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I studied Biology at the Ecole Normale Supérieure de Lyon (France) and then did my PhD at the Université Claude Bernard (Lyon 1) in interaction between the departments of Microbial Ecology and Biometry & Evolutionary Biology. There I studied how the history of homologous recombination and horizontal gene transfer along bacterial cladogenesis have shaped bacterial genomes through adaptive and non-adaptive processes. I notably used phylogenetic approaches to unravel past ecological adaptation of clade ancestors of the model taxon Agrobacterium tumefaciens, a rhizospheric bacterium. Methodological aspects involved reconstructing events of duplication and lateral gene transfer in the histories of genes to identify synapomorphic gene acquisitions or losses. I also tracked groups of genes sharing evolutionary paths across genomes (notably co-transfers) to unravel selective pressures on functional co-operation of genes.
I joined the team of Francois Balloux for a first postdoctoral position in 2014. Here, my work consists of studying the evolution of human pathogenic microbes from a phylogenetic and a population genomic perspective, with a particular focus on the role of recombination and gene transfer in shaping the genomic diversity of microbial genomes. Current projects include the study of evolution of human herpesviruses and the analysis of human oral microbiomes.
New methods will be developed to model the processes of gene flow within microbial populations, and notably the evolution of gene cassettes like integrative and conjugative elements (ICEs) across genomes. These elements often bear virulence and antibiotic resistance determinants that can cause a commensal bacterium to turn into a pathogenic one. Characterization of the processes governing their diversification and their spread within varied genomic backgrounds is the key to the identification of relevant selective pressures experienced by microbes and their own parasitic elements that will ultimately help us better prevent and manage epidemics.