Tempo and mode of evolutionary change in the gut microbiota as revealed by E. coli

Hundreds of different bacterial species inhabit our intestines and contribute to our health status. A great deal of variation is however hidden within each microbial species and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Yet our knowledge on this hidden diversity is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced.  We have been using experimental evolution and NGS to follow the emergence of intra-species diversity in Escherichia coli, a common commensal, when it colonizes the mouse gut. The data gathered so far indicates that a strong-mutation-strong selection regime drives the patterns of evolutionary change in this ecosystem. It further shows that E. coli evolution is characterized by the spread of similar adaptive mutations across different hosts. The repeatability in the dynamics and genetic basis of E. coli adaptation is also found to be much higher in healthy hosts than in immune-compromised ones. Overall these findings strongly suggest that levels of intra-species diversity may be large and highly dynamic, perhaps suggesting that rapid evolutionary change may be important to understand the high diversity levels observed in the mammalian microbiota