Gut microbiota and health

Gene-centric metagenomic analyses reveal microbiome functional insights into diseases

The paper develops MetaGEAR, a gene-centric metagenomic analysis framework, to investigate microbiome functionality in diseases and identify disease signature genes and mobile genetic elements.

Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial

This study evaluates the ecological fidelity of HMA mice in replicating human microbiome responses to a microbial consortium, finding they are more similar to other mice than their human donors.

Human gut metagenomes and assembled microbial genomes from an urban cohort from Colombia, South America

The paper reports shotgun gut metagenomes and assembled microbial genomes from an urban Colombian cohort, complementing existing 16S rRNA gene and host data.

Microbial lipid shifts in a multi-stage simulated gut

The paper uses a colon simulator to study microbial lipid shifts in the gut and validates findings using human samples.

Gut microbiota and bile acids changes in MASLD mice model with hepatic PLD1 knockout

This study shows hepatocyte PLD1 knockout changes gut microbiota and bile acid profiles in MASLD mice, suggesting PLD1 deficiency modulates disease progression via microbiota-bile acid homeostasis.

Microbial oral-gut translocation in advanced chronic liver disease is linked to exacerbation of intestinal barrier dysfunction and hepatic fibrosis

The paper identifies oral-gut microbial translocation in ACLD patients linked to intestinal barrier dysfunction and hepatic fibrosis, with prtC encoding bacteria as a biomarker.

Epithelial-intrinsic nitric oxide synthase 2 sustains host-microbiota dynamics that promote colitis

This study shows that epithelial nitric oxide synthase 2 (Nos2) influences host-microbiota interactions in IBD by regulating intestinal nitrates and nitrate-metabolizing bacteria, with implications for disease management.

Integrative Microbiome Profiling of Colorectal Cancer Across South Asian and Western Cohorts Using Interpretable Machine Learning

This study uses machine learning to identify microbial biomarkers for early colorectal cancer detection across South Asian and Western cohorts, finding distinct microbial signatures associated with CRC.

Compositional and Functional Profiling of the Gut Microbiome in Sarcoidosis

This study profiles the gut microbiome composition and function in sarcoidosis patients compared to healthy controls, finding significant functional differences in metabolic pathways.

A prebiotic-postbiotic combination supports dietary carbohydrate-targeting functional properties in a fiber-deprived microbiota

A prebiotic-postbiotic combination mitigates gut microbiota dysbiosis and restores mucus layer integrity in a fiber-deprived mouse model.

Characterizing the Microbiome of 'Sterile' Organs in Experimental Mice

This study identifies microbial presence in 'sterile' organs of experimental mice, showing 22.1% had high microbial burden and 40.4% had moderate burden, with 262 species identified through metagenomics.

Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake

This study shows that reduced dietary carbohydrate complexity decreases gut microbial diversity in mice, even when total carbohydrate intake is constant.

Akkermansia muciniphila mediates antibiotic-induced impairment of female preference in mice

This study shows that antibiotic treatment in mice impairs female preference, mediated by Akkermansia muciniphila and short chain fatty acids.

Activated carbon ameliorates type 2 diabetes via metabolic remodeling of the gut microbiota

This study shows activated carbon reduces blood glucose and obesity in T2D rats by altering gut microbiota composition and metabolism.

Single-cell quantification of the microbiota by flow cytometry: MicFLY

The paper develops MicFLY, a flow cytometry method to quantify and characterize intestinal microbiota at the single-cell level, revealing E. coli unbound by IgG and IgA is associated with necrotizing enterocolitis.

Bacterial suppression of intestinal fungi via activation of human gut γδ T-cells

The paper shows that bacterial metabolite HMB-PP activates human gut γδ T-cells to suppress fungal growth, but this mechanism is impaired in Crohn's disease.

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

The paper uses long-read metagenomics to analyze pet dog gut microbiomes, generating high-quality MAGs and identifying antimicrobial resistance elements in a Shanghai cohort.

DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales

This study identifies DNA-utilization loci in gut Bacteroidales that metabolize exogenous DNA into deaminated nucleobases, revealing a conserved pathway with implications for host-microbe interactions.

Isolation by distance promotes strain diversification in the wild mouse gut microbiota

The paper shows that geographic isolation, not host ancestry, drives strain diversification in the gut microbiota of wild deer mice.

Interspecies Functional Divergence: The Microbiome's Role in FLOT Response e Across Gastric Cancer Subtypes

This study examines how the FLOT chemotherapy regimen affects the gastric tumor microenvironment, revealing subtype-specific microbiome-host interactions that influence tumor behavior.

The fecal microbiota transplantation from drug-naive schizophrenia patients distinctively changes gut microbiome and metabolic profiles in male and female mice

This study uses fecal microbiota transplantation from schizophrenia patients in mice to show sex-specific effects on gut microbiome and metabolic profiles, particularly insulin resistance and short-chain fatty acid changes in females.

Intracellular acidification by bacteria-derived valeric acid is a mechanism of trans-kingdom ecology against Candida parapsilosis colonization

The paper uses machine learning to identify valeric acid as a bacterial metabolite that inhibits Candida parapsilosis growth through intracellular acidification, reducing fungal colonization in mice.

Meta-analysis reveals reproducible rapamycin-induced shifts in the mouse gut microbiome

This paper performs a harmonised meta-analysis of rapamycin's effects on the mouse gut microbiome, identifying reproducible taxonomic shifts and dose-dependent responses.

New Evidence of Altered Gut Microbiota in Autism Spectrum Disorders through Metagenomic Analysis

This study identifies altered gut microbiota in ASD children through metagenomic analysis, highlighting fungal dysbiosis and metabolic pathway changes linked to ASD pathogenesis.

The role of Akkermansia muciniphila sulfatases in colonic mucinutilisation

This study investigates the role of Akkermansia muciniphila sulfatases in colonic mucin utilization, revealing unique adaptations compared to Bacteroides species.

Gut Clostridia and Gammaproteobacteria metabolize dietary linoleic acid to produce a signature of microbial polyunsaturated fatty acids and associated lipids

This study identifies gut microbial taxa and pathways that metabolize dietary linoleic acid into polyunsaturated fatty acids and associated lipids, revealing their production dynamics and environmental influences.

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a new candidate biomarker of health

This study analyzes 11,115 global gut metagenomes to identify uncultured species linked to health and disease, finding CAG-170 as a potential biomarker of health.

No Distinct Gut Microbiome Signature in Alzheimer's Disease: A Reanalysis with Modern Tools

This study reanalyzes a 16S rRNA dataset to assess microbial composition differences between Alzheimer's patients and controls, finding no distinct gut microbiome signature.

Microbial dynamics inference at ecosystem-scale

The paper introduces MDSINE2, a Bayesian method for inferring microbial dynamics from time-series data, and shows it outperforms existing methods in identifying ecosystem-scale interactions.

Genetic variance in the murine defensin locus modulates glucose homeostasis

This study identifies a genetic locus affecting insulin sensitivity in mice, showing that Defa26 modulates glucose homeostasis through microbiome interactions.