M. Godfroid

Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes.

This study shows that horizontal gene transfer influences the likelihood of acquiring antibiotic resistance mutations in core genes of E. coli.

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.

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

Evo-Scope: Fully automated assessment of correlated evolution on phylogenetic trees

Evo-Scope is a fast, automated pipeline to assess correlated evolution on phylogenetic trees, improving previous tools and analyzing antibiotic resistance mutations in Streptococcus pneumoniae.

A minimal yet flexible likelihood framework to assess correlated evolution

This paper introduces a likelihood framework to assess correlated evolution between two traits on a phylogenetic tree, showing it performs well with datasets of fewer than 100 species.

Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.

This study identifies that insertions and deletions (indels) contribute to antibiotic resistance evolution in Mycobacterium tuberculosis during an outbreak, with indels showing a slower evolutionary rate than substitutions.