@article {pmid41748019,
year = {2026},
author = {Piccinno, G and Asnicar, F},
title = {Advanced computational analysis in metagenomic studies to support precision medicine.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {32},
number = {7},
pages = {1075-1080},
doi = {10.1016/j.cmi.2026.02.018},
pmid = {41748019},
issn = {1469-0691},
mesh = {Humans ; *Precision Medicine/methods ; *Metagenomics/methods ; *Computational Biology/methods ; *Microbiota/genetics ; },
abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a nondiseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.

OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.

SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.

CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multicohort data analysis, integration, and validation methods.

IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.},
}

Humans
*Precision Medicine/methods
*Metagenomics/methods
*Computational Biology/methods
*Microbiota/genetics

@article {pmid41850677,
year = {2026},
author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J},
title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {20},
number = {7},
pages = {101770},
pmid = {41850677},
issn = {2352-345X},
mesh = {Animals ; *Neutrophils/metabolism/immunology/drug effects ; *Hepatolenticular Degeneration/pathology/immunology/microbiology/metabolism ; *Propionates/metabolism/pharmacology ; Mice ; Mice, Knockout ; *Gastrointestinal Microbiome/immunology ; Transforming Growth Factor beta1/metabolism ; *Liver/pathology/immunology/metabolism ; Fecal Microbiota Transplantation ; Copper-Transporting ATPases/genetics ; Disease Models, Animal ; Male ; Humans ; Hydroxamic Acids ; },
abstract = {BACKGROUND & AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.

METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-β1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.

RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-β1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-β1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-β1.

CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-β1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.},
}

Animals
*Neutrophils/metabolism/immunology/drug effects
*Hepatolenticular Degeneration/pathology/immunology/microbiology/metabolism
*Propionates/metabolism/pharmacology
Mice
Mice, Knockout
*Gastrointestinal Microbiome/immunology
Transforming Growth Factor beta1/metabolism
*Liver/pathology/immunology/metabolism
Fecal Microbiota Transplantation
Copper-Transporting ATPases/genetics
Disease Models, Animal
Male
Humans
Hydroxamic Acids

@article {pmid41951175,
year = {2026},
author = {Rana, N and Tiewsoh, K and Ray, P and Angrup, A},
title = {Automating Microbial Community Analysis (AMCA): Development and application of an amplicon based graphical pipeline in patients with Chronic Kidney Disease.},
journal = {Indian journal of medical microbiology},
volume = {61},
number = {},
pages = {101110},
doi = {10.1016/j.ijmmb.2026.101110},
pmid = {41951175},
issn = {1998-3646},
mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Workflow ; Phylogeny ; Computational Biology/methods ; Bacteria/classification/genetics ; Software ; },
abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.

METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.

RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.

CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.},
}

Humans
*Renal Insufficiency, Chronic/microbiology
*Metagenomics/methods
*Microbiota/genetics
Workflow
Phylogeny
Computational Biology/methods
Bacteria/classification/genetics
Software

@article {pmid41966472,
year = {2026},
author = {Merkhan, K and Chaudhry, AS},
title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.},
journal = {Anaerobe},
volume = {98},
number = {},
pages = {103046},
doi = {10.1016/j.anaerobe.2026.103046},
pmid = {41966472},
issn = {1095-8274},
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Methane/metabolism/biosynthesis ; Fermentation ; *Animal Feed/analysis ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; Archaea/metabolism ; Bacteria/classification/genetics/metabolism ; *Food Additives ; },
abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.

METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72 h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20 g kg[-1] DM) for each PFA.

RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20 g kg[-1] DM, followed by GBL with a 28.5% reduction at 10 g kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.

CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.},
}

Animals
*Rumen/microbiology/metabolism
Cattle
*Methane/metabolism/biosynthesis
Fermentation
*Animal Feed/analysis
*Microbiota/drug effects
Fatty Acids, Volatile/metabolism
Archaea/metabolism
Bacteria/classification/genetics/metabolism
*Food Additives

@article {pmid41974712,
year = {2026},
author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y},
title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41974712},
issn = {2041-1723},
support = {R21 AI180737/AI/NIAID NIH HHS/United States ; R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Animals ; *Lupus Erythematosus, Systemic/microbiology/immunology/therapy ; Multiomics ; Male ; Mice ; *Faecalibacterium prausnitzii/physiology ; Disease Models, Animal ; Th17 Cells/immunology ; *Dysbiosis/microbiology/therapy/immunology ; Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Feces/microbiology ; *Probiotics/administration & dosage ; T-Lymphocytes, Regulatory/immunology ; Mice, Inbred C57BL ; Metagenome ; Metabolomics ; },
abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.},
}

Animals
*Lupus Erythematosus, Systemic/microbiology/immunology/therapy
Multiomics
Male
Mice
*Faecalibacterium prausnitzii/physiology
Disease Models, Animal
Th17 Cells/immunology
*Dysbiosis/microbiology/therapy/immunology
Humans
*Gastrointestinal Microbiome/immunology/genetics
Feces/microbiology
*Probiotics/administration & dosage
T-Lymphocytes, Regulatory/immunology
Mice, Inbred C57BL
Metagenome
Metabolomics

@article {pmid41975031,
year = {2026},
author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE},
title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41975031},
issn = {2399-3642},
support = {DairyBio//Dairy Australia/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Methane/metabolism ; Metagenome ; *Gastrointestinal Microbiome ; *Microbiota ; Australia ; },
abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.},
}

Animals
*Rumen/microbiology
Cattle/microbiology
*Methane/metabolism
Metagenome
*Gastrointestinal Microbiome
*Microbiota
Australia

@article {pmid41975041,
year = {2026},
author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , },
title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.},
journal = {British journal of cancer},
volume = {135},
number = {1},
pages = {139-151},
pmid = {41975041},
issn = {1532-1827},
support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; },
mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy/methods ; *Gastrointestinal Microbiome ; *Biomarkers, Tumor ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).

METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.

RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa -notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.

CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.

PROSPERO: CRD42023433704.},
}

Humans
*Rectal Neoplasms/microbiology/therapy
*Neoadjuvant Therapy/methods
*Gastrointestinal Microbiome
*Biomarkers, Tumor
Treatment Outcome

@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
mesh = {Animals ; *Ticks/microbiology ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenome ; Sheep/microbiology ; Soil Microbiology ; Marmota/microbiology ; *Livestock/microbiology ; *Animals, Wild/microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Caves/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}

Animals
*Ticks/microbiology
Gene Transfer, Horizontal
Metagenomics/methods
*Bacteria/genetics/classification/drug effects/isolation & purification
Metagenome
Sheep/microbiology
Soil Microbiology
Marmota/microbiology
*Livestock/microbiology
*Animals, Wild/microbiology
Microbiota
*Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial
Caves/microbiology
Genes, Bacterial
Anti-Bacterial Agents/pharmacology

@article {pmid41986664,
year = {2026},
author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J},
title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41986664},
issn = {2399-3642},
mesh = {*Soil Microbiology ; *Microbiota/genetics ; Arctic Regions ; *Metagenomics ; *Metagenome ; Russia ; *Bacteria/genetics ; *Genes, Microbial ; },
abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.},
}

*Soil Microbiology
*Microbiota/genetics
Arctic Regions
*Metagenomics
*Metagenome
Russia
*Bacteria/genetics
*Genes, Microbial

@article {pmid41991911,
year = {2026},
author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q},
title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41991911},
issn = {2041-1723},
support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; China ; Animals ; Fermentation ; Metagenome ; Food Microbiology ; Polymorphism, Single Nucleotide ; Lactobacillus helveticus/genetics ; Phylogeny ; Metagenomics ; Biodiversity ; beta-Galactosidase/metabolism ; },
abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.},
}

*Cheese/microbiology
*Microbiota/genetics
China
Animals
Fermentation
Metagenome
Food Microbiology
Polymorphism, Single Nucleotide
Lactobacillus helveticus/genetics
Phylogeny
Metagenomics
Biodiversity
beta-Galactosidase/metabolism

@article {pmid42041249,
year = {2026},
author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS},
title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.},
journal = {mBio},
volume = {17},
number = {6},
pages = {e0286825},
pmid = {42041249},
issn = {2150-7511},
support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; R01AI153332,R21AI186346//National Institute of Allergy and Infectious Diseases/ ; F32AI186285//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Female ; *Streptococcus agalactiae/genetics/growth & development/physiology ; *Vagina/microbiology ; Humans ; *Streptococcal Infections/microbiology ; Pregnancy ; Epithelial Cells/microbiology ; Animals ; Bacterial Adhesion ; Microbiota ; Akkermansia ; Mice ; },
abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.},
}

Female
*Streptococcus agalactiae/genetics/growth & development/physiology
*Vagina/microbiology
Humans
*Streptococcal Infections/microbiology
Pregnancy
Epithelial Cells/microbiology
Animals
Bacterial Adhesion
Microbiota
Akkermansia
Mice

@article {pmid42057198,
year = {2026},
author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J},
title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42057198},
issn = {1756-994X},
support = {2021-01637//Vetenskapsrådet/ ; 967569//Västerbotten Läns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; 09150162410022/ZONMW_/ZonMw/Netherlands ; },
mesh = {Humans ; *COVID-19/epidemiology/microbiology ; *Life Style ; Infant ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; Pandemics ; Feces/microbiology ; Metagenome ; Male ; Female ; Longitudinal Studies ; Hygiene ; },
abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.

METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.

RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.

CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.},
}

Humans
*COVID-19/epidemiology/microbiology
*Life Style
Infant
SARS-CoV-2
*Gastrointestinal Microbiome
Pandemics
Feces/microbiology
Metagenome
Male
Female
Longitudinal Studies
Hygiene

@article {pmid42103932,
year = {2026},
author = {Wang, F and Zeng, W and Zhang, Z and Li, N and Cui, Z and Bai, J and Yan, J and Zhang, Y and Miao, Y and Gu, L and Xiong, B},
title = {Gut microbiota-modulated glutamic acid rejuvenates the quality of oocytes deteriorated by advanced reproductive age.},
journal = {EMBO molecular medicine},
volume = {18},
number = {6},
pages = {2404-2435},
pmid = {42103932},
issn = {1757-4684},
support = {2023YFD1300502//MOST | National Key Research and Development Program of China (NKPs)/ ; BYSYSZKF2023029//State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital/ ; KYCX25_1007//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
mesh = {Animals ; *Oocytes/physiology/drug effects/metabolism/cytology ; Female ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome ; Mice ; Fecal Microbiota Transplantation ; Aging ; Metabolome ; Fertility ; },
abstract = {The gut microbiota plays a vital role in maintaining the physiological function of host health and the pathogenesis of various diseases. However, its relationship with maternal age-associated decline in oocyte quality remains elusive. Here, we report that establishment of gut microbiota from young donors in aged mice by fecal microbiota transplantation (FMT) is an effective method to rejuvenate the quality of maternally aged oocytes. Specifically, young gut microbiota promoted the ovulation and maturation of aged oocytes, and inhibited occurrence of cytoplasm fragmentation and spindle/chromosome abnormalities, hence enhancing the oocyte quality and female fertility. By integrating metagenome and untargeted metabolome of intestinal digesta, as well as targeted metabolome of ovaries and micro-transcriptome of oocytes, we identified that Bacteroides_caecimuris-modulated glutamic acid levels mediated the restorative effects of young gut microbiota on the aged oocytes through strengthening the mitochondria function. In addition, we demonstrated that in vivo supplementation of glutamic acid also enhanced the quality of aged oocytes, and the improvement of oocyte quality by glutamic acid was conserved across species. Altogether, our findings highlight the importance of gut microbiota in the oocyte aging and provide potential improvement strategies for age-related decline in oocyte quality and female fertility.},
}

Animals
*Oocytes/physiology/drug effects/metabolism/cytology
Female
*Glutamic Acid/metabolism
*Gastrointestinal Microbiome
Mice
Fecal Microbiota Transplantation
Aging
Metabolome
Fertility

@article {pmid42119030,
year = {2026},
author = {Yu, J and Tang, SN and Lee, PKH},
title = {Host-linked virome assembly and turnover predict bacterial community structure in wastewater treatment systems.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag120},
pmid = {42119030},
issn = {1751-7370},
support = {//TAL Apparel Limited/ ; 9231297//City University of Hong Kong/ ; },
mesh = {*Bacteria/virology/genetics/classification ; *Wastewater/microbiology/virology ; *Virome ; Sewage/virology/microbiology ; Metagenomics ; Bioreactors/virology/microbiology ; Water Purification ; *Microbiota ; *Host Microbial Interactions ; Ecosystem ; },
abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1046 and 1386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.},
}

*Bacteria/virology/genetics/classification
*Wastewater/microbiology/virology
*Virome
Sewage/virology/microbiology
Metagenomics
Bioreactors/virology/microbiology
Water Purification
*Microbiota
*Host Microbial Interactions
Ecosystem

@article {pmid42139081,
year = {2026},
author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Dietary niches drive microbial community assembly, network reorganization, and symbiont evolution in freshwater fish gut microbiomes.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42139081},
issn = {1751-7370},
support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; },
mesh = {Animals ; *Symbiosis ; Fresh Water ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; China ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.},
}

Animals
*Symbiosis
Fresh Water
*Fishes/microbiology
*Gastrointestinal Microbiome
Metagenomics
China
*Diet
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Sequence Analysis, DNA

@article {pmid42172982,
year = {2026},
author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C},
title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {157},
number = {},
pages = {158288},
doi = {10.1016/j.phymed.2026.158288},
pmid = {42172982},
issn = {1618-095X},
mesh = {Animals ; Homeostasis/drug effects ; Male ; *Zonula Occludens-1 Protein/metabolism ; *Bile Acids and Salts/metabolism ; Liver/drug effects/metabolism ; Rats ; Rats, Sprague-Dawley ; *Quinazolines/pharmacology ; *Cholestasis/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Liver Diseases/drug therapy/metabolism ; },
abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.

OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.

METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and α-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.

RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.

CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.},
}

Animals
Homeostasis/drug effects
Male
*Zonula Occludens-1 Protein/metabolism
*Bile Acids and Salts/metabolism
Liver/drug effects/metabolism
Rats
Rats, Sprague-Dawley
*Quinazolines/pharmacology
*Cholestasis/drug therapy/metabolism
Gastrointestinal Microbiome/drug effects
Intestines/drug effects
Fecal Microbiota Transplantation
Disease Models, Animal
*Liver Diseases/drug therapy/metabolism

@article {pmid42176010,
year = {2026},
author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E},
title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42176010},
issn = {1432-184X},
mesh = {Animals ; *Isopoda/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; *Hepatopancreas/microbiology ; Metagenome ; Metagenomics ; Lignin/metabolism ; Phylogeny ; Italy ; },
abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.},
}

Animals
*Isopoda/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
*Hepatopancreas/microbiology
Metagenome
Metagenomics
Lignin/metabolism
Phylogeny
Italy

@article {pmid42176589,
year = {2026},
author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q},
title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128552},
doi = {10.1016/j.micres.2026.128552},
pmid = {42176589},
issn = {1618-0623},
mesh = {*Phosphorus/metabolism ; Soil Microbiology ; *Trichoderma/physiology/metabolism ; Rhizosphere ; *Pseudomonas/metabolism/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Pyrus/microbiology/growth & development/metabolism ; Biomass ; Microbiota ; Metagenome ; Plant Roots/microbiology ; },
abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.},
}

*Phosphorus/metabolism
Soil Microbiology
*Trichoderma/physiology/metabolism
Rhizosphere
*Pseudomonas/metabolism/genetics
*Soil/chemistry
RNA, Ribosomal, 16S/genetics
*Pyrus/microbiology/growth & development/metabolism
Biomass
Microbiota
Metagenome
Plant Roots/microbiology

@article {pmid42217591,
year = {2026},
author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H},
title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.},
journal = {Pharmacological research},
volume = {229},
number = {},
pages = {108273},
doi = {10.1016/j.phrs.2026.108273},
pmid = {42217591},
issn = {1096-1186},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy ; Animals ; Metabolomics ; Precision Medicine ; },
abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.},
}

Humans
*Gastrointestinal Microbiome
*Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy
Animals
Metabolomics
Precision Medicine

@article {pmid42241861,
year = {2026},
author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L},
title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130128},
doi = {10.1016/j.jenvman.2026.130128},
pmid = {42241861},
issn = {1095-8630},
mesh = {Animals ; *Aquaculture ; *Nitrogen/metabolism ; Anti-Bacterial Agents ; *Probiotics ; Metagenomics ; China ; Microbiota ; Penaeidae ; },
abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.},
}

Animals
*Aquaculture
*Nitrogen/metabolism
Anti-Bacterial Agents
*Probiotics
Metagenomics
China
Microbiota
Penaeidae

@article {pmid42242027,
year = {2026},
author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M},
title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128569},
doi = {10.1016/j.micres.2026.128569},
pmid = {42242027},
issn = {1618-0623},
mesh = {Animals ; *Bifidobacterium longum/physiology ; *Metabolome ; Multiomics ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Mice ; Disease Models, Animal ; Liver/metabolism/pathology ; *Fatty Liver/metabolism/microbiology ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Male ; Metagenomics ; Intestinal Barrier Function ; Metabolomics ; *Metabolic Diseases ; },
abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.},
}

Animals
*Bifidobacterium longum/physiology
*Metabolome
Multiomics
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
Mice
Disease Models, Animal
Liver/metabolism/pathology
*Fatty Liver/metabolism/microbiology
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
Male
Metagenomics
Intestinal Barrier Function
Metabolomics
*Metabolic Diseases

@article {pmid42250135,
year = {2026},
author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M},
title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42250135},
issn = {1573-0972},
mesh = {*Agriculture/methods ; Soil Microbiology ; Climate Change ; Crops, Agricultural/microbiology/growth & development ; Microbiota ; Stress, Physiological ; Ecosystem ; Biotechnology ; Mycorrhizae ; },
abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.},
}

*Agriculture/methods
Soil Microbiology
Climate Change
Crops, Agricultural/microbiology/growth & development
Microbiota
Stress, Physiological
Ecosystem
Biotechnology
Mycorrhizae

@article {pmid42252802,
year = {2026},
author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M},
title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {3},
pages = {e70324},
pmid = {42252802},
issn = {2190-6009},
support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; },
mesh = {Humans ; *Cachexia/etiology ; *Bacteriophages/genetics ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; *Neoplasms/complications ; Metagenomics/methods ; Metagenome ; Feces/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.

METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67 ± 8 years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.

RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4 kg/m2), WL (mean -6.5 vs. -0.2 kg), survival (median 5 vs. 13 months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p < 0.001) but not for other clinical covariables (e.g., cancer type) (all p > 0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p < 0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p > 0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial β-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p < 0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p < 0.05; 2025: Myoviridae, Siphoridae, p < 0.05) but also single-stranded (2022: Inoviridae, Microviridae, p < 0.05; 2025: Inoviridae; p < 0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).

CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.

TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).},
}

Humans
*Cachexia/etiology
*Bacteriophages/genetics
Male
Female
*Gastrointestinal Microbiome
Aged
*Neoplasms/complications
Metagenomics/methods
Metagenome
Feces/microbiology
Middle Aged

@article {pmid42256221,
year = {2026},
author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V},
title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826972},
pmid = {42256221},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/therapy/microbiology ; *Inflammatory Bowel Diseases/therapy/microbiology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; Intestinal Barrier Function ; Animals ; Probiotics/therapeutic use ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.},
}

Humans
*Dysbiosis/therapy/microbiology
*Inflammatory Bowel Diseases/therapy/microbiology
*Precision Medicine/methods
*Gastrointestinal Microbiome
Intestinal Barrier Function
Animals
Probiotics/therapeutic use

@article {pmid42267567,
year = {2026},
author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL},
title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.},
journal = {Zoological research},
volume = {47},
number = {3},
pages = {827-842},
doi = {10.24272/j.issn.2095-8137.2025.141},
pmid = {42267567},
issn = {2095-8137},
mesh = {Animals ; *beta-Thalassemia/genetics/complications/veterinary/microbiology ; *Macaca fascicularis ; *Gastrointestinal Microbiome/physiology ; Mutation ; *Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics ; *beta-Globins/genetics/metabolism ; Male ; },
abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.},
}

Animals
*beta-Thalassemia/genetics/complications/veterinary/microbiology
*Macaca fascicularis
*Gastrointestinal Microbiome/physiology
Mutation
*Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics
*beta-Globins/genetics/metabolism
Male

@article {pmid42267859,
year = {2026},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70307},
pmid = {42267859},
issn = {2045-8827},
support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; },
mesh = {*Rhizosphere ; *Metagenomics ; Soil Microbiology ; *Allium/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fertilizers/analysis ; Soil/chemistry ; },
abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.},
}

*Rhizosphere
*Metagenomics
Soil Microbiology
*Allium/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fertilizers/analysis
Soil/chemistry

@article {pmid42268876,
year = {2026},
author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR},
title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351562},
pmid = {42268876},
issn = {1932-6203},
mesh = {Humans ; *Immunocompromised Host ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; *Microbiota/genetics ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/immunology ; Aged ; Healthy Volunteers ; Metagenomics ; Case-Control Studies ; Bacteria/genetics/isolation & purification/classification ; COVID-19 ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.

METHODS: BAL specimens from healthy control volunteers (n = 20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n = 52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).

RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p < 0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p = 0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q < 0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.

CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.},
}

Humans
*Immunocompromised Host
*Bronchoalveolar Lavage Fluid/microbiology
Male
*Microbiota/genetics
Female
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
*Pneumonia/microbiology/immunology
Aged
Healthy Volunteers
Metagenomics
Case-Control Studies
Bacteria/genetics/isolation & purification/classification
COVID-19
SARS-CoV-2

@article {pmid42269618,
year = {2026},
author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M},
title = {Variations in the latitudinal diversity gradients of the ocean microbiome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.016},
pmid = {42269618},
issn = {1934-6069},
abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.},
}

@article {pmid42269619,
year = {2026},
author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y},
title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.009},
pmid = {42269619},
issn = {1934-6069},
abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.},
}

@article {pmid42270094,
year = {2026},
author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B},
title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261460118},
pmid = {42270094},
issn = {1526-2359},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation & purification/genetics ; Aged ; Fungi/isolation & purification ; },
abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/microbiology/pathology
*Microbiota
*Lung Neoplasms/microbiology/pathology
Bronchoalveolar Lavage Fluid/microbiology
Female
Case-Control Studies
Male
Sputum/microbiology
Prospective Studies
Middle Aged
*Respiratory System/microbiology
Bacteria/isolation & purification/genetics
Aged
Fungi/isolation & purification

@article {pmid42270219,
year = {2026},
author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y},
title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119489},
doi = {10.1016/j.foodres.2026.119489},
pmid = {42270219},
issn = {1873-7145},
mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; },
abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.},
}

China
Fermentation
*Hot Temperature
*Microbiota
*Taste
*Food Microbiology
Bacteria/metabolism/classification/genetics
Rivers
Flavoring Agents
*Fermented Foods/microbiology

@article {pmid42270261,
year = {2026},
author = {Vandana, and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP},
title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119548},
doi = {10.1016/j.foodres.2026.119548},
pmid = {42270261},
issn = {1873-7145},
mesh = {Animals ; *Polyphenols/pharmacology ; *Plant Extracts/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Fruit/chemistry ; *Cognitive Dysfunction/chemically induced/prevention & control/drug therapy ; *Arsenic/toxicity ; Male ; *Rubus/chemistry ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; Disease Models, Animal ; },
abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.},
}

Animals
*Polyphenols/pharmacology
*Plant Extracts/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice
*Fruit/chemistry
*Cognitive Dysfunction/chemically induced/prevention & control/drug therapy
*Arsenic/toxicity
Male
*Rubus/chemistry
Oxidative Stress/drug effects
Antioxidants/pharmacology
Disease Models, Animal

@article {pmid42271572,
year = {2026},
author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E},
title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {6},
pages = {},
pmid = {42271572},
issn = {1574-6941},
support = {//CNRS/ ; ANR-24-CE01-6539-01//French National Research Agency/ ; },
mesh = {*Groundwater/microbiology/chemistry ; *Caves/microbiology/chemistry ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; South Africa ; *Geologic Sediments/microbiology ; Metagenome ; Oxidation-Reduction ; },
abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.},
}

*Groundwater/microbiology/chemistry
*Caves/microbiology/chemistry
*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics
South Africa
*Geologic Sediments/microbiology
Metagenome
Oxidation-Reduction

@article {pmid42272754,
year = {2026},
author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C},
title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779298},
pmid = {42272754},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *Metabolomics ; *Constipation/microbiology/immunology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; *Rhinitis, Allergic/microbiology/immunology/metabolism/complications ; Child ; Female ; Feces/microbiology ; Male ; Amino Acids/metabolism ; Multiomics ; Bacteria/classification/genetics ; Metabolome ; },
abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.

METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.

RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P = 0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and γ-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC = 0.946).

CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.},
}

Humans
*Metagenomics/methods
*Metabolomics
*Constipation/microbiology/immunology/metabolism/complications
*Gastrointestinal Microbiome/genetics
*Rhinitis, Allergic/microbiology/immunology/metabolism/complications
Child
Female
Feces/microbiology
Male
Amino Acids/metabolism
Multiomics
Bacteria/classification/genetics
Metabolome

@article {pmid42276515,
year = {2026},
author = {Hassanien, A and Saadaoui, I and Sayadi, S},
title = {Archaea as a Resource for Sustainable Biotechnology: From Extremophiles to Valuable Products.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2026.06.006},
pmid = {42276515},
issn = {1638-6183},
abstract = {Archaea, a remarkable domain of microorganisms, possess extraordinary survival capabilities that enable them to thrive in the most extreme environments on Earth, including high temperatures, extreme pH, oxygen-deprived habitats, and high salinity. Modern ecological studies have revealed their broad distribution and ecological roles, but traditional culture techniques do not accurately capture the structure of archaeal communities in such settings. This review provides an integrated and up-to-date synthesis of tools used to assess archaeal biodiversity, with particular emphasis on high-throughput culture-independent strategies, including metagenomics, functional metagenomics, and multi-omics. We also provide a quantitative, up-to-date mapping of archaeal biodiversity and bioproduct research (2010-2024), highlighting methodological trends and underexplored niches that are not emphasized in previous reviews. These advancements in archaeal studies have allowed scientists to investigate numerous archaeal strains for potential biotechnological applications and products, and to explore novel genes that lead to the discovery of new metabolites and bioactive molecules. Building on this framework, we critically analyze the current and emerging biotechnological applications of archaea. focusing on metabolites, enzymes, biopolymers, and biofuels, as well as identifying the major scientific and technical bottlenecks that hinder their translation into industrial scale. Finally, we outline key research priorities for utilizing archaeal resources in development of more sustainable and environmentally friendly biotechnologies.},
}

@article {pmid40903035,
year = {2026},
author = {Hou, Y and Wu, H and Zhang, Z and Wang, J and Chen, Q and Lian, C and He, D and Li, Z and Wei, W and Lin, X and Sun, D and Cao, B and Xu, T and Cai, M and Wang, G and Zhang, X and Duan, L and Hao, H and Zheng, X},
title = {Bacteroides intestinalis mediates the sensitivity to irinotecan toxicity via tryptophan catabolites.},
journal = {Gut},
volume = {75},
number = {7},
pages = {1322-1337},
doi = {10.1136/gutjnl-2024-334699},
pmid = {40903035},
issn = {1468-3288},
mesh = {Animals ; *Irinotecan/adverse effects/toxicity ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; *Tryptophan/metabolism ; *Diarrhea/chemically induced/microbiology ; Female ; Indoleacetic Acids/metabolism ; *Bacteroides/metabolism ; Male ; Intestinal Mucosa/drug effects/microbiology ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Late-onset diarrhoea remains a poorly managed concern for clinical irinotecan therapy. Although bacterial β-glucuronidases (β-GUS) mediated SN-38 production is prevailingly thought to mediate intestinal toxicity, β-GUS inhibitors confer limited benefits in the clinic.

OBJECTIVE: This study aimed to explore the role and mechanism of endogenous bacterial metabolites in susceptibility to irinotecan toxicity.

DESIGN: Gut microbiota profiles and metabolites in patients with colorectal cancer (CRC) with or without diarrhoea were investigated via 16S rRNA sequencing, shotgun metagenomics and metabolomics. The role of microbial metabolites was investigated in mice by metabolic bioengineering and intestinal organoid culture. The mechanism of microbial metabolites on intestinal stem cells was investigated by transcriptional profiling and chemical intervention.

RESULTS: Gut microbial configuration was differentially remodelled in diarrhoea and non-diarrhoea patients with irinotecan therapy, and the susceptibility was transmissible to recipient mice via transplantation of baseline faecal microbiome. Bacteroides intestinalis (B. intestinalis) was notably expanded in the diarrhoea-prone cohorts as well as in irinotecan-treated mice. B. intestinalis colonisation sensitised intestinal epithelia to irinotecan-induced chemical injury, partially via tryptophan metabolite indole-3-acetate (IAA). Both B. intestinalis and bioengineered bacteria that produce IAA exacerbated irinotecan-induced intestinal epithelial injury in mice. Mechanistically, IAA suppressed PI3K-Akt signalling, thereby impairing the renewal of intestinal epithelia under the insult of irinotecan. In clinical patients receiving irinotecan therapy, faecal IAA level was closely associated with the diarrhoea severity.

CONCLUSION: Our study uncovers the mechanism of endogenous bacterial metabolite in shaping the individual susceptibility to irinotecan toxicity and suggests IAA as a potential predictive biomarker.},
}

Animals
*Irinotecan/adverse effects/toxicity
Humans
Mice
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/drug therapy/microbiology
*Tryptophan/metabolism
*Diarrhea/chemically induced/microbiology
Female
Indoleacetic Acids/metabolism
*Bacteroides/metabolism
Male
Intestinal Mucosa/drug effects/microbiology
Mice, Inbred C57BL

@article {pmid41700755,
year = {2026},
author = {You, C and Ren, P and Guan, Y and Gong, K and Hua, Z and Zhou, W and Mei, X and Wang, Y and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {23},
pages = {e22628},
pmid = {41700755},
issn = {2198-3844},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; KJYQ2025034//Fundamental Research Funds for the Central Universities/ ; BK20240194//Natural Science Foundation of Jiangsu Province/ ; 42377118//National Natural Science Foundation of China/ ; 42277113//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Carbon Peak & Carbon Neutrality Science and Technology Innovation Special Fund/ ; 2024M760612//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Plant Diseases/microbiology/genetics ; Rhizosphere ; Machine Learning ; Metagenome/genetics ; *Microbiota/genetics ; Forecasting ; },
abstract = {Early diagnosis of soil-borne diseases like root rot is a long-standing challenge in agriculture. While microbial functional genes are recognized as potent indicators of soil healthy, their application has been primarily limited to current or past soil conditions. Here, we demonstrate that microbial functional genes can transition from descriptive indicators to reliable predictive biomarkers. By analyzing 199 paired metagenomes from healthy and diseased medicinal plants rhizosphere soil samples, we identified a conserved core set of functional genes, specifically those governing biofilm formation, stress response, and plant-microbe mutualism that are robustly associated with root rot disease. To bridge the gap between discovery and field application, we developed a framework that integrates cost-effective qPCR assay for these key genes and fused their abundance data with machine learning. This model achieved over 80% accuracy in predicting disease onset from independent, pre-symptomatic soil samples, identifying risks long before visible symptoms of infection appeared. Our findings suggest a practical path for moving beyond simple microbial correlations toward an active forecasting tool. By positioning microbial functional genes at the core of disease management, this framework provides a targeted approach for mitigating soil-borne risks and supporting sustainable agricultural practices.},
}

*Soil Microbiology
*Plant Roots/microbiology
*Plant Diseases/microbiology/genetics
Rhizosphere
Machine Learning
Metagenome/genetics
*Microbiota/genetics
Forecasting

@article {pmid41713061,
year = {2026},
author = {Cokro, A and Albert Ng, TC and Hill, ED and Lee, C and Chandra Segeran, US and Arumugam, K and Williams, RBH and Wuertz, S},
title = {Microbial community biomarkers can forecast methane production in full-scale anaerobic digesters.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128828},
doi = {10.1016/j.jenvman.2026.128828},
pmid = {41713061},
issn = {1095-8630},
mesh = {*Methane/biosynthesis ; *Bioreactors/microbiology ; Anaerobiosis ; Sewage/microbiology ; *Microbiota ; Biomarkers ; Wastewater/microbiology ; Singapore ; Machine Learning ; },
abstract = {Methane production from wastewater sludge via anaerobic digestion is a complex process and a disturbance in any one of the microbial stages can lead to eventual failure. Hence, it is desirable to detect disturbances as soon as possible. Although machine learning has been used to predict methane production from a variety of different substrates, there are no studies using metagenomic or -transcriptomic microbial community data as predictor variables. We used random forest analysis on a combination of physicochemical and microbial predictors to forecast methane production from three full-scale sludge digesters representing replicates of one another in a wastewater treatment plant in Singapore. Digesters were sampled for 25 weeks, and 42 physicochemical variables were measured along with shotgun metagenome and total RNA transcriptome sequencing. Models built using samples from a single digester yielded reactor-specific predictors, largely due to the limited sample size per reactor and the influence of rarer taxa. When data from the three digesters were combined, the best predictors included both substrate-related physicochemical parameters, such as chemical oxygen demand, and microbial taxa. Simulation using learning curves indicated that 150 to 200 samples instead of the 75 used would have yielded the most accurate methane prediction. The selection of many unidentified operational taxonomic units as microbial predictors suggests the existence of important yet unknown microorganisms in anaerobic digestion. The prediction model supports onsite digester surveillance by identifying digester-specific predictors through sufficient sampling, after which only those predictors need to be measured for subsequent monitoring.},
}

*Methane/biosynthesis
*Bioreactors/microbiology
Anaerobiosis
Sewage/microbiology
*Microbiota
Biomarkers
Wastewater/microbiology
Singapore
Machine Learning

@article {pmid41722567,
year = {2026},
author = {Thurimella, K and Wu, E and Li, C and Graham, DB and Owens, RM and Plichta, DR and Sokol, CL and Xavier, RJ and Bacallado, S},
title = {Identifying microbial protease allergens through protein language model-guided homology.},
journal = {Cell systems},
volume = {17},
number = {3},
pages = {101510},
pmid = {41722567},
issn = {2405-4720},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AI151163/AI/NIAID NIH HHS/United States ; },
mesh = {*Allergens/immunology ; Humans ; Animals ; *Serine Proteases/immunology/metabolism ; Metagenomics/methods ; Hypersensitivity/immunology ; Microbiota ; },
abstract = {Emerging research links the gut, skin, and oral microbiomes to allergies, with serine proteases (SPs) identified as potential allergens. This study leverages deep learning and pre-trained protein language models (pLMs) to uncover allergenic SPs in metagenomic data. First, we develop a model to identify the catalytic serine residue in serine hydrolases, demonstrating how pLMs capture structural information. Next, we create a deep learning framework to detect candidate SP allergens across gene catalogs, using the conserved catalytic triad to identify homologs in gut and oral sites despite low sequence identity. Our model predicts a putative SP allergen resembling V8 protease, a known trigger for protease-activated receptor 1. It also identifies a cysteine protease similar to Der f 1 from dust mites. Immunization with these proteases induced allergic responses, validating their allergenic potential experimentally. This approach uncovers candidate allergens beyond traditional methods, offering new targets for allergy research. A record of this paper's transparent peer review process is included in the supplemental information.},
}

*Allergens/immunology
Humans
Animals
*Serine Proteases/immunology/metabolism
Metagenomics/methods
Hypersensitivity/immunology
Microbiota

@article {pmid41762314,
year = {2026},
author = {Dabravolski, SA and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Orekhov, AN},
title = {A metagenomic perspective on microbial hydrocarbon degradation: uncovering novel pathways and community dynamics.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {5},
pages = {},
pmid = {41762314},
issn = {1573-2983},
support = {202760-2-000//RUDN University/ ; },
mesh = {Biodegradation, Environmental ; *Metagenomics ; *Hydrocarbons/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics ; Petroleum/metabolism ; Microbial Consortia ; Aerobiosis ; Polycyclic Aromatic Hydrocarbons/metabolism ; },
abstract = {The microbial degradation of petroleum hydrocarbons is a fundamental biogeochemical process and a cornerstone of environmental bioremediation. While traditional culture-based studies have outlined the basic principles, the advent of metagenomics has revolutionised our understanding by revealing the full genetic and functional diversity of hydrocarbon-degrading communities in situ. This review synthesises the current state of knowledge on both aerobic and anaerobic hydrocarbon biodegradation, providing a critical comparative analysis of traditional versus multi-omics methodologies. We provide an in-depth examination of aerobic mechanisms, initiated by oxygenases (e.g., alkB, PAH-RHDα), and contrast them with the diverse array of anaerobic activation pathways, including fumarate addition (bssA) and the recently elucidated direct carboxylation pathway for polycyclic aromatic hydrocarbons (PAHs). Furthermore, we highlight groundbreaking metagenomic insights into anaerobic benzene degradation and the critical role of syntrophic networks driven by interspecies electron transfer. Finally, we present specific case studies demonstrating the translation of genomic data into practical bioremediation strategies, such as the rational design of synthetic consortia. This review charts these recent advances, highlights remaining knowledge gaps, and outlines future directions for harnessing multi-omics to translate genomic potential into effective, field-scale environmental solutions.},
}

Biodegradation, Environmental
*Metagenomics
*Hydrocarbons/metabolism
Anaerobiosis
*Bacteria/metabolism/genetics
Petroleum/metabolism
Microbial Consortia
Aerobiosis
Polycyclic Aromatic Hydrocarbons/metabolism

@article {pmid41878990,
year = {2026},
author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B},
title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {32},
pages = {e17444},
pmid = {41878990},
issn = {2198-3844},
support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; },
mesh = {Animals ; China/epidemiology ; *Herbivory ; Humans ; *Animals, Domestic/virology ; *Virome/genetics ; *Viruses/genetics/classification ; },
abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.},
}

Animals
China/epidemiology
*Herbivory
Humans
*Animals, Domestic/virology
*Virome/genetics
*Viruses/genetics/classification

@article {pmid42139982,
year = {2026},
author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R},
title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128553},
doi = {10.1016/j.micres.2026.128553},
pmid = {42139982},
issn = {1618-0623},
mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; *Water Microbiology ; Carbon/metabolism ; Nitrogen/metabolism ; Eutrophication ; China ; Biodiversity ; },
abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.},
}

*Lakes/microbiology
*Metagenomics/methods
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Ecosystem
Metagenome
Phylogeny
*Water Microbiology
Carbon/metabolism
Nitrogen/metabolism
Eutrophication
China
Biodiversity

@article {pmid42161089,
year = {2026},
author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S},
title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.},
journal = {Placenta},
volume = {181},
number = {},
pages = {168-174},
doi = {10.1016/j.placenta.2026.05.010},
pmid = {42161089},
issn = {1532-3102},
mesh = {Female ; Humans ; Pregnancy ; *Placenta/virology ; *DNA, Viral/analysis ; *RNA, Viral/analysis ; Pre-Eclampsia/virology ; Adult ; *Virome ; Cesarean Section ; },
abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.

METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n = 6), (2) delivered by emergency caesarean section (n = 6), and (3) complicated by preeclampsia (n = 5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.

RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.

CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.},
}

Female
Humans
Pregnancy
*Placenta/virology
*DNA, Viral/analysis
*RNA, Viral/analysis
Pre-Eclampsia/virology
Adult
*Virome
Cesarean Section

@article {pmid42161263,
year = {2026},
author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {Cell host & microbe},
volume = {34},
number = {6},
pages = {1033-1049.e8},
pmid = {42161263},
issn = {1934-6069},
support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological/genetics ; DNA Methylation ; Fecal Microbiota Transplantation ; Infant ; *Bacteria/genetics/drug effects ; Metagenomics ; Probiotics ; Feces/microbiology ; Akkermansia ; },
abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.},
}

Humans
*Epigenesis, Genetic
*Gastrointestinal Microbiome/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Adaptation, Physiological/genetics
DNA Methylation
Fecal Microbiota Transplantation
Infant
*Bacteria/genetics/drug effects
Metagenomics
Probiotics
Feces/microbiology
Akkermansia

@article {pmid42176766,
year = {2026},
author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM},
title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.},
journal = {Neuroscience and biobehavioral reviews},
volume = {187},
number = {},
pages = {106775},
doi = {10.1016/j.neubiorev.2026.106775},
pmid = {42176766},
issn = {1873-7528},
mesh = {Humans ; *Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology ; *Oxidative Stress/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/immunology/metabolism ; *Neuroinflammatory Diseases/immunology/metabolism ; Probiotics ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.},
}

Humans
*Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology
*Oxidative Stress/physiology
Animals
*Gastrointestinal Microbiome/physiology
*Inflammation/immunology/metabolism
*Neuroinflammatory Diseases/immunology/metabolism
Probiotics

@article {pmid42184159,
year = {2026},
author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C},
title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {6},
pages = {},
pmid = {42184159},
issn = {1574-6941},
support = {//Scientific Committee on Antarctic Research/ ; 542264307//German Research Foundation/ ; 569718716//German Research Foundation/ ; },
mesh = {Antarctic Regions ; *Phytoplankton/metabolism/genetics/classification ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Diatoms ; Seawater/microbiology ; Polysaccharides/metabolism ; *Microbiota ; },
abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.},
}

Antarctic Regions
*Phytoplankton/metabolism/genetics/classification
Seasons
*Bacteria/metabolism/genetics/classification/isolation & purification
Diatoms
Seawater/microbiology
Polysaccharides/metabolism
*Microbiota

@article {pmid42202778,
year = {2026},
author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M},
title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.},
journal = {Cell host & microbe},
volume = {34},
number = {6},
pages = {1135-1150.e6},
doi = {10.1016/j.chom.2026.05.001},
pmid = {42202778},
issn = {1934-6069},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/surgery/metabolism ; Female ; *Feces/microbiology/chemistry ; *Adenoma/microbiology/surgery ; *Metabolome ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Aged ; Metagenomics ; Metagenome ; },
abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.},
}

Humans
*Colorectal Neoplasms/microbiology/surgery/metabolism
Female
*Feces/microbiology/chemistry
*Adenoma/microbiology/surgery
*Metabolome
*Gastrointestinal Microbiome
Case-Control Studies
Middle Aged
Aged
Metagenomics
Metagenome

@article {pmid42219044,
year = {2026},
author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A},
title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.},
journal = {Journal of microbiological methods},
volume = {246},
number = {},
pages = {107565},
doi = {10.1016/j.mimet.2026.107565},
pmid = {42219044},
issn = {1872-8359},
mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Pasteurellaceae/genetics/isolation & purification/classification ; Chickens/microbiology ; DNA Primers/genetics ; Cecum/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Poultry Diseases/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Pasteurellaceae Infections/veterinary/microbiology/diagnosis ; },
abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.},
}

Animals
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Pasteurellaceae/genetics/isolation & purification/classification
Chickens/microbiology
DNA Primers/genetics
Cecum/microbiology
DNA, Bacterial/genetics
Sequence Analysis, DNA
*Poultry Diseases/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
Phylogeny
*Pasteurellaceae Infections/veterinary/microbiology/diagnosis

@article {pmid42249511,
year = {2026},
author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H},
title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42249511},
issn = {2049-2618},
support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Aging/immunology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Adaptive Immunity ; *Vitamin B 6/blood/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/immunology/microbiology ; Immunity, Mucosal ; Ileum/immunology/microbiology ; },
abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.

RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced naïve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of naïve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.

CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.},
}

Animals
*Aging/immunology
Mice
*Gastrointestinal Microbiome/immunology
*Adaptive Immunity
*Vitamin B 6/blood/metabolism
Mice, Inbred C57BL
Intestinal Mucosa/immunology/microbiology
Immunity, Mucosal
Ileum/immunology/microbiology

@article {pmid42249721,
year = {2026},
author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W},
title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {11},
pages = {e70422},
doi = {10.1111/mec.70422},
pmid = {42249721},
issn = {1365-294X},
support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; Temperature ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota/genetics ; Seasons ; *Ecosystem ; Metagenomics ; },
abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.},
}

*Soil Microbiology
Temperature
*Bacteria/genetics/classification
*Archaea/genetics/classification
*Microbiota/genetics
Seasons
*Ecosystem
Metagenomics

@article {pmid40762941,
year = {2026},
author = {Wei, R and Long, J and Xia, H and Sun, Y and Zhang, L and Li, X and Zhang, H and Wang, R and Gao, S and Chen, Y and Gu, Y and Wang, X and Wang, J},
title = {Galacto-oligosaccharides enrich galactosidase-encoded rather than all Lachnospiraceae bacteria to redress abnormal gut microbiota and lipid metabolism in pregnancy.},
journal = {Science China. Life sciences},
volume = {69},
number = {6},
pages = {1858-1870},
pmid = {40762941},
issn = {1869-1889},
mesh = {Female ; Animals ; Pregnancy ; *Lipid Metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology ; *Diabetes, Gestational/microbiology/metabolism ; Mice ; Liver/metabolism/drug effects ; Dietary Supplements ; Blood Glucose/metabolism ; Dysbiosis/microbiology ; },
abstract = {Among the various pregnancy complications, gestational diabetes mellitus (GDM) is one of the most prevalent and damaging adverse conditions. GDM is characterised by dysregulated gut microbiota and dysglycaemia. There is a keen search for active ingredients that can modify gut dysbiosis and glycaemic imbalances. In this study, the effects of dietary supplementation with high fibre and galacto-oligosaccharides (GOS) on GDM were evaluated. We found that GOS effectively alleviated blood glucose, hepatic inflammatory response, and lipid metabolism in high-fat-induced GDM mice. Furthermore, GOS redressed GDM-associated gut dysbiosis and altered glycerolipid metabolic pathways. GOS supplementation significantly downregulated the levels of fat synthesis genes and inflammatory factors in the liver and upregulated the expression of lipolytic catabolic genes (Cyp4a10). In dietary GOS supplementation, Lachnospiraceae bacteria strongly co-occurred with saturated lysophosphatidylcholine in the glycerolipid metabolic pathway. Metagenomic analyses illustrated that Lachnospiraceae bacteria-hosted α-galactosidase genes enriched upon GOS intake. GOS supplementation reduces lipopolysaccharide (LPS) entry into the systemic circulation by repairing intestinal mucosal damage, inhibits inflammatory cell production by reducing hepatic and intestinal Toll-like receptor-4 (TLR-4) expression and potentially ameliorates blood glucose dysregulation in GDM by modulating glycerophospholipid metabolism. These results revealed that dietary supplementation of GOS during pregnancy may be a promising intervention against GDM.},
}

Female
Animals
Pregnancy
*Lipid Metabolism/drug effects
*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/pharmacology
*Diabetes, Gestational/microbiology/metabolism
Mice
Liver/metabolism/drug effects
Dietary Supplements
Blood Glucose/metabolism
Dysbiosis/microbiology

@article {pmid41275986,
year = {2026},
author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , },
title = {Prebiotic Administration to Chronic Kidney Disease Patients Modifies Their Fecal Microbiome and Host Metabolism.},
journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation},
volume = {36},
number = {3},
pages = {419-429},
doi = {10.1053/j.jrn.2025.10.015},
pmid = {41275986},
issn = {1532-8503},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Feces/microbiology ; *Renal Insufficiency, Chronic/microbiology/metabolism/therapy ; Female ; Male ; Inulin/administration & dosage ; Pilot Projects ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; Aged ; Oligosaccharides/administration & dosage ; Dysbiosis ; Amino Acids ; },
abstract = {OBJECTIVE(S): Prebiotics are believed to improve gut microbial dysbiosis and dysmetabolism in chronic kidney disease (CKD) patients. However, impact of prebiotics on gut microbial metagenome and dynamic changes in metabolome has not been clearly defined.

METHODS: We conducted a nonrandomized, open-label, three-phase pilot trial to investigate the effect of daily oral prebiotic, oligofructose-enriched inulin (p-inulin), on stool functional metagenome and changes in plasma, urine, and stool metabolites in 13 CKD patients. The study comprised a pretreatment phase (8 weeks), p-inulin treatment phase (12 weeks), and post-treatment phase (8 weeks).

RESULTS: During treatment phase, there was a significant increase in the abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Lachnospiraceae species. Microbial pathways related to carbohydrate degradation and amino acid biosynthesis were enriched during the treatment phase, but urea biosynthetic pathway was attenuated. In plasma, metabolic biosynthetic pathways for valine, leucine, and isoleucine were activated during the treatment phase. Microbial genes related to lipid metabolism were enriched during post-treatment. Abundance of several polar and nonpolar lipids were altered in plasma and stool samples during treatment and post-treatment phases. Pathway analysis for lipids indicated suppression of triglyceride biosynthesis in plasma and enhanced triglyceride degradation in stool during the treatment phase. Secondary bile acid levels in plasma, urine, and stool were significantly reduced during p-inulin consumption. Urine levels of indoxyl sulfate and p-cresol sulfate were reduced during treatment phase.

CONCLUSION(S): P-inulin administration to CKD patients resulted in a distinct shift in toxin-generating proteolysis to amino acid biosynthesis and favorable changes in lipid metabolism.},
}

Humans
*Prebiotics/administration & dosage
*Feces/microbiology
*Renal Insufficiency, Chronic/microbiology/metabolism/therapy
Female
Male
Inulin/administration & dosage
Pilot Projects
Middle Aged
*Gastrointestinal Microbiome/drug effects
Aged
Oligosaccharides/administration & dosage
Dysbiosis
Amino Acids

@article {pmid41652998,
year = {2026},
author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I},
title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.},
journal = {Biological research for nursing},
volume = {28},
number = {3},
pages = {406-417},
doi = {10.1177/10998004261423546},
pmid = {41652998},
issn = {1552-4175},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Infant ; *Selective Serotonin Reuptake Inhibitors/adverse effects/therapeutic use ; Pregnancy ; *Antidepressive Agents/adverse effects/therapeutic use ; Adult ; Infant, Newborn ; Feces/microbiology ; },
abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.},
}

Humans
Female
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Infant
*Selective Serotonin Reuptake Inhibitors/adverse effects/therapeutic use
Pregnancy
*Antidepressive Agents/adverse effects/therapeutic use
Adult
Infant, Newborn
Feces/microbiology

@article {pmid41680419,
year = {2026},
author = {Pedrazzini, C and Funari, R and Cucini, C and Nardi, F and Grabenweger, G and Widmer, F and Enkerli, J},
title = {Population genomics identifies Italian and North American origins of Popillia japonica in Switzerland.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41680419},
issn = {2045-2322},
support = {No. 861852//European Union's Horizon 2020/ ; },
mesh = {Animals ; Switzerland ; *Coleoptera/genetics/classification ; Phylogeny ; North America ; Introduced Species ; Italy ; Genetics, Population ; *Metagenomics/methods ; Genomics ; },
abstract = {The Japanese beetle (Popillia japonica), native to Japan, is a major invasive species in North America and Europe. Its colonization of Europe began on the Azores (1970s), followed by Italy (2014) and southern Switzerland (2017). In 2023, the presence of the pest was reported in three areas of Switzerland: Kloten (Canton of Zürich, north-eastern Switzerland), Basel (Canton of Basel-Landschaft, northern Switzerland), and in eastern Canton of Valais (South Switzerland) near the Italian border. In 2024, P. japonica individuals were discovered in several other Swiss Cantons. To trace P. japonica spread and origins in Switzerland, we investigated 42 individuals from infested areas, comprising scattered findings across Switzerland. Phylogenetic and population structure analyses using whole-genome resequencing, including data of previously sequenced samples from Japan, North America, the Azores, Italy, and Southern Switzerland, revealed distinct P. japonica migration patterns. Populations in Basel, Valais, and central Switzerland likely originated from Ticino/Northern Italy via road or rail transport. Conversely, the population near Zürich Airport was identified as an independent introduction from North America, likely through unintentional air transport. These findings offer insights into P. japonica spread across Switzerland, highlighting the need for enhanced monitoring and identification of invasion pathways.},
}

Animals
Switzerland
*Coleoptera/genetics/classification
Phylogeny
North America
Introduced Species
Italy
Genetics, Population
*Metagenomics/methods
Genomics

@article {pmid41692940,
year = {2026},
author = {Le, B and Jia, L and Pang, T and Han, S and Duan, Y and Zhao, XM},
title = {A review of computational approaches for metagenomics by long-read sequencing.},
journal = {Science China. Life sciences},
volume = {69},
number = {6},
pages = {1825-1839},
pmid = {41692940},
issn = {1869-1889},
mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Humans ; },
abstract = {The metagenomic next-generation sequencing (mNGS), also known as short-read sequencing (SRS), is widely used to explore microbial composition and function. However, short reads, due to their difficulty in crossing repetitive regions, can lead to fragmented assemblies, hampering the comprehensive characterization of microbial genomes. In contrast, long-read sequencing (LRS) technologies, such as those from Pacific Biosciences (PacBio) and Oxford Nanopore, can span these complex repetitive regions and reconstruct continuous genomes, which enables high-resolution taxonomic classification and the precise recovery of essential genetic elements. This review provides a systematic overview of the computational approaches for long-read metagenomics, highlighting the progress in taxonomic profiling strategies, assembly and binning methods, and the detection of genetic elements. Furthermore, the review discusses the application of LRS in detecting structural variations (SVs), identifying methylation patterns, and characterizing strains. By combining advanced technologies and computational improvements, this review indicates the transformative potential of LRS in enhancing our understanding of microbial diversity, functions, and interactions within microbial communities.},
}

*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Computational Biology/methods
Microbiota/genetics
Sequence Analysis, DNA/methods
Humans

@article {pmid41698031,
year = {2026},
author = {Meng, Q and An, X and Hu, W and Ma, M and Chen, Z and Wei, G and Chen, C},
title = {Nanopriming with Silicon Quantum Dots Strengthens Wheat Drought Tolerance through Physiological Regulation and Microbial Functions.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {7},
pages = {5989-6001},
doi = {10.1021/acs.jafc.5c11900},
pmid = {41698031},
issn = {1520-5118},
mesh = {Drought Resistance ; *Triticum/microbiology/physiology/growth & development/drug effects/metabolism ; *Silicon/chemistry/pharmacology ; *Quantum Dots/chemistry ; Bacteria/classification/genetics/isolation & purification/metabolism ; Rhizosphere ; Seeds/growth & development/microbiology/physiology/drug effects ; Droughts ; Plant Roots/microbiology/growth & development/metabolism ; Water/metabolism ; Microbiota ; Germination ; },
abstract = {Seed priming offers a promising approach to strengthening drought resilience in wheat. In this study, seeds were primed with silicon quantum dots (SiQDs) at concentrations of 0, 250, 500, 750, and 1000 mg L[-1]. Under drought stress induced by 15% PEG-6000, 500 mg L[-1] SiQDs increased the level of germination by 18.2%. In a 30 day pot experiment conducted under drought conditions at 40% field capacity, 500 mg L[-1] SiQDs significantly enhanced shoot biomass (157.1%) and the relative water content (26.7%), reduced root malondialdehyde (24.7%), and increased root proline (76.7%) and soluble sugar (68.7%). 16S rRNA gene and metagenomic sequencing analyses revealed that SiQDs enriched Proteobacteria in the rhizosphere, including the genera Sphingomonas, Lysobacter, and Variovorax, and activated functional pathways associated with biofilm formation and bacterial colonization. These results demonstrate that SiQD priming enhances drought tolerance by improving plant physiological responses and modulating rhizosphere microbial communities.},
}

Drought Resistance
*Triticum/microbiology/physiology/growth & development/drug effects/metabolism
*Silicon/chemistry/pharmacology
*Quantum Dots/chemistry
Bacteria/classification/genetics/isolation & purification/metabolism
Rhizosphere
Seeds/growth & development/microbiology/physiology/drug effects
Droughts
Plant Roots/microbiology/growth & development/metabolism
Water/metabolism
Microbiota
Germination

@article {pmid41785649,
year = {2026},
author = {Dong, W and Ye, T and Zhang, Z and An, L and Peng, Y and Chen, Y and Zhang, Y and Ke, L and Chen, S and Zhao, S and Hu, Y},
title = {Quorum sensing-associated acid adaptation in bacterial communities during pit fermentation of sauce-flavor Baijiu.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111715},
doi = {10.1016/j.ijfoodmicro.2026.111715},
pmid = {41785649},
issn = {1879-3460},
mesh = {*Quorum Sensing ; Fermentation ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Adaptation, Physiological ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Lactic Acid/metabolism ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Sauce-flavor Baijiu is produced by multi-round solid-state fermentation under progressively increasing acidity, yet how bacterial communities adapt to this extreme acid stress and whether quorum sensing (QS)-associated features are involved remain unclear. Here, fermented grains from eight pit-fermentation rounds under both traditional and mechanized processes were analyzed by metagenomic sequencing and physicochemical profiling. The traditional process showed higher moisture, stronger and faster acidification, greater lactic acid accumulation, and more rapid depletion of reducing sugars and starch than the mechanized process. These conditions coincided with a sharper decline in bacterial α-diversity and convergence toward a community overwhelmingly dominated by Acetilactobacillus jinshanensis (>90%) in the traditional process, whereas the mechanized process maintained higher diversity and a multi-species core dominated by A. jinshanensis, Lactobacillus acetotolerans, Bacillus, and actinomycetes. Canonical correspondence analysis identified acidity (lactic acid) as a major environmental factor associated with these divergent trajectories. QS gene profiling revealed process-specific signatures, with the LuxS/AI-2-associated module being the most abundant QS-related feature and significantly enriched in the traditional process. Functional annotation uncovered coordinated enrichment of acid-adaptation genes (ATPF1A, clpP, ATPF1B, dnaK, and groEL) during mid-to-late stages under high acidity. Network analysis further highlighted tighter co-associations among A. jinshanensis, QS modules, and acid-adaptation genes, supporting a community-level QS-associated functional framework for ecological convergence. Collectively, this study links LuxS/AI-2-associated features to acid-adaptation capacity and A. jinshanensis dominance in high-acidity environment. These findings provide ecological insight into microbial resilience in high-acidity solid-state fermentations and offer QS-informed perspectives for future targeted validation in Baijiu production.},
}

*Quorum Sensing
Fermentation
*Bacteria/genetics/classification/metabolism/isolation & purification
Adaptation, Physiological
Food Microbiology
*Fermented Foods/microbiology/analysis
Lactic Acid/metabolism
Microbiota
Hydrogen-Ion Concentration

@article {pmid41951635,
year = {2026},
author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S},
title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41951635},
issn = {2052-4463},
mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Sus scrofa/microbiology ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Archaea/genetics/classification ; Bacteria/genetics/classification ; },
abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.},
}

Animals
*Feces/microbiology
*Metagenome
*Sus scrofa/microbiology
*Gastrointestinal Microbiome/genetics
Swine/microbiology
Archaea/genetics/classification
Bacteria/genetics/classification

@article {pmid42032279,
year = {2026},
author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G},
title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.},
journal = {Nature microbiology},
volume = {11},
number = {6},
pages = {1739-1753},
pmid = {42032279},
issn = {2058-5276},
support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics/classification ; *Metagenomics/methods ; Colorectal Neoplasms/microbiology ; Substrate Specificity ; Carbohydrate Metabolism ; Mucins/metabolism ; },
abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .},
}

Humans
Metagenome
*Gastrointestinal Microbiome/genetics
*Bacteria/enzymology/genetics/classification
*Metagenomics/methods
Colorectal Neoplasms/microbiology
Substrate Specificity
Carbohydrate Metabolism
Mucins/metabolism

@article {pmid42032281,
year = {2026},
author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J},
title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.},
journal = {Nature microbiology},
volume = {11},
number = {6},
pages = {1626-1638},
pmid = {42032281},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; Polymorphism, Single Nucleotide ; Streptococcus pneumoniae/genetics ; Plasmodium falciparum/genetics ; Feces/microbiology ; COVID-19/transmission ; Malaria, Falciparum/transmission ; Gastrointestinal Microbiome/genetics ; Metagenome ; Infant ; High-Throughput Nucleotide Sequencing ; },
abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmission Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.},
}

Humans
*Metagenomics/methods
Algorithms
Polymorphism, Single Nucleotide
Streptococcus pneumoniae/genetics
Plasmodium falciparum/genetics
Feces/microbiology
COVID-19/transmission
Malaria, Falciparum/transmission
Gastrointestinal Microbiome/genetics
Metagenome
Infant
High-Throughput Nucleotide Sequencing

@article {pmid42059625,
year = {2026},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {14},
number = {6},
pages = {e0362625},
pmid = {42059625},
issn = {2165-0497},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; R01 DE03013, R01 DE022586, 2R01 DE016937/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Capnocytophaga/genetics/classification/isolation & purification/physiology ; *Mouth/microbiology ; Microbiota ; Phylogeny ; Dental Plaque/microbiology ; Genome, Bacterial ; Metagenomics ; Metagenome ; },
abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.

IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.},
}

Humans
*Capnocytophaga/genetics/classification/isolation & purification/physiology
*Mouth/microbiology
Microbiota
Phylogeny
Dental Plaque/microbiology
Genome, Bacterial
Metagenomics
Metagenome

@article {pmid42067625,
year = {2026},
author = {Liu, X and Zhang, H and Wang, YZ and Tu, X and Wen, J and Lei, S and Liu, N and Wei, X and Li, C and Li, Y and Liu, B and Feng, YQ and Zhu, QF and Liu, X and Ning, K},
title = {Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.},
journal = {Nature microbiology},
volume = {11},
number = {6},
pages = {1495-1510},
pmid = {42067625},
issn = {2058-5276},
support = {2023YFA1800900, 2018YFC0910502//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2022FYC3400800//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32071465, 31871334, 31671374//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22361132526, 22274119, 22474101//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Sepsis/microbiology/drug therapy/metabolism ; Humans ; Mice ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; Child ; Enterococcus/metabolism ; *Deoxycholic Acid/metabolism/analogs & derivatives ; Intestinal Barrier Function ; Male ; Child, Preschool ; Female ; Metabolomics ; },
abstract = {Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.},
}

Animals
*Sepsis/microbiology/drug therapy/metabolism
Humans
Mice
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/physiology
Disease Models, Animal
Child
Enterococcus/metabolism
*Deoxycholic Acid/metabolism/analogs & derivatives
Intestinal Barrier Function
Male
Child, Preschool
Female
Metabolomics

@article {pmid42093272,
year = {2026},
author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q},
title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.},
journal = {Cancer biology & medicine},
volume = {23},
number = {5},
pages = {737-754},
pmid = {42093272},
issn = {2095-3941},
support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; },
mesh = {Animals ; *CD8-Positive T-Lymphocytes/immunology/metabolism/drug effects ; Mice ; YAP-Signaling Proteins ; Humans ; *Bifidobacterium animalis/immunology ; *Melanoma, Experimental/immunology/pathology ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Cell Proliferation ; Disease Progression ; Cell Line, Tumor ; Gastrointestinal Microbiome ; *Transcription Factors/metabolism ; },
abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.

METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.

RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.

CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.},
}

Animals
*CD8-Positive T-Lymphocytes/immunology/metabolism/drug effects
Mice
YAP-Signaling Proteins
Humans
*Bifidobacterium animalis/immunology
*Melanoma, Experimental/immunology/pathology
*Probiotics/pharmacology
Mice, Inbred C57BL
Cell Proliferation
Disease Progression
Cell Line, Tumor
Gastrointestinal Microbiome
*Transcription Factors/metabolism

@article {pmid42142571,
year = {2026},
author = {Malešević, M and Matijašević, D and Kljajević, N and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Seasonal shifts in the Belgrade airborne resistome and virulome: A metagenomic perspective.},
journal = {Environmental research},
volume = {303},
number = {Pt 2},
pages = {124700},
doi = {10.1016/j.envres.2026.124700},
pmid = {42142571},
issn = {1096-0953},
mesh = {*Seasons ; *Air Microbiology ; Serbia ; *Microbiota ; *Metagenome ; Metagenomics ; *Bacteria/genetics ; Environmental Monitoring ; },
abstract = {The atmosphere is a dynamic reservoir for microorganisms and antimicrobial resistance genes (ARGs), yet the seasonal interplay of microbial communities, resistance and virulence determinants with environmental conditions remains poorly characterized, particularly in polluted urban areas. This study presents year-round (summer 2024-spring 2025) shotgun metagenomic monitoring of airborne microbiomes across the Belgrade metropolitan area, a European air pollution hotspot. While community composition shifted seasonally, with an enrichment of Bacillota in autumn and stress-tolerant genera in winter, opportunistic pathogens including Pseudomonas and Acinetobacter were detected year-round. The airborne resistome and mobilome exhibited pronounced seasonal restructuring, with winter showing the highest diversity of resistance genes and plasmid-associated sequences. Mobility-associated genes, including unique toxins and plasmid maintenance systems, were also most prominent in winter. Pathogen-host interaction profiling revealed a functional shift from respiratory and colonization-associated Gram-positive taxa such as Streptococcus pneumoniae and Staphylococcus aureus in autumn to enteric pathogens like Escherichia coli and Salmonella enterica in winter. Network analysis showed that winter formed the densest co-occurrence network, suggesting enhanced potential for co-selection of resistance and virulence traits. Specific plasmid-associated ARGs displayed seasonal patterns, with blaCTX-M linked to multiple plasmids in summer, while blaTEM and aph genes were more prominent in winter. Our findings illustrate that seasonal variations in the airborne genetic landscape are linked to environmental factors and fluctuating reservoirs of clinically relevant resistance and virulence determinants. This highlights the need for integrated longitudinal aerobiome surveillance to understand its implications for public health within the One Health framework.},
}

*Seasons
*Air Microbiology
Serbia
*Microbiota
*Metagenome
Metagenomics
*Bacteria/genetics
Environmental Monitoring

@article {pmid42172850,
year = {2026},
author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R},
title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {130036},
doi = {10.1016/j.jenvman.2026.130036},
pmid = {42172850},
issn = {1095-8630},
mesh = {Tibet ; *Wastewater/microbiology ; RNA, Ribosomal, 16S ; *Waste Disposal, Fluid ; *Microbiota ; Bacteria ; Altitude ; Metagenomics ; },
abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.},
}

Tibet
*Wastewater/microbiology
RNA, Ribosomal, 16S
*Waste Disposal, Fluid
*Microbiota
Bacteria
Altitude
Metagenomics

@article {pmid42176375,
year = {2026},
author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D},
title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.},
journal = {Water research},
volume = {302},
number = {},
pages = {126129},
doi = {10.1016/j.watres.2026.126129},
pmid = {42176375},
issn = {1879-2448},
mesh = {*Lakes/microbiology ; *Phosphorus/metabolism ; *Freezing ; *Microbiota ; Geologic Sediments ; },
abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.},
}

*Lakes/microbiology
*Phosphorus/metabolism
*Freezing
*Microbiota
Geologic Sediments

@article {pmid42176923,
year = {2026},
author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y},
title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.},
journal = {International journal of biological macromolecules},
volume = {368},
number = {},
pages = {152668},
doi = {10.1016/j.ijbiomac.2026.152668},
pmid = {42176923},
issn = {1879-0003},
mesh = {Animals ; *Atractylodes/chemistry ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism/pathology ; *Carbon/metabolism ; *Fatty Liver/drug therapy/metabolism ; Disease Models, Animal ; },
abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat and methionine/choline-deficient diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/d) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.},
}

Animals
*Atractylodes/chemistry
*Polysaccharides/pharmacology/chemistry
Mice
*Gastrointestinal Microbiome/drug effects
Male
Liver/drug effects/metabolism/pathology
*Carbon/metabolism
*Fatty Liver/drug therapy/metabolism
Disease Models, Animal

@article {pmid42190825,
year = {2026},
author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J},
title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.},
journal = {Environmental research},
volume = {304},
number = {},
pages = {124845},
doi = {10.1016/j.envres.2026.124845},
pmid = {42190825},
issn = {1096-0953},
mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis/chemistry ; *Geologic Sediments/chemistry/microbiology ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; Molecular Weight ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Microbiota ; },
abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.},
}

China
*Polycyclic Aromatic Hydrocarbons/analysis/chemistry
*Geologic Sediments/chemistry/microbiology
*Rivers/chemistry/microbiology
*Water Pollutants, Chemical/analysis
*Drug Resistance, Microbial/genetics
Molecular Weight
*Genes, Bacterial
Bacteria/genetics/drug effects
Environmental Monitoring
Microbiota

@article {pmid42208810,
year = {2026},
author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB},
title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.},
journal = {The Journal of infection},
volume = {93},
number = {1},
pages = {106774},
doi = {10.1016/j.jinf.2026.106774},
pmid = {42208810},
issn = {1532-2742},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Female ; Male ; *Carrier State/microbiology/epidemiology ; Aged, 80 and over ; *Bacteria, Anaerobic/drug effects ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Aged ; Nursing Home Residents ; Prevalence ; },
abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.

METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.

RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (β=1.36, P=0.010) and higher overall pathobiont relative abundance (β=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (β=1.60, P=0.007) and relative abundance (β=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.

CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.},
}

Humans
*Anti-Bacterial Agents/therapeutic use/adverse effects
Female
Male
*Carrier State/microbiology/epidemiology
Aged, 80 and over
*Bacteria, Anaerobic/drug effects
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Aged
Nursing Home Residents
Prevalence

@article {pmid42214595,
year = {2026},
author = {Pan, W and Zhang, L and Liang, L and Du, L and Guo, X},
title = {Nanoplastics reshape nitrogen cycling in submerged macrophyte systems: A metagenomic perspective.},
journal = {Environmental research},
volume = {304},
number = {},
pages = {124885},
doi = {10.1016/j.envres.2026.124885},
pmid = {42214595},
issn = {1096-0953},
mesh = {*Nitrogen Cycle/drug effects ; Metagenomics ; Rhizosphere ; *Water Pollutants, Chemical/toxicity ; Nitrogen/metabolism ; *Magnoliopsida/metabolism/drug effects ; Bacteria/metabolism/genetics ; Microbiota/drug effects ; },
abstract = {Nanoplastics (NPs) pose a potential risk to aquatic ecosystems. Submerged macrophytes are critical for nitrogen removal, but how nitrogen cycling responds to NP-induced stress remains unclear. This study used Myriophyllum aquaticum to evaluate nitrogen cycling in submerged macrophyte-sediment systems exposed to 100 nm polystyrene (PS) NPs at 10, 100, and 1000 μg/L, integrating stable isotope tracing and metagenomic profiling to explore microbial community and nitrogen-cycling gene responses across rhizosphere and non-rhizosphere compartments. Low PS-NP exposure (10 μg/L) slightly increased the NH4[+]-N removal efficiency to 81.5%, whereas medium and high PS-NP exposures (100 and 1000 μg/L) reduced the NH4[+]-N removal efficiency, with values around 70.9%. Low doses stimulated nitrification (NO3[-]-N accumulation) and high doses inhibited N2O emissions; δ[15]N tracing showed disrupted NH4[+]-N to N2 reduction. Plant-only microcosms had the highest N2O release (1.37 mg, 1.5% of total N). Metagenomics revealed concentration-dependent, spatially distinct microbial community shifts: low PS-NPs increased rhizosphere α-diversity, while high concentrations depleted Proteobacteria, enriched Acidobacteria/Bacteroidetes, and reduced key nitrogen-cycling genera (e.g., Dechloromonas, Accumulibacter). In the rhizosphere, denitrification genes (nirK/S,nosZ) were upregulated by 2.5- and 3-fold, respectively, while DNRA (nrfA) and nitrogen fixation (nifH) genes were downregulated by 1.7- and 2.3-fold. Network and canonical correspondence analyses indicated stronger environmental filtering in bulk sediments (explaining 52.0% of variance) and spatially structured nitrogen metabolic pathway reorganization. These findings show concentration-dependent PS-NP exposure differentially shapes microbial community composition and nitrogen-cycling functions in rhizosphere and bulk sediments.},
}

*Nitrogen Cycle/drug effects
Metagenomics
Rhizosphere
*Water Pollutants, Chemical/toxicity
Nitrogen/metabolism
*Magnoliopsida/metabolism/drug effects
Bacteria/metabolism/genetics
Microbiota/drug effects

@article {pmid42233252,
year = {2026},
author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR},
title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42233252},
issn = {1758-0463},
support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; },
mesh = {Biocuration ; Humans ; *Autoimmune Diseases/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity/immunology ; *Antigens, Bacterial/immunology ; Animals ; *Databases, Protein ; },
abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.},
}

Biocuration
Humans
*Autoimmune Diseases/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Autoimmunity/immunology
*Antigens, Bacterial/immunology
Animals
*Databases, Protein

@article {pmid42240631,
year = {2026},
author = {Hernández-Velázquez, R and Hernández-Avilés, JS},
title = {Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {6},
pages = {},
pmid = {42240631},
issn = {1465-2080},
mesh = {*Lakes/microbiology/chemistry ; Metagenomics ; Mexico ; *Metagenome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Sulfur/metabolism ; Tropical Climate ; Carbon/metabolism ; Phylogeny ; Biodiversity ; Nitrogen/metabolism ; },
abstract = {Warm monomictic maar lakes in tropical regions represent dynamic systems where thermal stratification generates strong vertical gradients in oxygen availability and redox conditions, shaping microbial community structure and function. Lake Atexcac (Puebla, Mexico) undergoes seasonal stratification and episodic whiting events that provide a framework to examine microbial responses to changing hydrodynamic conditions. In this study, we applied deep shotgun metagenomic sequencing to characterize the taxonomic composition and functional potential of microbial communities across the epilimnion, metalimnion and hypolimnion during two contrasting stratification phases: early stratification associated with a whiting event and a later, well-established stratification period.Metagenomic profiles revealed a clear vertical organization of microbial communities, with samples clustering primarily according to thermal strata and the metalimnion displaying the highest genetic differentiation. Genome-resolved analyses enabled the recovery of a large number of metagenome-assembled genomes, with marked differences in their vertical distribution between hydrodynamic phases. The recovered genomes encompassed diverse metabolic pathways related to carbon, nitrogen and sulphur transformations, reflecting the heterogeneous redox conditions along the water column. Notably, sulphur-related metabolisms were widespread across strata, and Chlorobiota-affiliated genomes and metagenomic reads were consistently detected in suboxic layers. These organisms were found to harbour diverse thiosulphate disproportionation pathways and are thought to play an important role in the sulphur cycle that has not previously been reported in this type of lacustrine system.Overall, this study provides a genome-resolved perspective on microbial diversity and metabolic potential in a stratified tropical maar lake and establishes a baseline for future comparative and process-oriented studies integrating water column and sediment microbial communities.},
}

*Lakes/microbiology/chemistry
Metagenomics
Mexico
*Metagenome
*Bacteria/classification/genetics/metabolism/isolation & purification
Sulfur/metabolism
Tropical Climate
Carbon/metabolism
Phylogeny
Biodiversity
Nitrogen/metabolism

@article {pmid42247440,
year = {2026},
author = {Levade, I and Delisle, B and Fournier, É and Therrien, C},
title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350663},
pmid = {42247440},
issn = {1932-6203},
mesh = {Animals ; Quebec ; *Metagenomics/methods ; Phylogeny ; *Culicidae/virology ; *Virome/genetics ; Genome, Viral ; Mosquito-Borne Diseases ; *Mosquito Vectors/virology ; *RNA, Viral/genetics ; Arboviruses/genetics/classification ; },
abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.},
}

Animals
Quebec
*Metagenomics/methods
Phylogeny
*Culicidae/virology
*Virome/genetics
Genome, Viral
Mosquito-Borne Diseases
*Mosquito Vectors/virology
*RNA, Viral/genetics
Arboviruses/genetics/classification

@article {pmid41759875,
year = {2026},
author = {Nuranindita, R and Natanegara, S and Wusono, AD and Amirudin, FA and Hitipeuw, D and Rahayu, AA and Daud, MM and Yuwanita, MR and Qanita, NG and Saputra, EY and Jun, H and Jeon, BY and Lee, MR and Ju, JW and Malik, MDA and Garjito, TA and Han, JH and Muh, F},
title = {Metatranscriptomic analysis of Anopheles species from Menoreh Hills endemic area in Central Java, Indonesia.},
journal = {Acta tropica},
volume = {277},
number = {},
pages = {108033},
doi = {10.1016/j.actatropica.2026.108033},
pmid = {41759875},
issn = {1873-6254},
mesh = {Animals ; *Anopheles/microbiology/virology/genetics/classification ; Indonesia ; *Microbiota ; *Mosquito Vectors/virology/microbiology ; Bacteria/classification/genetics/isolation & purification ; Gene Expression Profiling ; Transcriptome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The mosquito microbiome plays a crucial role in vector competence and disease transmission dynamics, yet comprehensive metatranscriptomic analyses of Anopheles species microbiomes remain limited, particularly in malaria-endemic regions like the Menoreh Hills of Central Java, Indonesia. This study aimed to characterize the microbial and viral community compositions of five Anopheles species and their potential implications for vectorial capacity.

METHODS: Metatranscriptomic analysis was performed on five Anopheles species (An. barbirostris, An. flavirostris, An. kochi, An. maculatus, and An. vagus) collected from the Menoreh Hills endemic area using RNA sequencing, taxonomic classification, and functional annotation approaches.

RESULTS: Proteobacteria emerged as the dominant bacterial phylum across all species, with variations in relative abundance of other taxa. Baculoviridae emerged as the overwhelmingly dominant viral family across all species, with other families including Bunyavirales, Herpesvirales, and Nucleocytoviricota present at much lower abundances. Diversity indices revealed An. vagus with the highest microbial diversity and An. barbirostris with the lowest. Adherence-related virulence factors were predominant, particularly in An. maculatus and An. vagus, while carbohydrate-active enzymes AA1 and GT35 were abundant across all species.

CONCLUSIONS: This study examines microbiome and virome across five Anopheles species from Menoreh Hills. Betabaculovirus dominated virome, while bacterial and fungal communities showed species-specific patterns. Analyses revealed virulence differences. Study limitations include pooled samples. The results provide data for malaria research.},
}

Animals
*Anopheles/microbiology/virology/genetics/classification
Indonesia
*Microbiota
*Mosquito Vectors/virology/microbiology
Bacteria/classification/genetics/isolation & purification
Gene Expression Profiling
Transcriptome
Metagenomics
*Viruses/classification/genetics/isolation & purification

@article {pmid42208188,
year = {2026},
author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S},
title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.},
journal = {Water research},
volume = {302},
number = {},
pages = {126138},
doi = {10.1016/j.watres.2026.126138},
pmid = {42208188},
issn = {1879-2448},
mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Wastewater/microbiology/chemistry ; Anaerobiosis ; Caffeine/metabolism ; Carbon Isotopes ; Bacteria/metabolism/genetics ; Naproxen/metabolism ; Demethylation ; Methane/metabolism ; Archaea/metabolism/genetics ; *Seawater/microbiology ; Oceans and Seas ; },
abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.},
}

*Water Pollutants, Chemical/metabolism
*Microbiota
Geologic Sediments/microbiology
*Wastewater/microbiology/chemistry
Anaerobiosis
Caffeine/metabolism
Carbon Isotopes
Bacteria/metabolism/genetics
Naproxen/metabolism
Demethylation
Methane/metabolism
Archaea/metabolism/genetics
*Seawater/microbiology
Oceans and Seas

@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 ; *Herbicides/toxicity ; *Nitrogen/metabolism ; *Toluidines/toxicity ; *Soil Pollutants/toxicity ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Agroecology ; Bacteria/drug effects/metabolism/genetics ; *Anti-Bacterial Agents ; },
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
*Herbicides/toxicity
*Nitrogen/metabolism
*Toluidines/toxicity
*Soil Pollutants/toxicity
*Drug Resistance, Microbial/genetics
*Microbiota/drug effects
Agroecology
Bacteria/drug effects/metabolism/genetics
*Anti-Bacterial Agents

@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 {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {56},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
mesh = {Animals ; *Heteroptera/microbiology/physiology/classification ; *Gastrointestinal Microbiome ; *Predatory Behavior ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Proteobacteria/isolation & purification/classification/genetics ; Adaptation, Physiological ; Biological Evolution ; Enterococcus/isolation & purification/genetics/classification ; Serratia/isolation & purification/genetics ; Bacillota/isolation & purification/genetics/classification ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.

RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.

CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}

Animals
*Heteroptera/microbiology/physiology/classification
*Gastrointestinal Microbiome
*Predatory Behavior
*Bacteria/classification/genetics/isolation & purification
Symbiosis
Phylogeny
Proteobacteria/isolation & purification/classification/genetics
Adaptation, Physiological
Biological Evolution
Enterococcus/isolation & purification/genetics/classification
Serratia/isolation & purification/genetics
Bacillota/isolation & purification/genetics/classification

@article {pmid41502126,
year = {2026},
author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM},
title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70226},
doi = {10.1111/1462-2920.70226},
pmid = {41502126},
issn = {1462-2920},
support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; },
mesh = {*Oxygen/analysis/metabolism ; *Seawater/microbiology/chemistry ; Metagenomics ; Pacific Ocean ; *Metagenome ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Photosynthesis ; Chlorophyll/analysis ; },
abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.},
}

*Oxygen/analysis/metabolism
*Seawater/microbiology/chemistry
Metagenomics
Pacific Ocean
*Metagenome
*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Photosynthesis
Chlorophyll/analysis

@article {pmid41502165,
year = {2026},
author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES},
title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70225},
pmid = {41502165},
issn = {1462-2920},
support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; },
mesh = {*Hot Springs/microbiology ; *Carbon/metabolism ; *Nitrogen/metabolism ; Iceland ; *Thermus/metabolism/genetics/growth & development ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; },
abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.},
}

*Hot Springs/microbiology
*Carbon/metabolism
*Nitrogen/metabolism
Iceland
*Thermus/metabolism/genetics/growth & development
Nitrogen Fixation
Carbon Dioxide/metabolism

@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/epidemiology/metabolism/etiology ; *Fatty Acids, Volatile/metabolism/analysis ; *Gastrointestinal Microbiome ; Indonesia/epidemiology ; *Liver Cirrhosis/complications ; *Brain/metabolism ; *Liver/metabolism ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}

Humans
*Hepatic Encephalopathy/epidemiology/metabolism/etiology
*Fatty Acids, Volatile/metabolism/analysis
*Gastrointestinal Microbiome
Indonesia/epidemiology
*Liver Cirrhosis/complications
*Brain/metabolism
*Liver/metabolism

@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; *Dysbiosis/virology/complications/microbiology ; Animals ; *Primary Ovarian Insufficiency/microbiology/virology/therapy/etiology ; Humans ; *Gastrointestinal Microbiome ; Rats ; *Virome ; Adult ; Fecal Microbiota Transplantation ; Feces/virology/microbiology ; Bacteria/classification/genetics/isolation & purification ; Ovary/physiopathology ; Young Adult ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.

RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.

CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}

Female
*Dysbiosis/virology/complications/microbiology
Animals
*Primary Ovarian Insufficiency/microbiology/virology/therapy/etiology
Humans
*Gastrointestinal Microbiome
Rats
*Virome
Adult
Fecal Microbiota Transplantation
Feces/virology/microbiology
Bacteria/classification/genetics/isolation & purification
Ovary/physiopathology
Young Adult

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Hyperuricemia/microbiology ; *Overweight/microbiology ; Female ; Male ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Adult ; Middle Aged ; *Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Hyperuricemia/microbiology
*Overweight/microbiology
Female
Male
Cross-Sectional Studies
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Adult
Middle Aged
*Metagenomics
Metagenome

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0305125},
pmid = {41504449},
issn = {2165-0497},
support = {32460813//National Natural Science Foundation of China/ ; 2022MS03074, 2025MS03005, 2023YFDZ0079, 2023YFDZ0068, 2025YFDZ0123//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; NJYT22054//Education Department of Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle/metabolism ; *Rumen/microbiology/metabolism ; Female ; *Dietary Fiber/metabolism ; *Animal Feed/analysis ; Fermentation ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Poaceae/metabolism ; Mongolia ; Metabolomics ; Digestion ; Fungi/classification/genetics/isolation & purification/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

Animals
Cattle/metabolism
*Rumen/microbiology/metabolism
Female
*Dietary Fiber/metabolism
*Animal Feed/analysis
Fermentation
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism
*Poaceae/metabolism
Mongolia
Metabolomics
Digestion
Fungi/classification/genetics/isolation & purification/metabolism
Gastrointestinal Microbiome

@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}

*Methane/metabolism
*Plant Bark/microbiology
Australia
*Microbiota
*Forests
*Hydrogen/metabolism
Carbon Monoxide/metabolism
Metagenomics
*Trees/microbiology
*Bacteria/metabolism/genetics/classification
Anaerobiosis

@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 = {China ; *Geologic Sediments/microbiology ; *Wetlands ; Aquaculture ; *Microbiota ; Bacteria/classification/genetics ; *Environmental Restoration and Remediation ; Ponds/microbiology ; },
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.},
}

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

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {415-428},
pmid = {41507585},
issn = {2058-5276},
support = {K99 AA031328/AA/NIAAA NIH HHS/United States ; R21 AA030654/AA/NIAAA NIH HHS/United States ; R01 AA020098/AA/NIAAA NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R00 AA031328/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Ethanol/metabolism ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metabolic Networks and Pathways/genetics ; Male ; Fermentation ; Female ; Fecal Microbiota Transplantation ; Escherichia coli/metabolism/genetics/isolation & purification ; Metagenomics ; Middle Aged ; Metabolomics ; Adult ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

Humans
*Ethanol/metabolism
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/genetics
Cohort Studies
Metabolic Networks and Pathways/genetics
Male
Fermentation
Female
Fecal Microbiota Transplantation
Escherichia coli/metabolism/genetics/isolation & purification
Metagenomics
Middle Aged
Metabolomics
Adult

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {126},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Microbiota/drug effects/genetics ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Animal Husbandry/methods ; *Drug Resistance, Bacterial ; Farms ; *Anti-Infective Agents/pharmacology ; Soil Microbiology ; Shotgun Sequencing ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

Animals
*Chickens/microbiology
*Microbiota/drug effects/genetics
*Bacteria/drug effects/genetics/classification/isolation & purification
*Anti-Bacterial Agents/pharmacology
Animal Husbandry/methods
*Drug Resistance, Bacterial
Farms
*Anti-Infective Agents/pharmacology
Soil Microbiology
Shotgun Sequencing

@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {130},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Retrospective Studies ; Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; *Lung/microbiology ; Aged ; Nontuberculous Mycobacteria/genetics/isolation & purification ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Middle Aged ; Mycobacterium tuberculosis/genetics/isolation & purification ; Bacilloscopy ; *Tuberculosis, Pulmonary/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.

OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.

METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.

RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.

CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}

Retrospective Studies
Humans
*Bronchoalveolar Lavage Fluid/microbiology
Female
Male
*Lung/microbiology
Aged
Nontuberculous Mycobacteria/genetics/isolation & purification
*Microbiota
High-Throughput Nucleotide Sequencing
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
Middle Aged
Mycobacterium tuberculosis/genetics/isolation & purification
Bacilloscopy
*Tuberculosis, Pulmonary/microbiology
Metagenomics

@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Feces/microbiology ; Female ; Prospective Studies ; *Gastrointestinal Microbiome/genetics ; Male ; Australia ; *Specimen Handling/methods ; Middle Aged ; Aged ; Occult Blood ; Surveys and Questionnaires ; Adult ; Metagenomics/methods ; *Neoplasms/microbiology ; Whole Genome Sequencing ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.

SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}

Humans
Pilot Projects
*Feces/microbiology
Female
Prospective Studies
*Gastrointestinal Microbiome/genetics
Male
Australia
*Specimen Handling/methods
Middle Aged
Aged
Occult Blood
Surveys and Questionnaires
Adult
Metagenomics/methods
*Neoplasms/microbiology
Whole Genome Sequencing

@article {pmid41508741,
year = {2026},
author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P},
title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70262},
pmid = {41508741},
issn = {1758-2229},
support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Geologic Sediments/virology ; *Lakes/virology ; Tibet ; *DNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; Metagenomics ; Biodiversity ; Metagenome ; },
abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.},
}

*Geologic Sediments/virology
*Lakes/virology
Tibet
*DNA Viruses/genetics/classification/isolation & purification/physiology
Phylogeny
Metagenomics
Biodiversity
Metagenome

@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 = {*Iron/metabolism/analysis ; *Plant Roots/microbiology/metabolism/growth & development/genetics ; *Microbiota ; *Azetidinecarboxylic Acid/analogs & derivatives/metabolism/pharmacology ; *Citrus/microbiology/metabolism/growth & development/genetics ; Bacteria/genetics/isolation & purification/classification/metabolism ; Rhizosphere ; Fertilizers/analysis ; *Proline/analogs & derivatives/metabolism ; Soil Microbiology ; },
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.},
}

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

@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
support = {INV-044643/GATES/Gates Foundation/United States ; },
mesh = {Animals ; *Feces/microbiology ; *Marsupialia/microbiology ; Phylogeny ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}