Gut microbiota and health

Interpreting graph neural networks reveals microbial association patterns in inflammatory bowel diseases

The paper uses graph neural networks to interpret microbial association patterns in IBD, showing that coordinated associations, not just abundance shifts, are predictive.

Metabolic cascades drive spatial prebiotic fermentation in a defined gut consortium

This study shows that spatial prebiotic fermentation in a gut microbiota consortium is driven by metabolic cascades, revealing how spatial gradients influence microbial function and prebiotic efficacy.

Dietary fibre responses emerge through host-dietary regime interplay: Apple pectin modulates immune reactivity in adult zebrafish

This study examines how different dietary fibre regimes affect the gut microbiome, SCFA profiles, and immune responses in zebrafish, showing context-specific effects influenced by sex and dietary context.

Genomic insights into the human gut commensal Megasphaera elsdenii: Relatedness and metabolic potential compared to animal isolates

This study compares Megasphaera elsdenii genomes from human and animal gut isolates, finding they are genetically similar and share metabolic functions, with no host-specific clustering or virulence genes.

High-resolution temporal profiling reveals synchronized dynamics of the mouse gut microbiome

This study reveals synchronized temporal dynamics in the mouse gut microbiome using high-resolution sampling and analysis methods, showing phase-coherent groups linked to host circadian cycles.

Fetal sex is associated with the maternal gut microbiota composition and its metabolic function

This study finds that fetal sex influences maternal gut microbiota composition and metabolic function, with female pregnancies showing higher diversity and increased beta-glucuronidase activity.

Genetic profiling via a novel PCR-RFLP method enabled identification of four genera of anaerobic gut fungi isolated from nyala, giraffe, and zebra hosts

A validated PCR-RFLP method enables efficient identification of anaerobic gut fungi from faecal samples, leading to isolation of four genera including a novel Piromyces species.

Indigenous Yanomami gut microbiota protects against diet-induced metabolic dysfunction

This study transplants gut microbiota from Indigenous Yanomami and urban donors into mice to show Yanomami microbiota protects against diet-induced metabolic dysfunction.

Comparisons among Yanomami populations reveal transitional gut microbiome configurations under urban influence

The paper compares gut microbiomes of Yanomami populations with varying urban influence and a Belgian urban cohort, finding urban-associated features and shifts in microbial composition and function.

Integrating stool chemistry measurements with metagenomics in adults reveals distinct gut health profiles

The paper integrates stool chemistry metrics with shotgun metagenomics in adults to identify distinct gut health profiles associated with microbial and inflammatory markers.

Engineering a gut bacterium depleted in industrialized microbiomes to survive malabsorption

The paper engineers a gut bacterium to enhance osmotic resistance, enabling it to survive malabsorption in industrialized microbiomes.

Perturbation-based propagation of bacterial composition uncertainty improves robustness and reproducibility of microbiome differential abundance analysis.

PARALLAX improves microbiome differential abundance analysis by addressing compositional data, uncertainty, and experimental design through a unified framework with stability-based metrics.

Taxon-in-context reveals ecological individuality in the human gut microbiome

The paper introduces taxon-in-context to capture individualized microbial context in the human gut microbiome, showing that microbes occupy different contexts across individuals and over time, improving recurrence prediction.

Culturomics-Guided Precision FMT Enables Stable Antibiotic-Independent Engraftment via Metabolic Niche Targeting

This paper develops a culturomics-guided FMT framework that enables stable, antibiotic-independent engraftment by targeting metabolic niches in recipient microbiomes.

Integrated microbiome and metabolomic profiling reveals alterations across the adenoma-colorectal cancer sequence

This study identifies microbial and metabolic changes across the adenoma-carcinoma sequence in colorectal cancer using 16S rRNA sequencing and metabolomic profiling.

Dietary fiber-type-specific gut microbiome preconditioning drives differential susceptibility to sporadic colon cancer development

The paper shows that inulin supplementation increases colon tumor incidence in mice by altering gut microbiome and metabolome, creating a tumor-promoting environment when exposed to carcinogens.

TRUEDA overturns replicated, decontaminated low-biomass disease-microbe associations and clinical decisions, recovers true pathogens and outperforms every decontamination method

TRUEDA identifies true pathogens in low-biomass disease-microbe associations by accounting for contamination, outperforming existing decontamination methods and correcting false associations.

Gut microbial interaction networks control autoimmunity to neuroretina

Akkermansia expansion reduces short-chain fatty acid-producing Firmicutes in human-flora uveitis mice, raising Th1 responses and disease; a Verrucomicrobia/Firmicutes ratio is elevated in uveitis, MS and Crohn's patients.

Habituation drives elevated antimicrobial resistance, functional, and compositional shifts in the black bear gut microbiome

This study shows that habituation in black bears alters their gut microbiome composition and function, leading to increased antimicrobial resistance and other health-related changes.

Conserved patterns of mammal-microbe codiversification and interspecific bacterial sharing

The paper investigates factors driving microbial strain sharing across host species, finding host phylogeny, not environment, is the primary driver, with implications for microbial dispersal constraints across mammals.

Integrated 16S rRNA Bioinformatics Analysis of Gut Microbiota, Predicted Pathways, and Candidate Biomarkers in Inflammatory Bowel Disease

This study analyzes gut microbiota and predicted functions in IBD patients and healthy controls, identifying microbial signatures and pathway associations.

Gut microbially produced phenolic acids have differential and sex-dependent effects on host metabolic health

The paper investigates the metabolic effects of phenolic acids produced by gut microbiota in a mouse model of diet-induced obesity, revealing sex-dependent impacts on glucose tolerance and lipid metabolism.

Shotgun metagenomic and untargeted metabolomic analysis of gut microbiome associated with peripheral artery disease

This study analyzes gut microbiome and metabolomic profiles in PAD patients to identify dysbiosis and microbial modules associated with disease subtypes.

A defined multi-kingdom microbial consortium naturalizes the immune system of laboratory mice

The paper identifies a multi-kingdom microbial consortium that normalizes immune responses in laboratory mice, altering cancer outcomes and CAR T cell therapy responses.

Shifts in the Maternal Gut Microbiome Across Pregnancy are Associated with Energetic Status in Phayre's Leaf Monkeys

This study shows that shifts in the gut microbiome during pregnancy in Phayre's leaf monkeys are linked to postpartum physical condition and energy status.

Replication of Host St6galnac1-Microbiome Association Across Distinct Experimental Conditions in Heterogeneous Stock Rats

The paper replicates the association between St6galnac1 and Paraprevotella abundance in stool samples from non-fasted HS rats, confirming the association across different experimental conditions.

The effect of minocycline on the gut microbiome in individuals with alcohol use disorder and healthy controls

This study compares gut microbiome features between individuals with AUD and healthy controls and examines minocycline's effects on the microbiome, finding distinct microbial composition in AUD and microbiome restructuring with minocycline.

Functional Divergence in Gut Clostridia from Hadza Hunter-Gatherers Reveals Diet-Adapted Metabolic Machinery That Shapes Gut Ecology

The paper identifies functional divergence in gut Clostridia from Hadza hunter-gatherers, revealing diet-adapted metabolic pathways that influence gut ecology.

Early-life vancomycin and meropenem treatment exert distinct effects on microbiota-gut-brain axis signalling in zebrafish larvae

This study examines how early-life antibiotic treatments affect microbiota-gut-brain axis signaling in zebrafish larvae, showing distinct impacts on behavior, neurotransmitters, and metabolism.

Supplementation with a Limosilactobacillus fermentum K73 synbiotic modulates gut microbiota function and behavior in gnotobiotic mice transplanted with microbiota from children diagnosed with autism spectrum disorder

This study shows that a synbiotic supplement improves gut microbiota function and behavior in mice transplanted with ASD microbiota from Colombian children.