The tempo and mode of bacteria evolution in the mammalian gut is still poorly understood. Here, by performing in vivo experimental evolution for thousands of generations in the mouse gut, we show that the successful colonization of a commensal invader strain of Escherichia coli depends on the species diversity of the existing gut microbiota. Following E. coli colonization, we found that two modes of selection are responsible for its evolutionary dynamics: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps intertwined with events of horizontal gene transfer. Two summary statistics of mutation trajectories are proposed, which allow to quantitatively determine the dominant modes of selection from time series sequencing data. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, indicative of rapid adaptation, and rates of mutation accumulation similar to those observed in vitro, where E. coli adapts to a much simpler environment. The experiments show how rapid ecotype formation and phage domestication can be in the mammalian gut. They further suggest that massive amounts of intra-species horizontal gene transfer can occur when strains stably co-exist in the same host.

More information: https://gulbenkian.pt/ciencia/research-groups/igordo/