Antoine Hocher

Mapping bacterial pan-genome function through pooled fitness experiments

Research Area

Our lab studies the evolution of chromosomes across the tree of life. We are interested in DNA as a substrate for information: how genomes are organized, how they vary between organisms, and how this variation affects fitness. Bacterial species are highly diverse, and closely related strains can differ by many accessory genes. This pan-genome diversity is likely to shape competition, environmental adaptation and interactions with phages, but its functional consequences remain difficult to measure systematically.

This project aims to develop high-throughput methods to study pan-genome function at scale. The initial focus would be on natural E. coli isolates, but the broader goal is to build a general framework for studying how bacterial genetic diversity shapes ecological and evolutionary outcomes. The project would combine microbial genetics, phage biology, pooled fitness assays, high-throughput sequencing and computational pan-genome analysis.

Project Interests

I am interested in projects asking how bacterial pan-genome diversity determines fitness in complex environments. A possible starting point would be to establish pooled competition assays using natural E. coli isolates with well-characterised genomes. These strains could then be competed under different conditions, including nutrient limitation, environmental stress and phage exposure.

The student could ask which accessory genes predict competitive success, how phage pressure reshapes strain composition, and whether pooled competitions can reveal functions for poorly annotated genes. The project would suit a student interested in interdisciplinary biology, with scope to focus on microbial genetics, phage-host interactions, high-throughput sequencing, or quantitative analysis of fitness, pan-genomes and community dynamics.