child
*DNA, Bacterial/blood
Cross-Sectional Studies
Feces/microbiology
Adolescent
Female
Male
RNA, Ribosomal, 16S/genetics
*Pediatric Obesity/microbiology/blood
Lipid Metabolism
Carbohydrate Metabolism
Obesity/microbiology/blood
*Gastrointestinal Microbiome

@article {pmid42573887,
year = {2026},
author = {Yang, L and Zhao, J and Han, T and Qi, H and Zhao, F and Sun, Z},
title = {Modulating the gut-joint axis: Bifidobacterium longum subsp. infantis B8762 is associated with selective gut microbial and metabolic alterations in knee osteoarthritis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42573887},
issn = {1573-0972},
support = {U25A20733//National Natural Science Foundation of China/ ; 2022YFD2100702//National Key Research and Development Program of China/ ; YLXKZX-NND-006//Inner Mongolia Agricultural University First-Class Discipline Scientific Research Special Program/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {Humans ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Osteoarthritis, Knee/microbiology/metabolism/therapy ; *Probiotics/administration & dosage ; Metabolome ; *Bifidobacterium/physiology ; Metabolomics ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics ; Female ; Knee Joint/microbiology/metabolism ; *Bifidobacterium longum ; },
abstract = {Knee osteoarthritis (KOA) is a debilitating degenerative joint disorder characterized by chronic low-grade inflammation and metabolic dysregulation. The gut microbiota has emerged as an important regulator of systemic inflammatory responses. Building upon our previous clinical findings that Bifidobacterium longum subsp. infantis B8762 (B8762) improved clinical symptoms and inflammatory markers in patients with KOA, the present study investigated the associated alterations in the gut microbiome and fecal metabolome. Fecal samples were collected from probiotic (n = 20) and placebo (n = 20) groups at baseline (0 M) and after a 1-month intervention (1 M). Integrated metagenomic and untargeted metabolomic analyses were performed to characterize changes in gut microbial composition, functional potential, and metabolic profiles. Metagenomic reads mapped to the B8762 reference genome showed a greater increase in B8762-associated mapping rates in the probiotic group than in the placebo group, supporting an association between B8762 supplementation and longitudinal changes in the gut microbiome. Longitudinal analysis further demonstrated greater increases in microbial alpha diversity in the probiotic group. Species-level analyses suggested selective alterations in gut microbial composition, with nominally higher relative abundances of Bifidobacterium pseudocatenulatum and Anaerostipes caccae and lower relative abundances of Holdemania filiformis and Lachnospira SGB5077 (nominal P < 0.05). HUMAnN3-based functional profiling identified enrichment of microbial pathways related to carbon utilization and amino acid biosynthesis, including the bifidobacterial shunt and branched-chain amino acid biosynthesis pathways. Untargeted metabolomics identified nominal between-group differences in metabolites primarily related to lipid metabolism, including lower relative abundances of aldosterone and 7α-hydroxy-4-cholesten-3-one in the probiotic group (nominal P < 0.05). Correlation analysis further revealed associations between differential taxa and selected metabolites, suggesting potential links between gut microbial alterations and steroid-related metabolic pathways. Overall, B8762 supplementation was associated with longitudinal changes in B8762-associated genomic signals, gut microbial diversity and composition, microbial functional potential, and fecal metabolic profiles. These findings provide exploratory multi-omics evidence supporting an association between B8762 supplementation and gut microbial-metabolic remodeling in KOA and generate hypotheses for future mechanistic studies of the gut-joint axis.},
}

Humans
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/drug effects
*Osteoarthritis, Knee/microbiology/metabolism/therapy
*Probiotics/administration & dosage
Metabolome
*Bifidobacterium/physiology
Metabolomics
Male
Bacteria/classification/genetics/isolation & purification/metabolism
Metagenomics
Female
Knee Joint/microbiology/metabolism
*Bifidobacterium longum

@article {pmid42575708,
year = {2026},
author = {de Oliveira, AFB and Carneiro, BS and de Carvalho, JB and de Oliveira, AR and da Costa da Silva, AL and de Oliveira Veras, AA and Baraúna, RA and das Graças, DA},
title = {Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70396},
pmid = {42575708},
issn = {1758-2229},
support = {445350/2024-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Metagenomics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism/drug effects ; *Xenobiotics/metabolism ; Brazil ; *Bathing Beaches ; *Drug Resistance, Bacterial ; Biodiversity ; *Drug Resistance, Microbial ; Phylogeny ; Biodegradation, Environmental ; Cities ; },
abstract = {Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.},
}

*Metagenomics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism/drug effects
*Xenobiotics/metabolism
Brazil
*Bathing Beaches
*Drug Resistance, Bacterial
Biodiversity
*Drug Resistance, Microbial
Phylogeny
Biodegradation, Environmental
Cities

@article {pmid41996042,
year = {2026},
author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS},
title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {6},
pages = {877-887},
pmid = {41996042},
issn = {1618-1905},
mesh = {Humans ; Female ; Skin Microbiome ; Republic of Korea ; *Skin/microbiology/metabolism ; Adult ; Middle Aged ; Young Adult ; Multiomics ; *Metabolome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Aging ; Metabolomics ; *Microbiota ; Fibroblasts/metabolism ; Asian People ; Skin Aging ; },
abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.},
}

Humans
Female
Skin Microbiome
Republic of Korea
*Skin/microbiology/metabolism
Adult
Middle Aged
Young Adult
Multiomics
*Metabolome
*Bacteria/classification/genetics/isolation & purification/metabolism
Aging
Metabolomics
*Microbiota
Fibroblasts/metabolism
Asian People
Skin Aging

@article {pmid42156414,
year = {2026},
author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and , and Guarner, F and Ehrlich, SD},
title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42156414},
issn = {2045-2322},
support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Feces/microbiology ; Female ; Adult ; Male ; Phenotype ; Middle Aged ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Inflammation/microbiology ; Recurrence ; Leukocyte L1 Antigen Complex/analysis ; Metagenomics ; Quality of Life ; },
abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.},
}

Humans
*Colitis, Ulcerative/microbiology/pathology
*Feces/microbiology
Female
Adult
Male
Phenotype
Middle Aged
*Gastrointestinal Microbiome
Cross-Sectional Studies
*Inflammation/microbiology
Recurrence
Leukocyte L1 Antigen Complex/analysis
Metagenomics
Quality of Life

@article {pmid42260652,
year = {2026},
author = {Le Moigne, A and Andrei, AŞ and Pernthaler, J},
title = {Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42260652},
issn = {2049-2618},
mesh = {*Bacteria/genetics/classification/metabolism ; Stochastic Processes ; Metagenomics/methods ; *Lakes/microbiology ; Genome, Bacterial ; *Microbiota/genetics ; Cellobiose/metabolism ; Ecosystem ; },
abstract = {BACKGROUND: Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-"functional dispersal limitation"-explained variation in cellobiose use.

RESULTS: Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of "functional dispersal limitation." We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.

CONCLUSIONS: Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.},
}

*Bacteria/genetics/classification/metabolism
Stochastic Processes
Metagenomics/methods
*Lakes/microbiology
Genome, Bacterial
*Microbiota/genetics
Cellobiose/metabolism
Ecosystem

@article {pmid42263665,
year = {2026},
author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA},
title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.},
journal = {Blood advances},
volume = {10},
number = {16},
pages = {5505-5517},
doi = {10.1182/bloodadvances.2026020270},
pmid = {42263665},
issn = {2473-9537},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Diet, Plant-Based ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Male ; Transplantation, Autologous ; *Microbiota ; Adult ; Aged ; },
abstract = {Plant-based whole food diets may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary end points were feasibility and tolerability, defined by successful enrollment and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary end points included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a potential influence of the dietary strategy on microbial metabolite production during the peritransplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial was registered at ClinicalTrials.gov as NCT06559709.},
}

Humans
*Hematopoietic Stem Cell Transplantation/methods/adverse effects
Diet, Plant-Based
Female
Middle Aged
*Gastrointestinal Microbiome
Male
Transplantation, Autologous
*Microbiota
Adult
Aged

@article {pmid42562511,
year = {2026},
author = {Lee, JW and Kim, YM and Kim, YJ and Jeong, KC and Kim, SA},
title = {Wastewater irrigation reshapes the microbiome and resistome of radish sprouts: Insights from 16S rRNA and shotgun metagenomic sequencing.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119739},
doi = {10.1016/j.foodres.2026.119739},
pmid = {42562511},
issn = {1873-7145},
mesh = {*Raphanus/microbiology/growth & development ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Agricultural Irrigation/methods ; Animals ; Metagenomics/methods ; Shotgun Sequencing ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Swine ; },
abstract = {Water scarcity is increasing the reliance on treated wastewater in fresh produce production, yet its effects on the microbial and hygienic quality of fresh produce remain unclear. This study evaluated the influence of wastewater irrigation on the microbiome and antibiotic resistance gene (ARG) profiles of radish sprouts grown under commercially relevant conditions. Using culture-dependent methods and integrated sequencing (16S rRNA and shotgun metagenomics), we tracked microbial and resistome dynamics across the sprout production process under three irrigation regimes: swine wastewater, treated wastewater, and sterile distilled water. Wastewater irrigation markedly increased microbial loads, with aerobic plate counts exceeding 8.0 log CFU/g in final radish sprouts. Both wastewater treatments were dominated by Pseudomonas and Acinetobacter. Resistome profiling showed persistent multidrug, bacitracin, and polymyxin resistance genes in wastewater-irrigated sprouts, while sulfonamide resistance genes occurred exclusively under wastewater irrigation, suggesting wastewater-associated environmental transmission. Higher ARG subtype richness in wastewater treatments suggested that conventional wastewater treatment processes do not completely eliminate diverse ARGs. ARG-host linkage analysis suggested an elevated potential for horizontal gene transfer within edible plant tissues. Overall, wastewater irrigation altered the microbiological quality of radish sprouts and facilitated ARG persistence, underscoring the need for improved post-treatment and preventive water management to safeguard fresh produce safety.},
}

*Raphanus/microbiology/growth & development
*Wastewater/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Agricultural Irrigation/methods
Animals
Metagenomics/methods
Shotgun Sequencing
Bacteria/genetics
Drug Resistance, Microbial/genetics
Swine

@article {pmid42562513,
year = {2026},
author = {Liu, QJ and Mei, JL and Wen, X and Lu, YH and Zeng, Y and Liu, ZY and Xu, HY and Wang, ST and Jiang, F and Yang, CB and Chi, YL and Xu, ZH},
title = {Cellar age reshapes Huangshui micro-ecosystem and metabolism to drive flavor formation in strong-aroma baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119740},
doi = {10.1016/j.foodres.2026.119740},
pmid = {42562513},
issn = {1873-7145},
mesh = {Fermentation ; Metabolomics ; *Odorants/analysis ; *Taste ; Bacteria/metabolism/genetics ; *Wine/analysis/microbiology ; *Alcoholic Beverages/analysis/microbiology ; Metagenomics ; *Microbiota ; Flavoring Agents ; },
abstract = {Huangshui, a slurry-like liquid exuded during strong-aroma Baijiu fermentation, serves as the core medium for material exchange between pit mud and fermented grains. However, how its micro-ecosystem evolves with cellar age and drives flavor formation remains unclear. Using Huangshui as a dynamic window, this study integrated metagenomics, metabolomics, and flavoromics to compare its temporal dynamics in new and old cellars over a complete fermentation cycle, systematically characterizing how cellar age is associated with the restructuring of the microbial community and metabolic functions of Huangshui, and how these changes are consistent with the flavor profiles observed in the final base liquor. The results showed that Huangshui from old cellars harbored a more diverse and stable microbial community, forming a syntrophic consortium of caproic acid-producing bacteria (Caproicibacterium, Caproiciproducens), syntrophic bacteria (Syntrophomonas), and methanogenic archaea (Methanosarcina), whereas new cellars were dominated by lactic acid bacteria (Acetilactobacillus). Metabolically, the old-cellar community exhibited a clear phase-dependent division. During the acid-producing phase, the TCA cycle, arginine biosynthesis, and pyruvate metabolism were preferentially activated to generate core precursors; during esterification, butanoate metabolism and acyl-CoA supply pathways were enhanced. This orderly shift was associated with higher concentrations of ethyl caproate and ethyl octanoate in old-cellar base liquor. Functional gene analysis revealed coordinated upregulation of chain-elongation, methanogenic, and acetate-activating pathways in old cellars. Network analysis revealed a tightly coupled caproic acid-producing co-occurrence module in old cellars, which was not observed in new ones. Together, these findings suggest that Huangshui may serve as a rapid proxy for assessing both the fermentation status and the maturity level of the cellar. This work identifies potential bioaugmentation targets to accelerate flavor development in new cellars and provides a theoretical basis for the precise micro-ecological management of strong-aroma Baijiu quality.},
}

Fermentation
Metabolomics
*Odorants/analysis
*Taste
Bacteria/metabolism/genetics
*Wine/analysis/microbiology
*Alcoholic Beverages/analysis/microbiology
Metagenomics
*Microbiota
Flavoring Agents

@article {pmid42562527,
year = {2026},
author = {Sun, Y and Guo, S and Kwok, LY and Guo, Y and Jiao, Y and He, Q and Zhang, H and Wang, J},
title = {Fermented milk derived from a novel probiotic strain enhances digestive function and attenuates dextran sulfate sodium-induced colitis via the microbiota-metabolite-immune axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119757},
doi = {10.1016/j.foodres.2026.119757},
pmid = {42562527},
issn = {1873-7145},
mesh = {Animals ; *Colitis/chemically induced/prevention & control/metabolism ; *Probiotics/pharmacology ; Dextran Sulfate ; Male ; Rats ; *Gastrointestinal Microbiome/physiology ; *Cultured Milk Products/microbiology ; Bifidobacterium animalis/metabolism ; *Digestion ; Rats, Sprague-Dawley ; Cytokines/metabolism ; Colon/pathology/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; },
abstract = {Probiotic-fermented dairy products are increasingly recognized for their dual role in nutrient optimization and disease prevention. This study investigated the mechanisms by which Bifidobacterium animalis subsp. lactis Probio-M8 fermented milk enhances digestive efficiency and protects against dextran sulfate sodium-induced colitis in rats. FM8 supplementation promoted weight gain without excessive adipogenesis, elevated leptin levels, and amplified sucrase, lactase, aminopeptidase, and lipase activities, outperforming conventional fermented milk. Metagenomic analysis revealed microbial restructuring with Corynebacterium glutamicum and Bifidobacterium animalis enrichment, and increased short-chain fatty acids.Untargeted metabolomics identified FM8-responsive metabolites, including p-hydroxybenzaldehyde and indole-3-carboxaldehyde, linked to anti-inflammatory pathways. In dextran sulfate sodium-challenged rats, FM8 pre-administration attenuated colitis severity by reducing disease activity index scores, normalizing colon histology, and suppressing interleukin (IL)-6 and IL-17 while elevating IL-10 and IL-22. Mechanistically, FM8 enriched Bifidobacterium animalis and butyrate levels, which inversely correlated with mucosal injury and pro-inflammatory cytokines. These findings demonstrate that FM8 enhances gastrointestinal health through tripartite microbiota-metabolite-immune interactions, highlighting its functional potential for metabolic optimization and colitis prevention.},
}

Animals
*Colitis/chemically induced/prevention & control/metabolism
*Probiotics/pharmacology
Dextran Sulfate
Male
Rats
*Gastrointestinal Microbiome/physiology
*Cultured Milk Products/microbiology
Bifidobacterium animalis/metabolism
*Digestion
Rats, Sprague-Dawley
Cytokines/metabolism
Colon/pathology/metabolism
Disease Models, Animal
Fatty Acids, Volatile/metabolism

@article {pmid42562842,
year = {2026},
author = {Lechleiter, N and Wedemeyer, J and Junker, J and Wilczek, M and Klich, D and Olech, W and Anusz, K and Homeier-Bachmann, T and Didkowska, A},
title = {Microbiome and resistome of the European bison (Bison bonasus).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42562842},
issn = {2045-2322},
mesh = {Animals ; *Bison/microbiology ; *Microbiota/genetics ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {After facing extinction in the early 20th century, populations of the two remnant genetic lines of European bison are now under continuous health monitoring. Faecal samples were taken from five Polish and one German herd of European bison over the course of several years. Through metagenomic sequencing, the bacterial and archaeal microbiome as well as the resistome of these samples could be characterized. Significant differences were mainly found between the bacterial microbiome of samples taken from droppings as opposed to rectal samples. Apart from this, the microbiome and resistome had low differentiation, showing no significant influence of individual factors or location. Oscillospiraceae, Lachnospiraceae and Bacteroidaceae were the dominant bacterial families, the archaeome was mostly made up by Methanobacteriaceae. Genes from resistance classes like Aminoglycosides and Macrolide, Lincosamide and Streptogramine were present. This study characterises the microbiome and resistome of the European bison with the help of metagenomics, providing novel insights into its biology.},
}

Animals
*Bison/microbiology
*Microbiota/genetics
Feces/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
Metagenomics
Anti-Bacterial Agents/pharmacology
Archaea/genetics/classification/isolation & purification
Phylogeny

@article {pmid42563165,
year = {2026},
author = {Richie, TG and Wiechman, H and Vogt, B and Ingold, C and Heeren, L and Kamke, A and Pogranichniy, S and Monk, K and Summers, T and Ran, Q and Sarkar, S and Plattner, BL and Sidebottom, AM and Chang, EB and Lee, STM},
title = {Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42563165},
issn = {2049-2618},
mesh = {*Oxidative Stress/drug effects ; Animals ; *Glutathione/metabolism/pharmacology ; Reactive Oxygen Species/metabolism ; Mice ; Colon/microbiology/metabolism ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; Nitric Oxide/metabolism ; Intestinal Barrier Function ; Gastrointestinal Microbiome ; Metagenomics ; Mice, Knockout ; Interleukin-10/genetics ; },
abstract = {BACKGROUND: Certain microbes inhabiting the gut have been implicated in maintaining gut homeostasis and promoting gut damage repair. Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment.

RESULTS: We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and reactive oxygen species (ROS) levels. Cell-free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells and colon organoids. CFSM-treated organoids showed reduced ROS accumulation, improved epithelial integrity, and partial recovery of barrier function compared to oxidatively stressed controls. We demonstrated through shotgun metagenomics, metabolomics, host RNA sequencing, and molecular techniques that glutathione (GSH) biosynthesized by E. rectale alleviated host ROS damage. We showed downregulation of cell stress and immune response genes, indicating recovery from ROS stress. Chemical depletion of GSH in CFSM confirmed the role of microbial derived GSH in alleviation of ROS in colon cells.

CONCLUSIONS: In this study, we identify E. rectale as a potential probiotic by lowering colon inflammation and ROS damage through production of reduced glutathione. Microbially derived GSH has not been well established in the Lachnospiraceae family which are a large member of the overall gut microbiota. Understanding more about the impacts of microbial functions including GSH on lowering inflammation is needed to develop potential probiotics or therapies for chronic inflammatory conditions. Video Abstract.},
}

*Oxidative Stress/drug effects
Animals
*Glutathione/metabolism/pharmacology
Reactive Oxygen Species/metabolism
Mice
Colon/microbiology/metabolism
*Intestinal Mucosa/metabolism/microbiology/drug effects
Nitric Oxide/metabolism
Intestinal Barrier Function
Gastrointestinal Microbiome
Metagenomics
Mice, Knockout
Interleukin-10/genetics

@article {pmid42564172,
year = {2026},
author = {Rojas, L and Zuluaga, J and Cardona, AF},
title = {Microbiome as a prediction of immunotherapy response in lung cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1849553},
pmid = {42564172},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/drug therapy/microbiology/therapy ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology/drug effects ; Treatment Outcome ; Animals ; *Microbiota/immunology ; },
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of lung cancer (LC), offering durable responses in non-small cell lung cancer (NSCLC) and, to a lesser extent, small cell lung cancer (SCLC). Nevertheless, clinical outcomes remain highly heterogeneous, with many patients experiencing primary or acquired resistance and/or immune-related adverse events (irAEs) that impair their quality of life and treatment adherence. The human microbiome, particularly in the gut and oral compartments, has emerged as a critical modulator of systemic antitumor immunity and a promising noninvasive predictive biomarker for ICI efficacy and toxicity. This narrative review synthesizes the current evidence on microbiome composition, diversity, and function in patients with LC receiving ICIs as monotherapy, dual blockade, or in combination regimens, as well as clinically relevant biomarkers associated with treatment response and toxicity. Higher gut microbial alpha diversity and enrichment of beneficial taxa (e.g., Akkermansia muciniphila, Faecalibacterium prausnitzii, and certain Firmicutes) are consistently linked to improved progression-free survival (PFS) and overall survival (OS), mediated by microbial metabolites such as short-chain fatty acids and inosine, which enhance T-cell priming, tumor microenvironment remodeling, and gut-lung axis communication. Microbiome-disruptive exposures, particularly antibiotics and proton pump inhibitors (PPIs), induce dysbiosis and are strongly associated with poorer survival outcomes. Mechanistic insights from preclinical models and clinical cohorts, alongside clinical confounders, underscore the complementary role of the microbiome relative to established markers such as programmed death-ligand 1 (PD-L1) and tumor mutational burden. Prospective standardization of metagenomic profiling and microbiome-modulating interventions represents a key next step in translating these findings into personalized immunotherapy strategies for LC.},
}

Humans
*Lung Neoplasms/immunology/drug therapy/microbiology/therapy
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology/drug effects
Treatment Outcome
Animals
*Microbiota/immunology

@article {pmid42566318,
year = {2026},
author = {Beaton, ADM and Croxford, JT and Díaz de Aguinaga, AC and Horsburgh, E and Mark, DR and McQueary, LS and Murray-Clelland, KR and Tucker, SK and Roe, AJ and McHugh, RE},
title = {Interactions at the Streptomyces - animal interface: ecology, defence and disease.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
pmid = {42566318},
issn = {1465-2080},
mesh = {*Streptomyces/physiology/genetics/metabolism ; Animals ; Humans ; Soil Microbiology ; Microbiota ; Insecta/microbiology ; Nematoda/microbiology ; },
abstract = {Streptomyces are filamentous, spore-forming members of the Actinomycetota, renowned for their capacity to produce chemically diverse, specialized metabolites with medically important properties. Traditionally, Streptomyces have been viewed as soil-dwelling microbes, and their roles in soil ecology, plant health and plant disease have been extensively studied. However, advances in metagenomic sequencing and molecular approaches have greatly expanded our ability to investigate interkingdom interactions between Streptomyces and more complex organisms, including animals. In recent years, a growing body of work has revealed diverse and often intimate associations between Streptomyces and members of the Animalia. These include interactions with microfauna such as nematodes (Nematoda), insects (Insecta), including bees and ants, mammals such as bats (Chiroptera) and humans (Homo sapiens). This review consolidates our current knowledge of Streptomyces - animal interactions, with a particular focus on chemical ecology and the roles of specialized metabolites in shaping these relationships. This work highlights the emerging body of work investigating the role of Streptomyces ecology beyond soil ecosystems and draws attention to the importance of exploring non-traditional niches, including animal-associated microbiomes, to deepen our understanding of microbial-animal interactions and to expand opportunities for natural product discovery.},
}

*Streptomyces/physiology/genetics/metabolism
Animals
Humans
Soil Microbiology
Microbiota
Insecta/microbiology
Nematoda/microbiology

@article {pmid42568080,
year = {2026},
author = {Ma, S and Zhang, C and Yao, Y and Zhou, M and Chen, A and Chen, Y and Chen, Y and Wang, J and Abudushalamu, G and Cai, S and Zhao, F and Chen, D and Li, X and Zheng, Y and Fan, J and Gao, X and Liu, Y and Fan, W and Zhu, F and Yang, J and Miao, M and Fan, X and Wu, G},
title = {A three-metabolite microbiota-associated signature for early risk stratification of gestational diabetes mellitus.},
journal = {Cardiovascular diabetology},
volume = {25},
number = {1},
pages = {},
pmid = {42568080},
issn = {1475-2840},
support = {82302609//National Natural Science Foundation of China/ ; 82373781//National Natural Science Foundation of China/ ; BK20230840//Natural Science Foundation of Jiangsu Province/ ; JSKLCCM202202015//Jiangsu Provincial Key Laboratory of Critical Care Medicine/ ; },
mesh = {Humans ; Female ; *Diabetes, Gestational/diagnosis/microbiology/blood ; Pregnancy ; *Metabolomics ; Risk Assessment ; Prospective Studies ; Risk Factors ; Biomarkers/blood ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Metagenomics ; Predictive Value of Tests ; Gestational Age ; *Propionates/blood ; Prognosis ; *Bacteria/metabolism/classification ; Multiomics ; },
abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes and long-term metabolic and cardiovascular risk. However, oral glucose tolerance testing at 24-28 gestational weeks limits early risk stratification. Gut microbiota-associated metabolites may reflect early metabolic abnormalities, including those relevant to cardiometabolic health, but robust early-pregnancy biomarkers remain limited.

METHODS: We conducted a multicenter nested case-control and prospective study involving 2,693 pregnant women. Untargeted metabolomics and metagenomics were integrated to identify GDM-associated metabolites and gut microbial alterations. Three consistently dysregulated metabolites, 3-hydroxydecanoic acid, γ-Glu-Leu, and propionic acid, were quantified by targeted LC-MS/MS. Candidate algorithms were compared using repeated 10-fold cross-validation, and a final generalized linear model was externally and prospectively validated.

RESULTS: Women who later developed GDM showed an adverse early-pregnancy metabolic profile, including higher BMI, triglycerides, and platelet count. Untargeted metabolomics identified 14 persistently altered metabolites enriched in energy, oxidative stress, and amino acid metabolism pathways. Metagenomics revealed taxonomic restructuring and coordinated microbiota-metabolite associations. The three-metabolite model achieved AUCs of 0.838 (95% CI, 0.791-0.885) in training, 0.840 (95% CI, 0.769-0.911) in internal validation, 0.955 (95% CI, 0.925-0.985) and 0.917 (95% CI, 0.875-0.958) in two external cohorts, and 0.969 (95% CI, 0.937-1.000) in the prospective cohort.

CONCLUSION: Early microbiota-associated metabolic dysregulation is detectable before routine GDM diagnosis. This compact three-metabolite panel may support early GDM risk stratification and provides metabolic evidence relevant to broader cardiometabolic risk assessment in pregnancy.},
}

Humans
Female
*Diabetes, Gestational/diagnosis/microbiology/blood
Pregnancy
*Metabolomics
Risk Assessment
Prospective Studies
Risk Factors
Biomarkers/blood
Case-Control Studies
*Gastrointestinal Microbiome
Adult
Metagenomics
Predictive Value of Tests
Gestational Age
*Propionates/blood
Prognosis
*Bacteria/metabolism/classification
Multiomics

@article {pmid42568342,
year = {2026},
author = {Tedersoo, L and Prous, M and Chen, M and Anslan, S and Saar, I and Dubois, B and Mikryukov, V},
title = {Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70189},
pmid = {42568342},
issn = {1755-0998},
support = {101200758//HORIZON EUROPE European Research Council/ ; TK200//Estonian Ministry of Education and Research/ ; 362828//Research Council of Finland/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; *Soil Microbiology ; *Metagenomics/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Benchmarking ; Biodiversity ; },
abstract = {Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (> 500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2 × 500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar-a bioinformatics pipeline presented here-had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.},
}

*DNA Barcoding, Taxonomic/methods/standards
*Soil Microbiology
*Metagenomics/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
DNA, Ribosomal Spacer/genetics/chemistry
Benchmarking
Biodiversity

@article {pmid42569915,
year = {2026},
author = {Lin, CP and Geroldi, A and Selem, N and Liti, G and Tsai, IJ},
title = {A Global Synthesis of Yeast in Microbiomes.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.70039},
pmid = {42569915},
issn = {1097-0061},
support = {Impulscience 2024 - SMIC//Fondation Bettencourt Schueller/ ; AS-IA-113-L04//Academia Sinica/ ; 114-2628-B-001-014-//National Science and Technology Council, R.O.C/ ; },
abstract = {Yeasts are widespread members of microbial communities across terrestrial, aquatic, and host-associated environments, yet they remain underrepresented in microbiome studies due to low abundance and methodological biases. By combining a literature review with a meta-analysis of ~44,000 fungal metabarcoding samples from the GlobalFungi database, we show that yeasts occur in over 90% of samples, confirming their global ubiquity. Basidiomycetous lineages-especially Agaricomycotina-were most frequently detected, whereas Saccharomycotina showed stronger signals in anthropogenic, aquatic, host-associated, and food-related settings depending on the dataset. Although yeasts typically comprised only ~0.1% of fungal reads, their distributions were structured rather than uniform and reflected distinct habitat associations across environments. In ~3% of samples, yeasts exceeded 25% of reads, with genera such as Aureobasidium, Hanseniaspora, and Saccharomyces episodically dominating nutrient-rich or human-influenced environments. Cosmopolitan genera including Vishniacozyma, Solicoccozyma and Rhodotorula were broadly distributed but remain underreported in microbiome surveys. Shotgun metagenomic data further confirmed yeast presence across diverse microbiomes, with yeast-derived reads being a small fraction of total metagenomic sequences, reflecting the 'curse of low abundance'. Despite their rarity, yeasts are likely to contribute to nutrient cycling, plant growth, and host interactions. We recommend inclusive multi-kingdom approaches-improved primer design, optimised fungal DNA recovery, long-read sequencing, and quantitative tools-to better integrate yeasts into microbiome research.},
}

@article {pmid42168837,
year = {2026},
author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T},
title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42168837},
issn = {1471-2180},
support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; },
mesh = {*Swimming Pools ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; *Water Microbiology ; Archaea/genetics/classification/isolation & purification ; *Microbiota/genetics ; Viruses/genetics/classification/isolation & purification ; China ; Metagenome ; Water Quality ; Biodiversity ; },
abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.},
}

*Swimming Pools
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
*Water Microbiology
Archaea/genetics/classification/isolation & purification
*Microbiota/genetics
Viruses/genetics/classification/isolation & purification
China
Metagenome
Water Quality
Biodiversity

@article {pmid42286394,
year = {2026},
author = {Shen, Q and Chen, J and Chen, Y and Liu, J and Mao, L and Shi, W and Ndjekadom, A and Wang, J and Wang, X and Liu, Y and Yang, S and Ji, L and Wu, P and Tong, F and Yang, H and Zhang, W},
title = {Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.},
journal = {Virus genes},
volume = {62},
number = {4},
pages = {533-541},
pmid = {42286394},
issn = {1572-994X},
support = {22KJA320001//Jiangsu Province Higher Education Basic Science (Natural Science) Research Project/ ; No. 2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Aedes/virology ; Phylogeny ; China ; Metagenomics/methods ; *DNA Viruses/genetics/classification/isolation & purification ; *Virome/genetics ; Genome, Viral ; *Parvoviridae/genetics/classification ; },
abstract = {Aedes albopictus is a globally important mosquito species capable of transmitting a variety of viruses. In this study, a total of 440 Ae. albopictus individuals were collected from Fanchang, Anhui Province, and 22 tissue libraries were constructed for metagenomic sequencing. A total of 649,930,614 reads were obtained and assembled into 209,335 contigs, of which 18,339 showed similarity to known viral proteins, spanning 13 viral families including both DNA and RNA viruses. Because several DNA virus-related sequences were recovered from the dataset, we further focussed on CRESS-DNA virus-related sequences and members of the family Parvoviridae. Phylogenetic analysis showed that three CRESS-DNA virus-related sequences clustered within Smacoviridae and Genomoviridae, while two Parvoviridae genomes were assigned to Brevihamaparvovirus and Protoparvovirus. These findings provide a metagenomic overview of the Ae. albopictus-associated virome in Anhui Province and provide baseline information on mosquito-associated DNA virus-related sequences in this region.},
}

Animals
*Aedes/virology
Phylogeny
China
Metagenomics/methods
*DNA Viruses/genetics/classification/isolation & purification
*Virome/genetics
Genome, Viral
*Parvoviridae/genetics/classification

@article {pmid42364737,
year = {2026},
author = {Hajjar, C and Saint-Criq, V and Thomas, M and Butel, MJ and Bazarbachi, A and Abifadel, M},
title = {The lung microbiome in hematopoietic stem cell transplantation: immune interactions, clinical consequences, and emerging interventions.},
journal = {Respiratory medicine},
volume = {261},
number = {},
pages = {109004},
doi = {10.1016/j.rmed.2026.109004},
pmid = {42364737},
issn = {1532-3064},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Microbiota/immunology ; *Lung/microbiology/immunology ; Graft vs Host Disease/immunology ; Dysbiosis/immunology ; *Lung Diseases/microbiology/immunology/etiology ; },
abstract = {Hematopoietic stem cell transplantation (HSCT) offers curative potential for hematologic malignancies and immune disorders, yet pulmonary complications remain major contributors to non-relapse morbidity and mortality. Traditionally attributed to immune suppression and graft-versus-host disease (GvHD), these complications are increasingly recognized to involve disruption of pulmonary microbial communities. A growing body of clinical and experimental evidence indicates that HSCT-associated perturbations in the lung microbiome, driven by conditioning, antimicrobials, immune injury, and infection, are associated with distinct post-transplant pulmonary phenotypes and, in some cohorts, with mortality risk. Whether these microbial shifts represent causal contributors to lung injury or contextual biomarkers of immune vulnerability remains unresolved, and this distinction carries direct implications for microbiome-targeted intervention. Dysbiotic shifts in the lung have been associated with both infectious and non-infectious complications, including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and fibrotic lung disease. Gut-lung microbial crosstalk may amplify or reflect systemic immune dysfunction, though the directionality of this relationship remains incompletely characterized. Multi-omics approaches, integrating metagenomics, metatranscriptomics, and metabolomics, are beginning to define the host-microbiome interaction signatures that distinguish injury subtypes and predict outcomes. This review synthesizes mechanistic insights into lung microbiome-immune interactions after HSCT, critically appraises the methodological constraints on the current evidence base, and evaluates microbiome-based interventions, including fecal microbiota transplantation, inhaled postbiotics, and precision antimicrobials, as candidate strategies for respiratory protection in transplant recipients, while acknowledging that prospective interventional evidence in this population remains limited.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*Microbiota/immunology
*Lung/microbiology/immunology
Graft vs Host Disease/immunology
Dysbiosis/immunology
*Lung Diseases/microbiology/immunology/etiology

@article {pmid42370747,
year = {2026},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.},
journal = {mBio},
volume = {17},
number = {8},
pages = {e0338225},
pmid = {42370747},
issn = {2150-7511},
support = {DE-FOA-0001858//Advanced Research Projects Agency - Energy/ ; OCE-1837116//National Science Foundation/ ; EF-2025217//National Science Foundation/ ; R01-ES030316/NH/NIH HHS/United States ; },
mesh = {Animals ; Polyphenols/metabolism ; Polysaccharides/metabolism ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Seaweed/metabolism/chemistry ; *Bacteria/metabolism/classification/genetics ; Biotransformation ; },
abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}

Animals
Polyphenols/metabolism
Polysaccharides/metabolism
*Fishes/microbiology
*Gastrointestinal Microbiome
*Seaweed/metabolism/chemistry
*Bacteria/metabolism/classification/genetics
Biotransformation

@article {pmid42476135,
year = {2026},
author = {Zhao, W and Wang, J and Chen, C and Jiang, A and Wang, Y and Hu, A and Qi, Q and Chen, Y and Sui, W and Dong, L and Zhang, Y and Xiao, X},
title = {Hadal topography incubates hidden microbial hotspots in the deepest ocean.},
journal = {Cell host & microbe},
volume = {34},
number = {8},
pages = {1523-1539.e7},
doi = {10.1016/j.chom.2026.06.015},
pmid = {42476135},
issn = {1934-6069},
mesh = {Oceans and Seas ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; Carbon Cycle ; Ecosystem ; Metagenomics ; *Microbiota ; Water Microbiology ; Bacteria/classification/genetics/isolation & purification ; Biomass ; },
abstract = {Plate subduction creates unique topographic features in hadal trenches, yet their influence on microbial ecosystems and the global ocean remains unclear. Here, we conducted a topography-targeted investigation across 6-11 km of water depth within the Mariana Trench, integrating metagenomic, metaproteomic, and geochemical analyses. Coupled with high-resolution topographic mapping, our analyses reveal topography as an overlooked determinant of hadal geochemical and microbial heterogeneity. Convex areas exhibit classical sediment-depth-decay patterns with sparse, cooperative microbial communities. Conversely, concave features maintain higher biomass and activity as well as dense microbial interactions. Critically, slope concave sites incubate previously unrecognized microbial hotspots and may serve as interchange hubs, potentially facilitating genetic exchange and upward dispersal of microorganisms from Earth's deepest regions to the broader ocean. Our findings demonstrate that topographic features, rather than water depth, significantly correlate with organic carbon influx and its microbial turnover rates, enabling predictive modeling of hadal carbon cycling with global implications.},
}

Oceans and Seas
*Seawater/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
Carbon Cycle
Ecosystem
Metagenomics
*Microbiota
Water Microbiology
Bacteria/classification/genetics/isolation & purification
Biomass

@article {pmid42520798,
year = {2026},
author = {Zhang, WJ and Hu, A and Wu, Z and Liu, L and Li, C and Wang, Y and Wei, Z and Lu, R and Li, J and He, Y and Zhang, T and Liu, S and Wang, J and Meng, L and Xiao, X and Zhao, W},
title = {Unveiling active microbial processes in Earth's deepest seawater.},
journal = {Cell host & microbe},
volume = {34},
number = {8},
pages = {1540-1559.e10},
doi = {10.1016/j.chom.2026.07.001},
pmid = {42520798},
issn = {1934-6069},
mesh = {*Seawater/microbiology ; *Microbiota/genetics ; Metagenome ; Ecosystem ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Oceans and Seas ; Earth, Planet ; Proteome ; Proteomics ; },
abstract = {Microorganisms dominate life in the hadal zone, yet extreme sampling difficulty and low biomass have precluded characterization of their in situ activities. Here, we analyze microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives. DNA-protein co-extraction and metagenome-guided metaproteomic analysis identify 135,073 non-redundant active proteins, with over 95% being hadal-specific. Metaproteomic quantification distinguishes highly active and less active taxa that differ in biogeographic origins and genomic traits. Hadal microorganisms operate a metabolic regime fundamentally distinct from the upper ocean, preferentially utilizing refractory organic matter (aromatics, halogenated compounds, and D-amino acids) and expanded electron acceptors (thiosulfate and heavy metals), collectively shaping hadal element cycling. Active viruses extend beyond "Piggyback-the-Winner" dynamics, enhancing host adaptation through auxiliary metabolic genes. These findings provide proteome-level evidence of hadal microbial activities and reveal biogeochemical cycling distinct from that of the upper ocean, highlighting the underappreciated significance of hadal microbiomes within global ocean ecosystems.},
}

*Seawater/microbiology
*Microbiota/genetics
Metagenome
Ecosystem
*Bacteria/genetics/classification/metabolism/isolation & purification
Oceans and Seas
Earth, Planet
Proteome
Proteomics

@article {pmid42562478,
year = {2026},
author = {Zhang, HY and Huang, TC and Chai, LJ and Shi, W and He, YX and Lu, ZM and Zhang, XJ and Wang, ST and Shen, CH and Shi, JS and Xu, ZH},
title = {Integrating ecological networks and metagenomics to decipher core microbial drivers of organic acid metabolism during heaped fermentation of sauce-flavor Baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119702},
doi = {10.1016/j.foodres.2026.119702},
pmid = {42562478},
issn = {1873-7145},
mesh = {*Fermentation ; *Metagenomics/methods ; *Food Microbiology ; *Bacteria/metabolism/genetics/classification ; Volatile Organic Compounds/metabolism/analysis ; Acetic Acid/metabolism/analysis ; Caproates/analysis ; Taste ; Lactic Acid/metabolism/analysis ; *Fermented Foods/microbiology ; *Microbiota ; Pentanoic Acids ; Hemiterpenes ; },
abstract = {Organic acids play crucial roles in both flavor quality and microbial succession of sauce-flavor Baijiu; however, the core microbial drivers responsible for their metabolism remain poorly understood. This study systematically investigated the microbial drivers of organic acid metabolism across six sequential rounds (R1-R6) of heaped fermentation. A total of 24 organic acids were identified, including nine non-volatile organic acids (NVOAs) and 15 volatile organic acids (VOAs). HPLC analysis revealed that the total content of acetic acid and nine NVOAs increased significantly across rounds, rising from 29.35 g/kg in R1 to 66.40 g/kg in R6. Lactic acid was the most abundant NVOA, while acetic acid, isovaleric acid, and hexanoic acid were the primary volatile contributors. Co-occurrence network analysis identified 488 consistently correlated bacterial pairs that clustered into two distinct guilds. Guild 2, mainly comprising Virgibacillus, Kroppenstedtia, Oceanobacillus, and Bacillus, exhibited high abundance (47%-78%) across all rounds and was defined as the core bacterial guild. Spearman correlation analysis revealed that guild 2 was positively correlated with NVOAs (69.41%) but negatively correlated with VOAs (63.02%). Metagenomic analysis reconstructed seven key pathways involved in organic acid biosynthesis. Kroppenstedtia, Lentibacillus, Desmospora, and Oceanobacillus were identified the taxa harboring the genetic potential most frequently detected across multiple pathways, with Kroppenstedtia and Lentibacillus exhibiting the highest gene abundances. These findings provide a theoretical foundation for targeted regulation of organic acid content in sauce-flavor Baijiu production.},
}

*Fermentation
*Metagenomics/methods
*Food Microbiology
*Bacteria/metabolism/genetics/classification
Volatile Organic Compounds/metabolism/analysis
Acetic Acid/metabolism/analysis
Caproates/analysis
Taste
Lactic Acid/metabolism/analysis
*Fermented Foods/microbiology
*Microbiota
Pentanoic Acids
Hemiterpenes

@article {pmid42562486,
year = {2026},
author = {Sehar, H and Chen, Z and Zhang, J and Wu, K and Li, BS and Yan, H},
title = {Microbial composition, dynamics, and functional roles in jinhua ham fermentation: integrating starter cultures and multi-omics for quality and safety.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119711},
doi = {10.1016/j.foodres.2026.119711},
pmid = {42562486},
issn = {1873-7145},
mesh = {*Fermentation ; *Meat Products/microbiology/analysis ; Multiomics ; *Food Microbiology ; Animals ; Bacteria/metabolism/classification ; *Microbiota ; Food Safety ; Swine ; Fungi/metabolism ; },
abstract = {Jinhua ham, a traditional Chinese dry-cured meat product with nearly a millennium of production history, derives its characteristic colour, layered aroma, and umami-rich taste from the coordinated biochemical activity of a dynamic microbial ecosystem across an eight-to-ten-month fermentation timeline. This review provides a critical synthesis of research between 2018 and 2025 on microbial composition, community dynamics, functional roles, safety risks, starter culture applications, and multi-omics characterisation of Jinhua ham fermentation, unified by precision fermentation as an organising framework. High-throughput sequencing has established that halotolerant bacterial genera, Staphylococcus, Psychrobacter, Halomonas, and Lactobacillus, and fungal communities comprising Aspergillus, Debaryomyces, Meyerozyma, and Penicillium undergo deterministic, physicochemically driven succession, with their enzymatic activities governing proteolysis, lipolysis, volatile compound formation, colour stabilisation, and the accumulation of biogenic amines, mycotoxins, and antimicrobial resistance genes (ARGs). Autochthonous starter cultures, including Staphylococcus xylosus, Lactiplantibacillus plantarum, and Penicillium aethiopicum, improve process controllability, safety, and sensory consistency, yet their mechanistic basis and validation remain incompletely established. Genomic and metabolomic approaches have generated datasets, but integrated metagenomics-metabolomics coupling, capable of linking microbial gene networks to flavour compound production, and metatranscriptomic characterisation of gene expression remain the unmet methodological needs. Five research directions are proposed: achieving species-level microbial resolution through long-read sequencing and longitudinal sampling; validating flavour-forming pathways through isotopic tracing and controlled inoculation; standardising analytical protocols for cross-study comparability; conducting starter culture and ARG safety validation; and developing low-salt fermentation strategies. Together, these directions define the research investment required to advance Jinhua ham production from empirical tradition to precision-engineered consistency.},
}

*Fermentation
*Meat Products/microbiology/analysis
Multiomics
*Food Microbiology
Animals
Bacteria/metabolism/classification
*Microbiota
Food Safety
Swine
Fungi/metabolism

@article {pmid42231385,
year = {2026},
author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N},
title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.},
journal = {Nutrition journal},
volume = {25},
number = {1},
pages = {},
pmid = {42231385},
issn = {1475-2891},
support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; },
mesh = {Humans ; Male ; *Altitude ; *Body Composition/drug effects ; *Curcumin/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Muscle, Skeletal/drug effects ; Young Adult ; Adult ; Acclimatization ; Electric Impedance ; },
abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.

METHODS: A total of 102 male Han participants was randomized to curcumin (812 mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.

RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P = 0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P < 0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P < 0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P < 0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.

CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.

TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.},
}

Humans
Male
*Altitude
*Body Composition/drug effects
*Curcumin/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
Muscle, Skeletal/drug effects
Young Adult
Adult
Acclimatization
Electric Impedance

@article {pmid42498043,
year = {2026},
author = {Kaki, D and Kore, U and Talari, A and Komati, A and Garlapati, C and Dondra, T and De, S and Mandava, K},
title = {Modern approaches to gut microbiome investigation: Sequencing, culturomics, metabolomics, and beyond.},
journal = {Journal of microbiological methods},
volume = {248},
number = {},
pages = {107636},
doi = {10.1016/j.mimet.2026.107636},
pmid = {42498043},
issn = {1872-8359},
mesh = {Humans ; *Metabolomics/methods ; Multiomics ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Host Microbial Interactions ; Bacteria/genetics/classification/isolation & purification ; Proteomics/methods ; },
abstract = {The human gut microbiome is a complex and constantly evolving community of trillions of microorganisms that are crucial to various aspects of health and disease. It impacts digestion, metabolism, immune function, neurological processes, and vulnerability to illnesses. Recent technological advancements in biology and engineering have transformed microbiome research, allowing for more detailed analysis of microbial composition, functions, and interactions with the host. This review offers a thorough overview of both current and emerging methods for studying the gut microbiome, including sample collection techniques, culture-based approaches like culturomics and microfluidics, as well as culture-independent methods such as 16S rRNA sequencing, shotgun metagenomics, and the integration of multi-omics approaches like metabolomics, proteomics, and transcriptomics. It also discusses innovative tools including single-cell genomics, spatial transcriptomics, and microbiome-on-a-chip platforms, which hold promise for revealing host-microbe interactions at unprecedented levels of detail. The review underscores the importance of combining biological insights with engineering innovations particularly microfluidics and organ-on-a-chip models to recreate gut environments that mimic physiological conditions. Additionally, it explores the potential of artificial intelligence and machine learning in analyzing data and developing predictive models for personalized microbiome-based diagnostics and therapies. Acknowledging challenges such as microbial diversity, environmental sensitivity, and technical hurdles, this review aims to guide researchers in choosing optimal tools to study the gut microbiota, deepen mechanistic understanding, and translate findings into clinical applications that enhance human health.},
}

Humans
*Metabolomics/methods
Multiomics
*Gastrointestinal Microbiome/genetics/physiology
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Host Microbial Interactions
Bacteria/genetics/classification/isolation & purification
Proteomics/methods

@article {pmid42501556,
year = {2026},
author = {Bhuyan, B},
title = {Enhancing crop productivity under stress through plant growth-promoting bacterial consortia: Relevance to sustainable development goals.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128641},
doi = {10.1016/j.micres.2026.128641},
pmid = {42501556},
issn = {1618-0623},
mesh = {*Stress, Physiological ; *Sustainable Development ; *Crops, Agricultural/microbiology/growth & development ; *Plant Development ; *Microbial Consortia/physiology ; *Bacteria/metabolism ; Soil Microbiology ; Rhizosphere ; Plant Growth Regulators/metabolism ; *Crop Production/methods ; },
abstract = {Abiotic and biotic stresses significantly threaten global food security and agricultural sustainability. Achieving the United Nations Sustainable Development Goals (SDGs), particularly SDG 2 (Zero Hunger), SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), SDG 13 (Climate Action), and SDG 15 (Life on Land), requires sustainable agricultural approaches. Recently, plant growth-promoting bacterial (PGPB) consortia have emerged as an effective strategy for enhancing crop productivity under stress conditions. These microbial communities improve plant growth through mechanisms such as nitrogen fixation, phosphate solubilization, phytohormone production, siderophore secretion, ACC deaminase activity, induction of systemic resistance, while enhancing nutrient uptake, antioxidant activity, osmotic regulation, and stress-responsive signalling pathways, thus improving plant health and productivity. Compared with single-strain inoculants, consortia provide synergistic effects that enhance rhizosphere colonization, microbial survival, and plant-microbe interactions, thus contributing to the achievement of the SDGs. Recent advances in modern tools such as metagenomics, metatranscriptomics, metabolomics, and machine learning for predictive microbiome modelling, as well as field-level engineering approaches such as encapsulation technologies, biochar-based carriers, seed coating, and root microbiome editing, have accelerated the development of efficient microbial formulations for sustainable agriculture. This review discusses the potential of PGPB consortia as a sustainable solution for boosting crop productivity under stress. The integration of consortia into modern agricultural practices can play a crucial role in supporting resilient farming systems and advancing the global SDG agenda. This review highlights the key limitations, challenges, and research gaps associated with PGPB consortia, as well as future prospects for enhancing crop productivity.},
}

*Stress, Physiological
*Sustainable Development
*Crops, Agricultural/microbiology/growth & development
*Plant Development
*Microbial Consortia/physiology
*Bacteria/metabolism
Soil Microbiology
Rhizosphere
Plant Growth Regulators/metabolism
*Crop Production/methods

@article {pmid42520350,
year = {2026},
author = {Chen, Q and Niu, X and Wu, W and Shi, H and Liu, G and Chen, L and Wang, H and Zhang, Y},
title = {Composted cattle manure enhances microbial nitrogen retention and increased seed watermelon yield in saline-alkali soil.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128647},
doi = {10.1016/j.micres.2026.128647},
pmid = {42520350},
issn = {1618-0623},
mesh = {*Manure/microbiology/analysis ; Animals ; *Soil Microbiology ; *Soil/chemistry ; Cattle ; *Nitrogen/metabolism/analysis ; *Composting/methods ; Salinity ; Alkalies ; Bacteria/metabolism/classification/genetics ; Nitrogen Cycle ; Nitrification ; Microbiota ; },
abstract = {Soil salinity and alkalinity represent a global environmental challenge that severely hampers agricultural productivity. While composted manure amendment represents a sustainable strategy relates to nutrient supplementation and soil health improvement. However, the influence of composted manure on microbial nitrogen cycles in a saline-alkali soil remains obscure. Saline-alkali soil amendment with cattle manure (CM) and composted CM (CCM) were conducted to systematically evaluate their efficacy in ameliorating soil physicochemical properties and enhancing crop productivity under saline-alkaline stress conditions. Physicochemical properties of saline-alkali soils under different amendments were investigated. The changes in microbial communities and nitrogen metabolism were analyzed using metagenomic sequencing and qPCR. Furthermore, the correlations between microbial nitrogen cycle and soil physicochemical factors were assessed. Compared to control (CK), soil salinity was significantly mitigated by 43.0%% and 51.9% in CM and CCM treatments. The organic matter, humus and nitrogen contents were also significantly increased in CM and CCM treatments. CCM significantly improved abundance of nrf in dissimilatory nitrate reduction to ammonium (DNRA), while reducing amoA abundance in nitrification. These findings suggest a potential redirection of microbial nitrogen fluxes toward retention rather than loss pathways, thereby enhances soil fertility. And the seed yield in CCM treatment was significantly higher than those of CM and CK. Our results provided mechanistic evidence for the use of composted manure as a sustainable strategy for enhancing soil fertility, mitigating salinization, and increasing crop yield of saline-alkali soils.},
}

*Manure/microbiology/analysis
Animals
*Soil Microbiology
*Soil/chemistry
Cattle
*Nitrogen/metabolism/analysis
*Composting/methods
Salinity
Alkalies
Bacteria/metabolism/classification/genetics
Nitrogen Cycle
Nitrification
Microbiota

@article {pmid42531353,
year = {2026},
author = {Riddell V, J and Shatadru, RN and Smith, GJ and McGivern, BB and Ellenbogen, JB and Jurgensen, SK and Fofana, A and Tfaily, MM and Wrighton, KC and Sullivan, MB},
title = {Viruses help shape microbiome response to polyphenol rewiring of methane-suppressed peat microcosms.},
journal = {PLoS biology},
volume = {24},
number = {7},
pages = {e3003925},
doi = {10.1371/journal.pbio.3003925},
pmid = {42531353},
issn = {1545-7885},
mesh = {*Methane/metabolism ; *Microbiota/drug effects/physiology/genetics ; *Soil Microbiology ; *Polyphenols/metabolism ; Soil/chemistry ; },
abstract = {Human activities are accelerating permafrost thaw and subsequent methane emissions from increased microbial activity, prompting microbiome engineering efforts as an emissions mitigation strategy. We recently demonstrated that catechin amendment could drastically reduce methane emissions (>80%) in peat microcosms by enriching catechin-degrading prokaryotes that outcompeted methanogens for hydrogen. However, viral contributions to such microbiome-level responses remain unexplored and we hypothesized that viral dynamics could help shape the microbiome response as nutrient amendments may alter cellular physiology in ways that could induce lytic viral activity. Here, we performed virus eco-genomics analyses of the previously-studied time-resolved multi-omics data collected from catechin-amended peat microcosms. We conservatively identified 900 putatively lytic viral operational taxonomic units (vOTUs), with 41% predicted to infect active host genomes including the most transcriptionally active vOTUs predicted to infect key catechin-degrading genera (Clostridium and undescribed Bacillota JAGFXR01). Notably, a single JAGFXR01-targeting vOTU dominating the viral response (>40% of community viral transcription; 20-156-fold more abundant than its host), which we interpreted as induction resulting in intense lytic activity that could release catechin degradation intermediates to other community members. Consistent with this, gene expression analysis revealed elevated catechin-intermediate degradation and hydrogenase signals in 34 additional polyphenol-degrading metagenome-assembled genomes. These findings support a model consistent with a viral shunt-like process that extends our previous prokaryote-centric model: viral lysis of fast-growing catechin degraders redistributes phenolic intermediates to diverse phenol-degrading taxa that sustain methane suppression via hydrogen consumption. Beyond carbon cycling importance in this system, elucidating unintended virus-mediated responses to nutrient and prebiotic interventions will enable more predictable and effective microbiome engineering strategies across soil, ocean, and human ecosystems.},
}

*Methane/metabolism
*Microbiota/drug effects/physiology/genetics
*Soil Microbiology
*Polyphenols/metabolism
Soil/chemistry

@article {pmid42558343,
year = {2026},
author = {Liu, L and Lin, J and Sang, K and Lai, J and Huang, N and Zhong, P and Liu, Y and Chen, S},
title = {Bile acid signaling at the gut-vascular interface: a novel modulator of hantavirus endothelial barrier dysfunction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1883162},
pmid = {42558343},
issn = {2235-2988},
mesh = {Animals ; Humans ; *Orthohantavirus/pathogenicity/physiology ; *Bile Acids and Salts/metabolism ; *Signal Transduction ; Receptor, Farnesoid X-Activated ; Rats ; *Endothelial Cells/virology/metabolism ; Gastrointestinal Microbiome ; *Hantavirus Infections/virology/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; NF-kappa B/metabolism ; Lung/virology/microbiology ; Vascular Cell Adhesion Molecule-1/metabolism/genetics ; },
abstract = {Hantavirus infection triggers life-threatening hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), driven by severe endothelial barrier breakdown and systemic capillary leakage. Clinical severity varies widely with undefined host regulators, and no targeted endothelial-protective treatments exist. Recent data link hantaviruses to gut microbiome remodeling, while bile acid (BA) receptors FXR and TGR5 potently inhibit NF-κB-mediated endothelial inflammation. We synthesize four core lines of evidence. First, metagenomic reports confirm hantavirus reshapes gut/lung microbiota in rodent reservoirs. Second, we re-analyzed three public GEO datasets via standardized RNA-seq/microarray pipelines: (i) GSE245916: SEOV-infected human/rat lung ECs show conserved VCAM1/ICAM1 upregulation (human VCAM1 log2FC=+1.17, P = 0.023; rat Icam1 log2FC=+0.32, padj=0.016) with unaltered FXR; (ii) GSE7271: SEOV-infected rat lung displays sustained Nfkb1 suppression (all timepoints, P<0.05) and day-15 Slc10a2 downregulation (P = 0.028); (iii) GSE270172: PUUV 3D vessel chips feature robust IL6 elevation (log2FC=+1.22, P = 3.1×10[-8]) and disrupted BA transporters (ABCC3 log2FC=-1.44, P = 7.4×10[-][12]). TGR5 (GPBAR1) was undetectable in endothelial cells across all datasets. Third, FXR/TGR5 agonists repress NF-κB inflammation and mitigate lung vascular injury. Fourth, HTNV upregulates CH25H to block HMGCR-dependent cholesterol synthesis, depleting BA precursor substrates. We propose a unified pathogenic model: hantavirus-triggered gut dysbiosis plus virus-impaired cholesterol metabolism deplete circulating FXR/TGR5 agonistic BAs, relieving constitutive inhibition of endothelial NF-κB and monocyte NLRP3 inflammasomes to exacerbate capillary leakage. We define tiered testable predictions covering clinical multi-omics cohorts, in vitro receptor modulation assays and in vivo pharmacological interventions. This gut microbiota-BA-FXR/TGR5 axis represents a repurposable therapeutic target for hantavirus diseases, though direct causal evidence connecting BA signaling to viral vascular damage remains absent; our framework offers a rigorous testable roadmap for subsequent validation.},
}

Animals
Humans
*Orthohantavirus/pathogenicity/physiology
*Bile Acids and Salts/metabolism
*Signal Transduction
Receptor, Farnesoid X-Activated
Rats
*Endothelial Cells/virology/metabolism
Gastrointestinal Microbiome
*Hantavirus Infections/virology/metabolism
Receptors, G-Protein-Coupled/metabolism
Receptors, Cytoplasmic and Nuclear/metabolism
NF-kappa B/metabolism
Lung/virology/microbiology
Vascular Cell Adhesion Molecule-1/metabolism/genetics

@article {pmid42559206,
year = {2026},
author = {Viver, T and Gago, JF and Bustos-Caparros, E and Aldeguer-Riquelme, B and Rodriguez Rojas, LM and Ramírez, AS and Albuquerque, L and Amiour, S and Oren, A and Mutlu, MB and Venter, SN and Baxter, BK and Llames, ME and González, B and Rodríguez-Valdecantos, G and Banciu, HL and Stott, MB and Santos, F and Hedlund, BP and Antón, J and Amann, R and Konstantinidis, KT and Rossello-Mora, R},
title = {Metagenomics reveal unrestricted dispersal of extreme halophiles and higher connectivity among coastal vs. inland solar salterns and hypersaline lakes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag165},
pmid = {42559206},
issn = {2730-6151},
abstract = {Hypersaline environments constitute ideal systems for studying evolutionary processes and microbial diversification due to their relatively low (and thus tractable) diversity and geographically isolated nature. Based on metagenomic sequencing of samples from 25 hypersaline sites in 11 countries taken within a single year, we explored the relationships between environmental factors, geographic distance, and microbial community structure and diversification. Our results revealed that microbial communities of coastal sites were more similar to each other than those of the inland sites, reflecting higher connectivity due to ocean currents and nearly unrestricted dispersal. Conversely, inland hypersaline environments showed less connectivity and higher genetic and taxonomic dissimilarities that did not correlate with the distance between the sampled sites. The latter results reflect reduced species migration characterizing inland sites as well as site-specific environmental factors selecting for divergent taxa. The 484 MAGs recovered, representing 284 distinct species, revealed a striking global ubiquity, with 62.5% of the species showing cosmopolitanism, defined as being present at both coastal and inland sites. Most cosmopolitan species showed allopatric differentiation, reflected by an increased frequency of non-synonymous substitutions between MAGs of the same species recovered from more distant sites. However, a few cases of truly cosmopolitan genomovars (average nucleotide identity, or ANI > 99.8%), were also observed. Our results suggest that extreme halophiles have nearly unrestricted global dispersal among ocean-connected sites, and to a lesser extent, among geographically isolated inland sites, although cases of allopatric diversification were also observed.},
}

@article {pmid42560299,
year = {2026},
author = {Liang, F and Li, J and Yue, Y and Pan, J and Liu, C and Cheng, D and Zhang, N and Li, K and Chu, F and Wu, H},
title = {Distinct Gut Microbiome and Metabolome Profiles Associate with Differential Responses to Immunotherapy in Colorectal Cancer.},
journal = {Polish journal of microbiology},
volume = {75},
number = {2},
pages = {168-194},
pmid = {42560299},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/metabolism ; *Metabolome ; *Immunotherapy ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; Male ; Middle Aged ; Aged ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The composition of the intestinal microbiome has been identified as a key factor influencing the efficacy of immune checkpoint inhibitors. This study aimed to systematically evaluate the potential associations among gut microbiota, metabolic profiles, and clinical outcomes in patients with MSI-H advanced colorectal cancer (CRC) treated with immunotherapy. Twenty advanced CRC patients receiving immunotherapy were enrolled and categorized into clinical benefit response (CBR) and non-benefit (NCB) groups based on treatment efficacy. Fecal samples were analyzed using metagenomic sequencing and untargeted metabolomics. The results revealed significant enrichments of s_Clostridium unclassified and metabolites such as guanosine, 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid, and quercetin 3-(6"-malonyl-glucoside) in the CBR group, suggesting their potential positive predictive value for immunotherapy response. Conversely, the NCB group showed significant enrichments of s_Roseburia hominis, s_Marseilla massiliensis, and metabolites including pyrophosphate, riboflavin, and PC(22:5(4Z,7Z,10Z,13Z,16Z)/14:0), indicating a possible association with treatment resistance. By integrating fecal metagenomics and metabolomics, this study reveals distinctive "flora-metabolite" interactions linked to therapeutic response in advanced CRC patients undergoing immunotherapy. Specific microbial and metabolic profiles were positively or negatively correlated with immunotherapy outcomes, highlighting their potential not only as predictive biomarkers but also as a theoretical foundation for developing individualized immunotherapy strategies based on microecological modulation.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology/metabolism
*Metabolome
*Immunotherapy
*Gastrointestinal Microbiome
Female
Feces/microbiology
Male
Middle Aged
Aged
Metabolomics
Bacteria/classification/genetics/isolation & purification

@article {pmid42562454,
year = {2026},
author = {Zheng, X and Sun, P and He, C and Liu, M and Qiu, J and Ding, Z and Zhang, Y and Zhou, S and Zhou, J and Sun, J and Feng, W and Zhang, L and Cheng, N and Xu, Q and Li, X and Yang, L and Liang, A},
title = {Royal jelly enhances ovarian function by modulating taurocholic acid metabolism and attenuating oxidative stress in D-galactose-induced POI mice.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119500},
doi = {10.1016/j.foodres.2026.119500},
pmid = {42562454},
issn = {1873-7145},
mesh = {Animals ; Female ; *Oxidative Stress/drug effects ; Royal Jelly ; Galactose ; Mice ; *Fatty Acids/pharmacology ; *Ovary/drug effects/metabolism ; *Taurocholic Acid/metabolism ; Disease Models, Animal ; *Primary Ovarian Insufficiency/chemically induced/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Estradiol/blood ; },
abstract = {Premature ovarian insufficiency (POI) is a complex endocrine and metabolic disorder frequently associated with oxidative stress. Royal jelly (RJ) is a well-recognized natural functional food with multiple health benefits; however, its potential effects on POI remain unexplored. This study aimed to investigate the therapeutic potential and underlying mechanisms of RJ in a D-galactose (D-gal)-induced POI mouse model. The results showed that RJ increased serum estradiol (E2) levels, enhanced ovarian reserve and oocyte maturation, reduced ovarian oxidative stress, and ultimately improved the fertility of D-gal-treated mice. Integrated metagenomic and metabolomic analyses revealed that RJ alleviated D-gal-induced gut microbiota dysbiosis, notably increasing the abundance of Muribaculaceae bacterium, and restored levels of taurocholic acid (TCA), which positively correlated with both Muribaculaceae bacterium abundance and serum E2 levels. Importantly, TCA supplementation alone recapitulated the protective effects of RJ by reversing D-gal-induced reductions in E2 and anti-Müllerian hormone (AMH) levels, restoring follicle numbers, and alleviating oxidative stress. Mechanistically, TCA activated the nuclear factor erythroid 2-related factor 2 (NRF2) antioxidant pathway in ovarian tissue, while simultaneously enhancing intestinal β-glucuronidase activity to modulate systemic E2 metabolism. In conclusion, RJ alleviates D-gal-induced POI in mice by modulating the gut microbiota-bile acid-ovarian axis, providing novel insights into its potential application for POI prevention and treatment.},
}

Animals
Female
*Oxidative Stress/drug effects
Royal Jelly
Galactose
Mice
*Fatty Acids/pharmacology
*Ovary/drug effects/metabolism
*Taurocholic Acid/metabolism
Disease Models, Animal
*Primary Ovarian Insufficiency/chemically induced/drug therapy/metabolism
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Estradiol/blood

@article {pmid41604220,
year = {2026},
author = {Yao, ML and Lin, P and Hua, K and Zhang, W},
title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {53},
number = {},
pages = {},
doi = {10.1093/jimb/kuag005},
pmid = {41604220},
issn = {1476-5535},
support = {/DE/NIDCR NIH HHS/United States ; R01DE032732/NH/NIH HHS/United States ; No. DGE2146752//National Science Foundation/ ; //University of California/ ; },
mesh = {*Dental Caries/microbiology ; *Microbiota/genetics ; *Multigene Family ; Humans ; *Mouth/microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Biosynthetic Pathways/genetics ; },
abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have identified hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs and quantified their metagenomic abundance and transcriptional activity. We found that aryl polyene, ribosomally synthesized and posttranslationally modified peptide, and nonribosomal peptide encoding BGCs were the most prominent BGCs identified across the three metagenomic datasets. We grouped the identified BGCs into homology-based gene cluster families (GCFs) and found that specific GCFs were consistently associated with either health or caries across diverse taxa, suggesting that some specialized metabolites may perform conserved ecological functions. Conversely, other BGCs showed more restricted taxonomic distributions and were linked to disease-associated taxa, such as Propionibacterium acidifaciens, suggesting niche-specific biosynthetic capacities within the oral environment. Applying elastic-net regression to the metatranscriptomic dataset further identified a subset of 51 BGCs out >3,000 that distinguished healthy from caries samples, reinforcing the discriminatory power of BGC expression patterns. These results demonstrate that BGCs can provide functional resolution beyond taxonomic profiling and that BGC expression, rather than genomic presence alone, can differentiate oral microbial community states. This underscores the relevance of specialized metabolism to oral health and supports the use of BGC-centric analyses to interrogate microbial interactions underlying community stability and disease-associated shifts. One-sentence summary Specialized metabolites in oral bacteria are differentially expressed in healthy and cavity-affected communities.},
}

*Dental Caries/microbiology
*Microbiota/genetics
*Multigene Family
Humans
*Mouth/microbiology
Metagenomics
Metagenome
*Bacteria/genetics/classification/metabolism/isolation & purification
*Biosynthetic Pathways/genetics

@article {pmid42418904,
year = {2026},
author = {Yu, J and Wan, Y and Peng, Y and Liang, S and Chan, FKL and Ng, SC and Tun, HM},
title = {Multi-cohort evidence for impaired microbial support of the methionine cycle in children with autism spectrum disorder.},
journal = {Psychiatry research},
volume = {364},
number = {},
pages = {117317},
doi = {10.1016/j.psychres.2026.117317},
pmid = {42418904},
issn = {1872-7123},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/metabolism ; *Methionine/metabolism ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/metabolism ; Child ; Cohort Studies ; Male ; },
abstract = {The contribution of gut microbiota to outcomes of autism spectrum disorders (ASD) has been increasingly appreciated in recent years. With the accumulating evidence on ASD-driven alterations of the gut microbiota, heterogeneities arise across different reports. To account for variabilities in gut microbiota, clinical representations of ASD and data processing approaches, as well as limitations in sample sizes among the existing gut microbiota studies for ASD, the present multi-cohort analysis applied a standard bioinformatic and statistical pipeline on the publicly available gut metagenomic sequencing data for 674 samples, including 326 TD and 348 ASD individuals, collected from eight studies across three main geographical regions. Throughout the analysis, we identified taxonomic profiles of the gut microbiota exhibited more pronounced dysbiosis associated with ASD and between-study variations compared to functional profiles. Differentially abundant taxonomic and pathway markers were identified and validated for their consistent response to ASD across different studies. Co-occurring deficits in microbial pathways for salvaging adenosylcobalamin and S-adenosyl-L-methionine and biosynthesis of methionine in children with ASD point to a reduced microbial support for the host methionine cycle. Species from Faecalibacterium, Bacteroides, Blautia and Bifidobacterium were identified as microbial contributors to ASD-deficient microbial pathways, particularly those related to the methionine cycle. Therefore, the generalisable ASD-deficient contributors to the methionine cycle, such as Blautia wexlerae, Bacteroides stercoris and Streptococcus thermophilus, could be further investigated for their role in therapeutic applications for ASD.},
}

Humans
*Autism Spectrum Disorder/microbiology/metabolism
*Methionine/metabolism
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology/metabolism
Child
Cohort Studies
Male

@article {pmid42437546,
year = {2026},
author = {Fregolente, LG and Roth, FN and Warncke, JD and Macpherson, AJ and Yilmaz, B and Bassetti, CLA},
title = {The gut-sleep connection: a scoping review into microbiome alterations in sleep-wake and circadian disorders.},
journal = {Sleep medicine},
volume = {147},
number = {},
pages = {109136},
doi = {10.1016/j.sleep.2026.109136},
pmid = {42437546},
issn = {1878-5506},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sleep/physiology ; Sleep Duration ; *Sleep Wake Disorders/microbiology/physiopathology ; *Chronobiology Disorders/microbiology ; Circadian Rhythm/physiology ; },
abstract = {Sleep is fundamental to brain, body, mental, and social health. In parallel, the gut microbiome is increasingly recognized as a key regulator of immune, metabolic, endocrine, and neurophysiological processes. This scoping review explored current evidence on gut microbiome alterations in relation to sleep duration and sleep loss, sleep-wake disorders, and circadian rhythm-related phenotypes. Searches of MEDLINE, Embase, and Cochrane were conducted up to February 2024. Of 2059 records identified, 54 studies met the eligibility criteria. Thirty-eight studies were observational, nine interventional, and seven genome-wide association or Mendelian-randomization studies. The most frequently investigated phenotypes were insomnia (15 studies, 28%), obstructive sleep apnea (12 studies, 22%), circadian rhythm or circadian-misalignment phenotypes (10 studies, 19%), and sleep duration or sleep loss/deprivation (9 studies, 17%). Most studies used 16S rRNA gene sequencing to assess gut microbiota composition and diversity, while shotgun metagenomic sequencing and functional analyses were less common. Across disorders, studies reported alterations in microbial diversity, taxonomic composition, short-chain fatty acid-producing taxa, bile acid-related pathways, inflammatory markers, and cardiometabolic or neurophysiological correlates. However, findings were limited by heterogeneous sleep phenotyping, small sample sizes, cross-sectional designs, variable microbiome methods, and inconsistent control of diet, medication use, body mass index, comorbidities, and stool sampling protocols. Current evidence supports an association between sleep-wake and circadian disturbances and gut microbiome alterations, but causality and disorder-specific microbial signatures remain unresolved. Standardized longitudinal and multi-omics studies are needed to clarify mechanisms and therapeutic potential.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sleep/physiology
Sleep Duration
*Sleep Wake Disorders/microbiology/physiopathology
*Chronobiology Disorders/microbiology
Circadian Rhythm/physiology

@article {pmid42557906,
year = {2026},
author = {Teklay, YT},
title = {Integrative Bioinformatics Approaches in Environmental Biotechnology: A Review.},
journal = {TheScientificWorldJournal},
volume = {2026},
number = {1},
pages = {e3495506},
pmid = {42557906},
issn = {1537-744X},
mesh = {*Computational Biology/methods ; *Biotechnology/methods ; Multiomics ; Genomics ; Biodegradation, Environmental ; },
abstract = {Environmental biotechnology increasingly relies on bioinformatics to address global challenges in pollution control or degradation, biodiversity conservation, and sustainable resource management. By integrating genomics, computational tools, and artificial intelligence, bioinformatics enables the analysis of complex biological datasets, such as metagenomes and environmental DNA (deoxyribonucleic acid), to uncover microbial diversity, pollutant degradation pathways, and ecological resilience. High-throughput sequencing technologies and multiomics integration provide novel insights into microbial communities and their functional roles in bioremediation and ecosystem monitoring. Predictive modeling further enhances our ability to simulate microbial behavior in contaminated environments and assess the long-term impacts of biotechnological interventions. Despite increased progress, challenges remain in managing large-scale data, fostering interdisciplinary collaboration, and developing user-friendly bioinformatics platforms. Future directions emphasize the application of machine learning, sustainable resource management, and collaborative frameworks to bridge bioinformatics and environmental sciences. Unlike traditional descriptive reviews, this work provides a critical evaluation of the functional gaps between genomic potential and in situ microbial activity. It offers a novel synthesis of how multiomics integration and predictive modeling can move beyond species cataloging toward a more robust, evidence-based framework for environmental sustainability.},
}

*Computational Biology/methods
*Biotechnology/methods
Multiomics
Genomics
Biodegradation, Environmental

@article {pmid42558149,
year = {2026},
author = {Ding, R and Qi, F and Dai, Q and Li, K and Zhang, Y},
title = {Multi-omics analysis identifies a hepatocyte-associated signature in alcohol-related liver injury.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1844110},
pmid = {42558149},
issn = {1664-3224},
mesh = {Animals ; *Hepatocytes/metabolism ; Multiomics ; Humans ; *Liver Diseases, Alcoholic/metabolism/genetics/etiology ; Mice ; Male ; Ethanol/adverse effects ; Metabolomics/methods ; Transcriptome ; Feces/chemistry/microbiology ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Disease Models, Animal ; Liver/metabolism ; Metabolome ; Mice, Inbred C57BL ; Metagenomics ; },
abstract = {Alcohol-related liver disease (ALD) is a major cause of liver-related morbidity and mortality worldwide, yet the associations linking alcohol-induced gut microbial alterations to metabolic remodeling and hepatocyte dysfunction remain incompletely understood. Here, we applied an integrative multi-omics strategy combining untargeted fecal metabolomics, shotgun metagenomics, mouse liver bulk RNA sequencing, and reanalysis of publicly available human hepatic single-cell and bulk transcriptomic datasets to characterize alcohol exposure-associated gut-liver immunometabolic features. In a mouse model of acute ethanol-induced liver injury, fecal metabolomic and metagenomic profiling revealed marked alterations in microbial functional potential and fecal metabolic composition, identifying six convergent metabolic pathways across fecal multi-omics layers, including nucleotide metabolism, the pentose phosphate pathway, histidine metabolism, glycerophospholipid metabolism, glycine/serine/threonine metabolism, and the phosphotransferase system. Reanalysis of human ALD single-cell transcriptomes showed hepatocyte-enriched activity patterns for several corresponding pathways, suggesting potential pathway-level associations between fecal metabolic alterations and hepatic transcriptional responses. Integrative transcriptomic analysis further identified a ten-gene hepatocyte-associated signature, comprising LRG1, ORM1, ORM2, TAT, HP, FGB, FGG, ITIH3, NNMT, and AGT, which was associated with pathway activity and showed consistent upregulation across acute ethanol-induced liver injury and human ALD/AH transcriptomic datasets. In an external human cohort, this signature stratified patients into exploratory molecular subgroups with distinct metabolic pathway activities and clinical outcome distributions. Collectively, these findings provide a hypothesis-generating multi-omics framework for investigating alcohol-related liver injury and support further validation in chronic ethanol exposure models and functional studies.},
}

Animals
*Hepatocytes/metabolism
Multiomics
Humans
*Liver Diseases, Alcoholic/metabolism/genetics/etiology
Mice
Male
Ethanol/adverse effects
Metabolomics/methods
Transcriptome
Feces/chemistry/microbiology
Gene Expression Profiling
Gastrointestinal Microbiome
Disease Models, Animal
Liver/metabolism
Metabolome
Mice, Inbred C57BL
Metagenomics

@article {pmid42558207,
year = {2026},
author = {Yang, Y and Ren, L and Zhang, Y and Wang, X and Shang, J and Zhang, L},
title = {Microbiota in cholestatic diseases: crosstalk among bile composition, the biliary microbiome, and host immunity.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1884030},
pmid = {42558207},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Microbiota/immunology ; Bile Acids and Salts/metabolism ; *Cholestasis/microbiology/immunology/metabolism ; *Bile/metabolism/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Cholestatic liver diseases are a heterogeneous group of hepatobiliary disorders caused by impaired bile formation, secretion, or excretion, leading to hepatocyte injury, biliary inflammation, fibrosis, and eventually cirrhosis. Traditional studies have largely focused on isolated mechanisms, including bile acid toxicity, immune dysregulation, and genetic susceptibility. However, recent advances in metagenomics, metabolomics, and immunology have highlighted the critical role of the gut and biliary microbiota in disease pathogenesis. This review proposes the core concept of a "tripartite interplay among bile composition, biliary microbiome, and host immunity," integrating the dynamic crosstalk among these three axes in cholestatic liver diseases. Bile composition shapes microbial communities and modulates immune responses through receptors such as FXR and TGR5. In turn, the biliary microbiome regulates bile acid metabolism and immune activity through microbial metabolites. Meanwhile, the host immune system senses microbial signals via pattern-recognition receptors, triggering inflammatory pathways and influencing microbial colonization and metabolism. These reciprocal interactions form complex feedback loops that drive disease progression from early inflammation to chronic fibrosis and cirrhosis. Based on this framework, emerging diagnostic approaches combine microbial signatures, bile acid profiles, and immune markers into multidimensional biomarker systems. Therapeutically, integrated strategies targeting the microbiome, bile acid metabolism, and immune pathways may offer synergistic benefits. Despite challenges including sampling difficulty, interindividual variability, and limitations of current models, future technologies such as single-cell sequencing, spatial transcriptomics, and multi-omics integration may enable precision diagnosis and targeted therapy.},
}

Humans
Animals
*Microbiota/immunology
Bile Acids and Salts/metabolism
*Cholestasis/microbiology/immunology/metabolism
*Bile/metabolism/immunology/microbiology
*Gastrointestinal Microbiome/immunology

@article {pmid42362546,
year = {2026},
author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42362546},
issn = {2041-1723},
mesh = {*Alzheimer Disease/pathology/metabolism/genetics/microbiology/blood ; *Imidazoles/blood/metabolism ; Animals ; Humans ; Male ; *Gastrointestinal Microbiome/physiology ; Glycogen Synthase Kinase 3 beta/metabolism/antagonists & inhibitors ; tau Proteins/metabolism ; Mice ; Female ; Neurons/metabolism/drug effects/pathology ; Phosphorylation ; Aged ; *Propionates/metabolism/blood ; Mice, Inbred C57BL ; Feces/microbiology ; Biomarkers/blood ; Brain/pathology/metabolism ; },
abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.},
}

*Alzheimer Disease/pathology/metabolism/genetics/microbiology/blood
*Imidazoles/blood/metabolism
Animals
Humans
Male
*Gastrointestinal Microbiome/physiology
Glycogen Synthase Kinase 3 beta/metabolism/antagonists & inhibitors
tau Proteins/metabolism
Mice
Female
Neurons/metabolism/drug effects/pathology
Phosphorylation
Aged
*Propionates/metabolism/blood
Mice, Inbred C57BL
Feces/microbiology
Biomarkers/blood
Brain/pathology/metabolism

@article {pmid42385873,
year = {2026},
author = {Chen, P and Si, H and Wang, J and Xie, J and Gu, C and Ma, W and Liu, X and Sun, Q},
title = {Metagenomic insights into microbial responses to soil amendments and oat cultivar identity in saline-alkali soils.},
journal = {Environmental research},
volume = {306},
number = {Pt 2},
pages = {125147},
doi = {10.1016/j.envres.2026.125147},
pmid = {42385873},
issn = {1096-0953},
mesh = {*Avena/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Metagenomics ; Rhizosphere ; *Microbiota ; Bacteria/genetics/classification ; Manure ; },
abstract = {Host cultivar identity can influence rhizosphere microbiomes, yet its relative importance compared with soil amendment regime in saline-alkali farmland remains insufficiently resolved. Here, we compared how two oat (Avena sativa) cultivars shape soil microbial communities and functions under contrasting amendment regimes. In a field experiment, two oat cultivars, Tianyan 60 (TY60) and Musite (MST), were grown under five treatments: control, bacterial agent, organic manure, silica fume, and their combination. Soil physicochemical properties, enzyme activities, and metagenomic sequencing were used to characterize microbial taxonomic and functional profiles. Amendment regimes strongly altered soil nutrient and enzyme variables, whereas cultivar identity explained more variation than amendment regime in microbial community structure and beta diversity under the tested field conditions. Taxonomically, TY60 showed stronger amendment-associated reassembly, including enrichment of Bacteroidota, Pseudomonadota, and Ascomycota under selected treatments, whereas MST retained a comparatively more stable higher-rank backbone. Network analysis further indicated cultivar-associated differences in microbial community organization. Functionally, organic manure and the combination treatments (MIX3) produced the broadest shifts in C, N, P, and S cycling gene modules, particularly in TY60-associated soils. Null-model analyses showed that stochastic assembly dominated overall, but the dominant stochastic component differed among kingdoms, with bacteria mainly governed by drift, archaea by homogeneous dispersal, and fungi by a more balanced contribution of the drift and homogeneous dispersal. These results indicate that cultivar identity played a stronger role than amendment regime in shaping amendment-associated microbiome and functional shifts in this two-cultivar comparison, highlighting the potential value of combining cultivar choice with organic-microbial inputs to improve rhizosphere multifunctionality in saline-alkali agroecosystems.},
}

*Avena/microbiology
*Soil Microbiology
*Soil/chemistry
Metagenomics
Rhizosphere
*Microbiota
Bacteria/genetics/classification
Manure

@article {pmid42476406,
year = {2026},
author = {Li, N and Yi, J and Zhu, L and Chen, D and Wang, M and Huang, D},
title = {Nanoconfined humic acid-supported nZVI enhances imidacloprid remediation without compromising soil microbiome or exacerbating ARG health risks.},
journal = {Environmental research},
volume = {306},
number = {Pt 3},
pages = {125277},
doi = {10.1016/j.envres.2026.125277},
pmid = {42476406},
issn = {1096-0953},
mesh = {*Neonicotinoids/chemistry ; *Humic Substances/analysis ; *Nitro Compounds/chemistry ; *Soil Pollutants/chemistry ; *Microbiota/drug effects ; *Soil Microbiology ; *Environmental Restoration and Remediation/methods ; },
abstract = {Pesticide contamination of agricultural soils poses persistent risks to ecosystem function and agricultural sustainability, yet the application of reactive nanomaterials for remediation remains constrained by physicochemical instability and uncertain ecological consequences. Here, we synthesized a nanoconfined humic acid-supported nZVI composite (HA-nZVI) and evaluated its performance in imidacloprid (IMI)-contaminated soil through kinetic analysis, interfacial characterization, metagenomic sequencing, and dual-framework ARG risk assessment. HA nanoconfinement improved particle dispersion, increased active-site accessibility, and facilitated interfacial electron shuttling. These effects accelerated predominantly abiotic IMI dissipation, raising the degradation rate by 3.8-fold relative to the unamended control and shortening the half-life to 18.56 d. Despite the accelerated removal, dominant phylum-level abundances fluctuated by less than 3%, suppression of plant-beneficial bacteria (PBB) observed with pristine nZVI was alleviated, and no measurable increase in human- or livestock-associated ARG risk was detected among the 525 identified ARG subtypes. Collectively, these findings show that HA nanoconfinement can couple improved pesticide dissipation with phylum-level microbiome compatibility and no detectable increase in resistome-associated health risk, supporting the design of iron-based nanomaterials for sustainable agricultural remediation.},
}

*Neonicotinoids/chemistry
*Humic Substances/analysis
*Nitro Compounds/chemistry
*Soil Pollutants/chemistry
*Microbiota/drug effects
*Soil Microbiology
*Environmental Restoration and Remediation/methods

@article {pmid42520901,
year = {2026},
author = {Zhang, L and Zhao, B and Zhang, X and Li, Y and Li, H and Yuan, S and Ning, H and Lv, B and Li, L and Fan, X and Yue, X},
title = {Fe[2+] alters carbon and nitrogen metabolic networks in a composite microbial consortium: Metagenomic insights into the shift from denitrification to DNRA.},
journal = {Environmental research},
volume = {306},
number = {Pt 3},
pages = {125349},
doi = {10.1016/j.envres.2026.125349},
pmid = {42520901},
issn = {1096-0953},
mesh = {*Denitrification ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Microbial Consortia/drug effects ; Metabolic Networks and Pathways/drug effects ; Metagenomics ; *Iron/metabolism ; Metagenome ; Bacteria/metabolism/genetics ; },
abstract = {Conventional biological nitrogen removal processes are constrained by lengthy treatment trains and dependence on organic carbon sources, necessitating the development of novel enhanced nitrogen removal strategies that integrate multiple functions and ensure operational stability. In this study, a synthetic bacterial consortium was constructed, comprising the aerobic denitrifier Pseudomonas stutzeri, the facultative anaerobic denitrifier Klebsiella sp., and the heterotrophic nitrifying-aerobic denitrifying bacterium Alcaligenes sp. The effects of five iron species as well as their combined effects with polyacrylamide (PAM), on nitrogen removal performance and oxidative stress responses of the consortium were investigated, and metagenomic sequencing was employed to elucidate the regulatory mechanisms of Fe[2+] on metabolic processes. The results showed that, compared with the other iron species, the Fe[2+] group achieved a 20-30% increase in nitrate-N removal efficiency. The addition of PAM attenuated the specific regulatory effects of different iron species through physical mass-transfer limitation. Metagenomic analysis revealed that Fe[2+] modulated the carbon and nitrogen metabolic networks: in the carbon metabolic network, enrichment of the por gene in the glycolytic pathway generated substantial reducing power in the form of reduced ferredoxin; concomitantly, the transcript abundance of the dissimilatory nitrate reduction to ammonium pathway increased from 775 to 802, whereas that of the denitrification pathway decreased from 1259 to 1222. This study elucidates the intrinsic mechanism by which Fe[2+] promotes synergistic carbon and nitrogen removal, providing a theoretical foundation for the development of a multi-process coupled deep nitrogen removal system integrating bioaugmentation, chemical regulation, and physical sedimentation.},
}

*Denitrification
*Nitrogen/metabolism
*Carbon/metabolism
*Microbial Consortia/drug effects
Metabolic Networks and Pathways/drug effects
Metagenomics
*Iron/metabolism
Metagenome
Bacteria/metabolism/genetics

@article {pmid42372963,
year = {2026},
author = {Cui, Q and Wang, F and Shan, X and Ding, L and Qiu, X and Zhang, B and Li, X and Liang, X and Guo, X},
title = {Biodegradable polylactic acid microplastics affect nutrient cycling during the entire crop growth cycle: Implications for soil ecosystem multifunctionality.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {406},
number = {},
pages = {128664},
doi = {10.1016/j.envpol.2026.128664},
pmid = {42372963},
issn = {1873-6424},
mesh = {*Polyesters ; *Soil Microbiology ; Soil/chemistry ; *Soil Pollutants/metabolism/toxicity ; *Microplastics/metabolism ; Ecosystem ; Microbiota ; Biodegradation, Environmental ; *Crops, Agricultural/growth & development ; Zea mays/growth & development ; Nitrogen ; },
abstract = {While microplastics (MPs) have been extensively studied for their effects on soil nutrient cycling, their influence on ecosystem multifunctionality (EMF) across the entire crop growth cycle remains poorly understood. This study systematically investigated the impacts of a model biodegradable MP, polylactic acid (PLA), on soil microbiomes and EMF across different maize incubation periods. Results of 16S rRNA amplicon sequencing and metagenomic analysis revealed that PLA-MPs decreased bacterial community α-diversity, co-occurrence network complexity, and stability throughout the 120-day incubation period. Particularly, PLA-MPs exerted more pronounced effects at early incubation stages (30 and 60 days), and these effects were intensified with increasing PLA-MP concentrations. PLA-MPs suppressed anaerobic carbon fixation (porA, porB, frda) and pyruvate metabolism (ppdk), while promoting fermentation (L-lactate dehydrogenase), nitrogen fixation (nifD, nifH, nifK, anfG), and microbial phosphorus (P) acquisition (phoD, phn cluster). Over the entire incubation period, PLA-MP-induced shifts in nutrient cycling enhanced soil carbon (C) function by 37.6-569%, while decreasing nitrogen (N) and P functions by 8.40-22.4% and 16.8-56.2%, respectively. Path analysis revealed that PLA-MPs altered soil properties and bacterial community diversity, which in turn regulated functional genes and these individual soil functions, thereby reducing EMF by 2.05-27.0% (R[2] = 0.923), with bacterial community diversity as the primary driver of EMF (standardized path coefficient of 0.978). These findings underscore the impacts of PLA-MPs on EMF in the soil-crop system throughout the entire maize growth cycle, advancing the understanding of the agroecological safety of biodegradable MPs.},
}

*Polyesters
*Soil Microbiology
Soil/chemistry
*Soil Pollutants/metabolism/toxicity
*Microplastics/metabolism
Ecosystem
Microbiota
Biodegradation, Environmental
*Crops, Agricultural/growth & development
Zea mays/growth & development
Nitrogen

@article {pmid42385828,
year = {2026},
author = {Yin, Z and Zhang, Y and Song, S and Li, C and Shi, J and Yin, Y and Cai, Y},
title = {Co-contamination of antimony and arsenic reshapes resistome, virulome, and virome in poultry feces near the world's largest antimony mine.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {406},
number = {},
pages = {128684},
doi = {10.1016/j.envpol.2026.128684},
pmid = {42385828},
issn = {1873-6424},
mesh = {Animals ; Mining ; *Arsenic/analysis ; *Antimony/analysis ; *Feces/microbiology/virology ; *Virome ; Poultry ; Drug Resistance, Microbial/genetics ; Microbiota ; },
abstract = {The poultry microbiome and virome are integral to the One Health framework, with significant implications for ecosystem and human health, but their responses to arsenic (As) and antimony (Sb) exposure remain overlooked. Here, we conducted a comprehensive metagenomic characterization of the metal resistome, antibiotic resistome, virulome, and virome in poultry feces collected from the world's largest antimony mining area. We found that As and Sb co-contamination was significantly associated with elevated resistance and virulence. The abundance of metal resistance genes (MRGs) was 1.8-fold higher in the high-Sb group than in the low-Sb group (15,022.27 ± 3538.47 vs 8370.24 ± 4502.07 TPM, P = 0.008), with arsR, arsB, and arsC dominating the MRG profiles. Similarly, antibiotic resistance genes (ARGs) abundance was 1.6-fold higher in the high-Sb group than in the low-Sb group (7251.00 ± 1844.34 vs 4478.95 ± 2302.69 TPM, P = 0.026), with multidrug resistance genes being the predominant class (8.09% - 58.48%). Metagenome-assembled genomes (MAGs) analysis and contig analysis suggest co-selection of MRGs, ARGs, and virulence factor genes (VFGs). We identified 100,819 viral contigs clustered into 91,004 viral operational taxonomic units (vOTUs), revealing a highly diverse viral community. Members of Enterobacteriaceae (e.g., Klebsiella) and Enterococcaceae (i.e., Enterococcus) were identified as key drivers mediating resistance and virulence dynamics, acting as resistome supercarriers, opportunistic pathogens, and viral hosts. These findings suggest that As-Sb co-contamination is an overlooked but potentially important driver of poultry antimicrobial resistance and pathogenicity, and highlight potential ecological and public health risks in mining-impacted poultry-associated environments.},
}

Animals
Mining
*Arsenic/analysis
*Antimony/analysis
*Feces/microbiology/virology
*Virome
Poultry
Drug Resistance, Microbial/genetics
Microbiota

@article {pmid42442277,
year = {2026},
author = {Zhang, X and Han, S and Zhao, A and Wei, B and Chang, X and Song, S and Zhao, Y and Zhao, Z and Zhang, X and Chen, J},
title = {Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120488},
doi = {10.1016/j.ecoenv.2026.120488},
pmid = {42442277},
issn = {1090-2414},
mesh = {*Pyrethrins/toxicity ; Animals ; *Rumen/microbiology/drug effects ; *Insecticides/toxicity ; *Drug Resistance, Microbial/genetics ; Metagenomics ; *Dietary Exposure/adverse effects ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.},
}

*Pyrethrins/toxicity
Animals
*Rumen/microbiology/drug effects
*Insecticides/toxicity
*Drug Resistance, Microbial/genetics
Metagenomics
*Dietary Exposure/adverse effects
*Gastrointestinal Microbiome/drug effects

@article {pmid42456442,
year = {2026},
author = {Wills, OC and Chua, XY and McEvoy, C and Fitzmaurice, M and El-Assaad, F and El-Omar, E and Probst, Y},
title = {A case-control study of the oral microbiome among Australian female adults with relapsing-remitting multiple sclerosis: A pilot study.},
journal = {Multiple sclerosis and related disorders},
volume = {113},
number = {},
pages = {107383},
doi = {10.1016/j.msard.2026.107383},
pmid = {42456442},
issn = {2211-0356},
mesh = {Humans ; Female ; Pilot Projects ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; *Microbiota ; Case-Control Studies ; Adult ; *Mouth/microbiology ; Australia ; Cross-Sectional Studies ; Middle Aged ; },
abstract = {BACKGROUND: There is growing evidence investigating the role of the gut microbiome in the onset and progression of multiple sclerosis (MS). However, the role of the oral microbiome in MS is poorly understood, despite its importance in immune regulation and systemic health.

METHODS: A cross-sectional, case-control, pilot study comparing the oral microbiome among adults with relapsing-remitting MS to matched controls based on age, sex and body mass index (BMI), was conducted. Participants provided fasting oral swabs where DNA was extracted and shotgun metagenomic sequencing performed. Comparative analyses between cases and controls explored alpha-and beta-diversities including differential abundance testing.

RESULTS: Across 24 oral microbiome samples, 355 species from 12 phylum were detected. Alpha diversity was lower in MS at the species level, however, did not reach statistical significance for either richness or Shannon diversity. Beta diversity demonstrated a significant difference using Bray-Curtis dissimilarity with group status accounting for ∼6.7% of the total variation in microbial community structure. Differential abundance testing highlighted Veillonella parvula as the most enriched species among cases (coef=2.56, stderr=0.74, FDR=0.17), while Porphyromonas pasteri (coef=-3.57, stderr=1.02, FDR=0.17) and s__GGB4936_SGB6889 (coef=-4.29, stderr=1.30, FDR=0.17) were predominant among controls.

CONCLUSION: The oral microbiome of Australian females with RRMS differs in a subtle but detectable manner from those without MS, characterised by a non-significant trend towards reduced microbial diversity and distinct compositional clustering based on Bray-Curtis dissimilarity. Findings support the emerging concept of an oral-immune axis in MS, underscoring the need for longitudinal and functional studies to explore causality.},
}

Humans
Female
Pilot Projects
*Multiple Sclerosis, Relapsing-Remitting/microbiology
*Microbiota
Case-Control Studies
Adult
*Mouth/microbiology
Australia
Cross-Sectional Studies
Middle Aged

@article {pmid42470960,
year = {2026},
author = {Chen, Y and Han, D and Hu, Q and Xiong, Y and Zhou, X and Wang, Y and Li, D and Yan, J and Yang, J and Zhang, F and Cao, H and Wu, P and Liu, Y and Xia, Y and Sun, J},
title = {Gut-liver axis through microbiota-metabolite interplay driving age-dependent susceptibility to arsenite-induced liver injury in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120522},
doi = {10.1016/j.ecoenv.2026.120522},
pmid = {42470960},
issn = {1090-2414},
mesh = {Animals ; *Arsenites/toxicity ; *Liver/drug effects/metabolism/pathology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/etiology ; Male ; Aging ; Intestinal Barrier Function ; Mice, Inbred C57BL ; Age Factors ; Signal Transduction/drug effects ; },
abstract = {Arsenic is a highly toxic metalloid that contributes to many chronic diseases. The liver is a primary target organ because it mediates detoxification and metabolism. However, the differences in susceptibility to age-related arsenic-induced liver injury and their underlying mechanisms remain unclear, particularly regarding the involvement of the gut-liver axis. Young, adult, and old mice ingested arsenic via drinking water. We assessed glucose metabolism, liver injury, and intestinal barrier integrity. To investigate the role of the gut microbiota, we performed metagenomic sequencing on fecal samples. Liver metabolic changes and signaling pathways were analyzed using non-targeted metabolomics and transcriptomics technologies, respectively. This study reveals that aged mice exhibit heightened susceptibility to arsenite-induced liver injury and metabolic disorders. Histological examination and reduced occludin expression confirm this is associated with impaired intestinal barrier function. Metagenomic analysis indicated that arsenite exposure was associated with gut microbiota remodeling in aged mice, characterized primarily by genus-level alterations, including reduced Muribaculaceae-related genera and relative enrichment of genera associated with altered mucosal homeostasis and inflammatory signaling. Metagenomic pathway analysis further suggested shifts in microbial metabolic and inflammatory signaling-related pathways, including changes in insulin/glucagon signaling, glycerolipid metabolism, and NOD-like receptor signaling. Metabolomics detection revealed significant accumulation of uridine diphosphate glucose (UDPG) in the livers of arsenite-exposed aged mice. Transcriptomic analysis revealed upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway, while western blotting confirmed its activation in the liver. These findings suggest that aging is associated with increased susceptibility to arsenite-induced liver injury, potentially involving gut microbiota remodeling, intestinal barrier dysfunction, and hepatic UDPG accumulation. UDPG may function as a metabolic stress-associated factor or potential amplifier of MAPK-related inflammatory signaling, thereby potentially contributing to liver injury. Consequently, a novel gut-liver axis mechanism is revealed, elucidating the intrinsic link between aging and susceptibility to environmentally induced toxic diseases.},
}

Animals
*Arsenites/toxicity
*Liver/drug effects/metabolism/pathology
Mice
*Gastrointestinal Microbiome/drug effects
*Chemical and Drug Induced Liver Injury/metabolism/etiology
Male
Aging
Intestinal Barrier Function
Mice, Inbred C57BL
Age Factors
Signal Transduction/drug effects

@article {pmid42557256,
year = {2026},
author = {Gicquel, M and Planillo, A and Heitlinger, E and Forslund-Startceva, SK and Kramer-Schadt, S and Ferreira, SCM and Jarquín-Díaz, VH},
title = {Farming practices exert selection pressures on the resistome of natural populations of house mice.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42557256},
issn = {2041-1723},
support = {FO1279/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; HE7320/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KR4266/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; F01KI1909A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01KI2404B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {Animals ; Mice/microbiology ; *Selection, Genetic ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Livestock/microbiology ; Genes, Bacterial ; *Agriculture ; Germany ; Swine ; },
abstract = {The factors maintaining antimicrobial resistance genes (ARGs) in non-domesticated animal microbiomes remain unclear for species inhabiting human-dominated or less human-impacted landscapes. We analysed 875 gut metagenomes from natural populations of house mice (Mus musculus) on German farms between 2016 and 2022 to identify environmental and host determinants of ARG occurrence. Using joint species distribution models, we quantified the influence of landscape, climate and mouse associated characteristics on the occurrence of individual ARGs and on trait dependence among genes. Environmental variables and livestock farming intensity explained 27% of ARG variation, whereas host characteristics accounted for 8%. Analysis of ARG traits revealed that agricultural land use and exposure to livestock increased the occurrence of potentially mobile ARGs. Pig density was strongly associated with an integron-encoded sulfonamide resistance gene (sul1) and genes conferring tetracycline (tet) and beta-lactam resistance (cblA-1) (posterior probability 0.75). Consistently, mouse resistomes have a distinctive resistome, but share more than 50% of ARGs with livestock manure, including widespread genes and those promoted in livestock. Here, we show that landscape conditions, particularly farming intensity, shape the distribution of specific ARGs and potentially mobile ARGs in house mice microbiomes.},
}

Animals
Mice/microbiology
*Selection, Genetic
Anti-Bacterial Agents/pharmacology
Metagenome
*Gastrointestinal Microbiome/genetics
Livestock/microbiology
Genes, Bacterial
*Agriculture
Germany
Swine

@article {pmid42557544,
year = {2026},
author = {Martínez-Cuesta, R and Craighero, A and Walch, S and Helmreich, B and Schloter, M and Schulz, S},
title = {Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42557544},
issn = {1471-2180},
mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Cities ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenomics/methods ; Plasmids/genetics ; Biodiversity ; },
abstract = {BACKGROUND: Urban green roofs are increasingly introduced to enhance urban biodiversity and ecosystem services, yet their role in shaping antimicrobial resistance in cities remains unclear. Using long-read metagenomic sequencing, we characterized antimicrobial resistance genes (ARGs) across an experimental extensive green roof system with plots under four different management regimes specifically designed to test the influence of vegetation and organic amendments, as green waste, which although widely used to improve substrate quality, has been flagged as a potential ARG source.

RESULTS: We detected 62 ARGs across the four management regimes, which were dominated by target-modification and mixed mechanisms conferring resistance to naturally occurring antibiotics such as bacitracin (bacA) and rifamycin (arr, rox, rph), rather than efflux-based multidrug resistance, which is typically co-selected by anthropogenic pollutants. The ARGs were mainly chromosomally encoded, with only two ARGs located on plasmids, and associated with non-pathogenic environmental taxa. The management regime had a significant effect on ARG richness, ARG composition and plasmid abundance, but not on average genome size-normalized ARG abundance. We also detected aph3-II and tlmA as enriched in the unamended samples, which were carried by oligotrophic bacteria, pointing towards microbial competition in a nutrient-limited environment.

CONCLUSIONS: Overall, our findings indicate that green roof management supports a substrate resistome driven by ecological constraints rather than clinical threats. However, further research is required to evaluate potential risks and support the safe integration of green roofs within a One Health framework.},
}

Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
Cities
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Metagenomics/methods
Plasmids/genetics
Biodiversity

@article {pmid42557545,
year = {2026},
author = {Rodríguez Del Río, Á and Cui, Y and Mansour, I and Rillig, MC},
title = {Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42557545},
issn = {1471-2164},
mesh = {*Soil Microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Genomics ; Phylogeography ; Phylogeny ; *Prokaryotic Cells ; *Archaea/genetics/classification ; },
abstract = {Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the genomic features and biogeography of uncultivated prokaryotic taxa at the large scale. Here, we analyze 40,039 genomic bins from cultivated and uncultivated soil taxa within the SMAG catalog, and examine the occurrence of uncultivated prokaryotes in 9,012 metagenomic samples from the Sandpiper resource. Compared to genera with cultivated representatives, uncultivated soil prokaryotes show smaller genomes, lower G + C content, tendency to acidophilic, non-alkaline, thermophilic and host-associated lifestyles, and slower growth rates, with the latter having the highest predictive power for cultivation status. Uncultivated soil microbes also show unique gene repertoires, characterized by a depletion of biosynthetic and motility genes. We also show that completely uncultivated genera are more abundant in tropical and arctic soils, indicating substantial hidden diversity in these regions. Our work emphasizes that current cultivation efforts systematically fail to capture a particular fraction of soil prokaryotic diversity, and provides guidelines for future cultivation strategies.},
}

*Soil Microbiology
Metagenomics
Metagenome
*Bacteria/genetics/classification
*Genome, Bacterial
*Genomics
Phylogeography
Phylogeny
*Prokaryotic Cells
*Archaea/genetics/classification

@article {pmid42153961,
year = {2026},
author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {44},
pages = {e17087},
pmid = {42153961},
issn = {2198-3844},
support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Metagenome/genetics ; Metagenomics/methods ; *Dysbiosis/microbiology ; },
abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
*Metagenome/genetics
Metagenomics/methods
*Dysbiosis/microbiology

@article {pmid42237409,
year = {2026},
author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X},
title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42237409},
issn = {2049-2618},
support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; },
mesh = {*Stenotrophomonas maltophilia/genetics/physiology/metabolism ; *Skin Microbiome ; Multiomics ; Humans ; Metabolomics ; *Skin Aging/physiology ; *Skin/microbiology/metabolism ; Acinetobacter/metabolism ; Oxidative Stress ; Glutathione/metabolism ; Melanins/metabolism ; Metagenomics ; Metabolic Networks and Pathways ; Fibroblasts/metabolism ; Phenotype ; },
abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.

RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.

CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.},
}

*Stenotrophomonas maltophilia/genetics/physiology/metabolism
*Skin Microbiome
Multiomics
Humans
Metabolomics
*Skin Aging/physiology
*Skin/microbiology/metabolism
Acinetobacter/metabolism
Oxidative Stress
Glutathione/metabolism
Melanins/metabolism
Metagenomics
Metabolic Networks and Pathways
Fibroblasts/metabolism
Phenotype

@article {pmid42237424,
year = {2026},
author = {Yang, L and Chen, J},
title = {mPower: a real data-based power analysis tool for microbiome study design.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42237424},
issn = {2049-2618},
support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; R01 GM144351/GM/NIGMS NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Software ; Humans ; *Metagenomics/methods ; Computer Simulation ; Research Design ; *Bacteria/classification/genetics ; Cross-Sectional Studies ; Case-Control Studies ; },
abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/ . Video Abstract.},
}

*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Software
Humans
*Metagenomics/methods
Computer Simulation
Research Design
*Bacteria/classification/genetics
Cross-Sectional Studies
Case-Control Studies

@article {pmid42243719,
year = {2026},
author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS},
title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42243719},
issn = {1471-2229},
support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; },
mesh = {*Energy Metabolism/genetics ; Rhizosphere ; *Microbiota/genetics ; Soil Microbiology ; Computer Simulation ; },
abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.

RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.

CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).},
}

*Energy Metabolism/genetics
Rhizosphere
*Microbiota/genetics
Soil Microbiology
Computer Simulation

@article {pmid42328985,
year = {2026},
author = {Pallotti, S and Nigro, ME and Albini, E and Russo, E and Carpi, FM and Falconi, M and Torbidoni-Baldassari, B and Giuliodori, AM and Petrelli, D and Beccacece, L and Pezzotti, G and Magistrali, CF and Massacci, FR and Napolioni, V},
title = {Long-read metagenomics reveals stable resistome and microbiome in treated Italian slaughterhouse wastewater: a preliminary study.},
journal = {Microbiology spectrum},
volume = {14},
number = {8},
pages = {e0156226},
pmid = {42328985},
issn = {2165-0497},
support = {RC 004/2022//Ministero della Salute/ ; },
mesh = {Abattoirs ; *Wastewater/microbiology ; Metagenomics ; *Microbiota/genetics ; Italy ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance (AMR) poses a major threat to global health, and food production environments are increasingly recognized as potential reservoirs and dissemination points for resistant bacteria and antimicrobial resistance genes (ARGs). Slaughterhouse wastewater contains complex microbial communities originating from multiple animal sources and processing activities, yet the effectiveness of current treatment processes in mitigating microbiological and resistome-associated risks remains poorly understood. In this study, we applied high-throughput long-read metagenomic sequencing to characterize microbial community composition and resistome profiles in wastewater samples collected before and after physicochemical treatment from four Italian slaughterhouses. Taxonomic profiling revealed a diverse microbiome dominated by Bacillota and Pseudomonadota, along with DNA assigned to potentially clinically relevant taxa, including members of the ESKAPE group. Resistome analysis identified 96 ARGs conferring resistance to 16 antimicrobial classes. Comparative analyses of pre- and post-treatment samples showed no significant changes in microbial community structure, alpha- and beta-diversity metrics, or ARG profiles. These findings indicate that the applied coagulation-flocculation-based treatment has limited effects on the relative composition of the wastewater microbiome and resistome, as detected by shotgun metagenomics. Our results suggest that slaughterhouse wastewater may act as a persistent environmental reservoir of antimicrobial resistance determinants and highlight the need for enhanced treatment strategies and resistome-oriented surveillance within a One Health framework. Given the limited sample size and the preliminary nature of this investigation, these findings should be interpreted as exploratory and hypothesis-generating, rather than broadly generalizable.IMPORTANCEAntimicrobial resistance is a growing global health concern that extends beyond clinical settings into agricultural and environmental systems. Slaughterhouses represent critical interfaces where microbial communities from livestock, processing environments, and wastewater converge, creating opportunities for the persistence and dissemination of antimicrobial resistance genes. Despite the widespread use of physicochemical treatments to reduce organic load and suspended solids in slaughterhouse wastewater, their impact on microbial communities and resistome remains poorly characterized. By applying long-read metagenomic sequencing, this study provides a comprehensive characterization of the microbiome and resistome in slaughterhouse wastewater before and after treatment. Our findings show that commonly applied coagulation-flocculation treatments do not substantially alter the relative structure of microbial communities or the diversity of resistance genes. These results highlight the potential role of slaughterhouse wastewater as an environmental reservoir for antimicrobial resistance and emphasize the need for improved treatment technologies and systematic surveillance strategies to mitigate the environmental dissemination of resistance determinants in line with the One Health approach.},
}

Abattoirs
*Wastewater/microbiology
Metagenomics
*Microbiota/genetics
Italy
*Bacteria/genetics/classification/drug effects/isolation & purification
Animals
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid42329047,
year = {2026},
author = {Villanelo, SAR and Vestergaard, SZ and Liu, L and Yang, Y and Pedersen, IS and Nielsen, PH and Dueholm, MKD},
title = {Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.},
journal = {Microbiology spectrum},
volume = {14},
number = {8},
pages = {e0147726},
pmid = {42329047},
issn = {2165-0497},
support = {NNF22OC0071498//Novo Nordisk Fonden/ ; },
mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation & purification/classification/genetics/drug effects ; Phylogeny ; DNA, Bacterial/genetics ; Wastewater/microbiology ; Microbiota/drug effects ; },
abstract = {The microbial communities in activated sludge (AS) drive pollutant degradation and nutrient transformation into biomass and gaseous products, while also enabling resource recovery processes. In these systems, microorganisms grow as flocs, whose aggregation properties are essential for retaining active biomass while producing a clarified effluent. Understanding the microbial composition of AS and the functions of individual taxa is crucial for improving wastewater treatment practices and developing new treatment technologies. Although DNA-based studies have identified abundant taxa and inferred their metabolic roles, many of these organisms remain uncultured, limiting experimental validation of genome-based predictions. Here, we investigated whether antibiotics can transiently reduce community complexity and alleviate competitive exclusion during cultivation, thereby facilitating isolation of previously uncultured activated sludge bacteria. Dispersed single cells from AS were cultivated on agarose plates containing filter-sterilized AS fluid and 1 of 11 antibiotics at three concentrations. Full-length 16S rRNA gene amplicon sequencing indicated that antibiotics reduced microbial diversity and altered community composition in an antibiotic- and concentration-dependent manner. Two antibiotic conditions were selected for pure-culture isolation, resulting in 74 isolates that represented 28 different species based on genomic average nucleotide identity. These include 13 putatively novel species based on GTDB classification, and 19 species belonging to nine globally abundant AS core genera. Although several isolates belonged to genera with cultured representatives, they likely represent distinct species with potentially different ecological functions and physiological traits. These findings demonstrate that antibiotics can function as ecological selectors during cultivation and aid the targeted isolation of ecosystem-relevant activated sludge bacteria.IMPORTANCEBiological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.},
}

*Sewage/microbiology
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Bacteria/isolation & purification/classification/genetics/drug effects
Phylogeny
DNA, Bacterial/genetics
Wastewater/microbiology
Microbiota/drug effects