I studied Biology at the Ecole Normale Supérieure de Lyon (France) and then did my PhD at the Université Claude Bernard (Lyon 1). There I 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. 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 then joined the team of Francois Balloux in University College London for a first postdoctoral position in 2014. There, I studied the evolution of human-associated microbes from a phylogenetic and a population genomic perspective. This included the study of the patterns of recombination in of human herpesviruses and how it impacts their patho-adaptive strategy. I also performed the analysis of human oral microbiomes from populations following diverse subsistence strategies, to determine how lifestyle and diet impacts their microbiome and heath.
Here in Imperial College DIDE, working with Xavier Didelot, I am developing new phylogenetic methods to model the processes of gene flow within microbial populations and reconstruct the history of diversification of their pangenomes, focusing on the (co-)evolution of "accessory" genes (as opposed to "core" conserved genes) and notably mobile genetic elements (MGEs) like plasmids. These MGEs often bear virulence and anti-microbial resistance (AMR) determinants that can cause a harmless commensal bacterium to turn into an untreatable pathogen. Characterization of the processes governing their diversification and the spread of MGEs and their cargo of genes within and across varied genomic backgrounds is the key to the identification of relevant selective pressures experienced by microbes and their own parasitic elements in the varied environments they experience. These inferences on the hidden ecology of bacteria should help us identify reservoirs of pathogenic genes and the environmental factors that foster their spread, and ultimately lead to better prevention and management of epidemics. This approach is applied to several biological models, including the Enterobacteriaceae family, which diverse member species (Escherichia coli, Klebsiella pneumoniae, ...) share all sorts of AMR and virulence gene-carrying MGEs, and cause a high-risk emerging threat to public health.
et al., Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales, The Isme Journal: Multidisciplinary Journal of Microbial Ecology, ISSN:1751-7362
et al., 2020, Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses, Virus Evolution, Vol:6
et al., 2019, Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
et al., 2019, Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments
et al., 2019, Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel