Gut microbiota and health

The network structure of cross-feeding impacts microbial community diversity under growth-inhibiting stresses

The paper models how cross-feeding network structures affect microbial community diversity under growth-inhibiting stresses, finding cyclic networks promote coexistence in narrow-spectrum inhibition but can be detrimental in broader contexts.

Gut immunity and the bacterial and eukaryotic microbiome of wild house mice.

The paper examines the gut microbiome of wild mice, finding site-specific differences and identifying factors like gut inflammation and IgA responses that influence microbiome diversity.

Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal

The paper investigates how different high-fat diets affect host and microbiome multi-omic states over time and shows that some changes persist even after returning to a control diet.

Interspecies interaction controls Escherichia coli growth in human gut microbiome samples

The paper tests how gut microbiome variation affects Escherichia coli growth across human samples, finding interspecies interactions influence growth outcomes.

Gut Microbiome as a Diagnostic Biomarker for Early Cancer Detection: A Systematic Review and Meta-Analysis of 18 Studies across Five Cancer Types

This paper reviews 18 studies on gut microbiome biomarkers for early cancer detection across five cancer types, finding AUC values between 0.78 and 0.85 and identifying shared microbial patterns.

Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest

This study shows that reducing dietary sodium alters gut microbial fermentation and decreases host energy absorption in rats.

Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection

The paper identifies metabiosis, an ecological dependency where Bacteroides supports Pseudomonadota growth, increasing gut-borne bloodstream infection risk in allo-HCT patients.

NETWORK-BASED FUNCTIONAL FRAGILITY REVEALS SYSTEM-LEVEL REORGANIZATION OF THE GUT MICROBIOME IN INFLAMMATORY BOWEL DISEASE

This study uses network analysis to show that IBD alters gut microbiome functional organization, leading to fragmented and fragile networks compared to healthy controls.

Probiotic-conditioned microbiota from preterm infants modulate immune response to pathogen challenge in a humanized mouse model

This study shows that probiotic-modified microbiota from preterm infants reduces innate immune cell populations in mice and impairs bacterial clearance during infection.

Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts

This study shows that probiotic Bifidobacteria in infants reduce antibiotic-resistant pathobionts by altering gut metabolism and resistome.

Pyruvate-driven hydrogen production promotes polyphenol bioconversion by gut bacteria

The paper develops a medium to enhance gut bacteria's conversion of polyphenols into bioactive metabolites by promoting pyruvate metabolism and hydrogen production.

Sexual dimorphism in the homeostasis of the gut microbiome-immune axis

The paper identifies sex-specific microbial regulators of immune homeostasis and shows how oral contraceptives disrupt this relationship.

Microbiome-Targeted Reduction of Circulating Trimethylamine N-Oxide Mitigates Ischemic Stroke Risk

This study identifies Paracoccus aminovorans BM109 as a microbiome-targeted therapy that reduces TMAO levels and mitigates ischemic stroke risk in animal models.

An Explainable Knowledge Graph-Driven Approach to Decipher the Link Between Brain Disorders and the Gut Microbiome

This paper introduces GNN-GBA, a graph neural network that identifies mechanistic pathways linking gut microbes to brain disorders using a large biomedical knowledge graph.

The Neuroactive Potential of the Elderly Human Gut Microbiome is Associated with Mental Health Status

This study links the neuroactive potential of the elderly gut microbiome to mental health and cognition in older adults with cognitive complaints.

Fiber Formulation-Dependent Modulation of Gut Microbial Metabolism in Parkinsons Disease

This study shows that multi-fiber formulations increase SCFA production and microbial biomass in PD fecal samples, suggesting formulation-dependent modulation of gut-brain signaling.

Gut Microbial Metabolic Disorder in Depression: Insights from Computational Modeling and Mediation Analysis

This study identifies differential gut microbiota species and metabolic fluxes associated with depression using computational modeling and mediation analysis.

Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface

This study investigates how dietary oxysterols affect the gut-liver axis in rats, revealing post-transcriptional metabolic changes and microbiome alterations.

Environmentally mediated interactions predict community assembly and invasion success in a gut microbiota SynCom

This study uses a synthetic gut microbiota community to predict invasion success and community stability by modeling interactions between species.

Predicted meta-omics: a potential solution to multi-omics data scarcity in microbiome studies

The paper predicts other meta-omics data from metagenomics using machine learning, showing reliable predictions for transcript and metabolite abundances but challenges in protein profiles, and demonstrates utility for inflammatory bowel disease classification.

Gut Microbiota Mediates the Association between Diet Quality and Ectopic Adiposity: The Multiethnic Cohort Adiposity Phenotype Study

This study shows that higher diet quality reduces ectopic adiposity, and this effect is partially mediated by gut microbiota, specifically four bacterial genera.

A conserved peptidase governs glucose homeostasis in Bacteroides

The paper identifies an M16 peptidase in Bacteroides that regulates glucose-dependent inhibition of Cur, affecting carbon metabolism and host-microbial interactions.

Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM

This paper introduces PALM, a quasi-Poisson regression framework for fast and reliable association discovery in large-scale microbiome studies and meta-analyses, showing improved control of false discovery rates and computational efficiency.

A Mixed Effect Similarity Matrix Regression Model (SMRmix) for Integrating Multiple Microbiome Datasets at Community Level

This paper introduces SMRmix, a mixed effect model for integrating multiple microbiome datasets to identify consistent community-level associations with outcomes.

LOCOM2: Robust Differential Abundance Analysis for Microbiome Data

LOCOM2 improves differential abundance analysis in microbiome studies by controlling error rates and handling challenges like relative abundance data and unbalanced designs.

Metabolite mimicry identifies butyrate analogs with select protective functions in the intestinal mucosa

This study identifies a butyrate analog, 3-chlorobutyrate, that enhances epithelial barrier formation and is protective in colitis without affecting intestinal stem cells.

Links Between Gut Microbiota of Uruguayan Infants, Breast Milk Composition, and Maternal Factors During Exclusive Breastfeeding

The paper examines the gut microbiota of Uruguayan infants during exclusive breastfeeding, linking it to breast milk composition, fecal IgA, and maternal factors, finding delivery mode influences microbiota composition and correlations.

Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling

This paper shows that engineered probiotics converting lactate to pyruvate acutely alter microbiota and host metabolism but fail to improve chronic obesity, highlighting homeostatic limits of gut-targeted therapies.

The human gut microbiome activity is resilient and stable for up to six months: a large stool metatranscriptomic study

This study shows the human gut microbiome remains stable in composition and function for up to six months, with resilience to short-term disruptions like colonoscopy preparation.

A class of metallohydrolases expands bile salt hydrolase activity in the gut

The paper identifies a new class of metal-dependent bile salt hydrolases (mBSHs) in gut bacteria that expand bile acid metabolism beyond previously known Ntn family enzymes.