@article {pmid41574290,
year = {2025},
author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719300},
pmid = {41574290},
issn = {2235-2988},
mesh = {*Feces/virology ; Animals ; Phylogeny ; *Metagenomics ; *DNA Viruses/genetics/classification/isolation & purification ; Tibet ; Cattle/virology ; *Virome ; *Picornaviridae/genetics/classification/isolation & purification ; Genome, Viral ; China ; },
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.

METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.

RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.

DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.},
}

*Feces/virology
Animals
Phylogeny
*Metagenomics
*DNA Viruses/genetics/classification/isolation & purification
Tibet
Cattle/virology
*Virome
*Picornaviridae/genetics/classification/isolation & purification
Genome, Viral
China

@article {pmid41534355,
year = {2026},
author = {He, S and Wang, Z and Zhong, Z and Shi, C and Li, D and Yin, F},
title = {Soil salinization alters biogeochemical cycles in agricultural ecosystems by reducing carbon-cycling microorganisms.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119706},
doi = {10.1016/j.ecoenv.2026.119706},
pmid = {41534355},
issn = {1090-2414},
mesh = {*Soil Microbiology ; *Salinity ; *Soil/chemistry ; *Carbon Cycle ; Ecosystem ; Agriculture ; Bacteria/genetics/metabolism ; Microbiota ; Metagenomics ; },
abstract = {Salinity stress can decline crop yield in agricultural systems. Beyond the environmental conditions that drive agricultural plant growth, the diverse roles of microbes represent a critical, often overlooked factor in shaping crop health and productivity. Salinization exerts a profound effect on soil microbial communities, with consequences for biogeochemical cycles. However, the salinity adaptation mechanisms of microorganisms participating in biogeochemical cycles remain incompletely understood, which hold considerable promise for microbial solutions in saline agriculture. In this study, metagenomics-based technology was employed to analyze agricultural soils within a region-scale irrigation area characterized by varying degrees of salinization. According to the results of generalized linear models, bell-shaped trends were observed for the diversity and abundance of biogeochemical cycling genes along the soil salinity gradient, all of which peaked at a salinity of approximately 7.5 ‰. Further comparisons indicated reduced total abundance of all biogeochemical cycling genes in high salinity soils (>7.5 ‰) compared to those in low salinity soils (<7.5 ‰). Furthermore, correlation analysis indicated the coupling of different biogeochemical cycling genes, which were observed to be possessed by similar functional microorganisms, with a predominance of Gammaproteobacteria and Alphaproteobacteria. The presence of elevated salt levels resulted in a decline in the abundance of various microorganisms that play roles in biogeochemical cycling, including members of the Alphaproteobacteria, Actinomycetia, Limnocylindira, and Gemmatimonadetes phyla. Concurrently, there was an enrichment of a limited number of salt-tolerant bacteria, predominantly classified under the Bacteroidia and Bacilli taxonomic groups. The coupling of different biogeochemical cycling genes in some metagenome-assembled genomes (MAGs) was confirmed through metagenomics binning. Three MAGs (strains of Methylophaga, Salinimicrobium, and Sediminibacterium, respectively) with diverse biogeochemical cycling functions were recognized as potential plant-growth-promoting bacteria under salinity stress. These findings contribute to the existing body of knowledge on the salinity adaptability of soil microbial communities and offer guidance for the management of saline agriculture.},
}

*Soil Microbiology
*Salinity
*Soil/chemistry
*Carbon Cycle
Ecosystem
Agriculture
Bacteria/genetics/metabolism
Microbiota
Metagenomics

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {241},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
mesh = {*Artificial Intelligence ; *Metagenome/genetics ; *Metagenomics/methods ; Microbiota/genetics ; Computational Biology/methods ; Machine Learning ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

*Artificial Intelligence
*Metagenome/genetics
*Metagenomics/methods
Microbiota/genetics
Computational Biology/methods
Machine Learning
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of sediment microbial community composition and function to mangrove restoration from an aquaculture pond in Southern China.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology ; China ; Aquaculture ; *Wetlands ; *Microbiota ; Ponds/microbiology ; Bacteria/classification ; *Environmental Restoration and Remediation ; },
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}

*Geologic Sediments/microbiology
China
Aquaculture
*Wetlands
*Microbiota
Ponds/microbiology
Bacteria/classification
*Environmental Restoration and Remediation

@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
mesh = {*Sulfamethoxazole/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; *Toluidines/toxicity ; *Microbiota/drug effects ; *Herbicides/toxicity ; *Soil Pollutants/toxicity ; Anti-Bacterial Agents ; Ecosystem ; Bacteria/drug effects ; },
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}

*Sulfamethoxazole/toxicity
*Soil Microbiology
*Nitrogen/metabolism
*Toluidines/toxicity
*Microbiota/drug effects
*Herbicides/toxicity
*Soil Pollutants/toxicity
Anti-Bacterial Agents
Ecosystem
Bacteria/drug effects

@article {pmid41499817,
year = {2026},
author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z},
title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119669},
doi = {10.1016/j.ecoenv.2025.119669},
pmid = {41499817},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Phthalic Acids/toxicity ; Mice, Inbred C57BL ; Mice ; Male ; *Plasticizers/toxicity ; Dysbiosis/chemically induced ; *Intestines/drug effects ; Cytokines/metabolism ; },
abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.

METHODS: C57BL/6 mice (n = 10 per group) were orally gavaged with DnPP (1-100 mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).

RESULTS: DnPP exposure induced dose-dependent villus degeneration (100 mg/kg/d, P < 0.05) and colon shortening (P < 0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-α) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P < 0.001) and elevated antibiotic resistance genes (CARD, P < 0.05).

CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Phthalic Acids/toxicity
Mice, Inbred C57BL
Mice
Male
*Plasticizers/toxicity
Dysbiosis/chemically induced
*Intestines/drug effects
Cytokines/metabolism

@article {pmid41411799,
year = {2026},
author = {Chen, M and Meng, S and Guan, R and Dong, Q and Dong, X and Shen, X and Fang, L and Zhao, F},
title = {Lead exposure changes carbohydrate and amino acid metabolism corresponding to a disturbed microbiota-gut-brain axis in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119554},
doi = {10.1016/j.ecoenv.2025.119554},
pmid = {41411799},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Amino Acids/metabolism ; Mice ; *Lead/toxicity ; *Brain/drug effects/metabolism ; *Carbohydrate Metabolism/drug effects ; Male ; Feces/chemistry/microbiology ; *Brain-Gut Axis/drug effects ; },
abstract = {Chronic lead exposure can cause irreversible neurological damage. The brain-gut axis's involvement in lead-induced neurotoxicity, a key factor in cognitive deficits, requires further exploration. To deepen our understanding of how lead exposure influences the brain-gut connection, we carried out the behavioral and morphological analysis, as well as metabolome and metagenome analysis associated with the gut-brain axis. The study results suggested that Pb exposure resulted in inflammation in both the brain and gut, along with decreased cognitive ability. The metagenomic data indicated that Pb exposure impacted microbial diversity and composition, with a marked increase in genes linked to carbohydrate and amino acid metabolism. Compared to control mice, the metabolic profiles of brain, feces and serum samples from Pb-exposed mice were differed, with higher levels of amino acids in serum and soluble sugars in feces, but lower levels of amino acids in brain. Key enriched microbial (eg: Tenericutes, Thermotogae, Alistipes_putredinis) was significantly negatively correlated with brain amino acid (eg: proline, asparagine, tryptophan) but positively correlated with serum amino acids (eg: valine, leucine, tyrosine). This research uncovers new perspectives on how lead exposure alters metabolites in the brain-gut axis, regulated by gut microbiota, highlighting the need for additional research on lead's health risks.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Amino Acids/metabolism
Mice
*Lead/toxicity
*Brain/drug effects/metabolism
*Carbohydrate Metabolism/drug effects
Male
Feces/chemistry/microbiology
*Brain-Gut Axis/drug effects

@article {pmid41408188,
year = {2025},
author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H},
title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {55},
pmid = {41408188},
issn = {1471-230X},
support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; },
mesh = {Humans ; Cholangitis, Sclerosing/microbiology/diagnosis ; *Microbiota ; Bile Duct Neoplasms/microbiology/diagnosis ; *Biliary Tract/microbiology ; *Pancreatic Neoplasms/microbiology/diagnosis ; Cholangiocarcinoma/microbiology/diagnosis ; Gallstones/microbiology/diagnosis ; *Pancreatic Diseases/microbiology/diagnosis ; *Biliary Tract Diseases/microbiology/diagnosis ; },
abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.

METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16 S rRNA gene sequencing or metagenomics.

RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.

CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.},
}

Humans
Cholangitis, Sclerosing/microbiology/diagnosis
*Microbiota
Bile Duct Neoplasms/microbiology/diagnosis
*Biliary Tract/microbiology
*Pancreatic Neoplasms/microbiology/diagnosis
Cholangiocarcinoma/microbiology/diagnosis
Gallstones/microbiology/diagnosis
*Pancreatic Diseases/microbiology/diagnosis
*Biliary Tract Diseases/microbiology/diagnosis

@article {pmid41380611,
year = {2026},
author = {Xie, C and Li, Y and Wulijia, B and Dong, X and Wang, L and Song, Y and Liao, X},
title = {Centennial Pb-Zn mining pollution: Spatial distance impacts on agricultural soil microbiota stress response.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119550},
doi = {10.1016/j.ecoenv.2025.119550},
pmid = {41380611},
issn = {1090-2414},
mesh = {*Mining ; *Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; China ; *Lead/analysis/toxicity ; *Microbiota/drug effects ; *Zinc/analysis/toxicity ; Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Bacteria/genetics/drug effects/classification ; Agriculture ; Soil/chemistry ; Cadmium/analysis/toxicity ; Stress, Physiological ; },
abstract = {Mining activities pose significant threats to agricultural ecosystems through heavy metals (HMs) contamination, particularly in acidic red soils. Since there was limited research on the response mechanisms of agricultural microorganisms at different distances within typical mining areas to HMs stress, This study investigated HMs pollution patterns, microbial community dynamics, and functional gene responses in farmland surrounding a century-old Pb-Zn mine in Shuikoushan, Hengyang City, China. Soil samples were collected from three zones: Short-Distance (SD, 0-10 km), Medium-Distance (MD, 10-15 km), and Long-Distance (LD, 15-25 km) from the mine. Results revealed a pronounced distance-dependent decline in composite HMs pollution, with Cd (R[2]=0.61) and As (R[2]=0.51) showing the strongest correlations to proximity. SD zone exhibited severe contamination, with Cd (8.25 ± 5.74 mg kg[-1]) and As (58.58 ± 49.63 mg kg[-1]) concentrations exceeding regulatory limits by 27.5 and 1.95 fold, respectively. Bacterial diversity demonstrated significant spatial stratification, with Shannon indices increasing from SD to LD zones (6.8→7.2), while β-diversity decreased, indicating reduced ecological heterogeneity at lower pollution levels. High HMs stress in SD zone favored anaerobic taxa like Thermomarinilinea and acid-tolerant phyla like Acidobacteriota, whereas aerobic taxa like Gaiella dominated less-polluted areas. Metagenomic analysis revealed upregulation of HMs resistance genes (czcABCD, cadCD, arsABCJR) in SD zone. Correlation network analysis highlighted intensified positive interactions among bacterial genus under HMs stress, suggesting cooperative survival strategies. These findings elucidate the dual pressure of HMs toxicity and soil acidification on microbial ecosystems, providing critical insights for ecological risk assessment and bioremediation strategies in mining-impacted agricultural lands. The study underscores the need for distance-based pollution control measures and highlights microbial genetic adaptation as a potential tool for rehabilitating heavy metal-contaminated red soils.},
}

*Mining
*Soil Microbiology
*Soil Pollutants/analysis/toxicity
China
*Lead/analysis/toxicity
*Microbiota/drug effects
*Zinc/analysis/toxicity
Environmental Monitoring
*Metals, Heavy/analysis/toxicity
Bacteria/genetics/drug effects/classification
Agriculture
Soil/chemistry
Cadmium/analysis/toxicity
Stress, Physiological

@article {pmid41569097,
year = {2026},
author = {Ayala-Montaño, S and Afolayan, AO and Kociurzynski, R and Loeber, U and Reuter, S},
title = {Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001609},
pmid = {41569097},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; Computational Biology/methods ; *DNA Contamination ; *Metagenome ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Infant, Newborn ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; },
abstract = {Metagenomic sequencing of clinical samples has significantly enhanced our understanding of microbial communities. However, microbial contamination and host-derived DNA remain a major obstacle to accurate data interpretation. Here, we present a methodology called 'Stop-Check-Go' for detecting and mitigating contaminants in metagenomic datasets obtained from neonatal patient samples (nasal and rectal swabs). This method incorporates laboratory and bioinformatics work combining a prevalence method, coverage estimation and microbiological reports. We compared the 'Stop-Check-Go' decontamination system with other published decontamination tools and commonly found poor performance in decontaminating microbiologically negative patients (false positives). We emphasize that host DNA decreased by an average of 76% per sample using a lysis method and was further reduced during post-sequencing analysis. Microbial species were classified as putative contaminants and assigned to 'Stop' in nearly 60% of the dataset. The 'Stop-Check-Go' system was developed to address the specific need of decontaminating low-biomass samples, where existing tools primarily designed for short-read metagenomic data showed limited performance.},
}

*Metagenomics/methods
Humans
Computational Biology/methods
*DNA Contamination
*Metagenome
Microbiota/genetics
Sequence Analysis, DNA/methods
Infant, Newborn
High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification

@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Rats, Inbred SHR ; *Drugs, Chinese Herbal/pharmacology ; Male ; Rats ; *Antihypertensive Agents/pharmacology ; *Lipid Metabolism/drug effects ; Blood Pressure/drug effects ; Dysbiosis/drug therapy ; Fecal Microbiota Transplantation ; Hypertension/drug therapy ; *Prehypertension/drug therapy ; Disease Models, Animal ; },
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Rats, Inbred SHR
*Drugs, Chinese Herbal/pharmacology
Male
Rats
*Antihypertensive Agents/pharmacology
*Lipid Metabolism/drug effects
Blood Pressure/drug effects
Dysbiosis/drug therapy
Fecal Microbiota Transplantation
Hypertension/drug therapy
*Prehypertension/drug therapy
Disease Models, Animal

@article {pmid41478064,
year = {2026},
author = {Zhang, H and Zhang, S and Li, X and Wang, W and Kuang, H},
title = {Bupleurum polysaccharide improves CUMS-induced depressive behavior in rats by regulating the "microbiota-gut-brain Axis": a mechanism study based on metabolomics and metagenomics.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1270},
number = {},
pages = {124905},
doi = {10.1016/j.jchromb.2025.124905},
pmid = {41478064},
issn = {1873-376X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Depression/metabolism/drug therapy/microbiology ; Male ; *Polysaccharides/pharmacology/chemistry ; Metabolomics/methods ; Metagenomics/methods ; Rats, Sprague-Dawley ; *Bupleurum/chemistry ; *Antidepressive Agents/pharmacology/chemistry ; Brain/drug effects/metabolism ; *Stress, Psychological/metabolism ; Metabolome/drug effects ; Disease Models, Animal ; Behavior, Animal/drug effects ; },
abstract = {This study aimed to comprehensively investigate the antidepressant mechanisms of Bupleurum polysaccharide (BP) through the microbiota-gut-brain axis, employing an integrated multi-omics approach. Using a chronic unpredictable mild stress (CUMS) rat model of depression, we evaluated BP's effects on depressive-like behaviors and analyzed its regulatory mechanisms on metabolites and gut microbiota through combined metabolomics and metagenomics. Structural characterization revealed that Bupleurum polysaccharide SPAP-1 is an acidic homogeneous polysaccharide with a molecular weight of approximately 100 kDa, primarily composed of glucose, mannose, rhamnose, and other monosaccharides. Pharmacodynamic assessments demonstrated that BP significantly ameliorated CUMS-induced depressive behaviors, including weight loss, reduced food intake, anhedonia, and behavioral despair (P < 0.05). Metabolomic analysis identified 19 differential metabolites, with BP reversing 11 of them, primarily involved in phenylalanine and tryptophan metabolism pathways. Western blot analysis confirmed BP's regulatory effects on key enzymes Got1 and Lta4h. Metagenomic results showed that BP remarkably reshaped gut microbiota structure, restored microbial diversity, optimized the Firmicutes/Bacteroidetes ratio, enriched beneficial genera (Agathobacter, Phocaeicola), and inhibited pathogenic genera (Ruminococcus). Crucially, integrated multi-omics analysis revealed significant microbiota-metabolite correlations, demonstrating that BP-promoted beneficial bacteria positively correlated with neurotransmitter precursors, while BP-inhibited pathogenic bacteria associated with pro-inflammatory mediators. Mediation analysis further established the "microbiota → metabolite → behavior" causal chain, with Ruminococcus → LTB4 → despair behavior accounting for 42.3 % of the mediation effect. In conclusion, Bupleurum polysaccharide ameliorates depressive-like behaviors through multi-target regulation of the metabolite-microbiota interaction network, highlighting its potential as an antidepressant agent or functional food and providing a novel research paradigm for understanding the multi-target characteristics of traditional Chinese medicine polysaccharides.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats
*Depression/metabolism/drug therapy/microbiology
Male
*Polysaccharides/pharmacology/chemistry
Metabolomics/methods
Metagenomics/methods
Rats, Sprague-Dawley
*Bupleurum/chemistry
*Antidepressive Agents/pharmacology/chemistry
Brain/drug effects/metabolism
*Stress, Psychological/metabolism
Metabolome/drug effects
Disease Models, Animal
Behavior, Animal/drug effects

@article {pmid41456557,
year = {2026},
author = {Li, Y and Chen, Y and Du, Z and Guo, Y and Zhang, W and Xu, X and Liu, Z and Duan, H and Duan, X and Zhang, A and Zhou, A and Li, X and Makinia, J},
title = {Oriented butyrate production through a novel bacteria-yeast microbiome: batch verification, key electron donor identification, and long-term validation.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133892},
doi = {10.1016/j.biortech.2025.133892},
pmid = {41456557},
issn = {1873-2976},
mesh = {*Saccharomyces cerevisiae/metabolism ; *Butyrates/metabolism ; Ethanol/metabolism ; *Microbiota ; Fermentation ; *Electrons ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; Clostridium/metabolism ; },
abstract = {Recovering butyrate from organic waste enables its high-value conversion, aligning with the principles of a circular economy. Traditional butyrate fermentation emphasizes carbohydrates and protein degradation, with limited focus on chain elongation (CE). This study, for the first time, systematically evaluated the effects of different Saccharomyces cerevisiae (SC) concentrations (1, 2, 4, 6, and 8 g/L) on ethanol production (a key electron donor) and subsequent CE for butyrate synthesis, identifying 2 g/L as the optimal SC dosage. At this concentration, butyrate production reached 15.41 ± 2.84 g COD/L, which was 2.72 times higher than that of the blank. Metabolic pathway analysis revealed that yeast not only enhanced substrate degradation (＞90 %) but also facilitated the in situ generation and utilization of ethanol. 16S rRNA indicated 54.10 % relative abundance of butyrate-producing bacteria (Clostridium). Long-term tests found that adding SC reversed the halt in production from prolonged distiller yeast inoculum, stabilising output at 15 g COD/L. Metagenomic analysis revealed that SC inoculation primarily enriched Clostridium luticellarii and Clostridium tyrobutyricum. In addition to raising reverse β-oxidation gene abundance, this treatment also enhanced lactate utilization genes, thereby strengthening acetyl-CoA to butyrate conversion. Through further experiments involving different electron donor ratios and long-term operation, this study highlights the critical role of yeast-bacteria synergy in enhancing butyrate synthesis, providing a theoretical foundation and technical strategy for food waste valorization in line with circular economy principles.},
}

*Saccharomyces cerevisiae/metabolism
*Butyrates/metabolism
Ethanol/metabolism
*Microbiota
Fermentation
*Electrons
*Bacteria/metabolism
RNA, Ribosomal, 16S/genetics
Clostridium/metabolism

@article {pmid41388485,
year = {2026},
author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL},
title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.},
journal = {Alcohol, clinical & experimental research},
volume = {50},
number = {1},
pages = {e70210},
doi = {10.1111/acer.70210},
pmid = {41388485},
issn = {2993-7175},
support = {AA029925/AA/NIAAA NIH HHS/United States ; AA029925/AA/NIAAA NIH HHS/United States ; },
mesh = {Animals ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Ethanol/administration & dosage ; *Up-Regulation/drug effects ; *Dysbiosis/metabolism/chemically induced ; *alpha7 Nicotinic Acetylcholine Receptor/metabolism/genetics/biosynthesis ; *Binge Drinking/metabolism ; *Limbic System/metabolism/drug effects ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.

METHODS: B6 mice were given ethanol (EtOH; 5 g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24 h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96 h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12 h, 24 h, and 192 h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-α, IL-1β, P2Y12, ITGβ2, and α7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.

RESULTS: Data revealed increased TNF-α expression in the Amg, Hyp, and NAc and increased IL-1β expression in the Amg and NAc, 12 h after the first EtOH injection. α7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24 h after the third EtOH dose, compared to the control group. α7nAChR expression in the Hyp was observed at 2 min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24 h after the third EtOH dose. ITGβ2 showed an increasing trend in the Amg at 12 h after the first dose, followed by a significant reduction at 24 h, and 192 h after the third dose. 16S rRNA sequencing revealed a significant difference in β-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.

CONCLUSION: This study showed that brain inflammation, indicated by α7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.},
}

Animals
Mice
Male
*Gastrointestinal Microbiome/drug effects
*Ethanol/administration & dosage
*Up-Regulation/drug effects
*Dysbiosis/metabolism/chemically induced
*alpha7 Nicotinic Acetylcholine Receptor/metabolism/genetics/biosynthesis
*Binge Drinking/metabolism
*Limbic System/metabolism/drug effects
Mice, Inbred C57BL

@article {pmid41568738,
year = {2026},
author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA},
title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71023},
doi = {10.1002/alz.71023},
pmid = {41568738},
issn = {1552-5279},
support = {//TMCity/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; },
abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.},
}

Humans
*Cognitive Dysfunction/microbiology
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Probiotics/therapeutic use
*Brain

@article {pmid41568034,
year = {2025},
author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS},
title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660973},
pmid = {41568034},
issn = {1664-302X},
abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.},
}

@article {pmid41565402,
year = {2026},
author = {Zhou, Y and Wang, H and Guo, L and Liu, X and Wang, X and Liu, Y and Shang, M and Zheng, B and Li, K and Liu, L and Li, J and Ding, G},
title = {Human umbilical cord MSC-derived exosomes attenuate radiation-induced pulmonary fibrosis via remodeling the gut-lung axis in mice.},
journal = {Life sciences in space research},
volume = {48},
number = {},
pages = {204-215},
doi = {10.1016/j.lssr.2025.11.011},
pmid = {41565402},
issn = {2214-5532},
mesh = {*Exosomes/metabolism ; Humans ; Animals ; Mice ; *Mesenchymal Stem Cells/cytology/metabolism ; *Pulmonary Fibrosis/etiology/therapy ; *Umbilical Cord/cytology ; Gastrointestinal Microbiome ; *Lung/radiation effects/metabolism/pathology ; Male ; Mice, Inbred C57BL ; },
abstract = {OBJECTIVE: To investigate whether human umbilical cord mesenchymal stem cell-derived exosomes (hUC-MSC-Exos) attenuate radiation-induced pulmonary fibrosis (RIPF) through modulation of the gut-lung axis.

METHODS: The therapeutic efficacy of hUC-MSC-Exos was evaluated in a mouse model of RIPF through histopathology and western blot analysis of fibrosis markers (α-SMA, Vimentin, and E-cadherin). Gut barrier integrity (ZO-1, Occludin) and intestinal inflammation (IL-6, IL-1β) were examined using immunohistochemistry, RT-qPCR, and ELISA. Gut microbial composition and metabolic profiles were characterized via metagenomics and untargeted metabolomics, followed by integrated bioinformatics analyses to identify key pathways and metabolites.

RESULTS: hUC-MSC-Exos significantly reduced pulmonary collagen deposition and restored fibrosis markers expression, concomitant with enhanced gut barrier function and attenuated intestinal inflammation. Multi-omics analysis revealed restoration of gut microbiota homeostasis and metabolic reprogramming, with the alanine, aspartate, and glutamate pathway being notably co-regulated. L-Glutamic acid was the most significantly altered metabolite and correlated significantly positively with the severity of pulmonary fibrosis and gut dysfunction. Gut microbiota associated with L-Glutamic acid (e.g., Duncaniella, Ruminococcus) were also significantly restructured.

CONCLUSIONS: hUC-MSC-Exos attenuate RIPF through a comprehensive remodeling of the gut-lung axis, in which L-Glutamic acid and its associated microbiota serve as potential mediators. These findings highlight the gut-lung axis as a promising therapeutic target for RIPF.},
}

*Exosomes/metabolism
Humans
Animals
Mice
*Mesenchymal Stem Cells/cytology/metabolism
*Pulmonary Fibrosis/etiology/therapy
*Umbilical Cord/cytology
Gastrointestinal Microbiome
*Lung/radiation effects/metabolism/pathology
Male
Mice, Inbred C57BL

@article {pmid41401858,
year = {2026},
author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L},
title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.},
journal = {Journal of invertebrate pathology},
volume = {215},
number = {},
pages = {108518},
doi = {10.1016/j.jip.2025.108518},
pmid = {41401858},
issn = {1096-0805},
mesh = {Animals ; *Bombyx/microbiology/virology/immunology ; *Gastrointestinal Microbiome ; *Nucleopolyhedroviruses/physiology ; *Disease Resistance ; Species Specificity ; },
abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (An3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.},
}

Animals
*Bombyx/microbiology/virology/immunology
*Gastrointestinal Microbiome
*Nucleopolyhedroviruses/physiology
*Disease Resistance
Species Specificity

@article {pmid41370957,
year = {2026},
author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G},
title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.},
journal = {Environment international},
volume = {207},
number = {},
pages = {109971},
doi = {10.1016/j.envint.2025.109971},
pmid = {41370957},
issn = {1873-6750},
mesh = {*Wastewater/microbiology ; *Gene Transfer, Horizontal ; *Microplastics/analysis ; *Microbiota ; Virulence Factors/genetics ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; },
abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.},
}

*Wastewater/microbiology
*Gene Transfer, Horizontal
*Microplastics/analysis
*Microbiota
Virulence Factors/genetics
Waste Disposal, Fluid
Drug Resistance, Microbial/genetics

@article {pmid41299176,
year = {2026},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {649},
number = {8098},
pages = {982-990},
pmid = {41299176},
issn = {1476-4687},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Bacteriophages/genetics/physiology/classification/isolation & purification ; Prophages/genetics/physiology/isolation & purification ; Feces/microbiology/virology ; *Bacteria/virology/genetics/classification ; Virus Integration ; Gene Transfer, Horizontal ; Male ; Female ; },
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics
*Bacteriophages/genetics/physiology/classification/isolation & purification
Prophages/genetics/physiology/isolation & purification
Feces/microbiology/virology
*Bacteria/virology/genetics/classification
Virus Integration
Gene Transfer, Horizontal
Male
Female

@article {pmid41562094,
year = {2025},
author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P},
title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1717935},
pmid = {41562094},
issn = {1664-3224},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Phlebotomus/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Leishmaniasis/parasitology ; *Insect Vectors/microbiology/parasitology ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.

METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.

RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).

DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.},
}

*Gastrointestinal Microbiome
Animals
*Phlebotomus/microbiology/parasitology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
*Leishmaniasis/parasitology
*Insect Vectors/microbiology/parasitology
Bacteria/genetics/classification

@article {pmid41561096,
year = {2025},
author = {Wan, L and Huang, C and Kong, W and Li, M and Lu, C},
title = {The analysis of gut microbiota characteristics in children with global developmental delay.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1606453},
pmid = {41561096},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Female ; Feces/microbiology ; Male ; *Developmental Disabilities/microbiology ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Child ; DNA, Bacterial/genetics ; Infant ; Biodiversity ; China ; },
abstract = {OBJECTIVE: To explore the composition and functional changes of gut microbiota in children with Global Developmental Delay(GDD),and to explore the role of gut microbiota in the pathogenesis of GDD using high-throughput sequencing.

METHODS: A prospective study was conducted to select 26 children diagnosed with GDD at Longgang District Maternal and Child HealthCare Hospital of Shenzhen City from January 2024 to December 2024 as the disease group(GDD), and 59 healthy children of the same age were selected as the healthy group(HC).General information of the children was collected through a questionnaire survey, and fecal samples from all participants were collected. Total DNA was extracted and amplified, and high-throughput sequencing of the 16S rRNA gene was performed for biological analysis of the sequencing results.

RESULTS: The alpha diversity analysis revealed a significant reduction in microbial diversity in the GDD group (Chao1 index, P = 0.007), while the beta diversity showed significant segregation between groups (R² = 0.067, P = 0.001);At the phylum level, the relative abundance of Actinobacteria was significantly increased (P < 0.01), while the abundance of Bacteroidetes was significantly decreased (P < 0.05) in the GDD group;At the genus level, the abundance of Bifidobacterium, Fusicatenibacter, and Erysipelatoclostridium were significantly increased in the GDD group (all P < 0.001), while the abundance of Faecalibacterium, Phascolarctobacterium, and Alistipes were significantly reduced (all P < 0.001);Functional prediction based on 16S rRNA data suggested potential differences in microbial metabolic pathways, including mRNA surveillance, proteasome, and atrazine degradation, in the GDD group. These findings hypothesize a functional shift in the gut microbiome associated with GDD, which requires validation by direct metagenomic or metabolomic methods.

CONCLUSION: Children with GDD have significant differences in gut microbiota composition and diversity compared to HC,and the abundance and abnormal metabolic pathway may be closely related to the neuroinflammatory process, suggesting that intestinal microecological regulation may become a new intervention target for GDD.},
}

Humans
*Gastrointestinal Microbiome/genetics
Prospective Studies
RNA, Ribosomal, 16S/genetics
Female
Feces/microbiology
Male
*Developmental Disabilities/microbiology
Child, Preschool
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Child
DNA, Bacterial/genetics
Infant
Biodiversity
China

@article {pmid41561086,
year = {2025},
author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX},
title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1740322},
pmid = {41561086},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Gastrointestinal Diseases/therapy/microbiology ; Probiotics/therapeutic use ; Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Phage Therapy ; Dysbiosis/therapy ; },
abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Gastrointestinal Diseases/therapy/microbiology
Probiotics/therapeutic use
Animals
Fecal Microbiota Transplantation
Gastrointestinal Tract/microbiology
Phage Therapy
Dysbiosis/therapy

@article {pmid41558481,
year = {2026},
author = {Keller, V and Calchera, A and Otte, J and Tuovinen Nogerius, V and Schmitt, I},
title = {Ubiquitous occurrence of the black fungus Melanina gundecimermaniae in the lichen Umbilicaria pustulata.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.12.046},
pmid = {41558481},
issn = {1879-0445},
abstract = {Lichen symbioses frequently include additional fungal associates beyond the canonical mycobiont (fungus) and photobiont (alga/cyanobacterium). Despite the prevalence and diversity of these lichen cohabitants, their geographic distribution and role within the lichen consortium remain poorly understood. Combining genomics, metagenomics, and advanced microscopy, we identified the black fungus Melanina gundecimermaniae as a constant cohabitant in the lichen Umbilicaria pustulata. We analyzed metagenomes from 149 individuals across 15 populations, spanning the Europe-wide range of U. pustulata. Additionally, we screened pooled metagenomes of U. pustulata and Umbilicaria phaea along five elevation gradients (Europe and North America). Genome mapping, using a near-complete reference genome of M. gundecimermaniae, revealed that the black fungus was present in 100% of the screened lichen metagenomes, with 0.85%-3.78% of reads mapping against the reference. Among all lichen-associated fungi, it was one of the most common. These findings indicate that the black fungus is widely distributed and associated with different lichen species, underscoring its potential ecological significance. Using fluorescence in situ hybridization coupled with confocal laser scanning microscopy, we confirmed the presence of M. gundecimermaniae within various structures of U. pustulata, including vegetative symbiotic propagules involved in dispersal. Elucidating its widespread occurrence across continents, consistent presence in U. pustulata, and ability to be dispersed together with the lichens' canonical partners, our findings suggest a potential interaction of M. gundecimermaniae that extends beyond incidental colonization. Our study contributes to the growing body of evidence that organismal complexity within lichens is a prevalent and largely unexplored dimension of the lichen symbiosis.},
}

@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {2},
pages = {1998-2011},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
mesh = {*Citrus/metabolism/microbiology/growth & development/physiology/genetics ; *Plant Roots/metabolism/microbiology/physiology/growth & development ; Microbiota/drug effects ; *Iron/metabolism/analysis ; Rhizosphere ; Bacteria/genetics/isolation & purification/classification/metabolism ; *Azetidinecarboxylic Acid/analogs & derivatives/metabolism/pharmacology ; Soil Microbiology ; *Proline/analogs & derivatives/metabolism/pharmacology ; Fertilizers/analysis ; },
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}

*Citrus/metabolism/microbiology/growth & development/physiology/genetics
*Plant Roots/metabolism/microbiology/physiology/growth & development
Microbiota/drug effects
*Iron/metabolism/analysis
Rhizosphere
Bacteria/genetics/isolation & purification/classification/metabolism
*Azetidinecarboxylic Acid/analogs & derivatives/metabolism/pharmacology
Soil Microbiology
*Proline/analogs & derivatives/metabolism/pharmacology
Fertilizers/analysis

@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {2},
pages = {2438-2451},
doi = {10.1021/acs.jafc.5c13269},
pmid = {41505640},
issn = {1520-5118},
mesh = {*Silage/analysis/microbiology ; Fermentation ; Animals ; Rumen/metabolism/microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Lactiplantibacillus plantarum/metabolism ; Animal Feed/analysis ; Digestion ; Gastrointestinal Microbiome ; },
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}

*Silage/analysis/microbiology
Fermentation
Animals
Rumen/metabolism/microbiology
Bacteria/genetics/classification/metabolism/isolation & purification
*Lactiplantibacillus plantarum/metabolism
Animal Feed/analysis
Digestion
Gastrointestinal Microbiome

@article {pmid41478124,
year = {2026},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
mesh = {*Rhizosphere ; Mining ; *Antimony/toxicity ; *Microbiota ; *Soil Pollutants/toxicity ; Adaptation, Physiological ; Soil Microbiology ; Plant Roots/microbiology/growth & development ; },
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}

*Rhizosphere
Mining
*Antimony/toxicity
*Microbiota
*Soil Pollutants/toxicity
Adaptation, Physiological
Soil Microbiology
Plant Roots/microbiology/growth & development

@article {pmid41453903,
year = {2025},
author = {Lin, Z and Li, S and Liu, M and Li, J and Liu, F and Cao, J and Chen, S and Huang, K and Wang, Y and Li, H and Wang, Y and Yang, B and Xing, D and Wang, Q and Ji, X and Bai, X and Hu, D and Zhang, M and Guo, D and Huang, J and Geng, B and Gu, D and Lu, X},
title = {Gut microbiota-derived metabolite isovalerylcarnitine modulates salt sensitivity of blood pressure and incident hypertension: a multicenter dietary salt intervention trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {808},
pmid = {41453903},
issn = {2041-1723},
support = {91857118//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 12126602//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Hypertension/metabolism/microbiology ; Male ; *Carnitine/analogs & derivatives/metabolism/blood ; *Blood Pressure/drug effects/physiology ; Female ; *Sodium Chloride, Dietary/adverse effects ; Middle Aged ; Animals ; Rats ; Feces/microbiology ; Metabolome ; },
abstract = {This study aims to investigate the roles of gut microbiota and plasma metabolites in salt sensitivity (SS) of blood pressure (SSBP) and hypertension. A 23-day, multicenter, dietary salt intervention trial (the MetaSalt study) recruited 528 participants who underwent a baseline observation, low-salt, and high-salt interventions. SSBP was assessed and used as the primary outcome, and fecal shotgun metagenome and plasma targeted metabolome were measured. We found that high salt significantly altered 85 gut-microbial species (p < 9.42 × 10[-5]) and 70 metabolites (p < 2.26 × 10[-4]). Among them, the changes in 22 species and 8 metabolites were associated with SSBP (p < 0.05), and a gut microbiota-acylcarnitine network implicated in SSBP was identified, with a gut microbiota-derived metabolite, isovalerylcarnitine, as the core metabolite. Isovalerylcarnitine was also inversely associated with SSBP in the GenSalt study (p = 0.0102). Importantly, increased isovalerylcarnitine attenuated SS hypertension and improved endothelial function in rats, and was associated with reduced risk (ranging from 13% to 19%) of BP progression and incident hypertension in a prospective cohort (n = 3907, median follow-up = 5.5 years). This study demonstrated that the gut-acylcarnitine axis may play roles in the development of SS hypertension. Trial number: ChiCTR1900025171.},
}

*Gastrointestinal Microbiome/physiology/drug effects
Humans
*Hypertension/metabolism/microbiology
Male
*Carnitine/analogs & derivatives/metabolism/blood
*Blood Pressure/drug effects/physiology
Female
*Sodium Chloride, Dietary/adverse effects
Middle Aged
Animals
Rats
Feces/microbiology
Metabolome

@article {pmid41448087,
year = {2026},
author = {Yi, J and Li, Z and Han, X and Li, J and Liu, H and Zhu, L and Wang, M},
title = {Metformin drives the antibiotic resistome in activated sludge by reshaping microbial communities and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140887},
doi = {10.1016/j.jhazmat.2025.140887},
pmid = {41448087},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Metformin/pharmacology ; *Microbiota/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics/drug effects ; },
abstract = {Aerobic granular sludge (AGS) serves as a major reservoir and dissemination hotspot for human bacterial pathogens (HBPs) and antibiotic resistance genes (ARGs). Metformin (MET) as an emerging contaminant, which exacerbates antibiotic resistance and poses a problem for the stable operation of the activated sludge process in wastewater treatment plants. However, the specific mechanisms underlying the effects of MET stress on microbial communities and ARGs propagation in activated sludge remain poorly understood. In this study, we employed metagenomic analysis to investigate the effects of MET exposure, under a composite antibiotic background, on microbial community dynamics and resistome profiles in AGS systems and interpreted these effects from the perspectives of energy metabolism and community competition. Our findings demonstrate that MET exposure significantly enriched HBPs and multidrug resistance-related ARGs. Co-occurrence network analysis further identified that, among all sludge samples, 27 high-risk HBPs were strongly correlated with ARGs, virulence factor genes, and mobile genetic elements. Additionally, MET was also found to enhance ATP production in specific HBPs, conferring a competitive edge that facilitates ARG accumulation. Furthermore, the natural transformation and conjugation experiments further demonstrated the key role of MET in promoting horizontal gene transfer. In summary, this study underscores the role of MET in exacerbating the ecological risk of antibiotic resistance in AGS systems by concurrently enriching pathogenic bacteria and facilitating the horizontal transfer of ARGs, thereby highlighting the potential environmental impacts of MET as a pervasive contaminant on the propagation of resistance within wastewater treatment ecosystems.},
}

*Sewage/microbiology
*Gene Transfer, Horizontal/drug effects
*Metformin/pharmacology
*Microbiota/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
Genes, Bacterial
*Drug Resistance, Bacterial/genetics/drug effects

@article {pmid41421350,
year = {2026},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {7},
number = {1},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
mesh = {*Autism Spectrum Disorder/microbiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Host Microbial Interactions/genetics ; Metagenomics/methods ; Male ; Female ; Genomics/methods ; Polymorphism, Single Nucleotide/genetics ; Dysbiosis/microbiology ; Metabolomics/methods ; Genetic Variation ; Multiomics ; },
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}

*Autism Spectrum Disorder/microbiology/genetics/metabolism
Humans
*Gastrointestinal Microbiome/genetics
Child
*Host Microbial Interactions/genetics
Metagenomics/methods
Male
Female
Genomics/methods
Polymorphism, Single Nucleotide/genetics
Dysbiosis/microbiology
Metabolomics/methods
Genetic Variation
Multiomics

@article {pmid41412053,
year = {2026},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; Pacific Ocean ; *Temperature ; Halogenation ; Phylogeny ; *Bacteria/genetics/metabolism ; Microbiota ; },
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}

*Geologic Sediments/microbiology
Pacific Ocean
*Temperature
Halogenation
Phylogeny
*Bacteria/genetics/metabolism
Microbiota

@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {40},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Sheep/microbiology/metabolism ; *Animal Feed/analysis ; *Diet/veterinary ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metabolome ; Metabolomics ; Metagenomics ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}

Animals
*Rumen/microbiology/metabolism
Sheep/microbiology/metabolism
*Animal Feed/analysis
*Diet/veterinary
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Fermentation
Metabolome
Metabolomics
Metagenomics

@article {pmid41398277,
year = {2025},
author = {Xiao, Y and Liu, H and Wang, P and Zhang, Y and Wang, F and Jing, H},
title = {Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {16},
pmid = {41398277},
issn = {1741-7007},
support = {424MS115//the Hainan Provincial Natural Science Foundation of China/ ; 424QN341//the Hainan Provincial Natural Science Foundation of China/ ; 2022YFC2805400//the National Key R&D Program of China/ ; 2022YFC2805505//the National Key R&D Program of China/ ; KJRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; },
mesh = {*Geologic Sediments/microbiology ; *Microbiota ; *Seawater/microbiology ; *Bacteria/classification/genetics ; Metagenome ; *Water Microbiology ; },
abstract = {BACKGROUND: Microbes are widespread from the marine surface to the hadal zones and play a significant role in global biogeochemical cycling. Physicochemical properties of hadal zone shift with depth, in turn influencing the distribution profiles, biogeochemical functions, and adaptative mechanisms of microbial communities in hadal trenches. However, the ecological functions and evolutions of microbial communities along the surface water down to the sediments in the Diamantina and Kermadec trenches have been rarely studied.

RESULTS: Here, we provided a detailed metagenomic analysis of samples along the water columns (0-6553 m) and sediments (3060-9232 m) in the Diamantina and Kermadec trenches. The euphotic waters had a significantly higher ɑ-diversity than the deep-sea waters and sediments (p < 0.05, ANOSIM). Clear inter/intra-trench discrepancies of microbial communities along water layers appeared, with remarkable vertical connectivity exhibited in the Diamantina Trench (97.5%) than the Kermadec Trench (88.8%). Positive correlations among Proteobacteria, Bacteroidota, Actinobacteria, and Thaumarchaeota in seawaters and between Proteobacteria and Chloroflexi in sediments were revealed from the co-occurrence network. Niche-specific microbial groups showed distinct dominant metabolic pathways in carbon fixation, nitrogen, and sulfur cycles. Furthermore, we reconstructed 119 metagenome-assembled genomes (MAGs) of Rhodobacterales, and their notably low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS, 0.23) and high carbon atoms per residue side chain (C-ARSC, 2.86) in deep-sea sediments suggested a pronounced selection critical for their survival.

CONCLUSIONS: We found a clear connectivity of microbial communities in vertical profile, and discrepancy existed between the Diamantina and Kermadec trenches; Rhodobacterales' evolutionary adaptation related to genomic features (pN/pS and SNVs/kbp) in the deep-sea trench environments. These findings provided new insights into the community succession and potential adaption mechanism along the water columns to sediments in deep trenches.},
}

*Geologic Sediments/microbiology
*Microbiota
*Seawater/microbiology
*Bacteria/classification/genetics
Metagenome
*Water Microbiology

@article {pmid41391314,
year = {2026},
author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J},
title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140802},
doi = {10.1016/j.jhazmat.2025.140802},
pmid = {41391314},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Nitrogen Cycle ; *Microplastics/toxicity ; Ecosystem ; *Water Pollutants, Chemical/toxicity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Polyethylene ; },
abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.},
}

*Geologic Sediments/microbiology/chemistry
*Nitrogen Cycle
*Microplastics/toxicity
Ecosystem
*Water Pollutants, Chemical/toxicity
RNA, Ribosomal, 16S/genetics
Microbiota
Bacteria/genetics/metabolism
Nitrogen/metabolism
Polyethylene

@article {pmid41371144,
year = {2026},
author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y},
title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140716},
doi = {10.1016/j.jhazmat.2025.140716},
pmid = {41371144},
issn = {1873-3336},
mesh = {*Microbial Consortia ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Trichloroethanes/metabolism ; Chloroflexi/metabolism/genetics ; Halogenation ; Bacteria/metabolism/genetics ; },
abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.},
}

*Microbial Consortia
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
*Trichloroethanes/metabolism
Chloroflexi/metabolism/genetics
Halogenation
Bacteria/metabolism/genetics

@article {pmid41371128,
year = {2026},
author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH},
title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140758},
doi = {10.1016/j.jhazmat.2025.140758},
pmid = {41371128},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal/drug effects ; Aquaculture ; *Gastrointestinal Microbiome/drug effects ; *Enrofloxacin/pharmacology ; Animals ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Fatty Acids, Volatile/metabolism ; Bacteriophages/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; },
abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.},
}

*Gene Transfer, Horizontal/drug effects
Aquaculture
*Gastrointestinal Microbiome/drug effects
*Enrofloxacin/pharmacology
Animals
*Anti-Bacterial Agents/pharmacology
Plasmids/genetics
*Drug Resistance, Bacterial/genetics
Fatty Acids, Volatile/metabolism
Bacteriophages/genetics
Bacteria/genetics/drug effects
Genes, Bacterial
Drug Resistance, Microbial/genetics

@article {pmid41352011,
year = {2026},
author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X},
title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140640},
doi = {10.1016/j.jhazmat.2025.140640},
pmid = {41352011},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Hydrocarbons, Chlorinated/metabolism ; *Bacteria/metabolism/genetics ; *Archaea/metabolism/genetics ; Microbiota ; },
abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.},
}

*Soil Pollutants/metabolism
Biodegradation, Environmental
*Soil Microbiology
*Hydrocarbons, Chlorinated/metabolism
*Bacteria/metabolism/genetics
*Archaea/metabolism/genetics
Microbiota

@article {pmid41339548,
year = {2026},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {649},
number = {8098},
pages = {971-981},
pmid = {41339548},
issn = {1476-4687},
mesh = {Denmark ; *Microbiota/genetics ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Humans ; Ecosystem ; Biodiversity ; *Environmental Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}

Denmark
*Microbiota/genetics
Metagenome/genetics
RNA, Ribosomal, 16S/genetics
Phylogeny
Humans
Ecosystem
Biodiversity
*Environmental Microbiology
Agriculture
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid41260011,
year = {2026},
author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J},
title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119004},
doi = {10.1016/j.marpolbul.2025.119004},
pmid = {41260011},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Nitrogen Cycle ; *Freezing ; *Bacteria/classification ; Seasons ; Ecosystem ; *Microbiota ; Ice Cover ; Geologic Sediments/microbiology ; Nitrogen ; },
abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.},
}

*Lakes/microbiology
*Nitrogen Cycle
*Freezing
*Bacteria/classification
Seasons
Ecosystem
*Microbiota
Ice Cover
Geologic Sediments/microbiology
Nitrogen

@article {pmid41556507,
year = {2026},
author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M},
title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70704},
doi = {10.1111/gcb.70704},
pmid = {41556507},
issn = {1365-2486},
support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; Metagenomics ; *Metagenome ; *Stress, Physiological ; Biodiversity ; *Climate Change ; Ecosystem ; Bacteria/genetics/classification ; },
abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.},
}

*Soil Microbiology
*Microbiota
Metagenomics
*Metagenome
*Stress, Physiological
Biodiversity
*Climate Change
Ecosystem
Bacteria/genetics/classification

@article {pmid41552949,
year = {2026},
author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B},
title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70124},
pmid = {41552949},
issn = {1529-8817},
support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; },
abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.},
}

@article {pmid41430427,
year = {2025},
author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M},
title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {2586},
pmid = {41430427},
issn = {2045-2322},
mesh = {Italy ; *Metals, Heavy/analysis ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants/analysis ; *Soil/chemistry ; Environmental Monitoring/methods ; Metagenomics ; Models, Statistical ; },
abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.},
}

Italy
*Metals, Heavy/analysis
*Soil Microbiology
*Microbiota
*Soil Pollutants/analysis
*Soil/chemistry
Environmental Monitoring/methods
Metagenomics
Models, Statistical

@article {pmid41395946,
year = {2026},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; IDN/20/024//Internal funds KU Leuven/ ; },
mesh = {Humans ; *Virome/genetics ; *Skin/virology/microbiology ; Male ; Female ; Adult ; *Hidradenitis Suppurativa/virology/microbiology ; Middle Aged ; Microbiota ; Bacteriophages/genetics ; Metagenomics ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}

Humans
*Virome/genetics
*Skin/virology/microbiology
Male
Female
Adult
*Hidradenitis Suppurativa/virology/microbiology
Middle Aged
Microbiota
Bacteriophages/genetics
Metagenomics

@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {118},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
mesh = {Humans ; *Pulpitis/microbiology ; Adult ; *Metagenomics ; Adolescent ; Young Adult ; *High-Throughput Nucleotide Sequencing ; Male ; *Microbiota/genetics ; Chronic Disease ; Female ; *Dental Pulp/microbiology ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.

METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906 million paired-end reads per specimen.

RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.

CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}

Humans
*Pulpitis/microbiology
Adult
*Metagenomics
Adolescent
Young Adult
*High-Throughput Nucleotide Sequencing
Male
*Microbiota/genetics
Chronic Disease
Female
*Dental Pulp/microbiology

@article {pmid41389008,
year = {2026},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics alter duodenal immune populations upon gluten exposure in mice: implications for non-coeliac gluten sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {330},
number = {2},
pages = {G137-G153},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Animals ; *Glutens/immunology ; *Anti-Bacterial Agents/pharmacology ; *Duodenum/immunology/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred BALB C ; Intestinal Mucosa/immunology/drug effects/microbiology ; Eosinophils/immunology/drug effects ; Male ; Feces/microbiology ; },
abstract = {A growing proportion of the non-celiac population experiences adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesized that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5 mg/kg) or PBS-vehicle daily for 5 days. Mice were then treated with a 3-mg wheat-gluten suspension, or vehicle, on days 4 and 5 before euthanasia on day 7. Duodenal immune cells were analyzed by histology and flow cytometry, whereas the duodenal MAM and fecal microbiome were characterized via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in feces, and resulted in altered microbial carbohydrate and lipid metabolism, compared with vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared with vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.NEW & NOTEWORTHY A mouse model examined how microbial modulation affects immune responses to gluten. Antibiotic treatment followed by gluten reintroduction reduced duodenal Staphylococcus and altered microbial carbohydrate and lipid metabolism pathways in the fecal microbiome. Antibiotics and gluten treatment resulted in increased abundance and activation of duodenal eosinophils and elevated γδ T-cells in the duodenal epithelium. These findings highlight the role the microbiome plays in gluten-induced immune responses, providing insights into mechanisms behind non-celiac gluten sensitivity.},
}

Animals
*Glutens/immunology
*Anti-Bacterial Agents/pharmacology
*Duodenum/immunology/drug effects/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred BALB C
Intestinal Mucosa/immunology/drug effects/microbiology
Eosinophils/immunology/drug effects
Male
Feces/microbiology

@article {pmid41387926,
year = {2025},
author = {Ma, X and Wang, B and Xu, M and Zhang, Y and Liu, N and Teng, L and Li, Z and Yang, H and Xie, X and Zhang, B and Wang, Z and Wang, Y and Liu, J and Bao, J and Luo, H},
title = {Multiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {30},
pmid = {41387926},
issn = {2049-2618},
support = {32192463//The Major Program of National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Grassland ; *Gastrointestinal Microbiome ; Sheep/microbiology ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics/methods ; Poaceae ; *Nutrients/metabolism ; Fermentation ; Multiomics ; },
abstract = {BACKGROUND: The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility of forage produced by rumen microorganisms. Thus, the interaction between grass intake and rumen microbial fermentation is a key driver of both ruminant productivity and grassland ecosystem health. However, interactions between grass species, supplementary feeding, rumen microbiome, and rumen epithelium function, remain poorly understood.

RESULTS: We employed metagenomic and metatranscriptomic analyses, coupled with single-cell RNA sequencing (scRNA-seq) of rumen wall and serum metabolomics, to investigate how the rumen microbiome regulates grass intake and host metabolism. In a two-factor (grazing intensity and concentrate supplementation) experiment with 72 lambs, supplementary feeding under moderate grazing increased dry matter intake but decreased grass consumption of Artemisia tanacetifolia. These shifts correlated with contrasting trends between metagenomic and metatranscriptomic profiles of Lachnospiraceae. scRNA-seq revealed an increased abundance of basal cells (BCs), terminally differentiated keratinocytes (TDKs), and differentiated keratinocytes (DKs) in the supplemented group, with solute carrier genes (e.g., SLC16A1) involved in short chain fatty acids (SCFAs) transport enriched in basal cells. We also identified interactions between the rumen microbiome and host epithelial cells, influencing gene expression and localization, which in turn mediated the animal serum nutrient metabolism, particularly in B vitamin, bile acids, and amino acids.

CONCLUSIONS: Our study identified key microbiome and epithelial cell subtypes involved in grass digestion and SCFAs metabolism in the rumen. This novel link between ruminal microbial function, epithelial cell cluster-based genes, and host metabolism provides critical insights into mechanisms underlying the interaction between grass intake and supplementary feeding for optimizing ruminant management strategies in sustainable grazing systems. Video Abstract.},
}

Animals
*Rumen/microbiology/metabolism
Grassland
*Gastrointestinal Microbiome
Sheep/microbiology
Animal Feed/analysis
Bacteria/classification/genetics/isolation & purification/metabolism
Metagenomics/methods
Poaceae
*Nutrients/metabolism
Fermentation
Multiomics

@article {pmid41384736,
year = {2026},
author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A},
title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0136425},
doi = {10.1128/msystems.01364-25},
pmid = {41384736},
issn = {2379-5077},
mesh = {Fermentation ; *Coffea/microbiology/metabolism/chemistry ; Metabolomics/methods ; Humans ; Metagenomics/methods ; Taste ; Metabolome ; Microbiota ; Coffee/microbiology ; },
abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.

IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.},
}

Fermentation
*Coffea/microbiology/metabolism/chemistry
Metabolomics/methods
Humans
Metagenomics/methods
Taste
Metabolome
Microbiota
Coffee/microbiology

@article {pmid41382192,
year = {2025},
author = {Xue, R and Li, Z and Qin, W and Wang, Y and Zhao, K and Liu, L and Bai, Y},
title = {Prolonged grazing reduces the diversity and weakens virus-host links of metagenome-assembled viral community in acidic karst soil.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {15},
pmid = {41382192},
issn = {1741-7007},
support = {41907025//National Natural Science Foundation of China/ ; 32160337//National Natural Science Foundation of China/ ; 2025ZNSFSC0202//Natural Science Foundation of Sichuan Province/ ; },
mesh = {*Soil Microbiology ; *Metagenome ; *Soil/chemistry ; Biodiversity ; *Virome ; *Herbivory ; Bacteria/genetics ; Microbiota ; },
abstract = {BACKGROUND: Soil viruses are fundamental yet often overlooked components of terrestrial ecosystems, where they profoundly influence microbial diversity, community assembly, and biogeochemical cycling through predator-prey dynamics and the carriage of auxiliary metabolic genes (AMGs). However, the impact of human-driven land use change on viral communities and their functional potential remains poorly understood.

RESULTS: In this study, we analyzed viral diversity, virus-host linkage, and functional profiles of AMGs across different land management regimes in acidic karst soil after reclamation. The results showed that both bacterial and viral communities significantly differ across the four land management regimes, which are unused land, grazing pastureland, abandoned pastureland, and fertilized grazing pastureland. Grazing led to a lower viral diversity, a decrease in lysogenic viral abundance, and fewer virus-host linkages. The diversity and function of AMGs were also significantly affected by land management regimes, with grazing leading to a reduction in both AMGs diversity and relative abundance. Furthermore, both the bacterial community and soil physiochemical properties were essential factors that shaped viral diversity and lifestyle.

CONCLUSIONS: Overall, our findings indicate that inappropriate land use (long-term grazing) disrupts the virus-host balance, thereby altering the functional profiles of the soil viral community.},
}

*Soil Microbiology
*Metagenome
*Soil/chemistry
Biodiversity
*Virome
*Herbivory
Bacteria/genetics
Microbiota

@article {pmid41552860,
year = {2026},
author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A},
title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70102},
doi = {10.1111/1755-0998.70102},
pmid = {41552860},
issn = {1755-0998},
support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; },
mesh = {*DNA, Environmental/isolation & purification/genetics ; *Biodiversity ; *Deoxyribonucleases/metabolism ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/classification/genetics ; Rivers/chemistry ; *Metagenomics/methods ; },
abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.},
}

*DNA, Environmental/isolation & purification/genetics
*Biodiversity
*Deoxyribonucleases/metabolism
*DNA Barcoding, Taxonomic/methods
Animals
*Fishes/classification/genetics
Rivers/chemistry
*Metagenomics/methods

@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}

*Metagenomics/methods
*Software
Workflow
*Computational Biology/methods
Microbiota

@article {pmid41549294,
year = {2026},
author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC},
title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {139},
pmid = {41549294},
issn = {1432-0991},
mesh = {*Lakes/virology ; *Metagenomics ; *Viruses/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; India ; Phylogeny ; Ecosystem ; Biodiversity ; Fresh Water/virology ; Bacteriophages/genetics/classification/isolation & purification ; },
abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.},
}

*Lakes/virology
*Metagenomics
*Viruses/genetics/classification/isolation & purification
*Virome
Genome, Viral
India
Phylogeny
Ecosystem
Biodiversity
Fresh Water/virology
Bacteriophages/genetics/classification/isolation & purification

@article {pmid41459742,
year = {2026},
author = {Kwon, Y and Choi, J and Kim, SH and Kim, PJ and Lee, SM and Cha, JK and Park, H and Kang, JW and Jo, S and Kwak, YS and Kim, D and Kim, WJ and Lee, JH and Ryu, CM},
title = {Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf284},
pmid = {41459742},
issn = {1751-7370},
support = {RS-2022-RD010405//Cooperative Research Program for Agriculture Science and Technology Development/ ; //Rural Development Administration/ ; //National Research Foundation/ ; NRF-2021M3A9I5021439//Ministry of Science and ICT/ ; RS-2023-00219213//Ministry of Science and ICT/ ; KRIBB//Korea Research Institute of Bioscience and Biotechnology/ ; //Initiative Program, South Korea/ ; },
mesh = {*Oryza/genetics/microbiology/metabolism ; *Rhizosphere ; *Methane/metabolism ; *Nitrogen/metabolism ; *Microbiota ; Soil Microbiology ; Alleles ; *Crops, Agricultural/genetics ; Metagenomics ; Metagenome ; Plant Roots/microbiology ; Nitrogen Fixation ; Bacteria/genetics/metabolism/classification ; },
abstract = {Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line Saeilmi particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation and promoting microbial nitrogen fixation. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele's dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. Our study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars.},
}

*Oryza/genetics/microbiology/metabolism
*Rhizosphere
*Methane/metabolism
*Nitrogen/metabolism
*Microbiota
Soil Microbiology
Alleles
*Crops, Agricultural/genetics
Metagenomics
Metagenome
Plant Roots/microbiology
Nitrogen Fixation
Bacteria/genetics/metabolism/classification

@article {pmid41388019,
year = {2025},
author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA},
title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {638},
pmid = {41388019},
issn = {2041-1723},
support = {K08 AI123494/AI/NIAID NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Cholera Vaccines/immunology/administration & dosage ; *Immunity, Innate/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; *Sphingolipids/metabolism/immunology ; Vibrio cholerae/immunology ; *Cholera/prevention & control/immunology/microbiology ; Administration, Oral ; Feces/microbiology ; Macrophages/immunology ; Bacteroides/metabolism/immunology ; Female ; Male ; Adult ; },
abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.},
}

Humans
*Cholera Vaccines/immunology/administration & dosage
*Immunity, Innate/immunology
*Gastrointestinal Microbiome/immunology/genetics
*Sphingolipids/metabolism/immunology
Vibrio cholerae/immunology
*Cholera/prevention & control/immunology/microbiology
Administration, Oral
Feces/microbiology
Macrophages/immunology
Bacteroides/metabolism/immunology
Female
Male
Adult

@article {pmid41385957,
year = {2026},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
pmid = {41385957},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; },
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}

Animals
*Ducks/microbiology/physiology
*Gastrointestinal Microbiome
Domestication
*Adaptation, Physiological
Cecum/microbiology
Ileum/microbiology
*Metabolome
Metabolomics
Multiomics

@article {pmid41330454,
year = {2026},
author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, JX and Su, KP and Wang, B},
title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.},
journal = {Brain, behavior, and immunity},
volume = {132},
number = {},
pages = {106203},
doi = {10.1016/j.bbi.2025.106203},
pmid = {41330454},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy ; *Dysbiosis/physiopathology/microbiology ; Animals ; Brain/physiopathology ; Probiotics/therapeutic use ; Sleep/physiology ; *Brain-Gut Axis/physiology ; },
abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
*Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy
*Dysbiosis/physiopathology/microbiology
Animals
Brain/physiopathology
Probiotics/therapeutic use
Sleep/physiology
*Brain-Gut Axis/physiology

@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41485252,
year = {2026},
author = {Xu, Y and Zhao, B and Li, F and Song, S and Liu, J and Liu, Z and Wang, Y and Ji, J and Liu, Z and Zhou, W and Wang, X and Zhou, M},
title = {Tucidinostat ameliorates DSS-induced ulcerative colitis by inhibiting cellular senescence, modulating the p53 signaling pathway and cell cycle, and restoring the gut microbiota-metabolite Axis.},
journal = {International immunopharmacology},
volume = {171},
number = {},
pages = {116155},
doi = {10.1016/j.intimp.2025.116155},
pmid = {41485252},
issn = {1878-1705},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism/pathology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Cellular Senescence/drug effects ; Mice, Inbred C57BL ; *Tumor Suppressor Protein p53/metabolism ; Signal Transduction/drug effects ; Mice ; Dextran Sulfate ; Male ; Disease Models, Animal ; Cell Cycle/drug effects ; Humans ; Colon/drug effects/pathology ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex etiology, and its pathological process is closely associated with cellular senescence. Based on an anti-senescence drug screening system, this study identified Tucidinostat (TUC) as an agent with anti-senescence properties and investigated its therapeutic potential and mechanisms of action in a DSS-induced ulcerative colitis model. Using an in vitro model of colonic epithelial cells and an in vivo C57BL/6 mouse model, both induced by DSS treatment, we systematically evaluated changes in body weight, colon length, histopathological scores, levels of inflammatory cytokines, and senescence-associated markers. Our results demonstrated that TUC significantly inhibited cellular senescence and effectively alleviated colitis-related symptoms. Transcriptomic analysis and Western blotting further revealed that TUC exerts its effects by modulating the p53 signaling pathway and cell cycle progression. Furthermore, integrated metagenomic and untargeted metabolomic analyses revealed that TUC reshapes the gut microbiota-metabolite axis by promoting the proliferation of beneficial bacteria (e.g., s__Eubacterium plexicaudatum and s__Ligilactobacillus murinus) and increasing the levels of beneficial metabolites, such as alpha-muricholic acid and kynurenic acid. In summary, this study provides the first evidence that Tucidinostat can ameliorate ulcerative colitis by targeting cellular senescence, regulating the p53/cell cycle signaling network, and restoring gut microbiota-metabolite homeostasis, offering a novel potential therapeutic strategy for this disease.},
}

Animals
*Colitis, Ulcerative/drug therapy/chemically induced/metabolism/pathology/microbiology
*Gastrointestinal Microbiome/drug effects
Cellular Senescence/drug effects
Mice, Inbred C57BL
*Tumor Suppressor Protein p53/metabolism
Signal Transduction/drug effects
Mice
Dextran Sulfate
Male
Disease Models, Animal
Cell Cycle/drug effects
Humans
Colon/drug effects/pathology

@article {pmid41468674,
year = {2026},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Angelica/microbiology/growth & development/metabolism ; *Metagenomics/methods ; Soil Microbiology ; Plant Roots/microbiology/chemistry ; *Metabolome ; Bacteria/classification/genetics/metabolism/isolation & purification ; Microbiota ; Soil/chemistry ; Coumarins/analysis/metabolism ; Quorum Sensing ; Metabolomics ; Acyl-Butyrolactones/metabolism ; },
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}

*Rhizosphere
*Angelica/microbiology/growth & development/metabolism
*Metagenomics/methods
Soil Microbiology
Plant Roots/microbiology/chemistry
*Metabolome
Bacteria/classification/genetics/metabolism/isolation & purification
Microbiota
Soil/chemistry
Coumarins/analysis/metabolism
Quorum Sensing
Metabolomics
Acyl-Butyrolactones/metabolism

@article {pmid41455311,
year = {2026},
author = {Kolathingal-Thodika, N and Elayadeth-Meethal, M and Dunshea, FR and Eckard, R and Flavel, M and Chauhan, SS},
title = {Harnessing methane proxies to understand and mitigate enteric emissions from ruminant production systems.},
journal = {The Science of the total environment},
volume = {1012},
number = {},
pages = {181258},
doi = {10.1016/j.scitotenv.2025.181258},
pmid = {41455311},
issn = {1879-1026},
mesh = {*Methane/analysis/metabolism ; Animals ; *Ruminants/metabolism ; *Environmental Monitoring/methods ; *Animal Husbandry ; Rumen/microbiology ; Gastrointestinal Microbiome ; *Air Pollutants/analysis ; },
abstract = {Methane emissions from livestock, particularly ruminants, significantly contribute to global warming, necessitating the development of accurate methane monitoring systems. Direct methane measurement is technically complex, time-consuming, labour-intensive, and costly. Recent advances in methane inhibitors, such as 3-nitrooxy propanol and halogenated analogues, plant secondary compounds, including polyphenols and essential oils, to reduce methane emissions have necessitated the discovery of processes underlying rumen methane synthesis and inhibition. The identification of methane proxies, such as behavioural and input proxies (dry matter intake, neutral detergent fibre), microbial community proxies (rumen metagenome profiles), metabolic pathway proxies (fatty acids), molecular and genetic proxies (microbial genes), and downstream and non-invasive proxies (milk fatty acids and faecal lipidomes), is leading to more viable solutions. New developments in 'omic' techniques, including lipidomics, metagenomics and metatranscriptomics, have enabled the detection of proxies at the molecular level utilising rumen liquor, milk, blood, urine, and faeces. In addition to traditional methane proxies, rumen microbiota profiles, and specific genes involved in rumen methanogenesis (such as mcr and mrt, which encode methyl coenzyme reductase 1 and 2), these markers can be used to identify methane-producing pathways. Protozoa-associated methanogens (PAMs), propionate-producing bacteria, and methane-oxidising methanotrophs (Methylocystis sp.) are emerging as new proxies. Methane proxies provide scalable, affordable, and mechanistically insightful alternatives to conventional direct measuring techniques, which improve the understanding of rumen function and the biological causes of methane releases, enabling large-scale methane monitoring and will enable designing effective methane mitigation strategies in livestock production systems.},
}

*Methane/analysis/metabolism
Animals
*Ruminants/metabolism
*Environmental Monitoring/methods
*Animal Husbandry
Rumen/microbiology
Gastrointestinal Microbiome
*Air Pollutants/analysis

@article {pmid41389850,
year = {2026},
author = {Petrov, VA and Schade, S and Laczny, CC and Hällqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {132},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; *Parkinson Disease/diet therapy/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; Inflammation/metabolism/diet therapy ; *Resistant Starch/administration & dosage ; *Starch ; Quality of Life ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; },
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids alongside a reduction in opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}

Humans
*Gastrointestinal Microbiome/physiology/drug effects
*Parkinson Disease/diet therapy/microbiology/metabolism
Male
Female
Aged
Middle Aged
Inflammation/metabolism/diet therapy
*Resistant Starch/administration & dosage
*Starch
Quality of Life
Dietary Fiber
Fatty Acids, Volatile/metabolism

@article {pmid41285454,
year = {2026},
author = {Safika, S and Nisa', C and Supratikno, and Cahyadi, DD},
title = {Gut microbiota profiling of Javan pangolin (Manis javanica).},
journal = {The Journal of veterinary medical science},
volume = {88},
number = {1},
pages = {191-195},
doi = {10.1292/jvms.25-0036},
pmid = {41285454},
issn = {1347-7439},
mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Pangolins/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; },
abstract = {Chitin digestion in pangolins and other anteaters is thought to be aided by commensal bacteria in the digestive tract, in addition to their chitinase. This study characterized the gut microbiota of captive Javan pangolins using amplicon sequencing. Fecal samples were collected from two individuals and were sampled twice over one week. The dominant bacterial phyla identified were Firmicutes (Bacillota), Bacteroidetes (Bacteroidota), Proteobacteria (Pseudomonadota), and Actinobacteria (Actinomycetota). The most prevalent genera included Clostridium, Bacteroides, Lactobacillus, Bifidobacterium, Streptococcus, and Sporosarcina. Alpha and beta diversity were relatively low between paired samples, but the short sampling interval limits conclusions about microbial stability. These findings provide insights into the Javan pangolin's gut microbiota and support future research on microbial contributions to their digestion, health, and conservation.},
}

Animals
*Gastrointestinal Microbiome
Feces/microbiology
*Pangolins/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Female

@article {pmid40275546,
year = {2025},
author = {Jungpraditphol, I and Sutthiboonyapan, P and Khamwachirapitak, C and Krasaesin, A and Srithanyarat, S and Porntaveetus, T and Wiriyakijja, P},
title = {Shotgun Metagenomics of Biofilm Microbiome in Oral Lichen Planus With Desquamative Gingivitis.},
journal = {Oral diseases},
volume = {31},
number = {11},
pages = {3069-3080},
doi = {10.1111/odi.15349},
pmid = {40275546},
issn = {1601-0825},
support = {68-032,68-059//Health Systems Research Institute/ ; HEA_FF_68_008_3200_001,HEA_FF_68_223_3200_015//Thailand Science Research and Innovation Chulalongkorn University/ ; DRF68_007//Faculty of Dentistry, Chulalongkorn University/ ; },
mesh = {Humans ; *Gingivitis/microbiology/complications ; *Lichen Planus, Oral/microbiology/complications ; *Biofilms ; *Metagenomics ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; Adult ; Dental Plaque/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {INTRODUCTION: Oral lichen planus (OLP) is a chronic inflammatory condition often associated with desquamative gingivitis (DG). The oral microbiome's role in OLP and DG (OLP-DG) is gaining recognition, but prior 16S rRNA studies lacked taxonomic resolution. This study introduced shotgun metagenomic sequencing to thoroughly compare the supragingival and subgingival plaque microbiomes of individuals with and without OLP-DG.

METHODS: Twenty-seven participants (9 OLP-DG, 18 non-OLP) were recruited. Supra- and subgingival plaque samples were collected separately. Genomic DNA was analyzed using shotgun metagenomic sequencing. Microbial abundance and diversity were assessed through bioinformatic and statistical analyses.

RESULTS: We observed significant changes in the supragingival and subgingival microbiomes in OLP-DG. Supragingival plaque showed reduced Corynebacteriaceae and Porphyromonadaceae, with enrichment of an unnamed Synergistaceae genus and three unnamed species (Candidatus Saccharibacteria bacterium oral taxon 955 and 488 and GGB10852_SGB17523). Subgingival plaque revealed increased Flavobacteriaceae and Rhodocyclaceae, and reduced Actinomycetaceae. Although alpha or beta diversity was not significantly different, common commensals like Corynebacterium matruchotii and Streptococcus mitis were less abundant in OLP-DG patients.

CONCLUSION: This first-time application of metagenomic sequencing revealed a distinct microbiome in OLP-DG, characterized by novel bacterial species and reduced commensals, suggesting a potential role in OLP-DG pathogenesis, and warranting further study.},
}

Humans
*Gingivitis/microbiology/complications
*Lichen Planus, Oral/microbiology/complications
*Biofilms
*Metagenomics
Male
Female
*Microbiota/genetics
Middle Aged
Adult
Dental Plaque/microbiology
RNA, Ribosomal, 16S

@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}

Animals
Male
*Lactiplantibacillus plantarum/physiology
*Probiotics/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects/physiology
Mice, Inbred C57BL
*Liver Diseases, Alcoholic/therapy/microbiology
Liver/metabolism
Mice
Dysbiosis
NF-E2-Related Factor 2/metabolism/genetics
Oxidative Stress
Bile Acids and Salts/metabolism
Disease Models, Animal

@article {pmid41499937,
year = {2026},
author = {Wu, X and Zhang, T and Feng, J and Park, S},
title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157758},
doi = {10.1016/j.phymed.2025.157758},
pmid = {41499937},
issn = {1618-095X},
mesh = {Humans ; *Parkinson Disease/drug therapy/microbiology/metabolism ; Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; Caco-2 Cells ; Animals ; *Methylamines/metabolism ; Rats ; *5-Hydroxytryptophan/metabolism ; PC12 Cells ; Male ; *Plant Extracts/pharmacology ; Female ; Faecalibacterium prausnitzii ; Aged ; },
abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.

PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.

METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPKα signaling pathways.

RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPKα signaling.

CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPKα signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.},
}

Humans
*Parkinson Disease/drug therapy/microbiology/metabolism
Gastrointestinal Microbiome/drug effects
*Probiotics/pharmacology
Caco-2 Cells
Animals
*Methylamines/metabolism
Rats
*5-Hydroxytryptophan/metabolism
PC12 Cells
Male
*Plant Extracts/pharmacology
Female
Faecalibacterium prausnitzii
Aged

@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
pmid = {41494287},
issn = {2213-2317},
mesh = {Animals ; *Citrobacter rodentium/drug effects/pathogenicity ; Oxidation-Reduction/drug effects ; Rats ; *Antioxidants/pharmacology/administration & dosage/chemistry ; *Colon/microbiology/drug effects/metabolism ; Delayed-Action Preparations/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy/metabolism ; Male ; Coumaric Acids/pharmacology/administration & dosage ; },
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}

Animals
*Citrobacter rodentium/drug effects/pathogenicity
Oxidation-Reduction/drug effects
Rats
*Antioxidants/pharmacology/administration & dosage/chemistry
*Colon/microbiology/drug effects/metabolism
Delayed-Action Preparations/pharmacology
*Gastrointestinal Microbiome/drug effects
*Enterobacteriaceae Infections/microbiology/drug therapy/metabolism
Male
Coumaric Acids/pharmacology/administration & dosage

@article {pmid41485293,
year = {2026},
author = {Meng, Y and Hou, Y and Zhang, R and Guo, Z and Zhang, Z and Li, J and Yan, Y and Chang, Y and Li, D and Chang, L and Li, M and Gao, H},
title = {Jinlida ameliorates diabetic kidney disease via gut microbiota-dependent production of pyridoxamine targeting renal AGEs/RAGE and TGF-β pathways.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157744},
doi = {10.1016/j.phymed.2025.157744},
pmid = {41485293},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Pyridoxamine/metabolism/pharmacology ; *Diabetic Nephropathies/drug therapy/metabolism ; Mice ; Male ; Transforming Growth Factor beta/metabolism ; Glycation End Products, Advanced/metabolism ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; Fecal Microbiota Transplantation ; Receptor for Advanced Glycation End Products/metabolism ; Kidney/drug effects/metabolism ; Signal Transduction/drug effects ; Vitamin B 6/metabolism ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and end-stage renal disease (ESRD), necessitating novel therapies beyond conventional approaches. Emerging evidence indicates that gut microbiota dysbiosis promotes DKD progression through metabolite-mediated renal injury. Jinlida (JLD) is a clinically validated traditional Chinese medicine with antidiabetic activity, but its microbiota-mediated renoprotective mechanism remains unclear.

PURPOSE: This study investigates whether JLD alleviates DKD by modulating gut microbiota and vitamin B6 metabolism, and elucidates the renoprotective mechanism of its key metabolite, pyridoxamine (PM).

METHODS: To assess JLD's microbiota-dependent effects, we employed antibiotic-induced pseudo-germ-free mice and fecal microbiota transplantation (FMT). Metagenomics and untargeted metabolomics delineated gut microbiota and metabolite compositional changes. Renal PM levels were quantified by LC-MS/MS. The renoprotective effects and mechanisms of direct PM supplementation against DKD were further evaluated in vivo and in vitro.

RESULTS: JLD's therapeutic effects on proteinuria and glomerulosclerosis were shown to partially depend on microbiota homeostasis. Metabolomic analysis demonstrated that JLD significantly upregulated the vitamin B6 metabolic pathway and increased levels of related metabolites, including PM and pyridoxine (PN). Metagenomic analyses indicated that JLD remodeled the gut microbiota composition and enriched pathways related to cofactor biosynthesis, and markedly increased the relative abundance of key enzyme genes involved in the de novo (DXP-dependent) vitamin B6 biosynthesis pathway - namely pdxJ, pdxB, dxs and dxr. Genes related to vitamin B6 activation and conversion (pdxH, aldH) showed no significant changes, suggesting that JLD may promote PM accumulation by enhancing the microbiota's capacity for vitamin B6 biosynthesis rather than its subsequent activation/conversion. Source-tracking pinpointed Paramuribaculum intestinale as the core functional species. In vitro culture experiments showed that JLD markedly promoted the growth of this strain and elevated PM production, and that the strain's conditioned culture medium effectively inhibited formation of advanced glycation end-products (AGEs). Notably, direct supplementation with PM recapitulated the renoprotective effects of JLD in vivo. Mechanistically, PM inhibited the AGEs-RAGE-NF-κB-AP-1 axis and TGF-β receptor signaling, thereby suppressing NF-κB-driven inflammation and Smad2-mediated fibrosis.

CONCLUSION: JLD remodels the gut microbiota and enhances its de novo vitamin B6 biosynthetic capacity, leading to accumulation of PM. Gut-derived PM enters the circulation and functions as an effector molecule targeting the kidney; through PM's direct carbonyl-trapping activity it scavenges AGEs and suppresses the AGEs-RAGE axis as well as downstream inflammatory and profibrotic signaling, thereby exerting renoprotective effects. This study reveals PM as a microbially derived metabolite with therapeutic potential in DKD and offers a new metabolism-directed strategy for DKD treatment.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Pyridoxamine/metabolism/pharmacology
*Diabetic Nephropathies/drug therapy/metabolism
Mice
Male
Transforming Growth Factor beta/metabolism
Glycation End Products, Advanced/metabolism
Mice, Inbred C57BL
*Drugs, Chinese Herbal/pharmacology
Fecal Microbiota Transplantation
Receptor for Advanced Glycation End Products/metabolism
Kidney/drug effects/metabolism
Signal Transduction/drug effects
Vitamin B 6/metabolism

@article {pmid41351981,
year = {2026},
author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X},
title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157610},
doi = {10.1016/j.phymed.2025.157610},
pmid = {41351981},
issn = {1618-095X},
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Male ; Mice ; *Reactive Oxygen Species/metabolism ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.

PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.

METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.

RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.

CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.},
}

Animals
*Drugs, Chinese Herbal/pharmacology
*Gastrointestinal Microbiome/drug effects
*Renal Insufficiency, Chronic/drug therapy/microbiology/metabolism
*Receptors, Aryl Hydrocarbon/metabolism
Male
Mice
*Reactive Oxygen Species/metabolism
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Mice, Inbred C57BL
Signal Transduction/drug effects

@article {pmid41316726,
year = {2026},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D902-D911},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}

*Genome, Viral
*Virome/genetics
*Metagenome
*Viruses/genetics/classification
*Databases, Genetic
Metagenomics/methods
Open Reading Frames
Microbiota/genetics
Humans
Software
Molecular Sequence Annotation

@article {pmid41277537,
year = {2026},
author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH},
title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D734-D742},
pmid = {41277537},
issn = {1362-4962},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Biomarkers/analysis ; RNA, Ribosomal, 16S/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Disease/genetics ; Phenotype ; Software ; },
abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.},
}

Humans
*Gastrointestinal Microbiome/genetics
Biomarkers/analysis
RNA, Ribosomal, 16S/genetics
*Databases, Genetic
Metagenome/genetics
Metagenomics/methods
Disease/genetics
Phenotype
Software

@article {pmid41263098,
year = {2026},
author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y},
title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D555-D563},
pmid = {41263098},
issn = {1362-4962},
support = {R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Multigene Family ; Metagenome ; *Databases, Genetic ; Polysaccharides/metabolism ; Metagenomics/methods ; *Glycoside Hydrolases/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; Genome, Bacterial ; },
abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Multigene Family
Metagenome
*Databases, Genetic
Polysaccharides/metabolism
Metagenomics/methods
*Glycoside Hydrolases/genetics/metabolism
*Bacteria/genetics/enzymology/classification
Genome, Bacterial

@article {pmid41261745,
year = {2026},
author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z},
title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D925-D931},
pmid = {41261745},
issn = {1362-4962},
support = {2022FY100905//Science & Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; },
mesh = {*Virome/genetics ; Animals ; *Metagenomics/methods ; *Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Chiroptera/virology ; *Software ; Ticks/virology ; Zoonoses/virology ; Humans ; Culicidae/virology ; Animals, Wild/virology ; Rodentia/virology ; Metagenome ; Genome, Viral ; },
abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.},
}

*Virome/genetics
Animals
*Metagenomics/methods
*Viruses/genetics/classification
High-Throughput Nucleotide Sequencing
Chiroptera/virology
*Software
Ticks/virology
Zoonoses/virology
Humans
Culicidae/virology
Animals, Wild/virology
Rodentia/virology
Metagenome
Genome, Viral

@article {pmid41243980,
year = {2026},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1743-D1752},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI)/ ; //Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Autónoma de México/ ; },
mesh = {*Rhizosphere ; *Crops, Agricultural/microbiology ; *Microbiota/genetics ; Soil Microbiology ; *Metagenomics/methods ; Metagenome ; Software ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}

*Rhizosphere
*Crops, Agricultural/microbiology
*Microbiota/genetics
Soil Microbiology
*Metagenomics/methods
Metagenome
Software

@article {pmid41207298,
year = {2026},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D763-D775},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Metagenome
*Databases, Genetic
Molecular Sequence Annotation
Bacteria/genetics/classification
Software
Internet

@article {pmid41171125,
year = {2026},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D826-D834},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; ERC-AdG-669830/ERC_/European Research Council/International ; },
mesh = {*Metagenomics/methods ; Animals ; Humans ; *Databases, Genetic ; Metadata ; Metagenome ; Data Curation ; Gastrointestinal Microbiome/genetics ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}

*Metagenomics/methods
Animals
Humans
*Databases, Genetic
Metadata
Metagenome
Data Curation
Gastrointestinal Microbiome/genetics

@article {pmid40888850,
year = {2026},
author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA},
title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1733-D1742},
pmid = {40888850},
issn = {1362-4962},
support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Skłodowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; },
mesh = {*Plant Roots/microbiology ; *Microbiota/genetics ; *Databases, Protein ; Metagenomics ; Molecular Sequence Annotation ; Metagenome ; },
abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.},
}

*Plant Roots/microbiology
*Microbiota/genetics
*Databases, Protein
Metagenomics
Molecular Sequence Annotation
Metagenome

@article {pmid41539854,
year = {2026},
author = {Choi, S and Kwon, H and Kim, WK and Ko, G},
title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510017},
doi = {10.4014/jmb.2510.10017},
pmid = {41539854},
issn = {1738-8872},
mesh = {*Clostridium Infections/microbiology/therapy/prevention & control ; Animals ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; *Clostridioides difficile ; Disease Models, Animal ; Feces/microbiology ; Metagenomics ; },
abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.},
}

*Clostridium Infections/microbiology/therapy/prevention & control
Animals
*Clostridium/physiology/genetics
Gastrointestinal Microbiome
Mice
*Clostridioides difficile
Disease Models, Animal
Feces/microbiology
Metagenomics

@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}

*Fermentation
*Moringa oleifera/microbiology/chemistry
*Taste
*Plant Leaves/microbiology/chemistry
Gas Chromatography-Mass Spectrometry
Volatile Organic Compounds/analysis
Odorants/analysis
Amino Acids/analysis
*Food Microbiology
Flavoring Agents
*Fermented Foods/microbiology
Bacteria/metabolism/classification/genetics
Microbiota
Metagenomics
Multiomics

@article {pmid41538522,
year = {2026},
author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S},
title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA viromeFIRST REVIEW ROUND - REVIEWERS COMMENTSAUTHORS RESPONSE TO REVIEWERSREVIEWERS COMMENTS.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {120},
number = {},
pages = {e250131},
pmid = {41538522},
issn = {1678-8060},
mesh = {Animals ; *Mosquito Vectors/virology/classification ; *Arboviruses/genetics/isolation & purification ; Colombia ; *Culicidae/virology/classification ; *Virome/genetics ; *RNA, Viral/genetics ; Metagenomics ; Seasons ; Caribbean Region ; *RNA Viruses/genetics/classification ; Arbovirus Infections/transmission ; },
abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.

OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.

METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across Córdoba, Sucre, Bolívar, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50™ platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.

FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.

MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.},
}

Animals
*Mosquito Vectors/virology/classification
*Arboviruses/genetics/isolation & purification
Colombia
*Culicidae/virology/classification
*Virome/genetics
*RNA, Viral/genetics
Metagenomics
Seasons
Caribbean Region
*RNA Viruses/genetics/classification
Arbovirus Infections/transmission

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
doi = {10.1371/journal.pcbi.1013883},
pmid = {41525322},
issn = {1553-7358},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Aging/genetics/physiology ; *Longevity/genetics/physiology ; Aged ; Male ; Computational Biology ; Female ; Aged, 80 and over ; Feces/microbiology ; Metagenome/genetics ; Middle Aged ; },
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Aging/genetics/physiology
*Longevity/genetics/physiology
Aged
Male
Computational Biology
Female
Aged, 80 and over
Feces/microbiology
Metagenome/genetics
Middle Aged

@article {pmid41514452,
year = {2026},
author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K},
title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {24},
pmid = {41514452},
issn = {2049-2618},
support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium für Forschung, Technologie & Raumfahrt/ ; },
mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics/classification/isolation & purification ; Metagenomics/methods ; *Eukaryota/genetics/classification ; Metagenome ; Genetic Variation ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.

RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.

CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.},
}

*Wastewater/microbiology/virology
*Microbiota/genetics
*Bacteria/genetics/classification
*Drug Resistance, Microbial/genetics
*Viruses/genetics/classification/isolation & purification
Metagenomics/methods
*Eukaryota/genetics/classification
Metagenome
Genetic Variation

@article {pmid41468660,
year = {2026},
author = {Yu, X and Huang, S and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Multi-omics reveals efficient thiamethoxam biodegradation but altered flavor profile by native microbiota during Pixian broad bean paste fermentation.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111600},
doi = {10.1016/j.ijfoodmicro.2025.111600},
pmid = {41468660},
issn = {1879-3460},
mesh = {Fermentation ; *Thiamethoxam/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Neonicotinoids/metabolism ; *Insecticides/metabolism ; *Vigna/microbiology/chemistry/metabolism ; Guanidines/metabolism ; Taste ; Metagenomics ; Multiomics ; Thiazoles ; },
abstract = {Thiamethoxam (TH), a systemic neonicotinoid insecticide, poses food safety risks due to its persistence and uptake in crops. Microbial degradation during fermentation offers a promising decontamination strategy, but the underlying mechanisms and impact on food quality remain unclear. This study investigated TH and its toxic metabolite clothianidin biodegradation in Pixian broad bean paste (PBP) fermentation, assessed the impact of residue dissipation on product quality, and revealed microbial responses and metabolic adaptations under pesticide stress. Results demonstrated that TH and clothianidin were nearly completely degraded in the PBP fermentation system within 16 days, with a half-life of 3.25 days. Metagenomic analysis revealed that TH stress enriched pollutant-degrading microbes (e.g., Aspergillaceae, Desulfobacterota) and upregulated xenobiotic degradation genes (e.g., drug metabolism). However, volatile flavor compounds analysis indicated that TH treatment altered the flavor profile by reducing esters and phenols while increasing ketones and acids. Integrated metabolomics demonstrated that TH may disrupt organic acid metabolism during early fermentation, suppressing downstream flavonoid transformation and amino acid biosynthesis, ultimately compromising nutritional quality and flavor attributes. Multi-omics integration revealed that TH stress reshaped microbial community structure and enabled dual regulation of pesticide degradation and fermentation pathways through coordinated gene expression, ultimately altering PBP fermentation quality. Therefore, these findings demonstrate that the native microbial community in PBP efficiently degrades neonicotinoid pesticides, providing a novel strategy for the bioremediation of fermented foods and serving as an emerging reservoir of potential safe degrading bacteria, while highlighting the necessity for optimized microbial interventions to minimize adverse effects on product quality.},
}

Fermentation
*Thiamethoxam/metabolism
*Microbiota
Biodegradation, Environmental
*Bacteria/metabolism/genetics/classification/isolation & purification
Neonicotinoids/metabolism
*Insecticides/metabolism
*Vigna/microbiology/chemistry/metabolism
Guanidines/metabolism
Taste
Metagenomics
Multiomics
Thiazoles

@article {pmid41388903,
year = {2026},
author = {Wutkowska, M and Nweze, JA and Tláskal, V and Nweze, JE and Daebeler, A},
title = {Uncovering hidden phylo- and ecogenomic diversity of the widespread methanotrophic genus Methylobacter.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaf127},
pmid = {41388903},
issn = {1574-6941},
support = {21-17322 M//Czech Science Foundation/ ; },
mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Methane/metabolism ; Genome, Bacterial ; *Methylococcaceae/genetics/classification ; Geologic Sediments/microbiology ; Biodiversity ; Metagenome ; Ecosystem ; },
abstract = {The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterize the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulfur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognized species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.},
}

*Phylogeny
RNA, Ribosomal, 16S/genetics
*Methane/metabolism
Genome, Bacterial
*Methylococcaceae/genetics/classification
Geologic Sediments/microbiology
Biodiversity
Metagenome
Ecosystem

@article {pmid40576662,
year = {2026},
author = {Goldschmidt, I and Kramer, M and Junge, N and Ouro-Djobo, N and Poets, A and Rathert, M and Geffers, R and Baumann, U and Hartleben, B and Schulze, KD and Woltemate, S and Vital, M},
title = {Short-term and long-term development of gut microbiota in children after liver transplantation-A prospective observational trial.},
journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society},
volume = {32},
number = {2},
pages = {176-194},
doi = {10.1097/LVT.0000000000000659},
pmid = {40576662},
issn = {1527-6473},
mesh = {Humans ; *Liver Transplantation/adverse effects ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Child ; Prospective Studies ; *Dysbiosis/microbiology ; Child, Preschool ; Adolescent ; *End Stage Liver Disease/surgery/microbiology ; Feces/microbiology ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Case-Control Studies ; Infant ; Graft Survival ; Treatment Outcome ; Follow-Up Studies ; Metagenomics ; Time Factors ; },
abstract = {In children, little is known about gut microbiota (GM) in end-stage liver disease and its association with graft function after pediatric liver transplantation (pLT). We analyzed GM composition and function in children before pLT, longitudinally post-pLT and in long-term survivors (LT-pLT) in order to assess the impact of disease severity, treatment, and pLT on GM and delineate associations with graft and patient health. Fecal samples (FS) of 29 children [17f (female), age 2.6 (0.2-15.7) years] awaiting pLT were included with longitudinal follow-ups until 12 months post-transplant in 18, and compared with 38 LT-pLT [21f, age 11 (2.7-17.7) years, 7.8 (1.0-17.0) years post-pLT] and 94 healthy controls (HCs). Samples were analyzed using quantitative 16S rRNA gene analyses combined with shotgun metagenomics (subset of samples). Pre-pLT patients showed reduced alpha-diversities and altered GM composition compared with LT-pLT and HC, associated with disease severity and anti-pruritic treatment with rifampicin. Dysbiosis increased after pLT and started to recover after 3M (months). Although bacterial concentrations, alpha diversity, and gene richness increased post-pLT, levels remained below those of HC. Abundances of key functions, for example, the capacity to synthesize butyrate, also remained reduced. Quantitative analyses revealed the true extent of differences between patients and HC that were underestimated using relative abundance data. GM diversity and functional capacities correlated negatively with transaminase levels mid-term and long-term after pLT. Random Forest analyses based on GM were able to predict hepatocellular damage at high accuracy (AUC: 0.89). We provide comprehensive, quantitative insights into GM composition and function before and after pLT. A link between GM alterations and (long-term) graft health was uncovered, providing possible targets to modulate GM function in order to increase graft and patient health.},
}

Humans
*Liver Transplantation/adverse effects
*Gastrointestinal Microbiome/genetics
Female
Male
Child
Prospective Studies
*Dysbiosis/microbiology
Child, Preschool
Adolescent
*End Stage Liver Disease/surgery/microbiology
Feces/microbiology
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
Severity of Illness Index
Case-Control Studies
Infant
Graft Survival
Treatment Outcome
Follow-Up Studies
Metagenomics
Time Factors

@article {pmid41536238,
year = {2026},
author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C},
title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2607043},
doi = {10.1080/19490976.2025.2607043},
pmid = {41536238},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; Longitudinal Studies ; Adult ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Pregnancy in Obesity/microbiology/metabolism ; Infant ; Male ; Body Mass Index ; Mexico ; },
abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.},
}

Humans
*Milk, Human/chemistry
Female
*Oligosaccharides/analysis/metabolism
*Gastrointestinal Microbiome
Infant, Newborn
Feces/microbiology
Longitudinal Studies
Adult
Pregnancy
*Bacteria/classification/genetics/isolation & purification/metabolism
*Pregnancy in Obesity/microbiology/metabolism
Infant
Male
Body Mass Index
Mexico

@article {pmid41532487,
year = {2026},
author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK},
title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2026.2614431},
pmid = {41532487},
issn = {1549-7828},
abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.},
}

@article {pmid41530170,
year = {2026},
author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S},
title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {29},
pmid = {41530170},
issn = {2052-4463},
support = {Laboratoire international associé program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; },
abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.},
}

Chile
France
Metagenomics
Ecosystem
*DNA Barcoding, Taxonomic
*Metagenome
Seawater/microbiology
Salinity
Microbiota

@article {pmid41406442,
year = {2026},
author = {Li, Y and Li, H and Lv, C and Hu, X and Zhang, B},
title = {Bacterial changes and quality deterioration of freshwater shellfish Hyriopsis cumingii meat under different temperature storage.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2025-0056},
pmid = {41406442},
issn = {1480-3275},
mesh = {Animals ; Temperature ; *Bacteria/genetics/classification/isolation & purification ; *Shellfish/microbiology ; RNA, Ribosomal, 16S/genetics ; *Food Storage ; China ; Fresh Water/microbiology ; Food Microbiology ; Microbiota ; },
abstract = {Hyriopsis cumingii is an important economic freshwater shellfish in China and there is a need to understand changes in the microbial community structure resulting in multidimensional quality degradation when the fish is stored at different temperatures. This study integrated 16S rRNA full-length sequencing with multidimensional quality indicators to investigate the temperature-regulated bacterial community shifts and quality deterioration mechanisms in stored H. cumingii meat. The results showed that bacterial richness (Chao1 index) decreased progressively with both refrigerated (4 °C) and room-temperature (25 °C) storage. Community composition underwent significant restructuring, with Bacteroidota decreasing at 25 °C while Bacillota increased compared to 4 °C storage. Additionally, the refrigerated group showed enrichment of Delftia turuhatensis and Chryseobacterium indologenes compared to the room-temperature storage group. Temperature significantly restructured bacterial communities, with notably higher pathogenic bacteria under refrigeration and spoilage bacteria dominance at room temperature. Metagenomic functional profiling revealed temperature-driven metabolic pathway divergence, indicating distinct spoilage mechanism. Predictable quality changes in H. cumingii correlated with temperature-imposed microbial composition.},
}

Animals
Temperature
*Bacteria/genetics/classification/isolation & purification
*Shellfish/microbiology
RNA, Ribosomal, 16S/genetics
*Food Storage
China
Fresh Water/microbiology
Food Microbiology
Microbiota

@article {pmid41398180,
year = {2025},
author = {Song, X and Fu, Y and Xu, H and Wang, H and Chen, J and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W},
title = {Maternal health status is associated with paired maternal and cord blood virome and mother-to-infant transmission.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {14},
pmid = {41398180},
issn = {2055-5008},
support = {JSYGY-1-2023-03(03)//Jiangsu Provincial Hospital Association/ ; SH2023058//Social Development Projects in Zhenjiang/ ; 2023YFD1801300//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Fetal Blood/virology ; Female ; *Virome ; *Infectious Disease Transmission, Vertical ; Pregnancy ; Phylogeny ; Infant, Newborn ; *Viruses/classification/genetics/isolation & purification ; *Maternal Health ; Metagenomics ; Adult ; Genome, Viral ; Health Status ; },
abstract = {The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 near-complete genomes from four core viral families (Anelloviridae, Circoviridae, Parvoviridae, Flaviviridae). MPB viromes were primarily composed of bacteriophages and Anelloviridae, while UCB exhibited relatively increased abundances of Parvoviridae and Human Endogenous Retroviruses. Maternal disease correlated with reduced α-diversity in MPB but elevated richness in UCB. β-Diversity varied significantly with both health status and sample type. Differential abundance analysis identified health-specific signatures, including enriched Parvoviridae in diseased UCB. Phylogenetic evidence indicated possible vertical transmission and high genetic diversity among identified viruses. This study systematically characterizes the maternal-fetal blood virome and reveals associations between maternal health status and viral community structure, providing a basis for understanding early-life viral exposure and informing future preventive strategies.},
}

Humans
*Fetal Blood/virology
Female
*Virome
*Infectious Disease Transmission, Vertical
Pregnancy
Phylogeny
Infant, Newborn
*Viruses/classification/genetics/isolation & purification
*Maternal Health
Metagenomics
Adult
Genome, Viral
Health Status

@article {pmid41392116,
year = {2025},
author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H},
title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1801},
pmid = {41392116},
issn = {2045-2322},
support = {81860142//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ketamine/adverse effects ; *Cystitis/chemically induced/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Rats ; Metabolomics/methods ; Male ; Rats, Sprague-Dawley ; Urinary Bladder/metabolism ; *Metabolome ; Disease Models, Animal ; Bacteria/genetics/classification ; },
abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.},
}

Animals
*Ketamine/adverse effects
*Cystitis/chemically induced/metabolism/microbiology
*Gastrointestinal Microbiome/drug effects
Rats
Metabolomics/methods
Male
Rats, Sprague-Dawley
Urinary Bladder/metabolism
*Metabolome
Disease Models, Animal
Bacteria/genetics/classification

@article {pmid41382244,
year = {2025},
author = {Bae, IH and Kim, H and Kim, SM and Lee, YH},
title = {Multi-meta-omics reveal unique symbiotic synchronization between ectomycorrhizal fungus and soil microbiome in Tricholoma matsutake habitat.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {23},
pmid = {41382244},
issn = {2049-2618},
support = {RS-2022-NR072199//National Research Foundation of Korea/ ; RS-2025-00512558//National Research Foundation of Korea/ ; },
mesh = {*Mycorrhizae/physiology/genetics ; *Symbiosis ; *Soil Microbiology ; *Microbiota ; *Tricholoma/physiology ; Soil/chemistry ; Nitrogen/metabolism ; Plant Roots/microbiology ; Ecosystem ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: Ectomycorrhizal (ECM) fungi establish symbiotic relationships with plant roots, enhancing nutrient uptake, improving plant health, and boosting ecosystem resilience. Although previous studies reported molecular interactions among plant-ECM fungi-surrounding microbes near plant roots, microbiome-wide metabolic shifts and associations with the fungi remain unclear.

RESULTS: Using Tricholoma matsutake as a model, we initially found that T. matsutake induced remarkable microbial community turnover linked to altered soil moisture, nitrogen, and phosphorus levels. Parallel with the compositional alteration, microbiome-wide metabolic capacities, including glutamate metabolism, oligopeptide transport, and siderophore activity, were enriched in the T. matsutake-colonizing soil compared to the soils where the fungus was not colonized. From metatranscriptome data, we found that T. matsutake induced functional remodeling in nitrogen metabolism. Notably, the fungus and soil microbiome were metabolically synchronized with the upregulation of nitrate reduction, glutamate biosynthesis, tryptophan biosynthesis, and indole-3-acetic acid (IAA) biosynthesis. Metabarcoding and metatranscriptome-guided microbial associations revealed potential T. matsutake helper bacteria consisting of Conexibacter and Paraburkholderia. Phage community analyses further showed that the colonization of the ECM fungus influenced phage distributions along with the increase in temperate phage populations. The differential expression of auxiliary metabolic genes also demonstrated that phages could influence bacterial fitness in response to T. matsutake colonization.

CONCLUSION: Our multi-meta-omics-based approaches revealed unique environmental changes by T. matsutake compared to other mycorrhizal systems, as well as metabolic synchronization between the ECM fungus and surrounding microbiomes. These findings will expand our understanding of ECM symbiotic frameworks by highlighting integrated microbial and viral metabolic dynamics. Video Abstract.},
}

*Mycorrhizae/physiology/genetics
*Symbiosis
*Soil Microbiology
*Microbiota
*Tricholoma/physiology
Soil/chemistry
Nitrogen/metabolism
Plant Roots/microbiology
Ecosystem
Bacteria/classification/genetics/metabolism

@article {pmid41372750,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Metagenomic insights into microbial communities and antibiotic resistance in treated wastewater for urban irrigation.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {26},
pmid = {41372750},
issn = {1471-2180},
mesh = {*Wastewater/microbiology/chemistry ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Agricultural Irrigation ; Metals, Heavy/analysis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Cities ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; },
abstract = {BACKGROUND: The increasing reuse of treated wastewater for urban irrigation globally has raised ecological and public health concerns associated with microbial contaminations, antibiotic resistance genes (ARGs), and pathogen dissemination.

METHODS: Using a metagenomic approach, we analyzed microbial communities, ARGs, and pathogen profiles in three types of treated wastewater (W1, W2, W3) used for urban irrigation. Physicochemical properties, including nutrients and heavy metals, were also assessed to identify potential drivers of microbial and resistance patterns.

RESULTS: Significant variations in water quality and microbial community were observed across wastewater treatments. W2 showed the highest nutrient and organic pollution levels, while W3 exhibited elevated heavy metals such as zinc (83.37 µg/L), chromium (1.89 µg/L), and nickel (4.93 µg/L). Treated wastewater harbored significantly higher microbial diversity than tap water (P < 0.05), with W3 showing the most unique amplicon sequence variants (ASVs; 1 945, 7.31%). ARGs analysis revealed treatment-specific profiles: W1 was enriched in mupirocin and tetracycline resistance, W2 was dominated with beta-lactams and sulfonamides (P < 0.05), and W3 was enriched in fosfomycin and diaminopyrimidine resistance. Multidrug resistance genes dominated across all samples. PCoA revealed distinct microbial and ARGs structures across treatments (P < 0.05). Pathogens such as Salmonella enterica and Pseudomonas aeruginosa were abundant in treated wastewater, with Escherichia coli and Staphylococcus aureus identified as key pathogen hubs in ARG-pathogen co-occurrence networks. Nutrients (total nitrogen, phosphorus) and heavy metals (Fe and Pb) were key drivers of microbial community composition, ARGs abundance and pathogen prevalence.

CONCLUSIONS: This study underscores the ecological risks of using treated wastewater in urban environment, particularly due to the persistence of ARGs and pathogenic bacteria. Targeted removal of nutrients and heavy metals during wastewater treatment could help reduce microbial and resistance-related contamination, improving the safety of treated wastewater reuse.},
}

*Wastewater/microbiology/chemistry
*Metagenomics/methods
*Bacteria/genetics/drug effects/classification/isolation & purification
*Agricultural Irrigation
Metals, Heavy/analysis
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Cities
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Water Microbiology

@article {pmid39364864,
year = {2025},
author = {Dong, W and Hu, S and Yu, J and Liu, Y and Zeng, S and Duan, X and Deng, Y and Wang, Y and Yin, J and Xing, B and Shu, Z},
title = {Study on the Antidepressant Effect of Zhizichi Decoction by Regulating Metabolism and Intestinal Flora.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {28},
number = {16},
pages = {2826-2841},
pmid = {39364864},
issn = {1875-5402},
support = {82004245//National Natural Science Foundation of China/ ; 2018M641887//National Postdoctoral Science Foundation of China/ ; 822RC705//Natural Science Foundation of Hainan Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Antidepressive Agents/pharmacology/chemistry ; Rats ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Depression/drug therapy/metabolism ; Male ; Rats, Sprague-Dawley ; Disease Models, Animal ; Metabolomics ; Stress, Psychological/drug therapy ; },
abstract = {BACKGROUND: The incidence of depression is increasing year by year, and Zhizichi Decoction.ZZCD.has shown significant efficiency in the clinical treatment of mild depression, but its mechanism of action is still unclear. In this research, network pharmacology and metagenomics combined and metabolomics were used as research methods to explain the scientific connotation of the antidepressant effect of ZZCD from the aspects of the overall effect of organisms and microbial structure and function.

METHODS: The rat model of depression was established by chronic unpredictable mild stress (CUMS), and the improvement of depressive symptoms was evaluated by behavioral and histopathological methods. Network pharmacology predicted possible targets and important pathways of ZZCD. Metabolomics revealed its possible related biological pathways. Metagenomics showed the disturbance of ZZCD on intestinal microbial diversity structure and associated biological functions in depressed rats.

RESULTS: ZZCD can improve the behavioral performance of CUMS rats, and can significantly regulate the content of 5-HT, NE and other neurotransmitters in serum and brain tissue, and improve the damaged state of neurons in the hippocampus. Network pharmacology predicts that it mainly acts on biological processes such as inflammatory response and oxidative stress response. Metabolomics found that it affected metabolic pathways such as amino acid metabolism and lipid metabolism. The results of metagenomics showed that it significantly regulated the abundance of Firmicutes and Bacteroidetes. The above results predicted that it may affect signaling pathways such as the nervous system, inflammatory diseases and cell processing.

CONCLUSION: ZZCD may play an antidepressant role by regulating intestinal probiotics, energy metabolism, and inflammation reduction. This provides a scientific basis for the clinical application of ZZCD in traditional Chinese medicine and also makes it an optional alternative for the treatment of depression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Antidepressive Agents/pharmacology/chemistry
Rats
*Drugs, Chinese Herbal/pharmacology/chemistry
*Depression/drug therapy/metabolism
Male
Rats, Sprague-Dawley
Disease Models, Animal
Metabolomics
Stress, Psychological/drug therapy

@article {pmid41531093,
year = {2026},
author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W},
title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {650-662},
doi = {10.13227/j.hjkx.202411219},
pmid = {41531093},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Gossypium/growth & development ; Metagenomics ; Soil/chemistry ; Biodegradation, Environmental ; *Agriculture/methods ; Microbiota ; },
abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.},
}

*Soil Microbiology
*Gossypium/growth & development
Metagenomics
Soil/chemistry
Biodegradation, Environmental
*Agriculture/methods
Microbiota