Gut microbiota and health

Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure

EukDetect2 improves eukaryote detection in metagenomes with a larger database and quantitative metrics, revealing Blastocystis and Dientamoeba as prevalent gut eukaryotes.

Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics

This study investigates interactions between low-calorie sweeteners and xenobiotics on gut bacteria, finding synergistic effects that alter bacterial growth and host cell responses.

Enhanced Prediction of Gut Microbiome-Related Diseases Using Hybrid Machine Learning Models

This paper develops hybrid ensemble models for predicting gut microbiome-related diseases, achieving high accuracy and robustness across diverse datasets.

Enriching the Human Stool Microeukaryotes for Shotgun Sequencing

This study develops a method to enrich microeukaryotes in human stool samples for shotgun sequencing, improving their representation and taxonomic diversity in metagenomic libraries.

Fasting primes small intestinal regeneration after damage via a microbiome metabolite chromatin axis

The paper identifies a fasting-induced microbiome-metabolite-chromatin axis that primes intestinal stem cells for regeneration after radiation injury.

Gut Microbiota Alterations and Probiotic Intervention in Asian Elephants (Elephas maximus) with Gastrointestinal Distress

This study examines gut microbiota changes in Asian elephants with GI issues and evaluates the impact of probiotic treatment on microbial composition and fecal health.

A Scalable Framework for Species-Resolved Human Gut Microbiome Profiling Using Full-Length 16S rRNA Sequencing

This study evaluates a full-length 16S rRNA sequencing framework for species-resolved human gut microbiome profiling, showing improved taxonomic resolution compared to short-read methods.

Microbiome histidine competition mediates dietary control of systemic imidazole propionate

This study shows dietary glutamate influences ImP production via microbial competition, affecting glucose tolerance and systemic ImP levels.

Antibiotic-induced Malassezia spp. expansion in infants promotes early-life immune dysregulation and airway inflammation in mice

Multi-component functionalized Bifidobacterium longum hydrogel for multi-target integrated therapy of colitis-associated anxiety and depression

This paper develops a hydrogel-based therapy using functionalized Bifidobacterium longum to treat colitis-associated anxiety and depression by targeting both gut and brain inflammation.

The primate gut bacterial microbiome: a systematic review of research methodologies, taxonomic coverage, and conservation implications

This paper reviews primate gut microbiome research, identifying gaps in taxonomic coverage, geographic representation, and methodology, and proposes a standardized reporting framework for better conservation applications.

Neuroendocrine arylhydrocarbon receptor regulates gut microbiome of C. elegans via redox tone

This study shows that neuronal AHR-1 in C. elegans regulates gut microbiome composition by modulating intestinal redox tone through a neuroendocrine cascade.

Indole-3-acetic acid production is rare among gut bacteria and reflects OFOR-driven amino acid oxidation in acetogens

The paper identifies rare IAA-producing gut bacteria and links IAA synthesis to OFOR-driven amino acid oxidation in acetogens.

Integrative Multi-Omics Analysis of Gut Microbiota Dysbiosis and Host-Microbiome Interaction Mechanisms in Hypertension

The paper investigates gut microbiota dysbiosis in hypertension and its interactions with the host immune system using multi-omics data and single-cell analysis.

Spatial atlas highlights contribution of C. difficile in early-stage colorectal cancer

The paper creates a spatial atlas of early-stage colorectal cancer tumors to identify bacterial niches and their impact on tumor transcriptomes, highlighting C. difficile's significant influence despite low abundance.

Host-derived bile acids drive dysbiosis by selecting bile-resistant epimerizing bacteria in inflammatory bowel disease

The paper identifies epimerized host-derived bile acids as a driver of dysbiosis in IBD by selecting for bile-resistant bacteria that disrupt host bile acid feedback signaling.

The gut microbiota directs vitamin A flux to regulate intestinal T cell development

This paper shows the gut microbiota regulates intestinal T cell development by directing vitamin A flux through a sequential pathway involving epithelial, myeloid, and T cells.

Environmental microbial extracts for longitudinal studies of gut microbiome assembly and maintenance

The paper introduces a method using environmental microbial extracts to study gut microbiome dynamics in C. elegans over time, showing stable composition and age-related changes in Enterobacteriaceae abundance.

Effects of intergenerational transmission of small intestinal bacteria cultured from stunted Bangladeshi children with enteropathy

This study shows that a perturbed small intestinal microbiota from stunted children can induce EED-like features in offspring through inflammation and immune changes.

Social network cycle motifs and gut microbiome strain-sharing

The paper examines how social network cycles influence microbial strain-sharing in Honduran villages, finding that microbial transmission often occurs within clustered groups but not always aligned with social ties.

Vancomycin promotes key microbiota-pathogen interactions and removes protective bottlenecks to enteric infection

This study shows that vancomycin alters gut microbiota-pathogen interactions, removes infection bottlenecks, and promotes pathogen colonization in mice.

Distinct types of gut dysbiosis and oral-gut microbial signatures differentiate C. difficile, Campylobacter, and Salmonella infections: a cross-sectional study

This study identifies distinct gut dysbiosis patterns and oral-gut microbial signatures for C. difficile, Campylobacter, and Salmonella infections using 16S rRNA gene sequencing and machine learning.

Bile Salts and Bacterial Bile Salt Hydrolase Activity Differentially Influence Escherichia coli Colonization and FXR Signaling in Colorectal Cancer Organoids

Small intestine microbiota development prevents early-life adiposity via IL-22-mediated intestinal PPARα suppression

This study shows that early-life small intestine microbiota prevents adiposity by suppressing PPARα via IL-22, and antibiotic disruption increases adiposity.

Human footprints in the gut: how anthropogenic environments reshape the microbiome of chacma baboons

This study examines how different anthropogenic environments affect the gut microbiome of chacma baboons, finding reduced diversity and compositional shifts in human-altered areas, but distinct patterns in cultivated regions.

Bias-mitigated microbiome inference refines coronary artery disease signature

This paper introduces BootDA, a method to mitigate biases in microbiome differential abundance analysis, refining the coronary artery disease signature to two genera.

Identification of the complete pathway for conversion of bilirubin to urobilinogen by human gut bacteria

The paper identifies the complete pathway for bilirubin conversion to urobilinogen by human gut bacteria, revealing two enzymes and their specific reactions.

Beyond single markers: bacterial synergies identified by Multidimensional Feature Selection reveal conserved microbiome disease signatures

This paper introduces a framework to identify synergistic microbial pairs in metagenomic data that carry more disease information than individual features, showing improved performance in colorectal cancer classification.

The Critical Period Microbiota Shape Brain Plasticity

This study shows that gut microbiota disruption during critical periods of visual cortex development impairs ocular dominance plasticity in mice, and fecal transplantation restores it.

Disruption of the spinal cord-gut axis alters gut microbial dynamics and carbohydrate cross-feeding

This study shows that disrupting the spinal cord-gut axis alters gut microbial dynamics and carbohydrate cross-feeding, with interventions restoring health.