@article {pmid41602774,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1766907},
doi = {10.3389/fmicb.2025.1766907},
pmid = {41602774},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].},
}

@article {pmid41602101,
year = {2025},
author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H},
title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730098},
pmid = {41602101},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Nanopore Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Metagenomics/methods ; Microbiota ; Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.

METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.

RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.

CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Nanopore Sequencing/methods
Male
Female
Middle Aged
Aged
Sputum/microbiology
*Precision Medicine/methods
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
Metagenomics/methods
Microbiota
Bacteria/genetics/isolation & purification/classification
Sensitivity and Specificity
Adult
Aged, 80 and over

@article {pmid41601218,
year = {2025},
author = {Li, CT},
title = {[Applications and challenges of forensic microbiomics].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {441-442},
doi = {10.12116/j.issn.1004-5619.2025.551105},
pmid = {41601218},
issn = {1004-5619},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; },
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Forensic Medicine/methods
*Gastrointestinal Microbiome
China
Genomics
Human Genome Project
*Forensic Sciences
Metagenome

@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020330},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Carotenoids/pharmacology/chemistry
*Computational Biology
Humans
Fermentation
Lycopene/pharmacology
Lutein/pharmacology
Bacteria/drug effects/genetics/classification
beta Carotene/pharmacology

@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010055},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Female ; Cohort Studies ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}

Humans
*Metagenomics/methods
*Tuberculosis/microbiology/diagnosis/blood
Microbiota/genetics
*Cell-Free Nucleic Acids/blood/genetics
*Coronary Artery Disease/microbiology/diagnosis/blood
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Female
Cohort Studies

@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010146},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@article {pmid41597216,
year = {2026},
author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP},
title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020141},
pmid = {41597216},
issn = {2073-4409},
support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Homeostasis/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Azoxymethane ; Dextran Sulfate ; *Antineoplastic Agents/pharmacology ; Male ; Humans ; },
abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
*Homeostasis/drug effects
*Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL
Azoxymethane
Dextran Sulfate
*Antineoplastic Agents/pharmacology
Male
Humans

@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021014},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy
Male
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Azoxymethane
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Dextran Sulfate
*Plant Extracts/pharmacology
Bacteria/genetics/classification

@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020838},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}

Humans
*Psoriasis/microbiology
*Pemphigus/microbiology
Female
Male
*Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
Adult
*Hidradenitis Suppurativa/microbiology
Feces/microbiology
*Bacteria/genetics/classification
Aged

@article {pmid41595535,
year = {2026},
author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y},
title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010116},
pmid = {41595535},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; Animals ; Genomics/methods ; Probiotics ; },
abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods
Animals
Genomics/methods
Probiotics

@article {pmid41595438,
year = {2025},
author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D},
title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010018},
pmid = {41595438},
issn = {2073-4425},
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pilot Projects ; *Cervix Uteri/microbiology ; Greece ; *Lactobacillus/genetics/isolation & purification/classification ; Adult ; Middle Aged ; Vagina/microbiology ; },
abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.},
}

Female
Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Pilot Projects
*Cervix Uteri/microbiology
Greece
*Lactobacillus/genetics/isolation & purification/classification
Adult
Middle Aged
Vagina/microbiology

@article {pmid41595429,
year = {2025},
author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F},
title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010009},
pmid = {41595429},
issn = {2073-4425},
support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen Cycle/genetics ; Metagenomics/methods ; Nitrogen/metabolism ; China ; Zea mays/growth & development ; Fertilizers ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification ; Charcoal ; },
abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.

METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.

RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.

CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.},
}

*Soil Microbiology
Soil/chemistry
*Nitrogen Cycle/genetics
Metagenomics/methods
Nitrogen/metabolism
China
Zea mays/growth & development
Fertilizers
*Microbiota/genetics
Metagenome
Bacteria/genetics/classification
Charcoal

@article {pmid41594879,
year = {2026},
author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L},
title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020144},
pmid = {41594879},
issn = {2079-7737},
support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; },
abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.},
}

@article {pmid41594560,
year = {2025},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.},
journal = {Biomolecules},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/biom16010018},
pmid = {41594560},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Amyloid beta-Peptides/metabolism ; Aged ; Feces/microbiology/chemistry ; Middle Aged ; Alzheimer Disease/metabolism ; Cognition ; },
abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.},
}

Humans
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
Female
Male
*Amyloid beta-Peptides/metabolism
Aged
Feces/microbiology/chemistry
Middle Aged
Alzheimer Disease/metabolism
Cognition

@article {pmid41593747,
year = {2026},
author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S},
title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03960-z},
pmid = {41593747},
issn = {1474-760X},
support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; },
abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.

RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves > 90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.

CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.},
}

@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}

*Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
*Databases, Genetic
Microbiota/genetics
Environmental Pollutants/metabolism
Metagenome
Metagenomics

@article {pmid41591576,
year = {2026},
author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ},
title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {62},
pmid = {41591576},
issn = {1573-0972},
support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG Nº 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Mycobiome/genetics ; Soil/chemistry ; Islands ; Phylogeny ; Biodiversity ; Nitrogen/analysis ; },
abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.},
}

Antarctic Regions
*Soil Microbiology
*Fungi/genetics/classification/isolation & purification
*Metagenomics/methods
*Mycobiome/genetics
Soil/chemistry
Islands
Phylogeny
Biodiversity
Nitrogen/analysis

@article {pmid41590723,
year = {2026},
author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A},
title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.},
journal = {Marine drugs},
volume = {24},
number = {1},
pages = {},
doi = {10.3390/md24010026},
pmid = {41590723},
issn = {1660-3397},
support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; },
mesh = {*Cyanobacteria/isolation & purification/genetics/metabolism ; *Microalgae/isolation & purification/genetics ; Salinity ; Slovenia ; Metagenomics/methods ; Biodiversity ; Biotechnology/methods ; Ecosystem ; },
abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.},
}

*Cyanobacteria/isolation & purification/genetics/metabolism
*Microalgae/isolation & purification/genetics
Salinity
Slovenia
Metagenomics/methods
Biodiversity
Biotechnology/methods
Ecosystem

@article {pmid41589896,
year = {2026},
author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT},
title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0258925},
doi = {10.1128/aem.02589-25},
pmid = {41589896},
issn = {1098-5336},
abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.},
}

@article {pmid41586370,
year = {2025},
author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L},
title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718782},
pmid = {41586370},
issn = {1664-302X},
abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.

METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.

RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.

DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.},
}

@article {pmid41586308,
year = {2025},
author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L},
title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695928},
pmid = {41586308},
issn = {2235-2988},
mesh = {Humans ; Cross-Sectional Studies ; *Metagenomics ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Microbiota/genetics ; Aged ; Severity of Illness Index ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Inflammation/microbiology ; *Abscess/microbiology ; },
abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.

METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.

RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.

CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.},
}

Humans
Cross-Sectional Studies
*Metagenomics
Male
Female
Retrospective Studies
Middle Aged
*Microbiota/genetics
Aged
Severity of Illness Index
*Bacteria/classification/genetics/isolation & purification
Adult
*Inflammation/microbiology
*Abscess/microbiology

@article {pmid41582618,
year = {2026},
author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J},
title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {1},
pages = {e70212},
pmid = {41582618},
issn = {2190-6009},
mesh = {Humans ; Male ; Female ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Soybean Proteins/administration & dosage/pharmacology ; Aged, 80 and over ; *Muscle, Skeletal/physiology ; *Meals ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; *Sarcopenia/diet therapy ; },
abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.

METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).

RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.

CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.},
}

Humans
Male
Female
Aged
*Gastrointestinal Microbiome/drug effects
*Soybean Proteins/administration & dosage/pharmacology
Aged, 80 and over
*Muscle, Skeletal/physiology
*Meals
Feces/microbiology
Fatty Acids, Volatile/metabolism
*Sarcopenia/diet therapy

@article {pmid41535719,
year = {2026},
author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L},
title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.},
journal = {Cell research},
volume = {36},
number = {2},
pages = {103-120},
pmid = {41535719},
issn = {1748-7838},
support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/immunology/microbiology/complications ; Risk Factors ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.},
}

Humans
*Dysbiosis/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Neoplasms/immunology/microbiology/complications
Risk Factors
Immune Checkpoint Inhibitors/therapeutic use
Animals

@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {39},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Salt-Tolerant Plants/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Metagenome ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}

*Plant Leaves/microbiology
*Bacteria/genetics/classification/isolation & purification
*Microbiota
*Salt-Tolerant Plants/microbiology
Soil Microbiology
Plant Roots/microbiology
Metagenome

@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3801},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Myositis/microbiology ; Middle Aged ; Adult ; China ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; Bacteria/genetics/classification ; Virome ; Machine Learning ; Case-Control Studies ; Metagenome ; Asian People ; Aged ; East Asian People ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
Female
Male
*Myositis/microbiology
Middle Aged
Adult
China
Feces/microbiology
Metagenomics/methods
Dysbiosis/microbiology
Bacteria/genetics/classification
Virome
Machine Learning
Case-Control Studies
Metagenome
Asian People
Aged
East Asian People

@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0112625},
doi = {10.1128/aem.01126-25},
pmid = {41493379},
issn = {1098-5336},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}

Humans
*Metagenomics/methods
*Microbiota
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid41457319,
year = {2026},
author = {Smith, DDN and Subasinghe, RM and Kehoe, C and Grégoire, DS},
title = {Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0198425},
pmid = {41457319},
issn = {1098-5336},
support = {GRDI-AMR2 One Health,STAGE//Environment and Climate Change Canada/ ; 2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Microbial Consortia ; Ammonia/metabolism ; *Nitrification ; Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification ; Multiomics ; },
abstract = {UNLABELLED: Microbial consortia show promise for bioremediation of environmental pollution, but performance optimization and risk assessment remain challenging due to unculturable species and limitations of traditional biochemical and sequencing tools. This study demonstrates how a multi-omics approach can provide deeper insight into the performance and risks of using a model aerobic ammonia-oxidizing consortium under conditions representative of wastewater treatment. Long-read DNA sequencing recovered several high-quality genomes, revealing dominance by an unclassified Nitrosospira species with expected ammonia oxidation capabilities. Lower-abundance taxa with nitrogen cycling potential were also detected, though species-level identification was limited by poor taxonomic database representation. Multi-omics and nitrogen analyses showed shifts in community composition and nitrogen cycling activity when the consortium was grown along a redox gradient typical of wastewater. All cultures accumulated ammonia over 4 weeks, with only aerobic cultures reducing ammonia levels thereafter. The dominant Nitrosospira population declined in abundance and activity in aerobic cultures while shifting toward nitrogen reduction under anoxic conditions. This metabolic shift would not have been detected using amplicon sequencing alone. Multi-omics also supported risk assessment through detection of waterborne pathogens from the Legionella genus and other lineages harboring virulence genes resembling those from known pathogens. This study highlights the value of multi-omics for optimizing microbial consortia and assessing biosafety risks but also underscores challenges related to effective data analyses and the feasibility of risk assessment under realistic conditions. Addressing these challenges will be essential to support the broader adoption of multi-omics strategies by stakeholders working with microbial consortia across diverse environmental applications.

IMPORTANCE: Microbial consortia are increasingly used to advance a sustainable bioeconomy. Optimizing consortia for environmental applications and ensuring regulatory compliance remains challenging, largely due to reliance on culturing microbes with unknown physiology. In this study, we apply cutting-edge sequencing to a consortium designed for ammonia removal from wastewater. Long-read DNA sequencing enabled complete genome recovery and revealed that populations integral to nitrogen cycling are poorly represented in taxonomic databases. By integrating multi-omics with biochemical assays, we uncovered how environmental conditions drive off-target nitrogen reactions and the potential risks of exposure to pathogens carrying virulence genes. Our findings underscore how whole-community approaches provide insights that are not obtainable with traditional amplicon sequencing and biochemical analysis methods. However, our study also provides recommendations on how hurdles related to data integration and environmental representation must be addressed to support stakeholders adopting such approaches in the context of commercializing microbial consortia.},
}

*Microbial Consortia
Ammonia/metabolism
*Nitrification
Wastewater/microbiology
*Bacteria/metabolism/genetics/classification
Multiomics

@article {pmid41443199,
year = {2026},
author = {Lucas, TN and Biehain, U and Gautam, A and Gemeinhardt, K and Lass, T and Konzalla, S and Ley, RE and Angenent, LT and Huson, DH},
title = {MMonitor for real-time monitoring of microbial communities using long reads.},
journal = {Cell reports methods},
volume = {6},
number = {1},
pages = {101266},
doi = {10.1016/j.crmeth.2025.101266},
pmid = {41443199},
issn = {2667-2375},
mesh = {Humans ; *Metagenomics/methods ; *Software ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; },
abstract = {Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source software platform for real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI) and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs. We compare MMonitor with other real-time metagenomic tools, outlining their strengths and limitations.},
}

Humans
*Metagenomics/methods
*Software
Metagenome/genetics
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Computational Biology/methods
Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing
Whole Genome Sequencing

@article {pmid41437386,
year = {2025},
author = {Aminu, S and Ascandari, A and Mokhtar, MM and Allali, AE and Benhida, R and Daoud, R},
title = {Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {45},
pmid = {41437386},
issn = {2049-2618},
mesh = {*Microbiota/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Sewage/microbiology ; Cities ; Metagenomics/methods ; Machine Learning ; Genome, Bacterial ; },
abstract = {BACKGROUND: Human-built environment microbiomes mediate pathogen persistence and antimicrobial resistance (AMR) circulation, yet their ecological organization and resilience remain poorly quantified. Hospitals, sewage systems, ambulances, and public transport form interconnected microbial networks where contamination potential and compositional stability define biosurveillance risk. Understanding these dynamics requires genome-resolved frameworks capable of linking community composition to ecological behavior.

METHODS: We analyzed 767 publicly available Illumina metagenomes from four urban environments using the GRUMB workflow. Quality-filtered reads were assembled into 10,834 metagenome-assembled genomes (MAGs) and dereplicated into 1542 species-level representatives. Functional annotation with CARD and VFDB identified ARG- and VF-carrying species, producing a genome-resolved abundance matrix used for ecological and predictive modeling. Alpha and beta diversity, indicator taxa, and prevalence were assessed in R, while machine learning (Random Forest, scikit-learn) achieved a nested cross-validation balanced accuracy of 0.97 ± 0.01. Synthetic donor-recipient simulations (α = 0-1) implemented in Python modeled compositional blending, entropy-based uncertainty, and Minimal Detectable Contamination (MDC) thresholds.

RESULTS: Microbial communities exhibited strong environment-specific structure (PERMANOVA R[2] = 0.12, p < 0.001). Hospital sewage contained the highest richness and compositional heterogeneity, whereas ambulances and hospital environments showed low-diversity, surface-filtered microbiomes. Machine learning identified consistent ecological predictors (Pseudomonas_E fragi, Sphingomonas sp000797515, Acinetobacter variabilis, Roseomonas mucosa) that delineated environmental identity. Synthetic blending revealed a directional source-sink hierarchy with hospital sewage acting as the primary donor (MDC = 0.2-0.3), while hospital environments displayed the greatest compositional resilience (MDC ≥ 0.8). Entropy-based uncertainty analysis identified tipping zones (α = 0.3-0.5), and dominance mapping highlighted hospital environments as stabilizing ecological nodes. WHO-priority pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli) occupied central positions in the network, bridging environmental and clinical compartments.

CONCLUSIONS: This genome-resolved and simulation-driven framework reveals a directional microbial continuum across urban infrastructures governed by dominance, resilience, and clinical connectivity. Hospital sewage functions as a microbial donor, while hospital environments act as ecological stabilizers anchoring built-environment microbiomes. These findings advance biosurveillance from descriptive profiling to predictive ecological modeling, offering quantitative metrics for risk-informed infrastructure design. Video Abstract.},
}

*Microbiota/genetics
Humans
*Bacteria/genetics/classification/isolation & purification
Metagenome
Sewage/microbiology
Cities
Metagenomics/methods
Machine Learning
Genome, Bacterial

@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {954},
pmid = {41423629},
issn = {2041-1723},
support = {109105z/15/a//Wellcome Trust (Wellcome)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; },
mesh = {Humans ; Malawi ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics/drug effects ; Female ; Male ; Bayes Theorem ; Antimicrobial Stewardship ; Bacteria/drug effects/genetics/classification ; Sepsis/drug therapy/microbiology ; Metagenomics ; Young Adult ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}

Humans
Malawi
*Gastrointestinal Microbiome/drug effects/genetics
*Anti-Bacterial Agents/pharmacology/therapeutic use
Adult
Feces/microbiology
*Drug Resistance, Bacterial/genetics/drug effects
Female
Male
Bayes Theorem
Antimicrobial Stewardship
Bacteria/drug effects/genetics/classification
Sepsis/drug therapy/microbiology
Metagenomics
Young Adult

@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {22},
pmid = {41422269},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; Metagenomics ; Virulence Factors/genetics ; Animal Migration ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics ; Metagenome ; Sequence Analysis, DNA ; },
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}

*Gastrointestinal Microbiome/genetics
Animals
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects
Metagenomics
Virulence Factors/genetics
Animal Migration
Phylogeny
*Drug Resistance, Bacterial/genetics
DNA, Bacterial/genetics
Metagenome
Sequence Analysis, DNA

@article {pmid41408356,
year = {2026},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {65},
number = {1},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
support = {202330//National Clinical Key Speciality Capacity Building/ ; 2021818//Hainan Province Clinical Medical Center/ ; YSPTZX202313//The Innovation Platform for Academicians of Hainan Province/ ; WSJK2024MS150//Joint Project on Health Science and Technology Innovation in Hainan Province/ ; Qhyb2022-133//Hainan Provincial Postgraduate Innovation Research/ ; hnjg2024-67//Hainan Province Education Reform/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; *Metabolome/physiology ; Feces/microbiology ; Metabolomics ; Adult ; Aged ; Case-Control Studies ; Metagenomics ; Tandem Mass Spectrometry ; Multiomics ; },
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.

METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted liquid chromatography-tandem mass spectrometry metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.

RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae and Parabacteroides distasonis were noticed. Conversely, Phocaeicola plebeius, Blautia hansenii and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.

CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}

Humans
*Scleroderma, Systemic/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
*Metabolome/physiology
Feces/microbiology
Metabolomics
Adult
Aged
Case-Control Studies
Metagenomics
Tandem Mass Spectrometry
Multiomics

@article {pmid41395968,
year = {2026},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0198525},
pmid = {41395968},
issn = {1098-5336},
support = {4421050//USDA-Evans-Allen/ ; 2021-38821-34583//USDA-CBG/ ; },
mesh = {Animals ; *Microbiota ; *Aquaculture/methods ; *Ostreidae/microbiology ; *Vibrio parahaemolyticus/genetics/isolation & purification ; *Vibrio vulnificus/genetics/isolation & purification ; *Vibrio ; Population Dynamics ; Metagenomics ; },
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}

Animals
*Microbiota
*Aquaculture/methods
*Ostreidae/microbiology
*Vibrio parahaemolyticus/genetics/isolation & purification
*Vibrio vulnificus/genetics/isolation & purification
*Vibrio
Population Dynamics
Metagenomics

@article {pmid41366061,
year = {2026},
author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY},
title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.},
journal = {British journal of cancer},
volume = {134},
number = {3},
pages = {469-476},
pmid = {41366061},
issn = {1532-1827},
support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology/diagnosis/etiology ; *Life Style ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Diet ; Adult ; Aged ; Cohort Studies ; Age of Onset ; },
abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.

METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.

RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC = 0.95, 95% CI = 0.92-0.98).

CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/epidemiology/diagnosis/etiology
*Life Style
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Diet
Adult
Aged
Cohort Studies
Age of Onset

@article {pmid41363534,
year = {2026},
author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y},
title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.},
journal = {mSphere},
volume = {11},
number = {1},
pages = {e0053925},
pmid = {41363534},
issn = {2379-5042},
mesh = {Animals ; China ; *Virome/genetics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Culicidae/virology ; Metagenomics ; *Mosquito Vectors/virology ; High-Throughput Nucleotide Sequencing ; *Genetic Variation ; Culex/virology ; },
abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.},
}

Animals
China
*Virome/genetics
Phylogeny
*RNA Viruses/genetics/classification/isolation & purification
*Culicidae/virology
Metagenomics
*Mosquito Vectors/virology
High-Throughput Nucleotide Sequencing
*Genetic Variation
Culex/virology

@article {pmid41358839,
year = {2026},
author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q},
title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0189025},
pmid = {41358839},
issn = {1098-5336},
mesh = {Animals ; *Chickens/microbiology/metabolism/growth & development ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Animal Feed/analysis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metabolomics ; Metagenomics ; Fermentation ; },
abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.

IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (≤20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.},
}

Animals
*Chickens/microbiology/metabolism/growth & development
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics/analysis
*Animal Feed/analysis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metabolomics
Metagenomics
Fermentation

@article {pmid41318814,
year = {2026},
author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C},
title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.},
journal = {British journal of cancer},
volume = {134},
number = {3},
pages = {439-446},
pmid = {41318814},
issn = {1532-1827},
mesh = {Humans ; *Stomach Neoplasms/therapy/immunology/pathology/drug therapy ; Male ; Female ; Middle Aged ; Aged ; Retrospective Studies ; *Immunotherapy, Adoptive/methods ; *Claudins/immunology ; Gastrointestinal Microbiome/drug effects ; Adult ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Granulocyte Colony-Stimulating Factor/administration & dosage/therapeutic use ; Antibodies, Monoclonal, Humanized/administration & dosage/therapeutic use ; Adrenal Cortex Hormones/administration & dosage/therapeutic use ; Treatment Outcome ; },
abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.

METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.

RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P < 0.001) and overall survival (OS) (3.9 vs. 9.5 months; P < 0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.

CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.

TRIAL REGISTRATION: NCT03874897.},
}

Humans
*Stomach Neoplasms/therapy/immunology/pathology/drug therapy
Male
Female
Middle Aged
Aged
Retrospective Studies
*Immunotherapy, Adoptive/methods
*Claudins/immunology
Gastrointestinal Microbiome/drug effects
Adult
Anti-Bacterial Agents/therapeutic use/administration & dosage
Granulocyte Colony-Stimulating Factor/administration & dosage/therapeutic use
Antibodies, Monoclonal, Humanized/administration & dosage/therapeutic use
Adrenal Cortex Hormones/administration & dosage/therapeutic use
Treatment Outcome

@article {pmid41015044,
year = {2025},
author = {Mukherjee, A and Mazumder, M and Verma, A and Tikariha, H and Bhattacharya, R and Ooi, QE and Swarup, S},
title = {A bacterial signal coordinates plant-microbe fitness trade-off to enhance sulfur deficiency tolerance in plants.},
journal = {Cell host & microbe},
volume = {33},
number = {10},
pages = {1748-1764.e6},
doi = {10.1016/j.chom.2025.09.007},
pmid = {41015044},
issn = {1934-6069},
mesh = {*Sulfur/deficiency/metabolism ; *Rhizosphere ; Soil Microbiology ; Microbiota ; *Glutathione/metabolism ; *Arabidopsis/genetics/growth & development/microbiology ; Brassicaceae/genetics/growth & development/microbiology ; Genetic Fitness ; Metagenome ; Plant Roots/microbiology ; },
abstract = {Plant-associated microorganisms interact with each other and with host plants via intricate chemical signals, offering multiple benefits, including enhanced nutrition. We report a mechanism through which the rhizosphere microbiome improves plant growth under sulfur (S) deficiency. Disruption of plant S homeostasis caused a coordinated shift in the composition and S-metabolism of the rhizosphere microbiome. Leveraging this, we developed an 18-membered synthetic rhizosphere bacterial community (SynCom) that rescued the growth of Arabidopsis and a leafy Brassicaceae vegetable under S-deficiency. This beneficial trait is taxonomically widespread among SynCom members, with bacterial pairs providing both synergistic and neutral effects on host growth. Notably, stronger competitive interactions among SynCom members conferred greater fitness benefits to the host, suggesting a trans-kingdom (plant-microbe) fitness trade-off. Finally, guided chemical screening, deletion knockout mutants, and targeted metabolomics identified and validated microbially released glutathione (GSH) as the necessary bioactive signal that coordinates the trans-kingdom fitness trade-off and improves plant growth under sulfur limitation.},
}

*Sulfur/deficiency/metabolism
*Rhizosphere
Soil Microbiology
Microbiota
*Glutathione/metabolism
*Arabidopsis/genetics/growth & development/microbiology
Brassicaceae/genetics/growth & development/microbiology
Genetic Fitness
Metagenome
Plant Roots/microbiology

@article {pmid41582543,
year = {2026},
author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF},
title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {1},
pages = {26-35},
doi = {10.3967/bes2025.089},
pmid = {41582543},
issn = {2214-0190},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Blood Pressure ; *Hypertension/microbiology ; Prospective Studies ; Aged ; Blood Pressure Monitoring, Ambulatory ; China ; Adult ; },
abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).

METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.

RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).

CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Blood Pressure
*Hypertension/microbiology
Prospective Studies
Aged
Blood Pressure Monitoring, Ambulatory
China
Adult

@article {pmid41581932,
year = {2026},
author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK},
title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.},
journal = {Advances in protein chemistry and structural biology},
volume = {149},
number = {},
pages = {171-201},
doi = {10.1016/bs.apcsb.2025.08.002},
pmid = {41581932},
issn = {1876-1631},
mesh = {*Biotechnology/economics ; *Antimicrobial Peptides/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; Humans ; Animals ; Delivery of Health Care/economics ; *Anti-Bacterial Agents/pharmacology/chemistry ; },
abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.},
}

*Biotechnology/economics
*Antimicrobial Peptides/chemistry/pharmacology
*Aquatic Organisms/chemistry
Humans
Animals
Delivery of Health Care/economics
*Anti-Bacterial Agents/pharmacology/chemistry

@article {pmid41581112,
year = {2026},
author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P},
title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {62},
pmid = {41581112},
issn = {1432-8798},
mesh = {*Plant Diseases/virology ; *Solanum lycopersicum/virology ; *Hemiptera/virology ; Animals ; Phylogeny ; *Virome/genetics ; Reunion ; Metagenomics ; *Luteoviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; },
abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.},
}

*Plant Diseases/virology
*Solanum lycopersicum/virology
*Hemiptera/virology
Animals
Phylogeny
*Virome/genetics
Reunion
Metagenomics
*Luteoviridae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing
Genome, Viral

@article {pmid41578762,
year = {2025},
author = {Shen, F and Xu, C and Wang, C},
title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.},
journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology},
volume = {37},
number = {1},
pages = {62-74},
pmid = {41578762},
issn = {2148-5607},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; Female ; Middle Aged ; *Biomarkers, Tumor/analysis ; Aged ; *Adenoma/microbiology/diagnosis ; Case-Control Studies ; Disease Progression ; Early Detection of Cancer/methods ; Fusobacterium nucleatum/isolation & purification ; Adult ; },
abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.

MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.

RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.

CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression.   Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
*Gastrointestinal Microbiome/genetics
Male
Feces/microbiology
Female
Middle Aged
*Biomarkers, Tumor/analysis
Aged
*Adenoma/microbiology/diagnosis
Case-Control Studies
Disease Progression
Early Detection of Cancer/methods
Fusobacterium nucleatum/isolation & purification
Adult

@article {pmid41485666,
year = {2026},
author = {He, H and Han, L and Ni, W and Yu, J and Liu, K and Li, W and Li, C and Hu, S and Li, C and Li, X},
title = {The horse gut microbiota genome represents a vast novel reservoir of CAZymes.},
journal = {International journal of biological macromolecules},
volume = {339},
number = {Pt 2},
pages = {150042},
doi = {10.1016/j.ijbiomac.2025.150042},
pmid = {41485666},
issn = {1879-0003},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Horses/microbiology ; Phylogeny ; *Glycoside Hydrolases/genetics/metabolism ; *Genome, Bacterial ; Metagenome ; Glycosyltransferases/genetics/metabolism ; Substrate Specificity ; },
abstract = {Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilization loci (PULs) discovered in Bacteroides species. Through comparative genomic screening, a total of 12,976 hypothetical genes were predicted in PULs. These genes represent a putative novel reservoir of CAZymes. We selected and identified a putative CAZyme, which encodes 452 amino acids and is designated H113. Our research has confirmed that H113 is a metal enzyme (Zn[2+] significantly enhancing its catalytic efficiency) capable of degrading α-1,4 glycosidic bonds in maltotriose and also exhibiting activity toward mannan, demonstrating optimal activity at pH 4.8 and 35 °C (specific activity: maltotriose: 82.2 U/mg, mannan: 2.3 U/mg). Phylogenetic analysis revealed H113 belongs to a conserved enzyme family with 1866 identified homologues. This study not only provides a reference for efficient discovery of novel CAZymes but also offers valuable resources for developing novel biocatalysts.},
}

Animals
*Gastrointestinal Microbiome/genetics
Horses/microbiology
Phylogeny
*Glycoside Hydrolases/genetics/metabolism
*Genome, Bacterial
Metagenome
Glycosyltransferases/genetics/metabolism
Substrate Specificity

@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