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Talk abstract:
How and at what pace commensal bacteria evolve as they colonize healthy hosts remains poorly understood. Escherichia coli is a generalist species whose molecular evolution is understudied in its natural environment. Here, using experimental evolution in vivo, we obtained the densest and longest sequencing time series to date to characterise the evolution of this bacterium in the mammalian gut. We show that two modes of evolution occur: one where an invader E. coli strain, which manages to colonize the gut for thousands of generations, co-evolves with a resident strain through a succession of selective sweeps intertwined with phage driven horizontal gene transfer; another where the same strain evolves through diversifying selection dominates. We find that co-evolution in the gut leads to rapid prophage domestication in the invader strain and also to convergent evolution for metabolic functions between the invader and the resident lineages.
