Mutation accumulation and horizontal gene transfer in Escherichia coli colonizing the gut of old mice

The ecology and environment of the microbes that inhabit the mammalian intestine undergoes several changes as the host ages. Here, we ask if the selection pressure experienced by a new strain colonizing the aging gut differs from that in the gut of young adults. Using experimental evolution in mice after a short antibiotic treatment, as a model for a common clinical situation, we show that a new colonizing E. coli strain rapidly adapts to the aging gut via both mutation accumulation and bacteriophage-mediated horizontal gene transfer (HGT). The pattern of evolution of E. coli in aging mice is characterized by a larger number of transposable element insertions and intergenic mutations compared to that in young mice, which is consistent with the gut of aging hosts harboring a stressful and iron limiting environment.