Gut microbiota and health

Gut Microbiota Shifts with Lifetime Duration of Oral Contraception Use

The paper reanalyzes 16S rRNA sequencing data to show that longer lifetime use of oral contraceptives is associated with decreased abundance of certain Clostridia species in the gut microbiome.

Identifying the non-Bifidobacterial hallmarks of a Bifidobacterium-receptive gut microbiome

The paper identifies non-Bifidobacterial microbiome features associated with Bifidobacterial colonization and develops tools to predict responses to probiotic interventions.

An RNA regulates iron homeostasis and host mucus colonization in Bacteroides thetaiotaomicron

This study identifies an RNA that helps Bacteroides thetaiotaomicron adapt to the mucus-rich, iron-limited gut niche by regulating capsule gene expression.

The gut microbiota of two rodents varies over fine spatial scales yet is minimally influenced by the environmental microbiota

This study examines gut microbiota variation in two rodent species across Wytham Woods, finding that local environmental factors have minimal influence compared to biotic factors.

GLP1 receptor agonists attenuate systemic inflammation through microbiota mediated enrichment of Faecalibacterium prausnitzii and Roseburia spp

This study shows GLP-1 receptor agonists reduce systemic inflammation by increasing Faecalibacterium prausnitzii and Roseburia spp. in the gut microbiota, unlike NSAIDs.

Reproducible Community States Resolve the Nasopharyngeal Diversity Paradox

The paper identifies six reproducible nasopharyngeal community state types (NPCSTs) that explain most microbiome variance and develop a health index to assess nasopharyngeal wellness.

Hexanoic acid improves metabolic health in mice fed high-fat diet.

This study shows hexanoic acid improves metabolic health in mice on a high-fat diet by reducing weight gain, fat accumulation, and glucose intolerance.

Synergy between Enterobacteriaceae and dietary components shapes the competition between the dominant anaerobes of the human gut

The paper investigates how dietary components and Enterobacteriaceae influence competition between Prevotellaceae and Bacteroidaceae in the gut microbiota, finding that Enterobacteriaceae enhance Prevotellaceae dominance under specific conditions.

Stability and Processing Impacts on Faecal Microbiota Transplant Products: An Integrated Metagenomic-Culturomic Analysis

This study evaluates the stability and viability of FMT products using metagenomic and culturomic analyses, showing high donor consistency and geographic specificity of gut microbiomes.

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

This study identifies host-specific genomic and microbiome adaptations in Bifidobacterium across diverse animal hosts, revealing co-evolutionary dynamics and functional traits shaped by diet and phylogeny.

Microbiome Data Integration via Shared Dictionary Learning

This paper introduces MetaDICT, a method for integrating microbiome data that reduces batch effects and preserves biological variation, improving analysis of microbial interactions and outcome prediction.

MicrobiomeKG: Bridging Microbiome Research and Host Health Through Knowledge Graphs

The paper introduces MicrobiomeKG, a knowledge graph linking microbiome taxa, pathways, and host health, derived from published microbiome studies.

Early-life microbiota disruption by antibiotics elicits fitness trade-offs that differ by sex

This study shows that early-life antibiotic exposure causes sex-specific fitness trade-offs in mice, with males showing reduced lean mass and increased adiposity, while females show no metabolic changes but worse fitness under caloric restriction.

The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Mitigates Gut Inflammation

This study identifies isopentenyladenine as a secreted metabolite from Faecalibacterium prausnitzii that modulates host immune responses and mitigates gut inflammation in murine models.

Multiomic Integration Reveals Taxonomic Shifts Correlate to Serum Cytokines in an Antibiotics Model of Gut Microbiome Disruption

The paper examines how antibiotic-induced changes in gut microbiota correlate with serum cytokine levels in mice, identifying specific microbial-taxa-cytokine relationships.

Comparison of iSeq and Miseq in 16S rRNA sequencing-based human gut microbiome analysis

This study compares the performance of Illumina MiSeq, MiSeqNano, and iSeq platforms in 16S rRNA sequencing of human gut microbiomes, finding similar biological patterns but differing in specific metrics.

B12 promotes gut dysbiosis and an inflammatory microenvironment that potentiates Tet2-deficient hematopoiesis.

This study shows that B12 supplementation promotes gut dysbiosis and inflammation, which enhances myelopoiesis in Tet2-deficient mice, suggesting a microbiome-mediated mechanism for clonal hematopoiesis.

DeepBioSim: Efficient and Versatile Methods for Microbiome Data Simulation with Minimal Statistical Assumptions

DeepBioSim generates realistic microbiome datasets using deep learning, without strong assumptions or phylogenetic input, and can also simulate single-organism omics profiles.

The Enterostat: a 3D-printed bioreactor for simulating gut microbiome dynamics

The paper introduces the Enterostat, a 3D-printed bioreactor that simulates gut microbiome dynamics across scales, showing it supports microbial community stability and responds to antibiotic perturbations.

Environmental and genetic drivers differentially shaped resident and transient gut microbiota during the Macaronesian chaffinch radiation

The paper investigates how environmental and genetic factors shape gut microbiota in Macaronesian chaffinches, showing that island size and isolation drive diversity, while host genetics influence microbial abundance.

Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota

This study uses metagenomics to characterize the caecal microbiota of red grouse, identifying novel microbial genomes and fiber fermentation pathways.

Assessment of neurobehavioural traits under axenic conditions: an approach for multiple longitudinal analyses in the same mouse.

This study assesses neurobehavioural traits in axenic mice to evaluate the impact of microbiota on anxiety-like behaviour and memory over time.

Pathogenic microbiota disrupts the intact structure of cerebral organoids by altering energy metabolism

This study shows pathogenic bacteria disrupt cerebral organoid structure and energy metabolism by altering glycolysis and increasing pentose phosphate pathway activity.

From Snapshots to Structure: A Novel Method for Reconstructing Directed Microbial Interaction Networks from Compositional Data

This paper introduces a method to reconstruct directed microbial interaction networks from static compositional data, revealing ecological dynamics and keystone taxa.

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

This study examines how early antibiotic and probiotic treatments affect the gut microbiome and resistome in preterm infants, finding that probiotics reduce antibiotic resistance genes and MDR pathogens but do not eliminate them.

The gut microbiome promotes detoxification responses to an environmental toxicant

This study shows the gut microbiome is necessary for host detoxification responses to deltamethrin, with both developmental and active microbial signaling contributing to hepatic and colonic detoxification.

The ontogeny of immune tolerance: a model of early-life secretory IgA - gut microbiome interactions

This paper develops a mathematical model to understand how early-life secretory IgA and gut microbiome interactions shape immune tolerance and homeostasis.

Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection

This study shows that a wild-derived Lactiplantibacillus plantarum strain protects Drosophila from Serratia marcescens infection by acidifying specific gut regions, creating a priority effect.

Dietary soy shapes murine microbiota to consolidate the mucosal IgA response through T follicular helper cells

This study shows dietary soy enhances T follicular helper cells and IgA in mice by promoting specific gut bacteria that drive mucosal immunity and protect against Salmonella.

A potential role of altered SIgA-targeting of gut microbiota in long-term dysbiosis in pediatric solid organ transplant recipients

This study investigates altered SIgA targeting of gut microbiota in pediatric solid organ transplant recipients and links it to dysbiosis severity.