Scientific activities of the Evolutionary Microbial Genomics Unit are centered on the bioinformatics and biostatistics analysis of genomes, at the crossroads of molecular evolution, population genetics, evolutionary ecology and molecular genetics.
We focus on four major questions: 1) How and why are genomes organized? 2) How are such organizational features evolving in face of the extensive genome dynamics? 3) What are the roles of mobile elements in the trade-offs between organization and dynamics? 4) What is the interplay between genome dynamics and bacterial pathogen emergence at the microevolutionary and epidemiological scale?
Bacterial viruses (phages) are ubiquitous and have a strong impact on microbial population dynamics. Additionally, temperate phages by integrating the genome contribute to the evolution of bacterial gene repertoires. We have been studying the determinants of the lytic lysogeny decision and what this informs about the opportunity costs of lysogeny and about bacteria evolvability. Phages integrate genomes in genetic hotspots that are distributed in ways that protect genome organisation. Importantly, our analysis of the evolutionary patterns of prophages in enterobacteria shows that a sizeable fraction of prophages undergoes purifying selection, a clear pattern of prophage domestication by the bacterial host. We were able to infer the putative function of many of these prophages, and the results point to a significant role of prophage-derived sequences in the establishment of ecological antagonistic interactions with both eukaryotes and prokaryotes.