J. F. Baines

Evolution of E. coli in a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance

This study shows that E. coli evolves specific genetic and phenotypic traits in an inflamed gut, leading to antibiotic collateral sensitivity and potential therapeutic implications.

A mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression

This study shows that dSirt4 in Drosophila controls lysozyme expression in the intestine, altering microbiota composition and reducing lifespan.

Closely related Bacteroides of the murine intestinal microbiota affect each other's growth positively or negatively

The paper tests growth interactions between closely related Bacteroides strains from mice and finds both positive and negative effects, with growth promotion more common than inhibition.

Functional host-specific adaptation of the intestinal microbiome in hominids

The paper analyzes gut microbiome composition and function across hominids to identify host-specific adaptations and evolutionary changes.

Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice

Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice

The paper isolates and characterizes two bacterial strains from wild-derived house mice, identifying them as a novel species of Bacteroides with distinct genomic and phylogenetic features.

Primate phageomes are structured by superhost phylogeny and environment

The study examines primate phageomes across 23 wild non-human primate taxa, revealing phylosymbiotic patterns and social transmission of phages.

Neutrality in the Metaorganism

This study shows that microbiota community structure across various host organisms aligns with neutral model predictions, suggesting neutral processes rather than host selection primarily shape microbial communities after colonization.

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

An integrated metagenome catalog reveals novel insights into the murine gut microbiome

The paper creates a comprehensive mouse gut metagenome catalog, iMGMC, which improves taxonomic resolution and functional prediction of gut microbiota compared to existing methods.