•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.
Hundreds of different bacterial species inhabit our intestines and contribute to our health status, with significant loss of species diversity typically observed in disease conditions. Within each microbial species a great deal of diversity is hidden and such intra-specific variation is also key to the proper homeostasis between the host and its microbial inhabitants. Indeed, it is at this level that new mechanisms of antibiotic resistance emerge and pathogenic characteristics evolve. Yet, our knowledge on intra-species variation in the gut is still limited and an understanding of the evolutionary mechanisms acting on it is extremely reduced. Here we review recent work that has begun to reveal that adaptation of commensal bacteria to the mammalian intestine may be fast and highly repeatable, and that the time scales of evolutionary and ecological change can be very similar in these ecosystems.
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