@article {pmid41524860,
year = {2026},
author = {Parab, C and Yadav, KD and Prajapati, V},
title = {Metagenomic Insights into Microbial Community Succession and its Functional Changes during Natural Fermentation of Food Waste.},
journal = {Applied biochemistry and biotechnology},
volume = {198},
number = {3},
pages = {2053-2081},
pmid = {41524860},
issn = {1559-0291},
mesh = {*Fermentation ; *Metagenomics ; *Microbiota ; *Bacteria/genetics/metabolism ; *Food ; Food Loss and Waste ; },
abstract = {Food waste is a global concern, necessitating sustainable management strategies. While fermentation offers a promising approach to valorizing food waste, studies about microbial dynamics and functionality assessment of semi-controlled naturally fermented food waste are still seldom. This study employed whole-genome metagenomic sequencing to investigate the microbial succession and functional pathways during natural fermentation of food waste over 15 days. Physicochemical analysis revealed that pH decreased from 5.20 to 4.32 on day 3 and then neutralized. Protein, lipids, and carbohydrate were in the range of 4.03-4.90%, 9.99-17.78%, and 85.44-77.84%, respectively. Taxonomic profiling revealed clear community restructuring from an initially diverse consortium dominated by Enterobacter, Klebsiella, Pseudomonas, and Acinetobacter (collectively > 45% relative abundance at day 0) to a highly specialized lactic acid bacteria (LAB) community (> 80% by day 15). Lactobacillus helveticus and Limosilactobacillus panis emerged as the late-stage co-dominant species, together accounting for 60-75% of the total reads. Functional annotation based on the PFAM, eggNOG, GO, and EC databases revealed a progressive reduction in gene family richness and metabolic breadth, with early samples being enriched in carbohydrate-active enzymes, membrane transporters, and amino acid metabolism pathways. By contrast, late-stage communities were dominated by LAB-associated fermentative functions, including lactate and acetate production, stress-response modules, and transport systems supporting acid tolerance, driven mainly by Lactobacillus, Weissella, Streptococcus, Gluconobacter, Aeromonas, Saccharomyces, Klebsiella, and Cronobacter. These findings provide insights into the microbial dynamics and functional adaptations during natural fermentation of food waste, contributing to the development of optimized waste valorization strategies.},
}

*Fermentation
*Metagenomics
*Microbiota
*Bacteria/genetics/metabolism
*Food
Food Loss and Waste

@article {pmid41762508,
year = {2026},
author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X},
title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129121},
doi = {10.1016/j.jenvman.2026.129121},
pmid = {41762508},
issn = {1095-8630},
mesh = {*Manure/microbiology ; Animals ; Swine ; Anaerobiosis ; *Metal-Organic Frameworks ; Drug Resistance, Microbial ; *Virome ; },
abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.},
}

*Manure/microbiology
Animals
Swine
Anaerobiosis
*Metal-Organic Frameworks
Drug Resistance, Microbial
*Virome

@article {pmid41835092,
year = {2026},
author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {130},
pmid = {41835092},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.},
}

@article {pmid41836173,
year = {2026},
author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL},
title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20880},
pmid = {41836173},
issn = {2167-8359},
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; *Metagenomics ; *Culicidae/virology ; Brazil ; Phylogeny ; Female ; *Mosquito Vectors/virology ; Virome ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
*Metagenomics
*Culicidae/virology
Brazil
Phylogeny
Female
*Mosquito Vectors/virology
Virome
Genome, Viral
High-Throughput Nucleotide Sequencing

@article {pmid41837347,
year = {2026},
author = {Arnold, MJ and Bergner, LM and Malik, H and Ten Doeschate, M and Davison, NJ and Brownlow, A and Mollentze, N and Babayan, SA and Streicker, DG},
title = {Drivers of Viral Diversity and Sharing in Marine Mammals.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70294},
pmid = {41837347},
issn = {1365-294X},
support = {217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 218518/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/V003798/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DEB 2011069/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PLP-2020-362//Leverhulme Trust/ ; NE/X01424X/1//Natural Environment Research Council/ ; INV-003079/GATES/Gates Foundation/United States ; INV-030025/GATES/Gates Foundation/United States ; MC_UU_00034/3/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Viruses/genetics/classification ; Scotland ; *Aquatic Organisms/virology ; *Cetacea/virology ; *Mammals/virology ; },
abstract = {Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.},
}

Animals
*Viruses/genetics/classification
Scotland
*Aquatic Organisms/virology
*Cetacea/virology
*Mammals/virology

@article {pmid41841491,
year = {2026},
author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A},
title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.},
journal = {Nucleic acids research},
volume = {54},
number = {5},
pages = {},
doi = {10.1093/nar/gkag227},
pmid = {41841491},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette & Yersin PhD Grant/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Metagenome ; Algorithms ; },
abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.},
}

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

@article {pmid41841524,
year = {2026},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y},
title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2645267},
doi = {10.1080/19490976.2026.2645267},
pmid = {41841524},
issn = {1949-0984},
mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; },
abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.},
}

*Mucins/metabolism
Animals
*Gastrointestinal Microbiome
Humans
Feces/microbiology
Metagenome
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics

@article {pmid41841712,
year = {2026},
author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE},
title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.},
journal = {Biomeditsinskaia khimiia},
volume = {72},
number = {1},
pages = {62-74},
doi = {10.18097/PBMCR1644},
pmid = {41841712},
issn = {2310-6972},
mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation & purification ; Prevotella ; },
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.},
}

Humans
Female
*Candidiasis, Vulvovaginal/microbiology/drug therapy
*Microbiota
Adult
Case-Control Studies
*Vagina/microbiology
Recurrence
Lactobacillus/genetics/isolation & purification
Prevotella

@article {pmid41220286,
year = {2026},
author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK},
title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.},
journal = {Gut and liver},
volume = {20},
number = {2},
pages = {199-212},
doi = {10.5009/gnl250360},
pmid = {41220286},
issn = {2005-1212},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/diagnosis/microbiology ; Biomarkers/analysis ; Metagenomics/methods ; Machine Learning ; Metabolomics/methods ; Proteomics ; Feces/chemistry/microbiology ; },
abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Inflammatory Bowel Diseases/diagnosis/microbiology
Biomarkers/analysis
Metagenomics/methods
Machine Learning
Metabolomics/methods
Proteomics
Feces/chemistry/microbiology

@article {pmid41622335,
year = {2026},
author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T},
title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.},
journal = {Journal of plant research},
volume = {139},
number = {2},
pages = {195-205},
pmid = {41622335},
issn = {1618-0860},
mesh = {*Lotus/microbiology/growth & development ; *Soil Microbiology ; Symbiosis ; *Mesorhizobium/physiology/genetics ; Root Nodules, Plant/microbiology ; *Microbiota ; Rhizobium/physiology ; Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.},
}

*Lotus/microbiology/growth & development
*Soil Microbiology
Symbiosis
*Mesorhizobium/physiology/genetics
Root Nodules, Plant/microbiology
*Microbiota
Rhizobium/physiology
Nitrogen Fixation
RNA, Ribosomal, 16S/genetics

@article {pmid41724250,
year = {2026},
author = {Li, Y and Kang, L and Qin, X and Fei, R and Lu, A and Qishuang, H},
title = {Dual mechanism of electrochemical regulation to reduce soil Nitrous Oxide emissions-microbial recruitment and electron transfer pathway optimization.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134255},
doi = {10.1016/j.biortech.2026.134255},
pmid = {41724250},
issn = {1873-2976},
mesh = {*Nitrous Oxide/metabolism ; *Soil/chemistry ; *Soil Microbiology ; Electron Transport ; Oxidation-Reduction ; Fertilizers ; Denitrification ; Nitrogen/metabolism ; Microbiota ; *Electrochemical Techniques/methods ; Urea ; },
abstract = {Greenhouse gas emissions from agricultural nitrogen cycling, primarily Nitrous Oxide (N2O), are intrinsically linked to fertilizer dynamics. Conventional mitigation strategies emphasize synthetic fertilizer reduction, yet suffer from inefficiency and lack of sustainability. This study introduces an electrochemical regulation approach and, through comparative analysis of two fertilizers (ammonium sulfate vs. urea), elucidates dual mechanisms (redox modulation and microbial community engineering). Key findings: (1) 500 mV electrostimulation enriched nitrate-reducing microbiota, reducing N2O by 11.9 ± 5.9% (sulfate) and 14.2 ± 4.4% (urea) via enhanced denitrification; (2) Electrode interventions accelerated N2O-to-N2 conversion (15.8 ± 1.4% and 14.9 ± 8.9%) by optimizing redox fluxes and boosting electroautotrophic Pseudomonas spp. activity; (3) Urea exhibited delayed electroresponsiveness (6-10 h lag) due to slower amide nitrogen hydrolysis kinetics compared to sulfate; (4) Metagenomics confirmed upregulation of nitrogen metabolic genes (norC: 2.9×, nirD: 2.7×, narI: 2.6 ×) and restructured microbial networks. This study elucidates a fundamental electro-microbial mechanism that reconfigures nitrogen-transforming networks, providing a novel paradigm for managing soil biogeochemical cycles.},
}

*Nitrous Oxide/metabolism
*Soil/chemistry
*Soil Microbiology
Electron Transport
Oxidation-Reduction
Fertilizers
Denitrification
Nitrogen/metabolism
Microbiota
*Electrochemical Techniques/methods
Urea

@article {pmid41793890,
year = {2026},
author = {Dong, M and Zhang, Q and Wang, Y and Wang, S and Feng, G and Qi, H},
title = {Restructuring tilth layers suppresses cotton Verticillium wilt through the niacinamide-mediated enrichment of beneficial Pseudomonas.},
journal = {Microbiological research},
volume = {307},
number = {},
pages = {128491},
doi = {10.1016/j.micres.2026.128491},
pmid = {41793890},
issn = {1618-0623},
mesh = {Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Verticillium/drug effects ; Soil Microbiology ; *Gossypium/microbiology ; *Niacinamide/metabolism/pharmacology ; *Pseudomonas/metabolism/drug effects/growth & development ; Metabolomics ; Microbiota ; Plant Roots/microbiology ; Metagenomics ; },
abstract = {Restructuring tilth layers (RTL) is an innovative tillage practice that involves the vertical exchange of topsoil and subsoil while the deeper layer is loosened, and this practice has been verified to significantly reduce the incidence of cotton Verticillium wilt. However, the ecological mechanisms underlying disease suppression remain unclear. In this study, we integrated field experiments, metagenomic sequencing, untargeted metabolomics, and functional validation to elucidate the effects of RTL on the rhizosphere ecosystem from the perspectives of microbe and metabolite interactions. RTL significantly altered the diversity and composition of the rhizosphere microbial communities and increased their network complexity and stability. Linear discriminant analysis effect size (LEfSe) revealed that RTL promoted the enrichment of beneficial taxa such as Pseudomonas, Lysobacter, and Mesorhizobium. Metabolomic profiling revealed that the abundance of niacinamide was 19.11-fold higher (P < 0.05) in the RTL rhizosphere than in the control rhizosphere. Exogenous supplementation and antagonistic assays demonstrated that niacinamide stimulated Pseudomonas enrichment and activation in the rhizosphere. Although niacinamide did not have direct antifungal activity, its coapplication with Pseudomonas reduced the disease index of Verticillium wilt by 81.89%. Overall, RTL suppresses Verticillium wilt through two pathways, by establishing a more stable and complex microbial network and regulating rhizosphere metabolite composition, particularly niacinamide accumulation, which drives the colonization and activation of defense mediated by beneficial microbes, forming an ecological defense mechanism that links metabolite signaling, microbial response, and pathogen suppression.},
}

Rhizosphere
*Plant Diseases/microbiology/prevention & control
*Verticillium/drug effects
Soil Microbiology
*Gossypium/microbiology
*Niacinamide/metabolism/pharmacology
*Pseudomonas/metabolism/drug effects/growth & development
Metabolomics
Microbiota
Plant Roots/microbiology
Metagenomics

@article {pmid41828538,
year = {2026},
author = {Chen, J and Xu, Y and Liu, Z},
title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
pmid = {41828538},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome ; Animals ; Biotransformation ; Mice ; *Stress, Physiological ; Fermentation ; *Metabolic Networks and Pathways ; Lactiplantibacillus plantarum/metabolism ; Metabolomics/methods ; Male ; },
abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.},
}

*Gastrointestinal Microbiome
Animals
Biotransformation
Mice
*Stress, Physiological
Fermentation
*Metabolic Networks and Pathways
Lactiplantibacillus plantarum/metabolism
Metabolomics/methods
Male

@article {pmid41829938,
year = {2026},
author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW},
title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.},
journal = {Nutrients},
volume = {18},
number = {5},
pages = {},
pmid = {41829938},
issn = {2072-6643},
support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Dietary Supplements ; Male ; Whey Proteins/administration & dosage ; Young Adult ; Adult ; Pea Proteins/administration & dosage ; *Plant Proteins/administration & dosage ; Oryza ; Resistance Training ; *Soccer ; RNA, Ribosomal, 16S/genetics ; Athletes ; *Animal Proteins, Dietary/administration & dosage ; Animals ; },
abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.

METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.

RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.

CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Dietary Supplements
Male
Whey Proteins/administration & dosage
Young Adult
Adult
Pea Proteins/administration & dosage
*Plant Proteins/administration & dosage
Oryza
Resistance Training
*Soccer
RNA, Ribosomal, 16S/genetics
Athletes
*Animal Proteins, Dietary/administration & dosage
Animals

@article {pmid41831863,
year = {2026},
author = {Patel, SS and Shree, T and Kumar, A},
title = {Microbial consortia interactions and bioremediation of pesticides: A review on designing, mechanism and efficacy.},
journal = {Pesticide biochemistry and physiology},
volume = {219},
number = {},
pages = {106993},
doi = {10.1016/j.pestbp.2026.106993},
pmid = {41831863},
issn = {1095-9939},
mesh = {*Pesticides/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; Soil Microbiology ; *Soil Pollutants/metabolism ; },
abstract = {Ecosystems and human health are at serious risk due to the extensive application of pesticides in the agricultural system for controlling pests and diseases. The use of microbial consortia (MicroCons) has emerged as a promising solution for the remediation of pesticide-contaminated soil, offering a sustainable and eco-friendly alternative to physical and chemical methods; however, a systematic review on this aspect is still lacking. This comprehensive review provides an in-depth analysis of the current knowledge on microbial consortia-based remediation of pesticides in agricultural soil. Efficacy of single-strain vs multiple strains in MicroCons have been discussed to unravel the workload distribution between microbial strains in pesticide degradation. We also discuss the design and optimization of microbial consortia for remediation, highlighting the role of advanced tools and the mechanisms of MicroCons action. Furthermore, emerging trends and future directions in the field, including the potential of synthetic biology, machine learning (ML), and artificial intelligence (AI) are also covered. This review aims to critically expand the mechanistic understanding of how microbe-mediated remediation strategies might reduce pesticide phytotoxicity, enhance crop production in pesticide-stressed soils, and inspire future research and practices in MicroCons-based remediation to achieve the Sustainable Development Goals (SDGs).},
}

*Pesticides/metabolism
Biodegradation, Environmental
*Microbial Consortia
Soil Microbiology
*Soil Pollutants/metabolism

@article {pmid41834952,
year = {2026},
author = {Tu, Y and Niu, C and Huang, Z},
title = {[Analysis of the Characteristics of the Oral Virome in Metabolic Dysfunction-Associated Fatty Liver Disease].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {65-72},
pmid = {41834952},
issn = {1672-173X},
mesh = {Humans ; *Virome ; *Saliva/virology ; Male ; Female ; Middle Aged ; Adult ; *Fatty Liver/virology ; *Mouth/virology ; *Dental Plaque/virology ; },
abstract = {OBJECTIVE: To investigate the characteristics of salivary and supragingival plaque viromes in patients with metabolic dysfunction-associated fatty liver disease (MAFLD), and provide new insights for noninvasive oral screening and ecological intervention for MAFLD.

METHODS: This study included 21 MAFLD patients and 20 healthy controls. Saliva and supragingival plaque samples were collected, and metagenomic sequencing was used to analyze the characteristics of the oral virome.

RESULTS: The α-diversity and β-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the α-diversity (Shannon index) and β-diversity (Bray-Curtis distance) of the supragingival plaque virome showed significant differences (P = 0.0303, P = 0.001). For species with a relative abundance greater than 0.1%, 14 viral species in saliva and 5 in supragingival plaque differed significantly in relative abundance between the two groups (P < 0.05), with multiple Streptococcus phages enriched in the saliva of MAFLD patients. LEfSe and random forest analyses identified potential biomarkers in saliva and supragingival plaque. Receiver operating characteristic (ROC) curve analysis showed strong diagnostic performance for these biomarkers in both saliva (area under the curve [AUC] = 0.9548, 95% CI: 0.8898-1.0000) and supragingival plaque (AUC = 0.8952, 95% CI: 0.7774-1.0000). Spearman correlation analysis revealed associations between viral species in saliva or supragingival plaque and various disease indicators (P < 0.05). Compared with healthy individuals, MAFLD patients showed higher node counts, significant relationship numbers, and average node degrees in the co-occurrence networks of salivary and supragingival plaque viromes.

CONCLUSION: Differences in the species composition and structure of the oral virome between MAFLD patients and healthy individuals suggest that oral viral species could serve as potential biomarkers for diagnosing MAFLD.},
}

Humans
*Virome
*Saliva/virology
Male
Female
Middle Aged
Adult
*Fatty Liver/virology
*Mouth/virology
*Dental Plaque/virology

@article {pmid40588027,
year = {2026},
author = {Zhang, J and Yu, Z and Gao, Y and Li, Y and Hu, X and Gu, H and Tang, C and Liu, J and Liu, J and Zhang, S and Sima, X and Wang, G and Liu, P and Rui, Y and Franks, A and Liu, X and Jin, J},
title = {Warming-induced unstable microbial community metabolically lowers straw-carbon sequestration in paddy soils.},
journal = {Journal of advanced research},
volume = {82},
number = {},
pages = {33-44},
doi = {10.1016/j.jare.2025.06.075},
pmid = {40588027},
issn = {2090-1224},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Oryza ; *Carbon/metabolism ; *Carbon Sequestration/physiology ; *Microbiota/physiology ; Temperature ; Global Warming ; },
abstract = {INTRODUCTION: Growing academic attention has been given to the crucial role of soil microorganisms in the net loss of soil organic carbon (SOC) under climate warming and the effectiveness of straw-C sequestration to replenish the SOC stock. However, the lack of empirical investigations in anaerobic paddy soils hinders accurate estimation of the global soil C-climate feedback and development of countermeasures.

OBJECTIVES: This study aimed to unravel the impact of warming on the complexity of the microbial community network of the paddy soil in response to warming, and correspondent changes of microbial metabolic functions relevant to the transformation of straw-C in SOC pools.

METHODS: We added [13]C/[15]N-labeled rice straw into a long-term paddy soil and incubated under three temperature treatments (25, 35 and 45 °C) for 140 days to quantify straw-C sequestration in various SOC fractions, and further deployed metagenomic sequencing and solid-state [13]C NMR analyses to explore relevant biochemical mechanisms.

RESULTS: Warming (35 °C and 45 °C vs. 25 °C) enhanced SOC decomposition, but straw amendment did not replenish the loss C in mineral-associated C, a major SOC fraction of this soil, especially at 45 °C. Compared to 25 °C, temperature increases to 35 °C and 45 °C led to decreases in microbial diversity indices by an average of 19 % and 43 %, respectively. Warming also destabilized the microbial community network with less connectivity and keystone nodes in the paddy soil. Furthermore, warming decreased the abundances of organic C- and N-mineralization genes. Those genes encode enzymes involved in the degradation of both labile and recalcitrant organic compounds, including starch, cellulose, hemicellulose, chitin, pectin and aromatics, as well as in N mineralization, such as glutamate dehydrogenase and glutamate synthase. A subsequent deficiency in the synthesis of those enzymes appeared to suppress the transformation of straw-C and N, thereby reducing their sequestration efficiency in the mineral-associated C fraction in the paddy soil.

CONCLUSION: The detrimental impact of warming on the microbial metabolic profiles lowered the role of straw amendment in sustaining SOC stability under warming. An improved understanding of the warming-induced loss of microbial community diversity and correspondent weakening metabolic functions for the turnover of exogenous C should be accounted for global mitigation practices in paddy fields under climate warming.},
}

*Soil Microbiology
*Soil/chemistry
Oryza
*Carbon/metabolism
*Carbon Sequestration/physiology
*Microbiota/physiology
Temperature
Global Warming

@article {pmid41702980,
year = {2026},
author = {Paoli, JE and Aung, O and Lilak, AA and Maw, MT and Cleary, NG and Watto, E and Hassell, J and Win, YT and Thein, WZ and Evans, TS and Valitutto, M and Goldstein, T and Johnson, CK and Mazet, JA and Fleischer, R and VanTassel, N and Subramaniam, K and Anderson, BD and von Fricken, ME and Mavian, CN and Murray, S},
title = {Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41702980},
issn = {2045-2322},
support = {AID-OAA-A-14-00102 , GHN-A-OO-09-0001000//United States Agency for International Development/ ; },
abstract = {UNLABELLED: Myanmar is one of the most biodiverse countries from a species perspective in Southeast Asia, yet there is minimal published data on zoonotic viruses in small mammals. From July 2017 to August 2018, wildlife sampling was conducted at human-animal interfaces at sites in the Yangon Region and Kayin State. To investigate virus diversity of commensal rodents and shrew, rectal swabs were collected from mice (Mus sp., N = 3), rats (Rattus norvegicus, N = 80; Rattus rattus, N = 6), and Southeast Asian shrews (Crocidura fuliginosa, N = 8). RNA was extracted from rectal swabs, made into cDNA, and subjected to metagenomic next-generation sequencing followed by phylogenetic analysis for virus identification and taxonomic placement. The study provides the first detection of Wencheng shrew virus (WESV) in Myanmar and the first report in C. fuliginosa. A novel member of the genus Cardiovirus was also detected in R. norvegicus and clustered with Cardiovirus theileri sequences previously identified in wild rats from China. Further characterization of viruses circulating in small mammals will help inform public health officials of potential zoonotic risks in a region with virus surveillance gaps and ongoing land use change which may be increasing the risk of zoonotic disease emergence.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38406-w.},
}

@article {pmid41748043,
year = {2026},
author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG},
title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.},
journal = {Experimental gerontology},
volume = {216},
number = {},
pages = {113079},
doi = {10.1016/j.exger.2026.113079},
pmid = {41748043},
issn = {1873-6815},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Middle Aged ; Male ; *Bed Rest/adverse effects ; Female ; *Frailty/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Feces/microbiology ; Aging/physiology ; RNA, Ribosomal, 16S/genetics ; Exercise ; },
abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.},
}

Humans
*Gastrointestinal Microbiome
Aged
Middle Aged
Male
*Bed Rest/adverse effects
Female
*Frailty/microbiology
Saliva/microbiology
*Mouth/microbiology
Feces/microbiology
Aging/physiology
RNA, Ribosomal, 16S/genetics
Exercise

@article {pmid41771404,
year = {2026},
author = {Zhang, C and Zheng, L and Zhang, Q and Zhang, Y and Zheng, X},
title = {Synergistic removal of methanethiol and other odorant gases by a metabolically complementary synthetic consortia isolated from food waste.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134313},
doi = {10.1016/j.biortech.2026.134313},
pmid = {41771404},
issn = {1873-2976},
mesh = {*Odorants/analysis ; *Sulfhydryl Compounds/isolation & purification/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Gases/isolation & purification/metabolism ; *Food ; Hydrogen Sulfide ; Food Loss and Waste ; },
abstract = {Methanethiol (MeSH), a typical volatile sulfur compound, contributes significantly to environmental malodor and poses ecological risks. In this study, three bacterial strains capable of MeSH removal efficiencies exceeding 40% were isolated from food waste. These strains were taxonomically identified asAgrobacterium cavarae,Mycolicibacterium neoaurum, andPseudomonas qingdaonensis. Metagenomic annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that all strains possess key enzymes for the methionine and cysteine metabolism pathway, suggesting potential for MeSH degradation. In binary consortia, the combination of A. cavarae R1 and P. qingdaonensis CF (5:1 ratio) exhibited the optimal degradation performance, achieving removal efficiency of 87.2% for MeSH, 98.7% for H2S, and complete NH3 elimination (100%) after a 6-day cultivation. Among ternary consortia, the A. cavarae R1/M. neoaurum CD/ P. qingdaonensis CF combination at 3:2:1 and 3:1:2 ratios demonstrated superior removal efficiency for all three target odorants. Specifically, the 3:2:1 ratio consortium achieved 94.7% MeSH degradation, while the 3:1:2 ratio showd 91.7% NH3 removal efficiency. These results demonstrate the feasibility of using composite microbial agents for odor control in waste management systems.},
}

*Odorants/analysis
*Sulfhydryl Compounds/isolation & purification/metabolism
Biodegradation, Environmental
*Microbial Consortia
*Gases/isolation & purification/metabolism
*Food
Hydrogen Sulfide
Food Loss and Waste

@article {pmid41780079,
year = {2026},
author = {Zhao, B and Xu, Y and Li, F and Song, S and Liu, Z and Liu, J and Liu, Z and Chen, X and Zhou, M and Zhao, L and Wang, X},
title = {Cyclosporine A ameliorates ulcerative colitis by inhibiting cellular senescence, modulating the JAK2-STAT3/NF-κB signaling pathway, and regulating the gut microbiota-metabolite axis.},
journal = {International immunopharmacology},
volume = {175},
number = {},
pages = {116452},
doi = {10.1016/j.intimp.2026.116452},
pmid = {41780079},
issn = {1878-1705},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/pathology/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; STAT3 Transcription Factor/metabolism ; *Cyclosporine/therapeutic use/pharmacology ; Signal Transduction/drug effects ; Janus Kinase 2/metabolism ; Cellular Senescence/drug effects ; NF-kappa B/metabolism ; Mice ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; Humans ; Disease Models, Animal ; *Immunosuppressive Agents/pharmacology/therapeutic use ; },
abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease characterized by immune dysregulation, compromised intestinal barrier integrity, and disruptions in the microbiota-metabolite axis. Current clinical management of UC remains limited, underscoring the need for novel therapeutic approaches. Cellular senescence is increasingly recognized as a significant contributor to the pathogenesis of this disease. Senescent cells promote inflammatory responses via the sustained release of pro-inflammatory mediators such as IL-6, IL-1β, and TNF-α. Conversely, persistent inflammation drives further cellular senescence, establishing a self-amplifying cycle that exacerbates disease progression. Additionally, gut microbiota dysbiosis (reduced Akkermansia abundance) and metabolic abnormalities (disrupted bile acid metabolism) may further compromise intestinal barrier integrity. Cyclosporine A (CsA), a classical immunosuppressant, has unclear mechanisms in UC, particularly regarding its potential effects on senescence and the microbiota-metabolite axis. In this investigation, using a dextran sulfate sodium (DSS)-induced UC model, we demonstrated that CsA significantly alleviated DSS-induced acute colitis in mice and senescence-associated pathological changes. Multi-omics analyses integrating network pharmacology, transcriptomics, metabolomics, and metagenomics demonstrated that CsA likely exerts its therapeutic effects through inhibition of the JAK2-STAT3/NF-κB signaling pathway. This leads to reduced release of pro-inflammatory cytokines, modulation of intestinal microbiota composition and metabolite profiles, and enhanced intestinal barrier function.These findings elucidate new mechanisms by which CsA improves DSS-induced colitis in mice through anti-senescence effects and microbiota-metabolic regulation, providing potential therapeutic targets for UC.},
}

Animals
*Colitis, Ulcerative/drug therapy/chemically induced/pathology/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
STAT3 Transcription Factor/metabolism
*Cyclosporine/therapeutic use/pharmacology
Signal Transduction/drug effects
Janus Kinase 2/metabolism
Cellular Senescence/drug effects
NF-kappa B/metabolism
Mice
Mice, Inbred C57BL
Dextran Sulfate
Male
Humans
Disease Models, Animal
*Immunosuppressive Agents/pharmacology/therapeutic use

@article {pmid41825251,
year = {2026},
author = {Chang, L and Su, X and Hu, W and Fang, Y and Liu, J and Li, J and Huang, L and Shu, W},
title = {Genomic insights into adaptation and microevolution of two novel non-AOA Nitrososphaeria, Acidarchaeum fankouense and Thermosulfuris yongpingense, in acid mine drainage ecosystems.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {3},
pages = {126711},
doi = {10.1016/j.syapm.2026.126711},
pmid = {41825251},
issn = {1618-0984},
abstract = {The class Nitrososphaeria is best known for ammonia-oxidizing archaea (AOA), yet deeply branching non-AOA lineages remain poorly characterized, leaving a critical gap in our understanding of the group's early evolution and ecological diversification. Herein, we recovered 44 non-AOA Nitrososphaeria metagenome-assembled genomes (MAGs) from acid mine drainage (AMD) sediments in diverse metal mines, representing two novel genera within the family Thermosulfuridaceae, Acidarchaeum and Thermosulfuris. A meta-analysis of 251 AMD-associated metagenomes worldwide showed that these potentially thermophilic lineages were detected only in China and were typically rare, with localized blooms (up to ∼7.65%) at a few sites, particularly Fankou lead-zinc mine. Metabolic reconstruction suggested a facultatively anaerobic, mixotrophic lifestyle capable of CO oxidation and sulfur reduction, and extensive acid- and heavy-metal resistance mediated primarily by ether-linked archaeal lipids, ion efflux systems, and enzymatic reduction. Genus-specific traits include dissimilatory sulfate reduction in Thermosulfuris and urea utilization in Acidarchaeum, illuminating distinct ecological niches. Population-genomic analyses reveal low homologous recombination and pervasive purifying selection in these non-AOA populations, together with local relaxation of selection and elevated diversity, the former being correlated with geochemical stressors (notably copper), pointing to long-term, geochemically driven adaptation. Overall, these findings provide insights into the biodiversity, ecophysiology, and evolutionary dynamics of non-AOA Nitrososphaeria.},
}

@article {pmid41821330,
year = {2026},
author = {Yi, XH and Zhu, HX and He, MY and Gao, S and Li, M},
title = {Decoding Links between Gut Microbiota and Metabolic-associated Fatty Liver Disease: Meta-analysis and Mediation Study Uncover Species-specific Taxa and a Novel Bile Acid Mediator.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {2},
pages = {202-214},
doi = {10.3967/bes2025.162},
pmid = {41821330},
issn = {2214-0190},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Bile Acids and Salts/metabolism ; Mendelian Randomization Analysis ; Species Specificity ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Fatty Liver/microbiology ; Bacteria/classification/genetics ; },
abstract = {OBJECTIVE: Previous Mendelian randomization (MR) studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease (MAFLD). However, the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights. To address this, we conducted a de novo MR analysis using species-level shotgun metagenomic data, combined it with a meta-analysis to consolidate the existing evidence, and explored metabolite-mediated pathways.

METHODS: Bidirectional MR analyses were performed between 883 gut microbiota taxa (derived from shotgun metagenomic genome-wide association study) and MAFLD. Published MR studies (up to December 1, 2024) were identified using PubMed, Embase, Web of Science, and the Cochrane Library for meta-analysis. Multivariable MR (MVMR) and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.

RESULTS: The de novo MR identified 25 MAFLD-associated microbial taxa. Integration with 7 published studies revealed 34 causal taxa, including 10 at the species level. Among the 1,400 metabolites, 53 showed causal links with MAFLD. MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk (22.06% mediation proportion).

CONCLUSION: This study elucidated the connections between species-level gut microbiota and MAFLD, highlighting the interplay between microbiota, metabolites, and disease pathogenesis. These findings provide novel insights into the potential therapeutic targets for MAFLD.},
}

*Gastrointestinal Microbiome
Humans
*Bile Acids and Salts/metabolism
Mendelian Randomization Analysis
Species Specificity
*Non-alcoholic Fatty Liver Disease/microbiology
*Fatty Liver/microbiology
Bacteria/classification/genetics

@article {pmid41820832,
year = {2026},
author = {Vela-Chauvin, MG and Ramirez-Villacis, DX and Armijos, CE and Narvaez, M and Quelal-Madrid, F and Bustamante, G and Torres-Sobrevilla, C and Debut, A and Corredor, F and Calero-Cáceres, W and Machado, A and Zapata-Mena, S},
title = {Characterization and evaluation of a phage cocktail targeting Salmonella enterica in a Turkey farm.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04849-4},
pmid = {41820832},
issn = {1471-2180},
support = {FSPI grant (Project ID 17827)//French Embassy in Ecuador/ ; Collaboration Grant (Project ID 23185)//Universidad San Francisco de Quito/ ; },
}

@article {pmid41730403,
year = {2026},
author = {Liu, W and Zhang, Z and Wu, W and Yan, X and Huang, Y and Feng, H and Mou, Q and Wan, J and Yan, M and Tang, H and Liang, J and Zhang, Y and Peng, C and Pan, X},
title = {Ligilactobacillus murinus confers a dual benefit: Counteracting crotonis fructus-induced intestinal toxicity and synergizing with its processed form against ulcerative colitis.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121420},
doi = {10.1016/j.jep.2026.121420},
pmid = {41730403},
issn = {1872-7573},
mesh = {Animals ; *Colitis, Ulcerative/chemically induced/microbiology/drug therapy/pathology ; Caenorhabditis elegans ; Gastrointestinal Microbiome/drug effects ; *Croton/chemistry/toxicity ; Mice ; *Probiotics/pharmacology/administration & dosage/therapeutic use ; Male ; Disease Models, Animal ; Dextran Sulfate ; *Lactobacillus ; Mice, Inbred C57BL ; *Plant Extracts/toxicity ; },
abstract = {Ulcerative colitis (UC) poses a major clinical challenge. Classical Chinese medical texts record the use of Crotonis Fructus (CF), the seeds of Croton tiglium L., for treating conditions like "chronic dysentery" presenting symptoms similar to UC. However, the clinical application of both raw and processed CF is limited due to intestinal toxicity.

AIM OF THE STUDY: This study investigates the role of gut microbiota in mitigating the intestinal toxicity induced by CF and in enhancing the anti-UC efficacy of its processed form.

METHODS: Metagenomic analysis investigated CF-induced intestinal toxicity. The benefits of probiotics combined with CF or processed CF cream were evaluated in Caenorhabditis elegans (C. elegans) and a dextran sulfate sodium (DSS)-induced mouse model. Their combined effect was further assessed in DSS-exposed C. elegans, with qRT-PCR measuring intestinal barrier integrity.

RESULTS: Metagenomic analysis revealed that CF-induced intestinal toxicity was associated with gut microbiota dysbiosis characterized by a pronounced reduction in Ligilactobacillus murinus (L. murinus). Supplementation with L. murinus alleviated CF-induced damage in C. elegans. In DSS-induced UC mice, both L. murinus and processed CF cream ameliorated colitis and suppressed TNF-α, IL-6, and IL-1β. When co-administered in DSS-exposed C. elegans, two agents acted synergistically, leading to greater restoration of intestinal barrier integrity and more pronounced upregulation of barrier-function genes.

CONCLUSION: This study demonstrates that L. murinus plays a dual role: it mitigates CF-induced intestinal toxicity and acts synergistically with processed CF cream to enhance UC treatment, providing a microbiome-based strategy for safer clinical application.},
}

Animals
*Colitis, Ulcerative/chemically induced/microbiology/drug therapy/pathology
Caenorhabditis elegans
Gastrointestinal Microbiome/drug effects
*Croton/chemistry/toxicity
Mice
*Probiotics/pharmacology/administration & dosage/therapeutic use
Male
Disease Models, Animal
Dextran Sulfate
*Lactobacillus
Mice, Inbred C57BL
*Plant Extracts/toxicity

@article {pmid41724049,
year = {2026},
author = {Wang, D and Xin, J and Lai, C and Sun, N and Yang, Y and He, Y and Duan, L and Luo, J and He, Y and Zhang, Y and Zhang, Y and Wang, H and Zeng, D and Bai, Y and Ni, X},
title = {High fluoride exposure disrupts gut microbiota and induces intestinal barrier damage via RhoA/ROCK-mediated cytoskeletal remodeling.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119898},
doi = {10.1016/j.ecoenv.2026.119898},
pmid = {41724049},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; rho-Associated Kinases/metabolism ; Mice ; Cytoskeleton/drug effects ; rhoA GTP-Binding Protein/metabolism ; *Fluorides/toxicity ; Male ; Intestinal Mucosa/drug effects ; Signal Transduction/drug effects ; Intestines/drug effects ; Permeability ; Mice, Inbred C57BL ; },
abstract = {Fluoride pollution-whether of geological or anthropogenic origin-disrupts gut microbiota-host homeostasis and compromises the intestinal barrier. We established an acute high-fluoride mouse model via intragastric NaF, integrating metagenomics, metabolomics, and molecular biological techniques to clarify the underlying mechanism of enhanced intestinal permeability caused by fluoride exposure in vivo. Mechanistically, high fluoride exposure activates the RhoA/ROCK signaling pathway, increases the level of phosphorylated myosin light chain (p-MLC), induces filamentous actin (F-actin) rearrangement, and disrupts the apical junctional complex (AJC)-characterized by downregulated expression or abnormal localization of AJC-related proteins (ZO-1, Claudin-1, β-catenin, Occludin). It also alters the morphology of intestinal epithelial cells, ultimately increasing ileal permeability. At the microbiota level, high fluoride disrupted the ileal microbiota; specifically, at the species level, Bifidobacterium sp. SO1 and Schaalia turicensis were identified as the key species with high specificity and high occupancy under fluoride exposure. Lactobacillus and Akkermansia were abnormally enriched in the intestines of mice exposed to fluoride. Metabolomic analysis revealed that high fluoride exposure enriched multiple pathways including linoleic acid metabolism and sphingolipid metabolism, altering the levels of 11 cytoskeleton-related metabolites. Correlation analysis confirmed that Bifidobacterium sp. SO1 and Schaalia turicensis were strongly correlated with damage phenotypes, pathway molecules, and metabolites, indicating that these two strains are closely associated with cytoskeleton changes and increased intestinal permeability under high fluoride exposure. Collectively, our findings reveal that gut microbiota drive fluoride-induced intestinal barrier dysfunction through the "microbiota-RhoA/ROCK-cytoskeleton" axis, highlighting a novel host-microbe interaction mechanism underlying environmental toxin-mediated gut injury.},
}

Animals
*Gastrointestinal Microbiome/drug effects
rho-Associated Kinases/metabolism
Mice
Cytoskeleton/drug effects
rhoA GTP-Binding Protein/metabolism
*Fluorides/toxicity
Male
Intestinal Mucosa/drug effects
Signal Transduction/drug effects
Intestines/drug effects
Permeability
Mice, Inbred C57BL

@article {pmid41713817,
year = {2026},
author = {Zhao, Q and Cao, Y and Zhang, Z and Yang, Y and Wang, L and Xu, M and Mao, Y and Zhang, X and Zeng, M and Yang, P and Chen, Q and Yan, H and Yang, G},
title = {Xiao-Chaihu-Tang preserves intestinal barrier and ameliorates irinotecan-evoked delayed diarrhea by anchoring endogenous tryptophol to modulate inflammation and oxidation dependent on AhR-UGT1A1-microbiota axis.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121380},
doi = {10.1016/j.jep.2026.121380},
pmid = {41713817},
issn = {1872-7573},
mesh = {Animals ; *Irinotecan/toxicity ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Male ; *Diarrhea/chemically induced/drug therapy/prevention & control/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Rats ; Rats, Sprague-Dawley ; Glucuronosyltransferase/metabolism ; *Indoles/metabolism ; Intestinal Mucosa/drug effects/metabolism ; Inflammation/drug therapy ; Oxidation-Reduction ; Fecal Microbiota Transplantation ; },
abstract = {Xiao-Chaihu-Tang (XCHT), a well-known traditional formula, is commonly used to treat various types of diarrhea. It also exhibits promising efficacy against chemotherapy irinotecan (CPT-11)-induced delayed diarrhea (DD). However, its underlying mechanisms, specifically concerning endogenous metabolites, key pathways, and functional gut bacteria at the species level, remain unclear, severely restricting its clinical application.

AIM OF THE STUDY: This study aimed to elucidate the biomarkers, pathways, and functional bacteria involved in XCHT's alleviating CPT-11-evoked DD using multi-omics approaches, antagonists, and fecal microbiota transplantation (FMT).

MATERIALS AND METHODS: First, the ingredients of XCHT and absorbed compounds in rat plasma were identified using liquid chromatography-mass spectrometry (LC-MS). Next, the therapeutic effects of XCHT were assessed by monitoring perianal status, body weight, disease activity index, food and water intake, and histopathological changes in the colon (hematoxylin and eosin, alcian blue-periodic acid-schiff staining). The underlying mechanisms were studied using metabolomics and network pharmacology, which highlighted the role of endogenous biomarkers and associated pathways. Tryptophol was identified as a key correlate, and its efficacy was further validated in rat and Caco-2 models using antagonists of potential targets (AhR and UGT1A1). The levels of inflammatory cytokines, and oxidative stress markers, intestinal barrier proteins, and mucins were detected by enzyme-linked immunosorbent assay (ELISA), Western blotting, and immunofluorescence. Furthermore, functional gut bacteria were identified using metagenomic sequencing and validated using FMT, while gut leakage was detected using fluorescence in situ hybridization (FISH). Finally, the interactions between tryptophol with targets of AhR and UGT1A1 were examined using molecular docking, molecular dynamics, and surface plasmon resonance.

RESULTS: LC-MS analysis identified 43 phytochemicals in XCHT and 17 compounds absorbed in plasma. XCHT, similar to tryptophol, attenuated DD by improving perianal status, disease activity index, and colon pathology, while increasing body weight, food intake, and water intake. Metabolomics analysis revealed 33 potential endogenous biomarkers, including PGB3, LysoPA, and so on. Integrated with network pharmacology, the results indicated that the therapeutic effect of XCHT involved the regulation of tryptophan metabolism, arachidonic acid metabolism, inflammation, and oxidative stress. Tryptophol, which exhibited a strong correlation with efficacy indices, reduced inflammation and oxidation in vivo/vitro, and enhanced intestinal barrier protein and mucin expression in an AhR-UGT1A1-dependent manner. Furthermore, metagenomic sequencing and FISH demonstrated that both XCHT and tryptophol normalized the abundance of 10 gut bacterial species (for example, Lactobacillaceae bacterium, Massiliimalia timonensis, and Limosilactobacillus reuteri) and inhibited bacterial invasion. Molecular interaction studies confirmed the strong binding between tryptophol with AhR and UGT1A1.

CONCLUSION: This study demonstrates that XCHT preserves intestinal barrier integrity in rats and alleviates CPT-11-induced DD. This protective effect is mediated by modulating inflammation and oxidative stress via the tryptophol- AhR-UGT1A1-microbiota axis, providing a novel paradigm for mechanistic studies on toxicity reduction in clinical chemotherapy drugs.},
}

Animals
*Irinotecan/toxicity
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Gastrointestinal Microbiome/drug effects
Male
*Diarrhea/chemically induced/drug therapy/prevention & control/metabolism
Receptors, Aryl Hydrocarbon/metabolism
Rats
Rats, Sprague-Dawley
Glucuronosyltransferase/metabolism
*Indoles/metabolism
Intestinal Mucosa/drug effects/metabolism
Inflammation/drug therapy
Oxidation-Reduction
Fecal Microbiota Transplantation

@article {pmid41688638,
year = {2026},
author = {Dekkers, KF and Pertiwi, K and Baldanzi, G and Lundmark, P and Hammar, U and Moksnes, MR and Coward, E and Nethander, M and Salih, GA and Miari, M and Nguyen, D and Sayols-Baixeras, S and Eklund, AC and Holm, JB and Nielsen, HB and Volpiano, CG and Méric, G and Thangam, M and Hakaste, L and Tuomi, T and Ahlqvist, E and Smith, CA and Allen, M and Reimann, F and Gribble, FM and Ohlsson, C and Hveem, K and Melander, O and Nilsson, PM and Engström, G and Smith, JG and Michaëlsson, K and Ärnlöv, J and Orho-Melander, M and Fall, T},
title = {Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.},
journal = {Nature genetics},
volume = {58},
number = {3},
pages = {540-549},
pmid = {41688638},
issn = {1546-1718},
support = {2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2020-02191//Vetenskapsrådet (Swedish Research Council)/ ; 2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; 521-2013-2756//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01236//Vetenskapsrådet (Swedish Research Council)/ ; 2021-02273//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01291//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01015, 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784, 2018-02837, EXODIAB 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20200173//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2022-0344//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2020-0711//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//Lars Erik Lundbergs Stiftelse för Forskning och Utbildning (Lundberg Foundation for Research and Education)/ ; CKFUU-1025348, 987986, 976460, 963488, 936407, 695401, and 797891//Centrum fÖr Klinisk Forskning Dalarna (Center for Clinical Research Dalarna)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genome-Wide Association Study ; Male ; Female ; Sweden ; Adult ; Polymorphism, Single Nucleotide ; Metagenomics ; Fatty Acids/metabolism ; Genetic Variation ; Middle Aged ; Galactoside 2-alpha-L-fucosyltransferase ; },
abstract = {Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 × 10[-11]) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Genome-Wide Association Study
Male
Female
Sweden
Adult
Polymorphism, Single Nucleotide
Metagenomics
Fatty Acids/metabolism
Genetic Variation
Middle Aged
Galactoside 2-alpha-L-fucosyltransferase

@article {pmid41651883,
year = {2026},
author = {Pantiukh, K and Org, E},
title = {Human gut archaea collection from Estonian population.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41651883},
issn = {2052-4463},
support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Estonia ; *Archaea/genetics ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Genome, Archaeal ; Metagenomics ; Feces/microbiology ; },
abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.},
}

Estonia
*Archaea/genetics
*Gastrointestinal Microbiome
Humans
*Metagenome
*Genome, Archaeal
Metagenomics
Feces/microbiology

@article {pmid41558076,
year = {2026},
author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S},
title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106427},
pmid = {41558076},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Chickens/immunology/microbiology/physiology ; *T-Lymphocytes, Regulatory/drug effects/immunology ; *Triterpenes/administration & dosage/metabolism/pharmacology ; Ursolic Acid ; Dietary Supplements/analysis ; Diet/veterinary ; *Intestines/drug effects/physiology/microbiology ; Animal Feed/analysis ; *Th17 Cells/drug effects/immunology ; Random Allocation ; Dose-Response Relationship, Drug ; Male ; },
abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Chickens/immunology/microbiology/physiology
*T-Lymphocytes, Regulatory/drug effects/immunology
*Triterpenes/administration & dosage/metabolism/pharmacology
Ursolic Acid
Dietary Supplements/analysis
Diet/veterinary
*Intestines/drug effects/physiology/microbiology
Animal Feed/analysis
*Th17 Cells/drug effects/immunology
Random Allocation
Dose-Response Relationship, Drug
Male

@article {pmid41544440,
year = {2026},
author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X},
title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106373},
pmid = {41544440},
issn = {1525-3171},
mesh = {Animals ; *Chickens/virology ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Bacteriophages/drug effects/physiology/genetics ; Dietary Supplements/analysis ; *Virome/drug effects ; Animal Feed/analysis ; Diet/veterinary ; *Chlortetracycline/pharmacology/administration & dosage ; *Plant Extracts/pharmacology/administration & dosage ; },
abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.},
}

Animals
*Chickens/virology
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Bacteriophages/drug effects/physiology/genetics
Dietary Supplements/analysis
*Virome/drug effects
Animal Feed/analysis
Diet/veterinary
*Chlortetracycline/pharmacology/administration & dosage
*Plant Extracts/pharmacology/administration & dosage

@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
pmid = {41539238},
issn = {1525-3171},
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Bacillus subtilis/chemistry ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Clostridium butyricum/chemistry ; Animal Feed/analysis ; Diet/veterinary ; *Metabolic Networks and Pathways/drug effects ; Thailand ; Metagenomics ; Dietary Supplements/analysis ; *Metagenome ; },
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}

Animals
*Probiotics/pharmacology/administration & dosage
*Bacillus subtilis/chemistry
*Chickens/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
*Clostridium butyricum/chemistry
Animal Feed/analysis
Diet/veterinary
*Metabolic Networks and Pathways/drug effects
Thailand
Metagenomics
Dietary Supplements/analysis
*Metagenome

@article {pmid41512665,
year = {2026},
author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY},
title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106384},
pmid = {41512665},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Poultry Diseases/microbiology/prevention & control ; Cecum/microbiology ; *Salmonella Infections, Animal/microbiology/prevention & control ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology/administration & dosage ; Random Allocation ; Anti-Bacterial Agents/pharmacology ; Amoxicillin/pharmacology ; *Bacillaceae/physiology ; *Lactobacillaceae/physiology ; },
abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.},
}

Animals
*Chickens
*Poultry Diseases/microbiology/prevention & control
Cecum/microbiology
*Salmonella Infections, Animal/microbiology/prevention & control
*Gastrointestinal Microbiome/drug effects
*Probiotics/pharmacology/administration & dosage
Random Allocation
Anti-Bacterial Agents/pharmacology
Amoxicillin/pharmacology
*Bacillaceae/physiology
*Lactobacillaceae/physiology

@article {pmid41814421,
year = {2026},
author = {Lee, CZ and Worsley, SF and Davies, CS and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS},
title = {Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41814421},
issn = {2049-2618},
mesh = {*Gastrointestinal Microbiome/genetics/immunology ; Animals ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Songbirds/microbiology/immunology/genetics ; *Major Histocompatibility Complex/genetics ; Animals, Wild/microbiology/immunology ; Immunogenetics ; },
abstract = {BACKGROUND: The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.

RESULTS: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts.

CONCLUSION: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics/immunology
Animals
Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
*Songbirds/microbiology/immunology/genetics
*Major Histocompatibility Complex/genetics
Animals, Wild/microbiology/immunology
Immunogenetics

@article {pmid41813975,
year = {2026},
author = {Telles-de-Deus, J and Claro, IM and Bertanhe, M and Whittaker, C and Port-Carvalho, M and Rocha, EC and Coletti, TM and da Silva, CAM and Valença, IN and Lima-Camara, TN and Bicudo de Paula, M and Cunha, MS and de Jesus, JG and Dos Santos Andrade, P and Cox, V and de Azevedo, NCCF and Guerra, JM and Summa, JL and Teixeira, APP and Bergo, ES and Pereira, M and Moreira, FRR and Felix, AC and de Paula, AV and de Araujo Eliodoro, RH and da Silva Lima, M and de Oliveira, FM and de Souza, VR and Franco, LAM and Nardi, MS and Sanches, TC and da Silva, ETBC and Coimbra, AAC and Dos Santos, PR and Lima de Gouveia, K and Vilela, FESP and Hill, SC and Oliveira, DAG and Piedade, HM and Guimarães-Luiz, T and Abreu, CMG and Casoni da Rocha, G and Abade, L and de Souza, WM and Lambert, B and Pereira de Souza, R and Pinter, A and Sabino, EC and Mucci, LF and Faria, NR},
title = {Evolution and spillover dynamics of yellow fever at the forest-urban interface in Brazil.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41813975},
issn = {2058-5276},
support = {316633/Z/24/Z//Wellcome Trust (Wellcome)/ ; 226075/Z/22/Z//Wellcome Trust (Wellcome)/ ; 226075/Z/22/Z//Wellcome Trust (Wellcome)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/X020258/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; },
abstract = {Yellow fever virus (YFV) continues to threaten human and wildlife populations in the Americas, yet its transmission at the forest-urban interface remains unclear. Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018. Our analyses reveal that transmission was primarily driven by a single genetic cluster introduced during a period of high abundance of the main vector, Haemagogus leucocelaenus mosquitoes. A near-complete hepatitis A virus genome was detected in a YFV-infected howler monkey, suggesting potential co-infections at the human-wildlife interface. Phylogenetic and epidemiological modelling estimated a basic reproduction number, R0, for sylvatic yellow fever of 8.2 (95% CI 5.1-12.2), substantially higher than previous estimates for urban outbreaks. Our findings demonstrate that multisource surveillance could provide actionable early warnings in regions at risk for zoonotic spillover.},
}

@article {pmid41811805,
year = {2026},
author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L},
title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344050},
pmid = {41811805},
issn = {1932-6203},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Adenoma/microbiology/metabolism/pathology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Case-Control Studies ; Aged ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.

OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.

MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.

RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K₂) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.

CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K₂ biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/pathology
*Adenoma/microbiology/metabolism/pathology
Female
Male
Middle Aged
*Gastrointestinal Microbiome
Colonoscopy
Case-Control Studies
Aged
*Vitamin K 2/metabolism
Cross-Sectional Studies
Feces/microbiology
Adult
Dysbiosis/microbiology

@article {pmid41791253,
year = {2026},
author = {Fu, CX and Cai, JJ and Liu, JL and Qiu, GY and Chen, XD and Zhang, JB and Qiao, M and Tong, WB and Guo, B},
title = {Mechanistic investigation of the associations between bacterial community composition and cadmium distribution in Zizania latifolia.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119972},
doi = {10.1016/j.ecoenv.2026.119972},
pmid = {41791253},
issn = {1090-2414},
mesh = {*Cadmium/metabolism/analysis ; *Soil Pollutants/metabolism/analysis ; Rhizosphere ; *Bacteria/metabolism/classification/genetics ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; *Poaceae/microbiology/metabolism ; Plant Leaves/metabolism/microbiology ; *Microbiota ; },
abstract = {The role of bacteria in external niches regulating cadmium (Cd(II)) in plant tissues remains unclear. We explored Cd(II) profiles and identified bacterial contributors among phyllosphere, rhizoplane, and rhizosphere of four Zizania latifolia varieties through integrated metagenomic and chemical analyses. Zizania latifolia accumulated Cd(II) in leaves (0.06-0.77 mg/kg), roots (0.73-1.57 mg/kg), and rhizosphere (0.43-3.15 mg/kg), respectively. The highest enrichment coefficient (leaf-Cd(II)/soil-Cd(II)) was observed in Genotype 3 (0.6). Among top 10 genus-level bacteria, Enterococcus in phyllosphere, Streptomyces and Dechloromonas in rhizoplane, and Bradyrhizobium, Pseudolabrys, Mycobacterium, and Dechloromonas in rhizosphere were significantly related to Cd(II). Enterococcus adsorbed Cd(II) by extracellular polysaccharides and precipitated Cd(II) sulfide. Rhizoplane and rhizosphere bacteria absorbed Cd(II) by cell-surface functional groups, and fixed Cd(II) through synthesizing polyphosphate and driving Fe (II) oxidation. Additionally, 64.4%-80% of bacteria were shared between rhizoplane and rhizosphere, 5.5%-6.9% between rhizoplane and phyllosphere, and 4.4%-6.1% between rhizosphere and phyllosphere. Metagenomic analysis indicated that Cd(II) disturbed bacterial secretion system and amino acid metabolic pathways. These findings provided comprehensive insights into interrelationships between Cd(II) and bacteria in leaves, roots, and rhizosphere of Zizania latifolia, offering valuable foundations for developing targeted strategies to mitigate Cd(II) accumulation in aquatic vegetables.},
}

*Cadmium/metabolism/analysis
*Soil Pollutants/metabolism/analysis
Rhizosphere
*Bacteria/metabolism/classification/genetics
Plant Roots/microbiology/metabolism
Soil Microbiology
*Poaceae/microbiology/metabolism
Plant Leaves/metabolism/microbiology
*Microbiota

@article {pmid41772715,
year = {2026},
author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD},
title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41772715},
issn = {2049-2618},
support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Caloric Restriction ; *Bacteria/virology/genetics/classification ; Longevity ; Genome, Viral ; Metagenome ; Male ; Longitudinal Studies ; Female ; },
abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.

RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.

CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Bacteriophages/genetics/classification/isolation & purification/physiology
*Caloric Restriction
*Bacteria/virology/genetics/classification
Longevity
Genome, Viral
Metagenome
Male
Longitudinal Studies
Female

@article {pmid41713162,
year = {2026},
author = {Liu, X and Cai, H and Zhao, L and Ke, D and Xu, X and Li, J and Yu, J and Shen, Y and Zhu, L and Jin, Y and Zhang, M and Liu, S and Du, J and Zheng, J and Dong, R},
title = {Microplastic-associated gut microbial profile and antibiotic resistance in preschool children: a multicentre cross-sectional study in China.},
journal = {EBioMedicine},
volume = {125},
number = {},
pages = {106177},
pmid = {41713162},
issn = {2352-3964},
mesh = {Humans ; China/epidemiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Cross-Sectional Studies ; Child, Preschool ; Female ; Male ; *Microplastics/adverse effects ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification ; },
abstract = {BACKGROUND: Microplastics (MPs) are ubiquitous in ecosystems and present in the human body, causing a worldwide environmental issue. However, the extent of human exposure to MPs remains largely unknown. Although mice exposed to MPs exhibit gut microbiota dysbiosis, the impact of MPs on the human intestinal microbiota remains unclear. Furthermore, MPs can carry and spread antibiotic resistance genes (ARGs). However, their potential influence on ARG abundance is underexplored.

METHODS: A multicentre cross-sectional study was conducted in Xiamen, Shanghai, and Nanjing in China from October 2022 to March 2023. A total of 335 couples of faecal samples were collected and analysed for MPs using Py-GC/MS and gut microbiota using 16S rRNA and metagenomic sequencing.

FINDINGS: Eight types of MPs were detected in 335 faecal samples, with a median concentration of 212.1 μg/g dw. MP exposure may be associated with the composition of the host gut microbiota. Microbial function analysis indicated the significant enrichment of 62 pathways primarily related to the metabolic pathways of macronutrients, vitamins, and bioactive substances. Total plastic concentration was significantly related to the relative abundance of species and ARGs, however this could not be attributed to specific plastic polymers after adjusting for covariates.

INTERPRETATION: This study provides baseline data on the gap in understanding of preschoolers' MP exposure, supporting the hypothesis that MP exposure might disrupt gut bacterial constitution and functions. This raises concerns regarding the potential adverse effects on the human gut when exposed to MPs, particularly drug resistance risks in younger populations.

FUNDING: Project of Shanghai Municipal Financial Professional foundation (Food Safety Risk Assessment) (grant number: RA-2023-10), National Natural Science Foundation of China (grant number: 2023YFF1104800), and Key Disciplines in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025) (grant number: GWVI-11.1-42).},
}

Humans
China/epidemiology
*Gastrointestinal Microbiome/drug effects/genetics
Cross-Sectional Studies
Child, Preschool
Female
Male
*Microplastics/adverse effects
*Drug Resistance, Microbial/genetics
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Bacteria/genetics/drug effects/classification

@article {pmid41691988,
year = {2026},
author = {Pan, Y and Zong, G and Liu, M and Wang, Z and Zhu, H and Wei, Z and Shan, Y and Lu, Y},
title = {Restoring gut microbiota homeostasis to ameliorate colitis via Huangqin decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {153},
number = {},
pages = {157929},
doi = {10.1016/j.phymed.2026.157929},
pmid = {41691988},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Mice, Inbred C57BL ; Homeostasis/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Disease Models, Animal ; Male ; *Colitis/drug therapy ; Wnt Signaling Pathway/drug effects ; Dextran Sulfate ; Anti-Inflammatory Agents/pharmacology ; Eubacteriales/drug effects ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory gut disorder involving dysregulated host-microbiota interactions. Huangqin decoction (HQD) is an herbal formula with known anti-inflammatory and microbiota-modulating effects, but its protective mechanism in ulcerative colitis remains unclear.

PURPOSE: To investigate whether HQD ameliorates colitis by rebalancing gut microbiota homeostasis and to elucidate the underlying immunological and regenerative mechanisms involved.

METHODS: A DSS-induced colitis mouse model was used to evaluate the effects of HQD. Colitis severity and inflammation were evaluated by the clinical disease index, histological analysis, and cytokine levels, and the gut microbiota profiles were analyzed via metagenomic sequencing. We used mechanistic assays to evaluate the effects of specific bacterial strains on intestinal organoids and neutrophil NETosis.

RESULTS: HQD significantly alleviated colitis symptoms and inflammation. It remodelled the gut microbiota, suppressing Desulfovibrionaceae while enriching Lachnospiraceae. This microbiota shift drove reduced NETosis and activated Wnt/β-catenin signaling to enhance intestinal stem cell (ISC) proliferation, thereby promoting mucosal repair. In organoid cultures, Lachnospiraceae promoted organoid growth, whereas Desulfovibrionaceae caused epithelial damage and, independently, triggered NETosis in immune contexts. Notably, administration of the Lachnospiraceae bacterium ameliorated colitis and increased colonic Wnt/β-catenin signaling, confirming its regenerative role.

CONCLUSION: HQD ameliorates colitis by rebalancing the gut microbiota, thereby suppressing harmful inflammation and promoting epithelial regeneration. These findings provide mechanistic support for HQD as a microbiota-mediated therapeutic strategy in colitis.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Drugs, Chinese Herbal/pharmacology
Mice
Mice, Inbred C57BL
Homeostasis/drug effects
*Colitis, Ulcerative/drug therapy/microbiology
Disease Models, Animal
Male
*Colitis/drug therapy
Wnt Signaling Pathway/drug effects
Dextran Sulfate
Anti-Inflammatory Agents/pharmacology
Eubacteriales/drug effects

@article {pmid41679496,
year = {2026},
author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y},
title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.},
journal = {Environmental research},
volume = {296},
number = {},
pages = {123973},
doi = {10.1016/j.envres.2026.123973},
pmid = {41679496},
issn = {1096-0953},
mesh = {*Microplastics/toxicity ; *Rivers/microbiology ; *Seawater/microbiology ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects ; Bacteria ; Environmental Monitoring ; Biofilms ; *Water Microbiology ; },
abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.},
}

*Microplastics/toxicity
*Rivers/microbiology
*Seawater/microbiology
*Water Pollutants, Chemical/toxicity
*Microbiota/drug effects
Bacteria
Environmental Monitoring
Biofilms
*Water Microbiology

@article {pmid41644553,
year = {2026},
author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J},
title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41644553},
issn = {2055-5008},
support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Echinococcus multilocularis/physiology ; Mice ; *Depression/microbiology/etiology ; *Echinococcosis/microbiology/psychology/parasitology ; Mice, Inbred BALB C ; Disease Models, Animal ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Behavior, Animal ; Metabolomics ; Metagenomics ; },
abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.},
}

Animals
*Gastrointestinal Microbiome
*Echinococcus multilocularis/physiology
Mice
*Depression/microbiology/etiology
*Echinococcosis/microbiology/psychology/parasitology
Mice, Inbred BALB C
Disease Models, Animal
Fecal Microbiota Transplantation
RNA, Ribosomal, 16S/genetics
Behavior, Animal
Metabolomics
Metagenomics

@article {pmid41558030,
year = {2026},
author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, A and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E},
title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.},
journal = {Blood advances},
volume = {10},
number = {6},
pages = {1979-1991},
doi = {10.1182/bloodadvances.2025016780},
pmid = {41558030},
issn = {2473-9537},
mesh = {Humans ; *Graft vs Host Disease/etiology/epidemiology/microbiology ; Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Female ; Male ; Incidence ; Middle Aged ; *Bacteria/metabolism ; Adult ; *Carbohydrate Metabolism ; Retrospective Studies ; *Gastrointestinal Diseases/etiology/epidemiology/microbiology ; Metagenomics ; },
abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of stool from patients with allo-HSCT (N = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate-degrading functionality of these bacteria, we investigated gene abundances for carbohydrate-active enzymes (CAZymes) and found that Parabacteroides merdae, P distasonis, and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared with those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with a reduced risk of LGI-GVHD. All these findings show the importance of the carbohydrate-degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.},
}

Humans
*Graft vs Host Disease/etiology/epidemiology/microbiology
Hematopoietic Stem Cell Transplantation/adverse effects
*Gastrointestinal Microbiome
*Feces/microbiology
Female
Male
Incidence
Middle Aged
*Bacteria/metabolism
Adult
*Carbohydrate Metabolism
Retrospective Studies
*Gastrointestinal Diseases/etiology/epidemiology/microbiology
Metagenomics

@article {pmid41544986,
year = {2026},
author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z},
title = {Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111205},
doi = {10.1016/j.ygeno.2026.111205},
pmid = {41544986},
issn = {1089-8646},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Fermentation ; Female ; Cattle/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; Pregnancy ; *Microbiota ; Metagenome ; },
abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.},
}

Animals
*Rumen/microbiology/metabolism
*Fermentation
Female
Cattle/microbiology/metabolism
*Metabolome
*Gastrointestinal Microbiome
Pregnancy
*Microbiota
Metagenome

@article {pmid41539415,
year = {2026},
author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL},
title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111204},
doi = {10.1016/j.ygeno.2026.111204},
pmid = {41539415},
issn = {1089-8646},
mesh = {*Fruit/metabolism/microbiology ; *Fermentation ; *Vegetables/metabolism/microbiology ; *Microbiota ; *Fertilizers ; Lactuca/growth & development ; Germination ; Sugars/metabolism ; },
abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.},
}

*Fruit/metabolism/microbiology
*Fermentation
*Vegetables/metabolism/microbiology
*Microbiota
*Fertilizers
Lactuca/growth & development
Germination
Sugars/metabolism

@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {33},
number = {4},
pages = {3203-3213},
pmid = {41524878},
issn = {1534-4681},
mesh = {Humans ; *Esophageal Neoplasms/therapy/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality ; Prognosis ; Survival Rate ; *Esophagectomy/mortality ; Aged ; Neoadjuvant Therapy/mortality ; Follow-Up Studies ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Bacteria/genetics/isolation & purification ; },
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.

PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.

RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.

CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}

Humans
*Esophageal Neoplasms/therapy/microbiology/pathology
Male
Female
*Microbiota
Middle Aged
*Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality
Prognosis
Survival Rate
*Esophagectomy/mortality
Aged
Neoadjuvant Therapy/mortality
Follow-Up Studies
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Bacteria/genetics/isolation & purification

@article {pmid41519314,
year = {2026},
author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K},
title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111198},
doi = {10.1016/j.ygeno.2026.111198},
pmid = {41519314},
issn = {1089-8646},
mesh = {Animals ; *Hyperlipidemias/metabolism/genetics ; *Circadian Rhythm/genetics ; *Liver/metabolism ; Mice ; *Gastrointestinal Microbiome ; Male ; Diet, High-Fat/adverse effects ; Lipid Metabolism/genetics ; Transcriptome ; Mice, Inbred C57BL ; Multiomics ; },
abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.

RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.

DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.

CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.},
}

Animals
*Hyperlipidemias/metabolism/genetics
*Circadian Rhythm/genetics
*Liver/metabolism
Mice
*Gastrointestinal Microbiome
Male
Diet, High-Fat/adverse effects
Lipid Metabolism/genetics
Transcriptome
Mice, Inbred C57BL
Multiomics

@article {pmid41811526,
year = {2026},
author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S},
title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.},
journal = {Cancer causes & control : CCC},
volume = {37},
number = {4},
pages = {},
pmid = {41811526},
issn = {1573-7225},
support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Adult ; Metagenomics/methods ; Risk Factors ; Finland/epidemiology ; Metagenome ; Diet ; },
abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.

METHODS: Our data included 1,228 adults aged 25-64 years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.

RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p < 0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (β 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (< 0.0001).

CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology/etiology
Middle Aged
*Life Style
*Gastrointestinal Microbiome/genetics
Female
Male
Adult
Metagenomics/methods
Risk Factors
Finland/epidemiology
Metagenome
Diet

@article {pmid41810553,
year = {2026},
author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ},
title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70264},
pmid = {41810553},
issn = {2045-8827},
support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovación/ ; },
mesh = {Humans ; *Glycoside Hydrolases/metabolism/genetics ; *Polysaccharides/metabolism ; Infant ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; Substrate Specificity ; Infant, Newborn ; },
abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.},
}

Humans
*Glycoside Hydrolases/metabolism/genetics
*Polysaccharides/metabolism
Infant
*Gastrointestinal Microbiome
*Metagenome
Feces/microbiology
Substrate Specificity
Infant, Newborn

@article {pmid41809656,
year = {2026},
author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M},
title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10894},
pmid = {41809656},
issn = {1535-3699},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology ; *Probiotics/administration & dosage/therapeutic use ; *Bifidobacterium bifidum/physiology ; Male ; Female ; Adult ; Middle Aged ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Obesity/microbiology
*Probiotics/administration & dosage/therapeutic use
*Bifidobacterium bifidum/physiology
Male
Female
Adult
Middle Aged
Dysbiosis/microbiology
Feces/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid41808525,
year = {2026},
author = {Jiménez, DJ and Rosado, AS},
title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70272},
pmid = {41808525},
issn = {1462-2920},
support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Microbiota ; *Polyethylene Terephthalates/metabolism ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biocatalysis ; *Bacteria/enzymology/genetics ; },
abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.},
}

*Microbiota
*Polyethylene Terephthalates/metabolism
*Hydrolases/metabolism/genetics
Metagenomics
Biocatalysis
*Bacteria/enzymology/genetics

@article {pmid41806446,
year = {2026},
author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C},
title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.},
journal = {The Science of the total environment},
volume = {1025},
number = {},
pages = {181655},
doi = {10.1016/j.scitotenv.2026.181655},
pmid = {41806446},
issn = {1879-1026},
abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.},
}

@article {pmid41759320,
year = {2026},
author = {Yin, Y and Wu, H and French, CE and Lu, Z},
title = {Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies.},
journal = {Water research},
volume = {296},
number = {},
pages = {125614},
doi = {10.1016/j.watres.2026.125614},
pmid = {41759320},
issn = {1879-2448},
mesh = {*Triclosan/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics ; },
abstract = {The widespread presence of emerging contaminants, such as triclosan (TCS), in environmental systems raises significant concerns regarding their ecological risks, particularly the propagation of antibiotic resistance genes (ARGs). In this study, sequencing batch reactors (SBRs) were exposed to a TCS concentration gradient to simulate the accumulation of TCS in activated sludge and to elucidate its effects on microbial community structure, ARG dissemination, and horizontal gene transfer (HGT). Using a multi-omics approach that integrated 16S rRNA amplicon sequencing, short- and long-read metagenomics, and genome-scale metabolic modeling, we demonstrated that increasing TCS concentrations progressively reduced microbial diversity and stability. At lower TCS concentrations (0-1.0 mg/L), ARG-carrying bacteria were enriched, whereas at higher concentrations (10 mg/L), TCS eliminated ARG-carrying bacteria and selected for strains rich in mobile genetic element (MGE). Notably, HGT led to genome expansion of Acidomonas methanolica (from 3.75 Mb to 7.13 Mb), disrupting the microbial interaction networks within the community. Additionally, the introduction of a triclosan-degrading hydrogel-magnetic biochar-engineered strain composite mitigated the destabilizing effects of TCS stress on the microbial community, enhanced its resilience, and facilitated TCS degradation, thus reducing associated environmental risks. Our findings highlight how gradient TCS exposure reshapes microbial communities, promotes the dominance of MGE-enriched taxa, and has profound implications for the ecological and evolutionary dynamics of microbial communities in aquatic ecosystems. This study provides novel insights into the role of emerging contaminants in the propagation of resistance and microbial adaptation.},
}

*Triclosan/pharmacology
*Sewage/microbiology
*Drug Resistance, Microbial/genetics
*Microbiota/drug effects
RNA, Ribosomal, 16S/genetics
Gene Transfer, Horizontal
Bacteria/genetics

@article {pmid41747725,
year = {2026},
author = {Chen, K and Liu, Y and Rong, J and Dai, N and Xu, C and Li, H and Zhong, L and Wang, B and Ji, Z and Xie, S and Xu, Y and Yang, F and Wang, J and Li, D and Gu, Y and Zhou, X and Li, Y and Chen, M and Chen, Y and Li, W and Tang, Z and Cai, J and Xu, J and Xia, S and Zhan, Q and Zhou, Z},
title = {Strain-level genetic heterogeneity and colonization dynamics drive microbiome therapeutic efficacy.},
journal = {Cell host & microbe},
volume = {34},
number = {3},
pages = {393-405.e5},
doi = {10.1016/j.chom.2026.02.002},
pmid = {41747725},
issn = {1934-6069},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Genetic Heterogeneity ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology ; *Lung Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Metagenome ; Female ; Bacteria/classification/genetics ; Male ; Phylogeny ; Treatment Outcome ; },
abstract = {Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise, yet its efficacy in non-small-cell lung cancer (NSCLC) remains unclear. We demonstrate that FMT improves anti-PD-1 efficacy and progression-free survival in a single-arm trial of advanced PD-L1-negative NSCLC. Analyzing over 2,000 metagenomes from diverse disease cohorts and healthy controls via a high-resolution strain-tracking framework, we reveal that phylogenetically distinct strains within identical species exert opposing therapeutic effects, resolving prior inconsistencies. We identify conserved ecological principles where engraftment relies on species-intrinsic metabolic and immune evasion traits. Crucially, successful colonization by specific beneficial strain variants correlates with positive clinical outcomes. Finally, we identify 38 priority species with robust engraftment potential and significant heterogeneity as candidates for precision therapeutics. These findings establish a strain-function-efficacy paradigm, elucidating the mechanistic basis of variable outcomes and guiding next-generation microbiome drug development.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Genetic Heterogeneity
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology
*Lung Neoplasms/therapy/microbiology
*Gastrointestinal Microbiome/genetics
*Microbiota/genetics
Metagenome
Female
Bacteria/classification/genetics
Male
Phylogeny
Treatment Outcome

@article {pmid41720032,
year = {2026},
author = {Kong, X and He, Y and Guo, J and Chen, Y and An, D},
title = {Chain-length-associated response patterns of chlorinated paraffins on activated sludge systems driven by microbial community response.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141542},
doi = {10.1016/j.jhazmat.2026.141542},
pmid = {41720032},
issn = {1873-3336},
mesh = {*Sewage/microbiology/chemistry ; *Water Pollutants, Chemical/chemistry/toxicity ; *Microbiota/drug effects ; *Paraffin/chemistry/toxicity ; Bioreactors/microbiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bacteria/genetics/drug effects/metabolism ; *Hydrocarbons, Chlorinated/chemistry/toxicity ; },
abstract = {Chlorinated paraffins (CPs) are emerging contaminants detected in wastewater treatment plants, yet their impacts on activated sludge systems remain poorly understood. In this study, parallel sequencing batch reactors were employed to comprehensively evaluate the effects of short-chain (SCCP), medium-chain (MCCP), and long-chain (LCCP) CPs on pollutant removal performance, sludge properties, and microbial ecological responses. Under the tested nominal loading, the C24-LCCP standard led to a clear reduction in nitrogen removal efficiency, whereas MCCP and SCCP maintained stable or even enhanced phosphorus removal performance. CP exposure generally increased oxidative stress and cytotoxicity, while SCCP and MCCP further stimulated extracellular polymeric substances secretion, consistent with an enhanced floc/cell-interface protective phenotype. Metagenomic analysis revealed that SCCP and MCCP enriched genera (Acinetobacter, Dechloromonas, Zoogloea) associated with phosphorus removal and increased the abundance of key nitrogen transformation genes, whereas the C24-LCCP standard exhibited comparatively weaker shifts in functional gene profiles. Metatranscriptomic profiling indicated treatment-associated differences in transcriptional responses under the tested nominal loading, with SCCP showing the largest DEG set (>30,000 genes) in this dataset. Integrated metagenomic and metatranscriptomic analyses revealed a coordinated stress‑response program under SCCP, characterized by activation of efflux pumps, DNA repair, redox regulation, environmental stress responses, and biofilm-associated functions, together with elevated energy metabolism and ABC transporter signals. These molecular and community-level patterns aligned with the observed variations in treatment performance and sludge properties, providing convergent evidence for a chain-length-associated response framework. These findings provide comparative molecular and phenotypic evidence that may inform future risk assessment and hypothesis-driven mitigation studies on CP impacts in biological wastewater treatment systems.},
}

*Sewage/microbiology/chemistry
*Water Pollutants, Chemical/chemistry/toxicity
*Microbiota/drug effects
*Paraffin/chemistry/toxicity
Bioreactors/microbiology
Nitrogen/metabolism
Phosphorus/metabolism
Bacteria/genetics/drug effects/metabolism
*Hydrocarbons, Chlorinated/chemistry/toxicity

@article {pmid41707391,
year = {2026},
author = {Werid, GM and Hemmatzadeh, F and Batterham, T and Miller, D and Edwards, R and Trott, DJ and Petrovski, K},
title = {Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110926},
doi = {10.1016/j.vetmic.2026.110926},
pmid = {41707391},
issn = {1873-2542},
mesh = {Animals ; Cattle ; *Lung/microbiology/virology ; *Cattle Diseases/microbiology/virology ; Metagenomics ; *Dysbiosis/veterinary/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Virome ; Microbiota ; Australia ; *Bovine Respiratory Disease Complex/microbiology/virology ; Bacteriophages/genetics ; },
abstract = {Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.},
}

Animals
Cattle
*Lung/microbiology/virology
*Cattle Diseases/microbiology/virology
Metagenomics
*Dysbiosis/veterinary/microbiology/virology
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Virome
Microbiota
Australia
*Bovine Respiratory Disease Complex/microbiology/virology
Bacteriophages/genetics

@article {pmid41697021,
year = {2025},
author = {Han, B and Wen, H and Li, Y and Wang, Y and Lv, X and Kang, M and Huang, W and Lan, Y and Tong, S and Zhang, M and Chen, D and Zhu, C and Jiang, Y and Tang, D},
title = {Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR-NF-κB axis.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag028},
pmid = {41697021},
issn = {1751-7370},
support = {LHGJ20250299//Henan Provincial Medical Science and Technology Research Joint Venture Project/ ; 2025M772035//China Postdoctoral Science Foundation/ ; 82460108//National Natural Science Foundation of China/ ; 2023GXNSFAA026135//Guangxi Natural Science Foundation/ ; 2025GXNSFDA069030//Key Project of Guangxi Natural Science Foundation/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Lithocholic Acid/metabolism ; Mice ; *Receptors, G-Protein-Coupled/metabolism/genetics ; NF-kappa B/metabolism/genetics ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Macrophages/metabolism/drug effects ; Humans ; Disease Models, Animal ; *Crohn Disease/drug therapy ; Fecal Microbiota Transplantation ; Colitis/drug therapy/chemically induced ; *Gastrointestinal Agents/therapeutic use/pharmacology ; Signal Transduction ; Metabolomics ; },
abstract = {Crohn's disease (CD) is a complex chronic transmural inflammatory bowel disease. Although vedolizumab (VDZ) markedly improves clinical outcomes in CD, treatment non-response remains a significant limitation, constraining its broader utility. Elucidating the mechanisms underlying VDZ responsiveness is thus critically needed. In this research, we employed a humanized mouse model of 2,4,6-trinitrobenzene sulfonic acid-induced colitis to investigate VDZ treatment response in CD. Our findings indicate that VDZ significantly alleviated disease phenotypes in a portion of CD mice. Integrated metagenomic and metabolomic profiling identified baseline gut microbiota-derived secondary bile acids as potential predictors of VDZ efficacy. Subsequent fecal microbiota transplantation from clinical donors into pseudo-germ-free mice confirmed that gut microbial composition critically influences VDZ responsiveness. Targeted metabolomics further pinpointed lithocholic acid (LCA) as a key microbially derived metabolite correlated with therapeutic remission. Single-cell RNA sequencing also revealed that intestinal macrophages serve as pivotal mediators of LCA-driven modulation of treatment outcomes. Furthermore, transcriptomic analyses demonstrated that LCA polarizes macrophages toward an M2-resolutive phenotype via concurrent engagement of the TGR5/FXR and their downstream nuclear factor kappa-B (NF-κB) pathways. Ultimately, using a conditioned medium co-culture system, we established that the regulatory effects of pro-resolutive macrophage niche on treatment response in a manner dependent on the TGR5/FXR-NF-κB axis. Taken together, our study elucidates a microbiota-immune circuit in which gut microbial metabolite LCA augments VDZ responsiveness in CD by reprogramming macrophages toward a pro-resolutive phenotype via the TGR5/FXR-NF-κB signaling network. These insights provide a mechanistic foundation for biomarker development and personalized therapeutic strategies in inflammatory bowel disease.},
}

*Gastrointestinal Microbiome
Animals
*Lithocholic Acid/metabolism
Mice
*Receptors, G-Protein-Coupled/metabolism/genetics
NF-kappa B/metabolism/genetics
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
*Macrophages/metabolism/drug effects
Humans
Disease Models, Animal
*Crohn Disease/drug therapy
Fecal Microbiota Transplantation
Colitis/drug therapy/chemically induced
*Gastrointestinal Agents/therapeutic use/pharmacology
Signal Transduction
Metabolomics

@article {pmid41666920,
year = {2026},
author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A},
title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.},
journal = {Cell host & microbe},
volume = {34},
number = {3},
pages = {379-392.e5},
doi = {10.1016/j.chom.2026.01.013},
pmid = {41666920},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Bacteria/classification/genetics/isolation & purification ; Vitamin B 12/biosynthesis ; Metagenomics ; },
abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenome
*Bacteria/classification/genetics/isolation & purification
Vitamin B 12/biosynthesis
Metagenomics

@article {pmid41633028,
year = {2026},
author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y},
title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.},
journal = {Research in veterinary science},
volume = {203},
number = {},
pages = {106092},
doi = {10.1016/j.rvsc.2026.106092},
pmid = {41633028},
issn = {1532-2661},
mesh = {Animals ; Cattle/growth & development/microbiology/metabolism ; *Rumen/microbiology/metabolism ; Male ; Metabolomics ; *Gastrointestinal Microbiome ; Metagenomics ; *Metabolome ; *Microbiota ; Multiomics ; },
abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.},
}

Animals
Cattle/growth & development/microbiology/metabolism
*Rumen/microbiology/metabolism
Male
Metabolomics
*Gastrointestinal Microbiome
Metagenomics
*Metabolome
*Microbiota
Multiomics

@article {pmid40757465,
year = {2026},
author = {Andréasson, K and Young, A and Joshi, S and Labus, JS and Low, AHL and Smith, V and McMahan, Z and Proudman, S and Valenzuela, A and Hunter, P and Kim, GH and Bozovic, G and Goldin, J and Aja, E and Jacobs, JP and Volkmann, ER},
title = {International Investigation of the Gut-Lung Axis in Systemic Sclerosis-Interstitial Lung Disease.},
journal = {Arthritis care & research},
volume = {78},
number = {3},
pages = {352-361},
doi = {10.1002/acr.25623},
pmid = {40757465},
issn = {2151-4658},
support = {K23 HL150237/HL/NHLBI NIH HHS/United States ; //Ulla och Roland Gustafssons Donationsfond, Alfred Österlunds Stiftelse and Anna-Greta Crafoords Stiftelse/ ; //Boehringer Ingelheim/ ; //Anonymous Patient Donation/ ; K23 HL150237/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications/diagnosis ; *Lung Diseases, Interstitial/microbiology/diagnostic imaging/etiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; *Lung/diagnostic imaging/microbiology ; Feces/microbiology ; Dysbiosis ; *Bacteria/genetics/classification ; Adult ; Severity of Illness Index ; },
abstract = {OBJECTIVE: Mounting evidence supports an association between the intestinal microbiota and diverse pulmonary pathologies (ie, gut-lung axis). Although intestinal dysbiosis is a feature of systemic sclerosis (SSc), no prior studies have investigated the relationship between intestinal microbiota and SSc-associated interstitial lung disease (ILD) in a multinational cohort. This study aimed to characterize the intestinal microbiota of SSc-ILD and determine whether specific bacterial species and functional pathways are associated with ILD severity.

METHODS: Patients with SSc with and without ILD from seven SSc Centers across five continents provided a stool sample. Shotgun metagenomic sequencing was performed using the Illumina NovaSeq 6000 to characterize microbial composition at the species level. Quantitative image analysis of high-resolution computed tomography scans of the chest was used to measure radiologic extent of ILD (QILD). Multivariate sparse partial least squares analyses were employed to identify a species signature of ILD and to determine whether specific species and functional pathways are associated with QILD.

RESULTS: Among 285 participants (mean disease duration of 9.8 years), 62.5% had ILD. In a multivariate analysis of all participants, patients with ILD had a unique microbial signature compared to those without ILD characterized by increased abundance of candidate pathobiont species. In a subgroup of participants with SSc-ILD (n = 103), specific bacterial species and functional pathways were associated with QILD.

CONCLUSION: This multicenter study demonstrates that distinct intestinal bacterial species are linked to the presence and radiologic extent of ILD in SSc. These species and/or their metabolic products may influence ILD pathogenesis and represent novel treatment targets.},
}

Humans
*Scleroderma, Systemic/microbiology/complications/diagnosis
*Lung Diseases, Interstitial/microbiology/diagnostic imaging/etiology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Aged
*Lung/diagnostic imaging/microbiology
Feces/microbiology
Dysbiosis
*Bacteria/genetics/classification
Adult
Severity of Illness Index

@article {pmid37329328,
year = {2023},
author = {Lledós, M and Prats-Sánchez, L and Llucià-Carol, L and Cárcel-Márquez, J and Muiño, E and Cullell, N and Gallego-Fabrega, C and Martín-Campos, JM and Aguilera-Simón, A and Guasch-Jiménez, M and Guisado-Alonso, D and Ramos-Pachón, A and Martínez-Domeño, A and Izquierdo, A and Marín, R and Camps-Renom, P and Martí-Fàbregas, J and Fernández-Cadenas, I},
title = {Ischaemic stroke patients present sex differences in gut microbiota.},
journal = {European journal of neurology},
volume = {30},
number = {11},
pages = {3497-3506},
doi = {10.1111/ene.15931},
pmid = {37329328},
issn = {1468-1331},
support = {//Centres de Recerca de Catalunya/ ; //ERA-NET NEURON/ ; //European Regional Development Fund/ ; //Instituto de Salud Carlos III/ ; //NextGeneration EU/ ; //RICORS-ICTUS/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Ischemic Stroke/microbiology/genetics ; Middle Aged ; Aged ; *Sex Characteristics ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; },
abstract = {BACKGROUND: Gut microbiota plays a role in the pathophysiology of ischaemic stroke (IS) through the bidirectional gut-brain axis. Nevertheless, little is known about sex-specific microbiota signatures in IS occurrence.

METHODS: A total of 89 IS patients and 12 healthy controls were enrolled. We studied the taxonomic differences of the gut microbiota between men and women with IS by shotgun metagenomic sequencing. To evaluate the causal effect of several bacteria on IS risk, we performed a two-sample Mendelian randomisation (MR) with inverse-variance weighting (IVW) using genome-wide association analysis (GWAS) summary statistics from two cohorts of 5959 subjects with genetic and microbiota data and 1,296,908 subjects with genetic and IS data, respectively.

RESULTS: α-Diversity analysis measured using Observed Species (p = 0.017), Chao1 (p = 0.009) and Abundance-based Coverage Estimator (p = 0.012) indexes revealed that IS men have a higher species richness compared with IS women. Moreover, we found sex-differences in IS patients in relation to the phylum Fusobacteria, class Fusobacteriia, order Fusobacteriales and family Fusobacteriaceae (all Bonferroni-corrected p < 0.001). MR confirmed that increased Fusobacteriaceae levels in the gut are causally associated with an increased risk of IS (IVW p = 0.02, β = 0.32).

CONCLUSIONS: Our study is the first to indicate that there are gut microbiome differences between men and women with IS, identifying high levels of Fusobacteriaceae in women as a specific risk factor for IS. Incorporating sex stratification analysis is important in the design, analysis and interpretation of studies on stroke and the gut microbiota.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
*Ischemic Stroke/microbiology/genetics
Middle Aged
Aged
*Sex Characteristics
Genome-Wide Association Study
Mendelian Randomization Analysis

@article {pmid41805117,
year = {2026},
author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE},
title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15254},
pmid = {41805117},
issn = {1520-5118},
abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.},
}

@article {pmid41804664,
year = {2026},
author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B},
title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70278},
doi = {10.1111/1462-2920.70278},
pmid = {41804664},
issn = {1462-2920},
support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; },
mesh = {Biodegradation, Environmental ; *Composting ; *Microplastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Polymers/metabolism/chemistry ; *Soil Microbiology ; Microbiota ; Polyesters/metabolism ; *Soil Pollutants/metabolism ; Soil/chemistry ; },
abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.},
}

Biodegradation, Environmental
*Composting
*Microplastics/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
*Polymers/metabolism/chemistry
*Soil Microbiology
Microbiota
Polyesters/metabolism
*Soil Pollutants/metabolism
Soil/chemistry

@article {pmid41738431,
year = {2026},
author = {Khade, K and Dadachanji, R and Bhonde, G and Patil, A and Bhor, VM and Mukherjee, S},
title = {Gut microbiota dysbiosis in Indian women with PCOS may be linked to metabolic and hormonal dysregulation.},
journal = {Future microbiology},
volume = {21},
number = {2},
pages = {153-165},
doi = {10.1080/17460913.2026.2634572},
pmid = {41738431},
issn = {1746-0921},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Polycystic Ovary Syndrome/microbiology/metabolism ; *Dysbiosis/microbiology/metabolism ; Adult ; India ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Fatty Acids, Volatile/metabolism/analysis ; Feces/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Protein Precursors ; Hyperandrogenism/microbiology/metabolism ; Sex Hormone-Binding Globulin/metabolism ; Haptoglobins ; },
abstract = {AIM: Polycystic ovary syndrome (PCOS) is a common gynecological and cardiometabolic disorder in reproductive-aged women. Recently gut microbiota alterations have been identified as key contributors to PCOS pathophysiology, but it remains understudied in Indian population.

METHODS: 16S rRNA gene amplicon sequencing using Illumina-MiSeq platform was conducted in 57 PCOS and 30 control women. Diversity indices were assessed and significantly altered taxa were identified by differential abundance tests (Wilcoxon-rank-sum test, ANCOMBC2 and LEfSe) in total and hyperandrogenism-based PCOS subgroups. We quantified levels of short-chain fatty acids (SCFAs) and gut barrier integrity marker, zonulin and LPS by HPLC and ELISA respectively.

RESULTS: Our study showed significantly altered beta diversity between PCOS and control groups, driven by hyperandrogenism. PCOS women demonstrate enrichment of Ligilactobacillus species, not previously reported to our knowledge, along with Collinsella species and markedly reduced SCFA-producing taxa, Oscillospiraceae. Additionally, levels of zonulin and fecal butyric acid, a potent SCFA, were significantly altered in PCOS women. Significantly altered taxa correlated with gonadotropin and SHBG levels and were involved in important metabolic pathways in total and PCOS subgroups.

CONCLUSION: Our study offers new insights into the mapping of gut microbiota in PCOS women from western India and implicates hyperandrogenism in driving dysbiosis.},
}

Humans
Female
*Gastrointestinal Microbiome/genetics
*Polycystic Ovary Syndrome/microbiology/metabolism
*Dysbiosis/microbiology/metabolism
Adult
India
RNA, Ribosomal, 16S/genetics
Young Adult
Fatty Acids, Volatile/metabolism/analysis
Feces/microbiology/chemistry
*Bacteria/classification/genetics/isolation & purification/metabolism
Protein Precursors
Hyperandrogenism/microbiology/metabolism
Sex Hormone-Binding Globulin/metabolism
Haptoglobins

@article {pmid41713270,
year = {2026},
author = {Jiao, X and Ji, W and Zhang, X and Zhang, S and Dolfing, J and Yang, K and Xie, B and Zhang, Y and Feng, J and Wu, D},
title = {Microcystins 'steer' antibiotic resistome dynamics by synergetic metabolism and horizontal gene transfer in a megacity's water supply catchment microbiota.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141525},
doi = {10.1016/j.jhazmat.2026.141525},
pmid = {41713270},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal ; *Microcystins/metabolism ; *Microbiota ; China ; *Microcystis/genetics/metabolism/growth & development ; *Drug Resistance, Microbial/genetics ; Water Supply ; Water Microbiology ; Drinking Water/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.},
}

*Gene Transfer, Horizontal
*Microcystins/metabolism
*Microbiota
China
*Microcystis/genetics/metabolism/growth & development
*Drug Resistance, Microbial/genetics
Water Supply
Water Microbiology
Drinking Water/microbiology
Anti-Bacterial Agents/pharmacology
Genes, Bacterial

@article {pmid41711070,
year = {2025},
author = {Beauvais, M and Schatt, P and Soulié, T and Lambert, S and Montiel, L and Gaudin, M and Chaffron, S and Logares, R and Bouget, FY and Galand, PE},
title = {Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag029},
pmid = {41711070},
issn = {1751-7370},
support = {ANR-24-CE02-7681//French Agence Nationale de la Recherche/ ; },
abstract = {Marine microbial communities are fundamental to nutrient and biogeochemical cycling, with intricate networks of metabolic interdependencies influencing their structure and dynamics. Among these, vitamins B1 (thiamin) and B12 (cobalamin) play crucial roles as enzymatic cofactors in central metabolic pathways. Despite their importance, the temporal dynamics of vitamin production, bioavailability, and associated microbial interactions remain poorly understood. Using a 7-year monthly metagenomic time series from the NW Mediterranean Sea (SOLA station), we found that vitamin B1/B12 auxotrophs (need for an exogenous vitamin source) were present throughout the year. Among B1 auxotrophs, those requiring the thiamin precursor pyrimidine were the most prevalent, with peak abundances in summer. Distinct metagenome-assembled genome co-abundance patterns between B1 and B12 producers/auxotrophs across seasons suggested mutualistic relationships. Double B1/B12 vitamin complementarities were more common in summer, and single vitamin complementarity was dominant in winter. As previously shown for vitamin B12, which is limiting during winter, bioassays revealed variable availability of vitamin B1 in winter seawater despite the abundance of its producers, suggesting potential transfer of vitamin B1 among microorganisms. Finally, microcosm experiments showed that B1 and B12 amendments significantly influenced the composition of microbial communities, with temporal variations in their impact. In some cases, B12 and B1 amendments favored both vitamin auxotrophs and producers, highlighting complex interdependencies between B1 and B12 producers and consumers. Our findings highlight the complexity of B vitamin-mediated metabolic interactions that shape microbial community dynamics and underscore the need for long-term, high-resolution studies to better understand vitamin-driven ecological processes in marine systems.},
}

@article {pmid41707423,
year = {2026},
author = {Francés, Á and López, M and González-Raurich, M and Cobo-Díaz, JF and Prieto, M and Allende, A and Gil, MI and Truchado, P and Alvarez-Ordóñez, A and Oliveira, M},
title = {Characterization of microbial diversity, chemical hazards and antimicrobial resistant bacteria in wash water from a fresh-cut vegetable processing plant.},
journal = {International journal of food microbiology},
volume = {452},
number = {},
pages = {111667},
doi = {10.1016/j.ijfoodmicro.2026.111667},
pmid = {41707423},
issn = {1879-3460},
mesh = {*Bacteria/drug effects/genetics/isolation & purification/classification ; *Vegetables/microbiology ; *Drug Resistance, Bacterial ; *Water Microbiology ; Food Handling ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Pesticides/analysis ; Microbial Sensitivity Tests ; },
abstract = {This study investigated the quality of process wash water (PWW) in an industrial fresh-cut produce facility. Traditional microbiological and physico-chemical parameters, such as aerobic mesophilic counts, coliforms, molds and yeasts, pH, free chlorine, oxidation-reduction potential, and organic matter indicators, were monitored to contextualize water quality dynamics across the workday. Additionally, untargeted analyses were performed to characterize the microbiome and resistome and identify chemical hazards in PWW, highlighting the occurrence of antimicrobial-resistant bacteria and the presence of some pesticides at low levels, including chlorantraniliprole, cyprodinil, fludioxonil, and propyzamide, in a real-world processing environment. Antimicrobial susceptibility tests and whole genome sequencing of twelve coliform isolates revealed multidrug-resistant strains, including Enterobacter mori, Enterobacter ludwigii, and Klebsiella oxytoca, carrying resistance genes such as oqxB, fosA, and blaACT-12, as well as the plasmid-borne blaOXY-2-2. Metagenome analyses revealed a microbial community dominated by the genus Pseudomonas, together with high abundance of Rheinheimera mangrovi and Pantoea agglomerans. Moreover, resistome analysis disclosed that 83% of detected antimicrobial resistance genes were associated with beta-lactam resistance. Additionally, the efficacy of chlorine against one K. oxytoca isolate obtained from PWW using a dynamic system simulating a produce washing operation confirmed that maintaining pH at 6.5 and stable free chlorine levels of 6 mg/L was sufficient for complete inactivation. These findings demonstrate the importance of implementing proper wash water management practices in fresh produce processing, including preventing excessive organic matter accumulation through adequate water replenishment and maintaining chemical parameters within the validated operational range, supported by systematic verification and monitoring.},
}

*Bacteria/drug effects/genetics/isolation & purification/classification
*Vegetables/microbiology
*Drug Resistance, Bacterial
*Water Microbiology
Food Handling
Anti-Bacterial Agents/pharmacology
Microbiota
Pesticides/analysis
Microbial Sensitivity Tests

@article {pmid41687578,
year = {2026},
author = {Zhou, Q and Liang, H and Huang, J and Klümper, U and Fang, P and Yu, Z and Wang, Y and Berendonk, TU and Lin, L and Li, X and Li, B},
title = {Impact of sulfonamides on microbial community and antibiotic resistome profiles in anaerobic digestion of swine wastewater.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141426},
doi = {10.1016/j.jhazmat.2026.141426},
pmid = {41687578},
issn = {1873-3336},
mesh = {Animals ; *Sulfonamides/pharmacology ; Swine ; *Wastewater/microbiology ; Anaerobiosis ; *Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; },
abstract = {Residual antibiotics in swine wastewater promote the proliferation of the antibiotic resistome, posing significant threats to environmental and human health. Although anaerobic digestion (AD) is widely applied for treating swine wastewater, the effects of antibiotics on the microbial community and resistome during AD remain unclear. This study employed amplicon and metagenomic sequencing, combined with long- and short-read hybrid assembly, to comprehensively investigate the impact of sulfonamides on the microbiome and resistome during AD. Enterococcus, a genus capable of utilizing exogenous folate, was identified as the dominant genus under sulfonamide stress. A total of 24 antibiotic resistance gene (ARG) types and 440 subtypes were identified. Sulfonamide stress selectively enriched sulfonamide resistance genes, with no notable co-selective effects on ARGs for other antibiotic classes. Short-term exposure significantly enriched sul2 (3.8-fold) and sul3 (4.0-fold), while long-term exposure enriched sul1 (1.6-fold). Sulfonamides especially promoted the proliferation of sulfonamide resistance genes on both mobilizable and non-mobilizable plasmids. The co-occurrence of multiple categories of mobile genetic elements and ARGs on contigs was inferred to play a critical role in driving ARG dissemination. Whereas a strain belonging to Enterococcus_I emerged as the dominant resistant bacterium in the AD system, a particular multidrug-resistance risk was identified for a strain belonging to the Filifactoraceae family. This work provides a new perspective on the impact of antibiotics on microbial community and antibiotic resistome composition and dynamics during the AD treatment process of swine wastewater.},
}

Animals
*Sulfonamides/pharmacology
Swine
*Wastewater/microbiology
Anaerobiosis
*Microbiota/drug effects
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Water Pollutants, Chemical
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects

@article {pmid41687083,
year = {2026},
author = {Olaniyi, K and Moodley, J and Moodley, R and Mackraj, I},
title = {Assessment of human placental microbial signatures in pre-eclampsia using shotgun metagenomics.},
journal = {Canadian journal of physiology and pharmacology},
volume = {104},
number = {},
pages = {1-11},
doi = {10.1139/cjpp-2025-0274},
pmid = {41687083},
issn = {1205-7541},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; *Placenta/microbiology ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/isolation & purification/classification ; *Microbiota ; },
abstract = {This study evaluated the presence of bacterial species in the placenta of women with pre-eclampsia and compared with that of normotensive women. One hundred and twenty participants, comprising 60 pre-eclamptic (30 early- and late-onset, respectively) and 60 age-matched normotensive women (30 early and late-gestation normotensive, respectively) were recruited. After informed consent was obtained, the placenta were obtained through caesarean section with sterile and standardized clinical procedures. DNA was extracted from each tissue, and the samples were pooled into six libraries and sequenced on Illumina NextSeq500 using a shotgun metagenomic approach. Bioinformatics was used to analyse the reads with the implementation of Kraken2/MetaPhlAn classification methods and complemented by multi-layered contamination assessment strategy that included frequency-based decontam filtering. Most reads were classified as belonging to the phyla Cutibacterium acnes, Staphylococcus epidermidis, and various Bradyrhizobium species. PE samples showed notable Corynebacterium tuberculostearicum and Pseudomonas species, while Bradyrhizobium and Cutibacterium acnes dominated normotensive samples. Further analysis showed no significant difference between bacterial species of pre-eclamptic and normotensive placental samples. The results show very low levels of bacteria in the placental samples. In addition, a little difference was observed between the bacterial compositions of pre-eclamptic and age-matched normotensive placental tissues, but not statistically significant.},
}

Humans
Female
Pregnancy
*Pre-Eclampsia/microbiology
*Placenta/microbiology
*Metagenomics/methods
Adult
*Bacteria/genetics/isolation & purification/classification
*Microbiota

@article {pmid41642002,
year = {2026},
author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB},
title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.},
journal = {mBio},
volume = {17},
number = {3},
pages = {e0364525},
doi = {10.1128/mbio.03645-25},
pmid = {41642002},
issn = {2150-7511},
support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; K01AI163413//National Institute of Allergy and Infectious Diseases/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; R01NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation/ ; },
mesh = {Female ; *Vagina/microbiology/immunology ; Humans ; *Microbiota/immunology/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Gardnerella/genetics/classification/immunology/isolation & purification ; Algorithms ; Metagenome ; Dysbiosis/microbiology ; Host Microbial Interactions/immunology ; },
abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.},
}

Female
*Vagina/microbiology/immunology
Humans
*Microbiota/immunology/genetics
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
*Gardnerella/genetics/classification/immunology/isolation & purification
Algorithms
Metagenome
Dysbiosis/microbiology
Host Microbial Interactions/immunology

@article {pmid41633137,
year = {2026},
author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R},
title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.},
journal = {Forensic science international. Genetics},
volume = {83},
number = {},
pages = {103435},
doi = {10.1016/j.fsigen.2026.103435},
pmid = {41633137},
issn = {1878-0326},
mesh = {*Lung/microbiology ; Animals ; *Drowning/diagnosis/microbiology ; Humans ; *Microbiota ; Metagenomics ; Mice ; Biomarkers ; Postmortem Changes ; Immersion ; Real-Time Polymerase Chain Reaction ; Male ; Bacteria/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.},
}

*Lung/microbiology
Animals
*Drowning/diagnosis/microbiology
Humans
*Microbiota
Metagenomics
Mice
Biomarkers
Postmortem Changes
Immersion
Real-Time Polymerase Chain Reaction
Male
Bacteria/genetics
Sequence Analysis, DNA
RNA, Ribosomal, 16S/genetics

@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41514203},
issn = {1471-2180},
mesh = {Animals ; Cattle/microbiology/growth & development ; *Gastrointestinal Microbiome ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation & purification ; Male ; RNA, Ribosomal, 16S/genetics ; *Diet/veterinary ; Fermentation ; Metagenomics ; DNA, Bacterial/genetics ; },
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}

Animals
Cattle/microbiology/growth & development
*Gastrointestinal Microbiome
*Animal Feed/analysis
*Bacteria/classification/genetics/isolation & purification
Male
RNA, Ribosomal, 16S/genetics
*Diet/veterinary
Fermentation
Metagenomics
DNA, Bacterial/genetics

@article {pmid41484024,
year = {2026},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {36},
number = {4},
pages = {104487},
doi = {10.1016/j.numecd.2025.104487},
pmid = {41484024},
issn = {1590-3729},
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/blood/diet therapy/microbiology ; Male ; Cross-Sectional Studies ; Female ; Adult ; *Glycemic Control ; *Blood Glucose/metabolism/drug effects ; Glycated Hemoglobin/metabolism ; *Bacteria/genetics/growth & development/classification ; Middle Aged ; Biomarkers/blood ; *Diet, Healthy ; Feces/microbiology ; Young Adult ; *Patient Compliance ; Treatment Outcome ; },
abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.

METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n = 103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1 % vs 7.7 %; p < 0.001), greater time in range (67.0 % vs 59.4 %; p-trend = 0.03), and higher HDL cholesterol (1.62 vs 1.39 mmol/L; p = 0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.

CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

Humans
*Diet, Mediterranean
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 1/diagnosis/blood/diet therapy/microbiology
Male
Cross-Sectional Studies
Female
Adult
*Glycemic Control
*Blood Glucose/metabolism/drug effects
Glycated Hemoglobin/metabolism
*Bacteria/genetics/growth & development/classification
Middle Aged
Biomarkers/blood
*Diet, Healthy
Feces/microbiology
Young Adult
*Patient Compliance
Treatment Outcome

@article {pmid41453848,
year = {2026},
author = {Li, XL and Li, ZQ},
title = {Gut microbiota of economically important termites: functional convergence, harmfulness and precision control.},
journal = {Pest management science},
volume = {82},
number = {4},
pages = {2808-2824},
doi = {10.1002/ps.70490},
pmid = {41453848},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Isoptera/microbiology ; *Gastrointestinal Microbiome ; *Insect Control/methods ; },
abstract = {As typical social insects and key decomposers in ecosystems, termites, like other insects, harbor a complex array of microbial communities with diverse functions in their gut. These microorganisms are not only closely related to key survival aspects of termites, including nutritional acquisition, metabolic adaptation and colony resilience, but also play crucial roles in their ecological adaptability. This demonstrates that termite survival strategies are highly dependent on the synergistic interactions within their gut microbiota. Notably, some termites, such as Coptotermes formosanus, exhibit both decomposition ability and damaging capacity. Whether their gut microbiota is closely related to their destructive potential has become one of the core issues of concern to researchers. Moreover, with the rapid development of metagenomics and bioinformatics technologies in recent years, an increasing number of termite gut microbiota functions have been predicted and validated, making it possible to analyze their destructive capacity from a microbial perspective. Therefore, based on a systematic synthesis of the functional commonalities and mechanistic roles of gut microbiota in economically significant termite species, this review further highlights evidence linking microbial functions with termite damaging capacity and discusses microbiota-based strategies for precision control of pest termites. It aims to provide comprehensive references and a solid theoretical foundation for in-depth research and rational utilization of termite gut microbiota, as well as scientifically grounded and targeted management of destructive termite pests. © 2025 Society of Chemical Industry.},
}

Animals
*Isoptera/microbiology
*Gastrointestinal Microbiome
*Insect Control/methods

@article {pmid37759740,
year = {2023},
author = {Witkowska, AM and Salem, JE},
title = {Pharmacological and Nutritional Modulation of Metabolome and Metagenome in Cardiometabolic Disorders.},
journal = {Biomolecules},
volume = {13},
number = {9},
pages = {},
pmid = {37759740},
issn = {2218-273X},
mesh = {Humans ; *Metabolome/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Cardiovascular Diseases/metabolism/microbiology/drug therapy ; *Metagenome/drug effects ; *Metabolic Diseases/metabolism/microbiology ; Animals ; Diet ; Metabolomics ; },
abstract = {Cardiometabolic disorders are major causes of morbidity and mortality worldwide. A growing body of research indicates that the gut microbiota, whether it interacts favorably or not, plays an important role in host metabolism. Elucidating metabolic pathways may be crucial in preventing and treating cardiometabolic diseases, and omics methods are key to studying the interaction between the fecal microbiota and host metabolism. This review summarizes available studies that combine metabolomic and metagenomic approaches to describe the effects of drugs, diet, nutrients, and specific foods on cardiometabolic health and to identify potential targets for future research.},
}

Humans
*Metabolome/drug effects
*Gastrointestinal Microbiome/drug effects
*Cardiovascular Diseases/metabolism/microbiology/drug therapy
*Metagenome/drug effects
*Metabolic Diseases/metabolism/microbiology
Animals
Diet
Metabolomics

@article {pmid37748344,
year = {2023},
author = {Yang, Y and Deng, Y and Liu, L and Yin, X and Xu, X and Wang, D and Zhang, T},
title = {Establishing reference material for the quest towards standardization in environmental microbial metagenomic studies.},
journal = {Water research},
volume = {245},
number = {},
pages = {120641},
doi = {10.1016/j.watres.2023.120641},
pmid = {37748344},
issn = {1879-2448},
mesh = {*Metagenomics/standards/methods ; Reference Standards ; Microbiota ; Sewage/microbiology ; *Environmental Microbiology ; Sequence Analysis, DNA ; },
abstract = {Breakthroughs in DNA-based technologies, especially in metagenomic sequencing, have drastically enhanced researchers' ability to explore environmental microbiome and the associated interplays within. However, as new methodologies are being actively developed for improvements in different aspects, metagenomic workflows become diversified and heterogeneous. Through a single-variable control approach, we quantified the microbial profiling variations arising from 6 common technical variables associated with metagenomic workflows for both simple and complex samples. The incurred variations were constantly the lowest in replicates of DNA isolation and DNA sequencing library construction. Different DNA extraction kits often caused the highest variation among all the tested variables. Additionally, sequencing run batch was an important source of variability for targeted platforms. As such, the development of an environmental reference material for complex environmental samples could be beneficial in benchmarking accrued non-biological variability within and between protocols and insuring reliable and reproducible sequencing outputs immediately upstream of bioinformatic analysis. To develop an environment reference material, sequencing of a well-homogenized environmental sample composed of activated sludge was performed using different pre-analytical assays in replications. In parallel, a certified mock community was processed and sequenced. Assays were ranked based on the reconstruction of the theoretical mock community profile. The reproducibility of the best-performing assay and the microbial profile of the reference material were further ascertained. We propose the adoption of our complex environmental reference material, which could reflect the degree of diversity in environmental microbiome studies, to facilitate accurate, reproducible, and comparable environmental metagenomics-based studies.},
}

*Metagenomics/standards/methods
Reference Standards
Microbiota
Sewage/microbiology
*Environmental Microbiology
Sequence Analysis, DNA

@article {pmid37713802,
year = {2023},
author = {Vieira, TR and de Oliveira, EFC and Cibulski, SP and Silva, NMV and Borba, MR and Oliveira, CJB and Cardoso, M},
title = {Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems.},
journal = {Poultry science},
volume = {102},
number = {11},
pages = {103002},
pmid = {37713802},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Animal Husbandry/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Interspersed Repetitive Sequences ; *Meat/microbiology ; Organic Agriculture ; *Bacteria/drug effects/genetics/isolation & purification ; *Microbiota ; Cross-Sectional Studies ; },
abstract = {The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.},
}

Animals
*Chickens/microbiology
*Animal Husbandry/methods
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Interspersed Repetitive Sequences
*Meat/microbiology
Organic Agriculture
*Bacteria/drug effects/genetics/isolation & purification
*Microbiota
Cross-Sectional Studies

@article {pmid37702790,
year = {2023},
author = {Zou, D and Chen, J and Zhang, C and Kao, SJ and Liu, H and Li, M},
title = {Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {22},
pages = {6897-6909},
pmid = {37702790},
issn = {1432-0614},
support = {32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 2022M722175//Postdoctoral Research Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Innovation Program/ ; },
mesh = {China ; *Estuaries ; *Archaea/classification/genetics/metabolism/physiology ; *Ammonia/metabolism ; Phylogeny ; Oxidation-Reduction ; Salinity ; Metagenomics ; *Adaptation, Physiological ; *Biodiversity ; Ecosystem ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.},
}

China
*Estuaries
*Archaea/classification/genetics/metabolism/physiology
*Ammonia/metabolism
Phylogeny
Oxidation-Reduction
Salinity
Metagenomics
*Adaptation, Physiological
*Biodiversity
Ecosystem

@article {pmid37690533,
year = {2023},
author = {Zhao, X and Zhao, J and Li, D and Yang, H and Chen, C and Qin, M and Wen, Z and He, Z and Xu, L},
title = {Akkermansia muciniphila: A potential target and pending issues for oncotherapy.},
journal = {Pharmacological research},
volume = {196},
number = {},
pages = {106916},
doi = {10.1016/j.phrs.2023.106916},
pmid = {37690533},
issn = {1096-1186},
mesh = {Humans ; Animals ; *Probiotics/therapeutic use ; *Neoplasms/microbiology/therapy/immunology/drug therapy ; *Gastrointestinal Microbiome ; Akkermansia ; },
abstract = {In the wake of the development of metagenomic, metabolomic, and metatranscriptomic approaches, the intricate interactions between the host and various microbes are now being progressively understood. Numerous studies have demonstrated evident changes in gut microbiota during the process of a variety of diseases, such as diabetes, obesity, aging, and cancers. Notably, gut microbiota is viewed as a potential source of novel therapeutics. Currently, Next-generation probiotics (NGPs) are gaining popularity as therapeutic agents that alter the gut microbiota and affect cancer development. Akkermansia muciniphila (A. muciniphila), a representative commensal bacterium, has received substantial attention over the past decade as a promising NGP. The components and metabolites of A. muciniphila can directly or indirectly affect tumorigenesis, in particular through its effects on antitumor immunosurveillance, including the stimulation of pattern recognition receptors (PRRs), which also leads to better outcomes in a variety of situations, including the prevention and curation of cancers. In this article, we systematically summarize the role of A. muciniphila in tumorigenesis (involving gastrointestinal and non-gastrointestinal cancers) and in tumor therapy. In particular, we carefully discuss some critical scientific issues that need to be solved for the future using A. muciniphila as a representative beneficial bacterium in tumor treatment, which might provide bright clues and assistance for the application of drugs targeting A. muciniphila in clinical oncotherapy.},
}

Humans
Animals
*Probiotics/therapeutic use
*Neoplasms/microbiology/therapy/immunology/drug therapy
*Gastrointestinal Microbiome
Akkermansia

@article {pmid37666200,
year = {2023},
author = {Xu, M and Wang, W and Su, S and Li, W and Hu, X and Zhang, J},
title = {Arecoline alleviated loperamide induced constipation by regulating gut microbes and the expression of colonic genome.},
journal = {Ecotoxicology and environmental safety},
volume = {264},
number = {},
pages = {115423},
doi = {10.1016/j.ecoenv.2023.115423},
pmid = {37666200},
issn = {1090-2414},
mesh = {*Constipation/chemically induced/drug therapy ; Loperamide/toxicity ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Colon/drug effects/metabolism ; Male ; *Arecoline/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Rats ; Fatty Acids, Volatile/metabolism ; Transcriptome/drug effects ; },
abstract = {This study aimed to investigate the effects of arecoline on constipation by intervening at different times to explore its preventive and therapeutic effects. Symptoms related to constipation, gut microbes, short-chain fatty acid (SCFA) content in the cecum, and gene expression in the colon were measured to examine the effect of arecoline on relieving constipation. The results showed that arecoline intervention alleviated loperamide-induced constipation, as evidenced by significantly shortened intestinal transit time, increased fecal water content, improved small bowel propulsion, and increased defecation frequency. In addition, arecoline significantly reduced the levels of gastrointestinal regulatory peptides such as somatostatin and vasoactive intestinal peptide in the serum, thereby regulating intestinal peristalsis. Histopathological analysis showed that arecoline ameliorated intestinal injury caused by constipation. Gut microbial analysis indicated that arecoline altered the taxonomic composition and levels of its metabolite SCFAs in the gut microbiota. Furthermore, the colonic transcriptome results indicated that genes expression related to intestinal diseases were significantly down-regulated by arecoline intervention. In conclusion, the results of the correlation analysis propose a possible mechanism of arecoline in alleviating constipation by modulating the gut microbes and their metabolites and regulating the gut genome.},
}

*Constipation/chemically induced/drug therapy
Loperamide/toxicity
*Gastrointestinal Microbiome/drug effects
Animals
*Colon/drug effects/metabolism
Male
*Arecoline/pharmacology/therapeutic use
Rats, Sprague-Dawley
Rats
Fatty Acids, Volatile/metabolism
Transcriptome/drug effects

@article {pmid37660873,
year = {2023},
author = {Bhardwaj, L and Reddy, B and Dubey, SK},
title = {Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {117033},
doi = {10.1016/j.envres.2023.117033},
pmid = {37660873},
issn = {1096-0953},
mesh = {*Herbicides/toxicity ; *Soil Microbiology ; Oryza/growth & development ; *Rhizosphere ; *Microbiota/drug effects ; Soil/chemistry ; *Soil Pollutants/analysis/toxicity ; Agriculture ; Bacteria/drug effects ; Fungi/drug effects ; Acetanilides ; Aniline Compounds ; },
abstract = {Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha[-1], respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.},
}

*Herbicides/toxicity
*Soil Microbiology
Oryza/growth & development
*Rhizosphere
*Microbiota/drug effects
Soil/chemistry
*Soil Pollutants/analysis/toxicity
Agriculture
Bacteria/drug effects
Fungi/drug effects
Acetanilides
Aniline Compounds

@article {pmid37641353,
year = {2023},
author = {Moore, SG and Feehily, C and Doyle, RC and Buckley, F and Lonergan, P and Cotter, PD and Butler, ST},
title = {Associations between the postpartum uterine and vaginal microbiota and the subsequent development of purulent vaginal discharge vary with dairy cow breed and parity.},
journal = {Journal of dairy science},
volume = {106},
number = {11},
pages = {8133-8151},
doi = {10.3168/jds.2022-22720},
pmid = {37641353},
issn = {1525-3198},
mesh = {Animals ; Female ; Cattle ; *Vagina/microbiology ; Postpartum Period ; *Microbiota ; *Uterus/microbiology ; *Vaginal Discharge/veterinary/microbiology ; Parity ; Pregnancy ; *Cattle Diseases/microbiology ; },
abstract = {The objective of this study was to characterize the species composition and functional potential of the vaginal and uterine microbiota at 1 wk postpartum in dairy cows diagnosed with or without purulent vaginal discharge (PVD) at 3 wk postpartum. The hypothesis was that differences in the vaginal and uterine microbiota between cows diagnosed with (PVD+) or without (PVD-) PVD were dependent on parity and breed. Cytobrush samples of the vagina and uterus were collected at 1 wk postpartum from 36 Holstein-Friesian (7 primiparous and 29 multiparous) and 29 Jersey (10 primiparous and 19 multiparous) cows. Microbial DNA was isolated from each sample and processed for shotgun metagenomic sequencing. The odds of multiparous cows being diagnosed as PVD+ was less compared with primiparous cows (OR = 0.21). Neither the α-diversity nor β-diversity of the uterine and vaginal microbiota were associated with PVD but the β-diversity was different between breeds and between parities. In the vagina of primiparous cows, differences in the microbiota of PVD- and PVD+ cows were minor, but the microbiota of multiparous PVD+ cows had greater relative abundance of Fusobacterium necrophorum, Trueperella pyogenes, Porphyromonas levii, and greater functional potential for amino acid and protein synthesis, energy metabolism, and growth compared with PVD- cows. The uterus of primiparous PVD+ cows had lesser relative abundance of Bacteroides heparinolyticus compared with PVD- cows. In the uterine microbiota, differences included greater functional potential for cellulose biosynthesis and fucose catabolism in multiparous PVD+ cows compared with PVD- cows. In the uterine microbiota of primiparous PVD+ cows, the functional potential for gram-negative cell wall synthesis and for negative regulation of tumor necrosis factor signaling was lesser compared with multiparous PVD+ cows. In the vagina of Holstein-Friesian PVD+ cows, the relative abundance of Caviibacter abscessus was greater whereas in the vagina of Jersey PVD+ cows the relative abundance of Catenibacterium mitsuokai, Finegoldia magna, Klebsiella variicola, and Streptococcus anginosus was greater compared with PVD- cows. In the uterine microbiota of Holstein-Friesian cows, the functional potential for spermidine biosynthesis was reduced compared with PVD- cows. In summary, differences in the species composition and functional potential of the vaginal and uterine microbiota between PVD- and PVD+ cows were dependent on parity and breed. The findings suggest that alternative strategies may be required to treat PVD for different parities and breeds of dairy cow.},
}

Animals
Female
Cattle
*Vagina/microbiology
Postpartum Period
*Microbiota
*Uterus/microbiology
*Vaginal Discharge/veterinary/microbiology
Parity
Pregnancy
*Cattle Diseases/microbiology

@article {pmid37638757,
year = {2023},
author = {Chaturvedi, A and Li, X and Dhandapani, V and Marshall, H and Kissane, S and Cuenca-Cambronero, M and Asole, G and Calvet, F and Ruiz-Romero, M and Marangio, P and Guigó, R and Rago, D and Mirbahai, L and Eastwood, N and Colbourne, JK and Zhou, J and Mallon, E and Orsini, L},
title = {The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.},
journal = {Nucleic acids research},
volume = {51},
number = {18},
pages = {9785-9803},
pmid = {37638757},
issn = {1362-4962},
support = {NE/N016777/1//NERC/ ; 965406//European Union/ ; 101028700//Marie Skłodowska-Curie/ ; IC160121//Royal Society International Collaboration Award/ ; },
mesh = {Animals ; *Daphnia/genetics/microbiology ; *DNA Methylation ; *Genome ; *Evolution, Molecular ; Metagenome ; *Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Transcriptome ; Daphnia magna ; },
abstract = {Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.},
}

Animals
*Daphnia/genetics/microbiology
*DNA Methylation
*Genome
*Evolution, Molecular
Metagenome
*Microbiota/genetics
Gastrointestinal Microbiome/genetics
Transcriptome
Daphnia magna

@article {pmid37558110,
year = {2023},
author = {Tian, F and Wang, Y and Guo, G and Ding, K and Yang, F and Wang, C and Wang, H and Yan, M},
title = {Meta-genome analysis of a newly enriched azo dyes detoxification halo-thermophilic bacterial consortium.},
journal = {Environmental research},
volume = {237},
number = {Pt 1},
pages = {116828},
doi = {10.1016/j.envres.2023.116828},
pmid = {37558110},
issn = {1096-0953},
mesh = {*Azo Compounds/metabolism ; *Coloring Agents/metabolism ; *Microbial Consortia/genetics ; *Genome, Bacterial ; *Water Pollutants, Chemical/metabolism ; *Bacteria/genetics/metabolism ; Wastewater ; Biodegradation, Environmental ; },
abstract = {Treating textile wastewaters were always inhibited by its higher salt concentration and temperature. In this study, a halo-thermophilic bacterial consortium YM was enriched with ability to decolorize acid brilliant scarlet GR (ABS) at 55 °C and 10% salinity. Under optimum conditions of pH (8), temperature (55 °C), and salinity (10%), YM decolorized 97% of ABS under anaerobic conditions. Alteribacillus was identified to be the dominant genus in consortium YM. Consortium YM showed significant decolorization ability under a wide range of salinity (1%-10%), pH (7-9) and temperature (45 °C-60 °C). The degradation pathway of ABS was proposed by the combination of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS), and metagenomic analysis. Azoreductase, which was an important enzyme in decolorization process, was identified with great variation in the genome of consortium YM. Meanwhile, the metabolic intermediates after decolorization was identified with low biotoxicity by phytotoxicity tests. This study first identified that Alterbacillus play an important role in azo dye decolorization and degradation process under halo-thermophlic conditions and provided significant knowledge for azo dye decolorization and degradation process.},
}

*Azo Compounds/metabolism
*Coloring Agents/metabolism
*Microbial Consortia/genetics
*Genome, Bacterial
*Water Pollutants, Chemical/metabolism
*Bacteria/genetics/metabolism
Wastewater
Biodegradation, Environmental

@article {pmid41803086,
year = {2026},
author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L},
title = {Water mass specific genes dominate the Southern Ocean microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41803086},
issn = {2041-1723},
support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Antarctic Regions ; *Bacteria/genetics/classification ; Sulfonium Compounds/metabolism ; Arctic Regions ; Plankton/genetics ; Phylogeny ; },
abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.},
}

*Microbiota/genetics
*Seawater/microbiology
Oceans and Seas
Metagenome/genetics
Antarctic Regions
*Bacteria/genetics/classification
Sulfonium Compounds/metabolism
Arctic Regions
Plankton/genetics
Phylogeny

@article {pmid41801404,
year = {2026},
author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH},
title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {4},
pages = {},
pmid = {41801404},
issn = {1432-0851},
support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Middle Aged ; Aged ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prospective Studies ; *Neoplasms/drug therapy/immunology/mortality ; Melanoma/drug therapy/immunology ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; },
abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Middle Aged
Aged
*Immunotherapy/methods
Retrospective Studies
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Prospective Studies
*Neoplasms/drug therapy/immunology/mortality
Melanoma/drug therapy/immunology
Carcinoma, Non-Small-Cell Lung/drug therapy/immunology

@article {pmid41798955,
year = {2026},
author = {Xiao, Y and Zhang, T and Chen, Q and Zhang, Y and Chen, B and Wang, M and Zhang, Y and Huang, M and Su, Y and Guo, J},
title = {Multi-omics analysis reveals the mechanism of verbenalin in treating gout via modulating purine metabolism, gut microbiota, and inflammatory pathways.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1761558},
pmid = {41798955},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Purines/metabolism ; Disease Models, Animal ; *Gout/drug therapy/metabolism ; Inflammation/drug therapy/metabolism ; Signal Transduction/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Hyperuricemia/drug therapy ; Rats, Sprague-Dawley ; Metabolomics/methods ; Arthritis, Gouty/drug therapy/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Gout is a prevalent metabolic disorder characterized by hyperuricemia and inflammation. Verbenalin, an iridoid glycoside from Verbena officinalis, possesses anti-inflammatory properties; however, its therapeutic potential and underlying mechanisms in gout remain underexplored.

OBJECTIVE: This study aimed to evaluate the pharmacological effects and elucidate the molecular mechanisms of verbenalin in a rat model of gout.

METHODS: Hyperuricemia and acute gouty arthritis were induced in rats using potassium oxonate/hypoxanthine and monosodium urate, respectively. Verbenalin was administered orally for 7 days. Therapeutic efficacy was assessed via physical symptom scores (inflammation, gait, swelling), renal/hepatic function indices, and histopathology. Furthermore, a multi-omics strategy integrating transcriptomics, metagenomics, and metabolomics, combined with Western blotting, was employed to investigate the pharmacological mechanisms.

RESULTS: Verbenalin treatment significantly alleviated joint inflammation and swelling while improving gait scores. It effectively lowered serum uric acid (UA), creatinine, and BUN levels, inhibited hepatic xanthine oxidase (XOD) activity, and promoted urinary UA excretion. Histopathological damage in the joints, kidneys, and liver was markedly mitigated. Mechanistically, verbenalin downregulated the expression of urate transporters (URAT1, GLUT9) and inflammatory mediators (NLRP3, IL-1β) by inhibiting the PI3K-AKT and MAPK signaling pathways. Multi-omics analysis further revealed that verbenalin restored gut microbiota diversity and modulated purine metabolism, correlating with reduced UA levels.

CONCLUSION: These findings demonstrate that verbenalin may exert anti-gout effects through the potential synergy of modulating purine metabolism, shifting gut microbiota composition, and suppressing PI3K-AKT and MAPK inflammatory signaling pathways. This study provides a preliminary scientific basis for further investigation into verbenalin as a prospective multi-target therapeutic candidate.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats
Male
*Purines/metabolism
Disease Models, Animal
*Gout/drug therapy/metabolism
Inflammation/drug therapy/metabolism
Signal Transduction/drug effects
*Anti-Inflammatory Agents/pharmacology
Hyperuricemia/drug therapy
Rats, Sprague-Dawley
Metabolomics/methods
Arthritis, Gouty/drug therapy/metabolism
Multiomics

@article {pmid41797508,
year = {2026},
author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W},
title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71656},
pmid = {41797508},
issn = {1530-6860},
support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Gallstones/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; Aged ; Multiomics ; Amidohydrolases ; },
abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bile Acids and Salts/metabolism
*Dysbiosis/microbiology/metabolism/complications
*Gallstones/microbiology/metabolism/etiology
Male
Female
Middle Aged
Feces/microbiology
Adult
Aged
Multiomics
Amidohydrolases

@article {pmid41673107,
year = {2026},
author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG},
title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41673107},
issn = {2045-2322},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/pathology/immunology/genetics/microbiology ; *Inflammation/pathology/genetics ; Mice, Knockout ; Disease Models, Animal ; Dysbiosis ; Autoimmunity ; Mice, Inbred C57BL ; },
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.},
}

Animals
Mice
*Gastrointestinal Microbiome
*Lupus Erythematosus, Systemic/pathology/immunology/genetics/microbiology
*Inflammation/pathology/genetics
Mice, Knockout
Disease Models, Animal
Dysbiosis
Autoimmunity
Mice, Inbred C57BL

@article {pmid41645054,
year = {2026},
author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H},
title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41645054},
issn = {1471-2164},
support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Enterocytozoon/physiology ; *Vitamin K 2 ; *Rodentia/microbiology ; *Microsporidiosis/microbiology/veterinary/metabolism ; Biosynthetic Pathways ; },
abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Enterocytozoon/physiology
*Vitamin K 2
*Rodentia/microbiology
*Microsporidiosis/microbiology/veterinary/metabolism
Biosynthetic Pathways

@article {pmid41448605,
year = {2026},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Johnson, S and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary Nitrate Intake and 16S rRNA-Inferred Nitrite-Generating Capacity of the Subgingival Microbiome May Influence Glucose Metabolism: Results From the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {Journal of clinical periodontology},
volume = {53},
number = {4},
pages = {508-519},
doi = {10.1111/jcpe.70084},
pmid = {41448605},
issn = {1600-051X},
support = {R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; DK-63608//Vagelos College of Physicians and Surgeons, Columbia University/ ; UL1TR001873/TR/NCATS NIH HHS/United States ; R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; UL1TR001873/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Female ; Cross-Sectional Studies ; Adult ; *RNA, Ribosomal, 16S/genetics ; Male ; *Insulin Resistance ; *Nitrates/administration & dosage/metabolism ; *Gingiva/microbiology ; *Microbiota/genetics ; *Nitrites/metabolism ; *Diet ; Blood Glucose/metabolism ; *Glucose/metabolism ; Biomarkers ; Cardiometabolic Risk Factors ; *Glucose Intolerance/metabolism/microbiology ; },
abstract = {AIMS: To investigate whether the association between the nitrite-generating capacity of the subgingival microbiome and early cardiometabolic risk biomarkers varies by dietary nitrate intake.

MATERIALS AND METHODS: Cross-sectional data from 668 participants (mean age 31 ± 9 years, 73% women) were analysed. Dietary nitrate intake was calculated from food frequency questionnaires. Subgingival 16S rRNA sequencing (Illumina, MiSeq) and PICRUSt2 estimated microbial genes. The Microbiome-Induced Nitric Oxide Enrichment Score (MINES) was calculated as a ratio of microbial gene abundances representing enhanced net capacity for NO generation. Adjusted multivariable linear models regressed cardiometabolic risk biomarkers (HbA1c, glucose, insulin, insulin resistance (HOMA-IR), blood pressure) on nitrate intake and MINES together with a MINES × nitrate intake interaction term.

RESULTS: Mean nitrate intake was 190 ± 171 mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA-IR (p < 0.05). Among participants with a low MINES, higher nitrate intake was associated with lower HOMA-IR (1.2 [1.1-1.4] vs. 1.5 [1.3-1.6]; p = 0.002), but levels were similar in those with high MINES (p = 0.84).

CONCLUSIONS: A biomarker of higher microbial NO-generating capacity in subgingival plaque is associated with lower insulin and insulin resistance among individuals with lower dietary nitrate intake. Future trials evaluating the cardiometabolic benefits of nitrate-rich diets should incorporate measures of the entire oral microbiome.},
}

Humans
Female
Cross-Sectional Studies
Adult
*RNA, Ribosomal, 16S/genetics
Male
*Insulin Resistance
*Nitrates/administration & dosage/metabolism
*Gingiva/microbiology
*Microbiota/genetics
*Nitrites/metabolism
*Diet
Blood Glucose/metabolism
*Glucose/metabolism
Biomarkers
Cardiometabolic Risk Factors
*Glucose Intolerance/metabolism/microbiology

@article {pmid37762509,
year = {2023},
author = {Zabolotneva, AA and Gaponov, AM and Roumiantsev, SA and Vasiliev, IY and Grigoryeva, TV and Kit, OI and Zlatnik, EY and Maksimov, AY and Goncharova, AS and Novikova, IA and Appolonova, SA and Markin, PA and Shestopalov, AV},
title = {Alkylresorcinols as New Modulators of the Metabolic Activity of the Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {24},
number = {18},
pages = {},
pmid = {37762509},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Resorcinols/pharmacology/metabolism ; Humans ; Mice ; Feces/microbiology/chemistry ; Mice, Inbred C57BL ; Male ; Fecal Microbiota Transplantation ; Receptors, LDL/genetics ; Female ; },
abstract = {Alkylresorcinols (ARs) are polyphenolic compounds with a wide spectrum of biological activities and are potentially involved in the regulation of host metabolism. The present study aims to establish whether ARs can be produced by the human gut microbiota and to evaluate alterations in content in stool samples as well as metabolic activity of the gut microbiota of C57BL, db/db, and LDLR (-/-) mice according to diet specifications and olivetol (5-n-pentylresorcinol) supplementation to estimate the regulatory potential of ARs. Gas chromatography with mass spectrometric detection was used to quantitatively analyse AR levels in mouse stool samples; faecal microbiota transplantation (FMT) from human donors to germ-free mice was performed to determine whether the intestinal microbiota could produce AR molecules; metagenome sequencing analysis of the mouse gut microbiota followed by reconstruction of its metabolic activity was performed to investigate olivetol's regulatory potential. A significant increase in the amounts of individual members of AR homologues in stool samples was revealed 14 days after FMT. Supplementation of 5-n-Pentylresorcinol to a regular diet influences the amounts of several ARs in the stool of C57BL/6 and LDLR (-/-) but not db/db mice, and caused a significant change in the predicted metabolic activity of the intestinal microbiota of C57BL/6 and LDLR (-/-) but not db/db mice. For the first time, we have shown that several ARs can be produced by the intestinal microbiota. Taking into account the dependence of AR levels in the gut on olivetol supplementation and microbiota metabolic activity, AR can be assumed to be potential quorum-sensing molecules, which also influence gut microbiota composition and host metabolism.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Resorcinols/pharmacology/metabolism
Humans
Mice
Feces/microbiology/chemistry
Mice, Inbred C57BL
Male
Fecal Microbiota Transplantation
Receptors, LDL/genetics
Female

@article {pmid37648194,
year = {2023},
author = {Kakakhel, MA and Narwal, N and Kataria, N and Johari, SA and Zaheer Ud Din, S and Jiang, Z and Khoo, KS and Xiaotao, S},
title = {Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {117002},
doi = {10.1016/j.envres.2023.117002},
pmid = {37648194},
issn = {1096-0953},
mesh = {Animals ; *Dysbiosis/chemically induced/veterinary/microbiology ; *Fishes/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Fish Diseases/microbiology/chemically induced ; },
abstract = {The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.},
}

Animals
*Dysbiosis/chemically induced/veterinary/microbiology
*Fishes/microbiology
*Gastrointestinal Microbiome/drug effects
*Water Pollutants, Chemical/toxicity
*Fish Diseases/microbiology/chemically induced

@article {pmid37634690,
year = {2023},
author = {Liu, L and Xin, Y and Guang, SB and Lin, GF and Liu, CX and Zeng, LQ and He, SQ and Zheng, YM and Chen, GY and Zhao, QB},
title = {Planktonic microbial community and biological metabolism in a subtropical drinking water river-reservoir system.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {116999},
doi = {10.1016/j.envres.2023.116999},
pmid = {37634690},
issn = {1096-0953},
mesh = {*Rivers/microbiology ; *Drinking Water/microbiology ; *Microbiota ; China ; *Plankton ; Bacteria/metabolism/classification ; *Water Microbiology ; Environmental Monitoring ; },
abstract = {To understand the dynamics of planktonic microbial community and its metabolism processes in subtropical drinking water river-reservoir system with lower man-made pollution loading, this study selected Dongzhen river-reservoir system in Mulan Creek as object to investigate spatial-temporal characteristics of community profile and functional genes involved in biological metabolism, and to analyze the influence of environmental factors. The results indicated that Proteobacteria and Actinobacteria were the most diverse phyla with proportion ranges of 9%-80% in target system, and carbohydrate metabolism (5.76-7.12 × 10[-2]), amino acid metabolism (5.78-7.21 × 10[-2]) and energy metabolism (4.07-5.17 × 10[-2]) were found to be the dominant pathways of biological metabolism. Although there were variations in biological properties both spatially and temporally, seasonal variation had a greater influence on microbial community and biological metabolism, than locational differences. Regarding the role of environmental factors, this study revealed that microbial diversity could be affected by multiple abiotic factors, with total organic carbon, total phosphorus and temperature being more influential (absolute value of standardized regression weights >2.13). Stochastic processes dominated the microbial community assembly (R[2] of neutral community model = 0.645), while niche-based processes differences represented by nutrients, temperature and pH level played secondary roles (R > 0.388, P < 0.01). Notably, the synergistic influences among the environmental factors accounted for the higher percentages of community variation (maximum proportion up to 17.6%). Additionally, pH level, temperature, and concentrations of dissolved oxygen, carbon and nitrogen were found to be the significant factors affecting carbon metabolism pathways (P < 0.05), yet only total organic carbon significantly affected on nitrogen transformation (P < 0.05). In summary, the microbial profile in reservoir is not completely dominated by that in feeding river, and planktonic microbial community and its metabolism in subtropical drinking water river-reservoir system are shaped by multiple abiotic and biotic factors with underlying interactions.},
}

*Rivers/microbiology
*Drinking Water/microbiology
*Microbiota
China
*Plankton
Bacteria/metabolism/classification
*Water Microbiology
Environmental Monitoring