Olivier Tenaillon

High-resolution lineage tracking maps the multi-phase evolution and adaptive potential of biofilms

This study tracks lineage evolution in biofilms using DNA barcoding and spatial sampling, revealing phases of segregation, migration, and adaptation that influence antibiotic resistance.

From diminishing returns to entrenchment: a unifying theory of epistasis along adaptive walks revealed by Fisher's geometric model

This paper uses Fisher's geometric model to show that epistasis along adaptive walks can be classified into diminishing returns, contingency, and entrenchment based on phenotypic complexity and selection pressure.

Collective protection drives human gut microbiota response to amoxicillin treatment.

This study examines how human gut microbiotas respond to amoxicillin treatment using an in vitro model, finding that initial community composition and antibiotic inactivation dynamics influence resilience and resistance selection.

Dietary emulsifiers and host inflammation synergistically drive genomic evolution of Crohn disease-associated E. coli toward enhanced pathogenicity

This study shows dietary emulsifiers and host inflammation together drive genomic changes in AIEC, increasing its pathogenicity.

Linking Codon- and Protein-Level Mutation Scores to Population Genetics Reveals Heterogeneous Selection Efficiency Across Escherichia coli Lineages

The paper quantifies selection efficiency across Escherichia coli lineages by linking mutation scores to population genetics, showing significant variation in selection intensity between synonymous and non-synonymous mutations and pathogenic populations.

High-Throughput Conjugation Reveals Strain Specific Recombination Patterns Enabling Precise Trait Mapping in Escherichia coli

This study uses high-throughput conjugation to map genetic traits in E. coli by analyzing recombination patterns and fragment sizes across strains.

Evidence for Neolithic acquisition of the high pathogenic island by Escherichia coli followed by recent selection

The paper traces the evolutionary origin and recent selection of the High Pathogenicity Island in Escherichia coli, linking its acquisition to Neolithic human-animal interactions and modern public health implications.

The evolution of robustness and fragility during long-term bacterial adaptation

This study shows that during long-term bacterial adaptation, fitness effects of mutations become less severe, but pleiotropic effects in new environments become more severe, indicating trade-offs between robustness and fragility.

The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France

This study analyzes the genomic evolution of commensal E. coli over 30 years in France, finding increases in virulence and antibiotic resistance genes through clonal expansion and gene frequency changes within clones.

Flux, toxicity and protein expression costs shape genetic interaction in a metabolic pathway

The paper quantifies fitness interactions between expression variants of two metabolic genes across environments and shows these can be explained by a model incorporating catabolic flux, metabolite toxicity, and expression costs.

Tempo and mode of genome evolution in a 50,000-generation experiment

The paper analyzes 264 genomes from 12 Escherichia coli populations over 50,000 generations to study genome evolution dynamics and finds that most fixed mutations are beneficial, with neutral mutations accumulating at a constant rate.

Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1

The paper develops a method to infer mutational landscapes and assesses context-dependent mutation effects in beta-lactamase TEM-1, improving explanatory power by 40% over methods ignoring epistasis.