Gut microbiota and health

Ecology and engineering to modify the bile acid output of a defined microbial community

The paper shows that modifying microbial community composition, specifically overexpressing bile acid metabolic genes in Lactobacillus strains, can alter bile acid pool size and composition in mice.

A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism

The paper uses a single-strain dropout screen in a defined microbial community to show how removing specific strains affects community composition and metabolic output.

Early-life canine gut microbiome maturation follows a shared age-diet trajectory within persistent host-specific structure

This study tracks the maturation of the canine gut microbiome through early life, showing it follows an age-diet trajectory but remains constrained by host-specific factors.

Rapid early life colonization of the intestinal tract by Akkermansia muciniphila after voluntary feeding

This study develops a voluntary feeding protocol to non-invasively colonize mice with A. muciniphila and shows rapid and stable colonization in both healthy and dysbiotic gut microbiota.

Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics

This study shows that gut microbiome recovery after antibiotics is path-dependent, shaped by ecological and evolutionary dynamics including strain sweeps, genetic changes, and phage activity.

A response-geometry framework separates microbiome movement magnitude from directional coherence in intervention studies

This paper introduces a response-geometry framework to distinguish microbiome response magnitude from directional coherence in intervention studies, showing it can detect shared-direction effects while accounting for heterogeneity.

Circadian Disruption Elicits Sex-Specific Gut Microbiota, Endocannabinoidome and Lipid Mediator Responses

This study shows that circadian disruption causes sex-specific changes in gut microbiota and bioactive lipid profiles, with distinct adaptations in males and females.

Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis

The paper develops PolyProf, a method to profile polymorphic toxin systems in metagenomes, showing it predicts microbiome development and disease-related dysbiosis.

Longitudinal Gut Microbiome Dynamics in Human CTLA-4 pathway Deficiencies: A One-Year Interventional Metagenomic Study

This study tracks gut microbiome changes in patients with CTLA-4 pathway deficiencies over one year of abatacept treatment, showing microbiome restructuring linked to disease improvement.

Preoperative biliary stenting is associated with functional dysbiosis and impaired bile acid metabolism in pancreatic cancer - Impact of preoperative biliary stenting on gut microbiota

This study examines how preoperative biliary stenting affects gut microbiota and bile acid metabolism in pancreatic cancer patients, finding reduced diversity and impaired metabolism linked to postoperative complications.

IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species

This study uses MIg-Seq to analyze IgA targeting in infant gut microbiota, finding increased targeting of Bifidobacterium and diet-specific associations with IgA binding.

Bacterial diversity and strain dynamics in the infant respiratory microbiome during the first year of life

The paper analyzes bacterial diversity and strain dynamics in the infant respiratory microbiome using whole genome sequencing and metagenomics, revealing age-dependent shifts in dominant taxa and expanding reference genomes for airway microbes.

Bidirectional interactions between gut microbiota and fluorochemical biotransformation and bioactivity

This study investigates bidirectional interactions between fluorinated chemicals and gut microbiota using ex vivo, in vitro, and in silico methods, revealing microbial biotransformation and potential detoxification effects.

Mapping the canine microbiome: Insights from the Dog Aging Project

The paper analyzes the canine gut microbiome across 900 dogs to identify factors influencing microbiome composition and develops a metagenomics-based aging clock.

A bidirectional nanAKE locus enables sialic acid catabolism in gut microbiome member Hungatella hathewayi

This paper identifies Hungatella hathewayi as a sialic acid degrader in the human gut microbiome and characterizes its bidirectional NanAKE pathway.

Microbial genome functions explain metabolite-driven dysbiosis and Pseudomonas-associated ammonium toxicity in Hydra

This study shows that specific metabolites can shift Hydra's microbiome composition and function, leading to ammonia toxicity and disease-like phenotypes.

The murine lung microbiome is dynamic and transient

This study shows the murine lung microbiome is dynamic and transient, with bacteria rapidly cleared by the immune system and not establishing stable colonization.

Elucidating the dysbiotic features of gut microbiome, interaction with the human genome, and utility as a biomarker for treatment of Parkinson disease.

This study identifies dysbiotic gut microbiome features in Parkinson's disease, links them to genetic variants, and proposes microbiome-based biomarkers for targeted treatment.

Machine learning-based Personalized Dietary Recommendations to Achieve Desired Gut Microbial Compositions

This paper develops a machine learning framework to provide personalized dietary recommendations for achieving desired gut microbial compositions using population-level cohort data.

A META-ANALYSIS OF GUT MICROBIOME RESEARCH IN MALNOURISHED AFRICAN POPULATIONS: A NATURAL LANGUAGE PROCESSING APPROACH

This paper uses NLP to analyze gut microbiome studies in malnourished African children, identifying microbial signatures and associations with malnutrition.

Comparative analysis of cloacal microbiota in Henophidia (non-venomous) and Caenophidia (venomous) snakes

This study compares cloacal microbiota between venomous and non-venomous snakes, finding higher bacterial richness and distinct community structures in non-venomous species.

Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine

The paper identifies region-specific host-microbiome associations in the human intestine using transcriptomic and microbiome data from non-inflamed tissue.

Microbiota-derived indole-3-propionic acid regulates glucose homeostasis via remodeling of hepatic mitochondrial metabolism

This study identifies indole-3-propionic acid (IPA), a microbial metabolite, as a regulator of hepatic glucose metabolism by remodeling mitochondrial function and improving glucose homeostasis in mice.

Meta-analysis reveals a distinct and uniform gut microbial signature associated with endocrine-disrupting chemicals-induced diabetes

This paper performs a meta-analysis of rodent studies to identify a common gut microbial signature associated with endocrine-disrupting chemicals-induced diabetes.

Integrative Analysis of the Mouse Cecal Microbiome Across Diet, Age, and Weight in the Diverse BXD Population

This study integrates microbiome and host transcriptome data from mice to show diet, age, and genetics influence gut microbiota, with machine learning models predicting body weight and age with high accuracy.

Roles of bacterial growth competition systems in colonization of the murine gut

This study examines how bacterial competition systems like CDI and colicins affect the colonization of the murine gut by an Escherichia coli isolate, showing their role in early competition and long-term persistence.

The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe

This study examines how western versus agrarian diets affect gut microbiome composition and immune function in HIV-positive individuals in rural and urban Zimbabwe.

Integrated Metagenomics and Metabolomics Studies Reveal Core Bacterial Guild Regulating Carbohydrate Metabolism in Pediatric MASLD

This study integrates metagenomics and metabolomics to identify core bacterial species regulating carbohydrate metabolism in pediatric MASLD, highlighting their role in metabolic disruption.

A Permutation-Based Framework for Evaluating Bias in Microbiome Differential Abundance Analysis

This study evaluates seven differential abundance methods across six datasets, finding that some produce biased p-values under null conditions, while classical tests perform reliably.

The Second Brain: Diffusion Models for Realistic Human Microbiome Generation

This paper introduces a diffusion model for generating realistic human microbiome data, achieving high sparsity preservation and competitive ecological distance metrics.