Gut microbiota and health

This study examines how ampicillin exposure via different routes affects bile acid metabolism in mice, finding significant changes in maternal bile acids and increased infant weight.

This study shows that succinate from the microbiota expands tuft cells in the colon, enhancing type 2 immunity and reducing C. difficile-induced disease.

The paper examines the association between Blastocystis carriage and gut microbiota composition in T2DM patients and non-diabetic individuals, finding increased alpha diversity and specific phylum shifts in Blastocystis-positive individuals.

This paper benchmarks nineteen methods for integrating metagenomics and metabolomics data, identifies top-performing approaches, and provides guidelines for their application.

MetaIBS performs a large-scale meta-analysis of 16S rRNA amplicon data from IBS patients and healthy controls, identifying consistent microbial taxa differences.

The paper isolates and characterizes novel Clostridium XIVa strains from the murine gut, revealing genomic diversity driven by mobile genetic element acquisition and expanded biosynthetic potential.

This study examines how birth weight and post-weaning antibiotics affect swine gut microbiota assembly and succession over time.

This study investigates how gut microbiome carbon and sulfur metabolisms support Salmonella during infection by analyzing multi-omics data from infected mice.

The paper identifies clonal Parabacteroides distasonis isolates from CD-associated gut fistulas that exhibit pathogenic traits in mouse models and show potential for transmissibility and adaptation to CD-like ileitis.

This study shows that lantibiotic resistance genes in gut bacteria affect microbiota composition and function, with implications for microbiome health and resistance strategies.

This study benchmarks a novel qPCR-based microbiome profiling platform against 16S amplicon and metagenomic sequencing methods, showing qPCR's superior accuracy and sensitivity for species-level detection.

The paper measures tryptophan metabolites in fecal samples from healthy individuals and links them to bacterial abundance and predicted microbial sources.

This study compares the pangenome of Bacteroides fragilis genomospecies to reveal genetic diversity and ecological roles, finding division I and II strains represent distinct species with different functional adaptations.

The paper uses Mendelian randomization to identify causal relationships between gut microbes and diabetic retinopathy, finding that Streptococcus salivarius affects DR through host fasting glucose levels.

This study shows that gut microbiota influences vagal nerve activity through metabolites, which activate specific receptors and neurons involved in gut-brain communication.

This paper characterizes two novel butyrate-producing Lachnospiraceae species isolated from swine feces, showing their metabolic versatility and potential probiotic role in swine gut health.

Micro-DeMix decomposes fecal microbiome composition to identify gut microbiome heterogeneity across GI locations and detect differentially abundant microbes in IBD patients.

The paper investigates how inflammatory radicals generate tartaric acid isomers, which serve as transient nutrients for gut pathogens in murine models.

The paper describes bacterial strains in the human gut using a statistical model based on their evolutionary history to predict metabolic phenotypes and engineer consortia.

The paper evaluates knowledge graphs for mechanistic inference of gut microbiome-disease relationships and highlights the need for semantic constraints and integrated resources.

This review examines how domestication and urbanization alter gut microbiomes in animals, comparing their effects on microbial communities and ecological implications.

This study uses FMT from BD and healthy donors to show distinct behavioral and metabolite profiles in mice, implicating gut-brain signaling in BD.

This study identifies gut microbial alterations associated with non-hepatitis virus related hepatocellular carcinoma using guild-based analysis of microbiome data.

This study confirms the production of esterified microbial bile acids (MCBAs) by human gut microbiota and identifies their distinct MS/MS fragmentation patterns.

This study shows that host-specific microbiota are essential for maintaining diet-specific metabolic homeostasis, while foreign microbiota impair metabolic fitness in germ-free mice.

MIOSTONE models microbiome-trait associations using taxonomy-adaptive neural networks to predict and interpret microbial impacts on host traits.

This study compares the effects of EFV and DTG on gut microbiome and intestinal barrier function in mice, finding both drugs impair gut barrier integrity, with EFV causing more severe metabolic and structural changes.

This study shows that Bacteroides fragilis from UC patients promotes colitis in genetically susceptible mice, suggesting a role for pathobionts in IBD.

This study compares the effects of beef, plant-based, and homemade meat substitutes on gut microbial metabolites using in vitro digestion models and metabolomics.

This study investigates how human infant gut microbiota affects mouse behavior, myelination, and dendritic morphology, finding that humanized mice show altered brain development compared to germ-free controls.