Research interests

Broadly speaking, I am interested in the inference of biological properties of ancient prokaryotic life and in how bacterial and archaeal communities evolve. My main interests focus on the study of genetic data (DNA, proteins) to understand the main evolutionary processes shaping their characteristics over evolutionary time, as well as driving the evolution of organisms. Most of my previous and current research interests include:

– Development of (non-homogeneous) substitution models
– Phylogenetic inference of early conditions of Life
– Molecular adaptation to hot/cold environmental temperatures in Prokaryotes
– Ancestral sequence reconstruction and protein resurrection
– Ancestral genome reconstruction
– Evolutionary genomics
– Evolution and ecology of microbial communities
– Gut microbiota and its impact on host biology


Current projects
My current research focuses on the evolution of gut microbiota in Vertebrates. My projects include: the development of evolutionary models aiming at capturing the evolutionary processes driving gut microbial composition over time; investigating the temporal dynamics of gut microbiota evolution; predicting diet from gut microbial composition; characterizing the intimate relationship between the host (immunity) and gut microbes after birth and during evolution.


Lyon, France: Manolo Gouy, Bastien Boussau, Gergely Szollosi, Celine Brochier-Armanet, Nicolas Lartillot, Laurent Gueguen

Paris, France: Simonetta Gribaldo

Grenoble, France: Dominique Madern, Florent Mazel

Lille, France: Samuel Blanquart

Hamilton, New Zealand: Joanne Hobbs (Now at Victoria University, Canada), Vic Arcus

London, England: Ziheng Yang

Geneva, Switzerland: Jan Pawlowski