Massive lateral gene transfer under strain coexistence in the gut

Mammals are colonized by multiple strains of Escherichia coli, yet how such strain coexistence affects their tempo and mode of evolution is poorly understood. Here, by following the colonization of two phylogenetic distinct strains of E. coli in the mouse gut, we find a strain-specific mode of evolution and a remarkable level of gene transfer between strains. In the same host, despite accumulating mutations at the same rate, one strain evolves by diversifying selection and the other by directional selection, and a rich dynamics of bacteriophage and plasmid transfer is found. Our results provide support for an important role of lateral transduction in the mammalian gut.