Evolution of E. coli in gnoto mice

In this project we followed the evolution of E. coli in the gut of monocolonized germ-free mice, i.e., in the absence of interspecies competition. Compared to microbiota-harboring animals, adaption of E. coli in the gnoto mouse gut occurred mainly through mutations involved in amino acid metabolism, notably a global regulator of this pathway, lrp. We showed that the metabolic environment in the gnoto gut is characterized by an abundance of amino acids that can be used as nutrient sources by E. coli. We further demonstrated that the presence of an additional competitor in the gnoto gut is enough to shift the metabolic profile of the environment and impact E. coli evolution. Our results evidence microbial metabolism as a driving force shaping the metabolic environment of the mouse gut and modulating the evolution of members of the microbiota.