Posted on September 26, 2025 by Bugembe Allan

Gut Microbiome & Human Health

Combined effect of probiotics and omega-3 fatty acids on blood and liver function biomarkers and gut microbiota diversity in male mice with high fat diet-induced obesity – Kwang Hee Son – PLOS ONE

Development and validation of a machine learning-based predictive model for clinical remission in Crohn’s disease patients receiving Adalimumab therapy – Pianpian Xia – PLOS ONE

Molecular mechanisms of dragon’s blood in treating ulcerative colitis based on NF-κb/NLPR3/Caspase-1 pyroptosis signaling pathway – Bilian Cai – PLOS ONE

Antimicrobial Resistance & Pathogens

Perinatal colonization with extended-spectrum beta-lactamase-producing and carbapenem-resistant gram-negative bacteria among home births in Bangladesh – Gregory S. Wu – PLOS ONE

Isolation, purification, and phenotypic characterization of virulent Klebsiella pneumoniae phages from environmental samples in Addis Ababa, Ethiopia – Assefa Asnakew Abebe – PLOS ONE

Other Microbiomes (Marine & Environmental)

Effects of repeated hemolymph sampling from adductor muscles of relaxed Pacific oysters (Magallana gigas) – Jingwei Song – PLOS ONE

Morphological differences in populations of Jacobaea erucifolia: Genetic differentiation, phenotypic plasticity or ecotypes? – Barbara Gawrońska – PLOS ONE

Reviews & Systematic Studies

Infection and telomere length: A systematic review – Louis Tunnicliffe – PLOS ONE

Cardiovascular & Comorbidities

Stratifying atherosclerotic cardiovascular disease by SMuRF burden in a Middle-Eastern country: A multiregistry study – Osama Alkouri – PLOS ONE

General Microbiome

The multi-kingdom cancer microbiome – Anders B. Dohlman – Nature Microbiology

Gut microbiome

Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection – Shrushti Shah – BMC Microbiology

Gut microbial production of imidazole propionate drives Parkinson’s pathologies – Hyunji Park – nature communications

Vaginal microbiome

Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis – Smrutiti Jena – bioRxiv

Animal microbiome

Longitudinal Long-Read Microbiome Profiling in a Canine Model Reveals How Age, Diet, and Birth Mode Shape Gut Community Dynamics – Md Asaduzzaman – bioRxiv

Water microbiome

Net rate of lateral gene transfer in marine prokaryoplankton – Ramunas Stepanauskas – The ISME Journal

Virome

Spatio-temporal factors shape mosquito virome diversity and composition in a host and virus phylogeny-dependent manner – Cassandra Koh – bioRxiv

Bioinformatics

Dietary Protein Source Shapes Gut Microbial Structure and Predicted Function: A Meta-Analysis with Machine Learning – SAMSON A. ADEJUMO – bioRxiv

Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Divergent pMMO Diversity – Magdalena J Mayr – The ISME Journal

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease – Stefano Romano – nature communications

Microbes on the market

Microbiome Manufacturing Market Size to Hit USD 130.37 Billion by 2034 – Deepa Pandey – Precedence Research

General microbiome

Conserved genetic basis for microbial colonization of the gut – Liu et al. – Cell

Human skin microbiome

Confounders of the skin microbiome and wound healing in burn patients – Pourali, Aali & Kamrava – Burns

Human vaginal microbiome

[PREPRINT]Temporal Dynamics of the Vaginal Microbiome and Host Immune Markers Before, During, and After Metronidazole Treatment for Bacterial Vaginosis – Williams et al. – bioRxiv

Human gut microbiome/mycobiome

Gut microbiome in patients with early-stage and late-stage endometriosis – Cai et al. – BMC Women’s Health

Effect, tolerability, and safety of exclusive palatable elemental diet in patients with intestinal microbial overgrowth – Rezaie et al. – Clinical Gastroenterology and Hepatology

[PREPRINT]Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome – Zheng et al. – bioRxiv

[PREPRINT]Investigating microbiota differences across chronic pancreatitis, influenced by lifestyle and genetic determinants – Ahmed et al. – bioRxiv

Animal microbiome

Gut microbiota contributes to protection against porcine deltacoronavirus infection in piglets by modulating intestinal barrier and microbiome – Zhang et al. – Microbiome

Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction – Yu et al. – The ISME Journal

[PREPRINT]Longitudinal study of the udder microbiome of Norwegian red dairy cows using metataxonomic and shotgun metagenomic approaches: Insights into pathogen-driven microbial adaptation and succession – da Silva Duarte et al. – bioRxiv

[PREPRINT]Characterizing the Microbiome of ‘Sterile’ Organs in Experimental Mice – Xu et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Environmental drivers of the resistome across the Baltic Sea – Serrana et al. – Microbiome

Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications – He et al. – Microbiome

Bioinformatics

Bayesian compositional generalized linear mixed models for disease prediction using microbiome data – Zhang et al. – BMC Bioinformatics

Techniques

[PREPRINT]Artificial soil systems: A tool for investigating microbial life strategy effects on substrate mineralization – Fujiwara, Makino & Hamamoto – bioRxiv

General microbiome

The Triple Alliance: Microbiome, Mitochondria, and Metabolites in the Context of Age-Related Cognitive Decline and Alzheimer’s Disease – Prajapiti et al. – The Journals of Gerontology: Series A

[REVIEW]Genomic surveillance for antimicrobial resistance — a One Health perspective – Djordjevic et al. – Nature Reviews Genetics

Human respiratory microbiome

[REVIEW]Lung Microbiome as a Treatable Trait in Chronic Respiratory Disorders – Scialo et al. – Lung

Human gut microbiome

[PREPRINT]Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation – Xue et al. – bioRxiv

[PREPRINT]A gut meta-interactome map reveals modulation of human immunity by microbiome effectors – Young et al. – bioRxiv

[PREPRINT]Association of homelessness and diet on the gut microbiome: A United States-Veteran Microbiome Project (US-VMP) study – Hoisington et al. – bioRxiv

Plant, root, and soil microbiome

Tomato growth stage modulates bacterial communities across different soil aggregate sizes and disease levels – Dong et al. – ISME Communications

Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation – Zhai et al. – Science of The Total Environment

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt, rocks)

Arctic bacterial diversity and connectivity in the coastal margin of the Last Ice Area – Girard, Vincent & Culley – ISME Communications

A glimpse of the paleome in endolithic microbial communities – Wegener et al. – Microbiome

Bioinformatics

A computational method to dissect colonization resistance of the gut microbiota against pathogens – Ke et al. – Cell Reports Methods

[PREPIRNT]SurvBal: Compositional Microbiome Balances for Survival Outcomes – Li et al. – bioRxiv

General microbiome

Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions – Zampieri, Efthimiou & Angione – Metabolic Engineering

[REVIEW]Advancing CAR T cell therapy through the use of multidimensional omics data – Yamg et al. – Nature Reviews Clinical Oncology

Pregnancy and early life

[REVIEW]Microbial transmission, colonisation and succession: from pregnancy to infancy – Xiao & Zhai – Gut

Human gut microbiome

Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome – Wang et al. – Microbiology Spectrum

[PREPRINT]Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization – Jansma et al. – bioRxiv

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice – Vallier et al. – Gut Microbes

Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid – Pruss et al. – Nature Communications

Disruption of the Intestinal Mucosal Barrier Induced by High Fructose and Restraint Stress Is Regulated by the Intestinal Microbiota and Microbiota Metabolites – Yu et al. – Microbiology Spectrum

[PREPRINT]Shift from a Simplified to Complex Gut Microbiota Reduces Adenoma Burden in a Preclinical Rat Model of Colon Cancer – Busi et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms – Vincent et al. – Nature Communications

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. – Microbiome

Bioinformatics

[PREPRINT]Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses – Gao & Wu – bioRxiv

Techniques

[PREPRINT]Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions – Alyami et al. – bioRxiv

Human oral microbiome

[PRIMER]A possible role for taste receptor cells in surveying the oral microbiome – Heisey & McCluskey – PLOS Biology

Type II taste cells participate in mucosal immune surveillance – Qin et al. – PLOS One

Human gut microbiome

[NEWS]How our microbiome is shaped by family, friends and even neighbours – Callaway – Nature

The person-to-person transmission landscape of the gut and oral microbiomes – Valles-Colomer et al. – Nature

[REVIEW]The gut microbiota in obesity and weight management: microbes as friends or foe? – van Hul & Cani – Nature Reviews Endocrinology

Dynamics of the gut microbiome, IgA response, and plasma metabolome in the development of pediatric celiac disease – Girdhar et al. – Microbiome

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes – Jacobs et al. – Microbiome

Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism – Xu et al. – mBio

Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets – Kim, Lee & Shim – Microbiology Spectrum

Harnessing gut microbes for glycan detection and quantification – Modesto, Pearce & Townsend Il – Nature Communications

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles – Malan – Müller et al. – Gut Microbes

Animal microbiome

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Li et al. – Microbiome

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions – Bay et al. – Microbiome

Plant, root, and soil microbiome

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data – Merihu et al. – Microbiome

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle – Kibegwa et al. – PLOS One

Bioinformatics

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples – Maki et al. – PLOS One