Evolution of commensal bacteria in the intestinal tract of mice

•The composition of the gut microbiota is shaped by positive and negative microbe–microbe and host-microbe interactions.•Evolution of a bacterial species in these complex ecosystems can be very rapid.•Natural selection overwhelms genetic drift in structuring the genetic composition of new emerging strains.•Experimental evolution combined with high-throughput sequencing can reveal the repeatability of evolution in the gut.