Escherichia coli cultures maintain stable subpopulation structure during long-term evolution

Significance Understanding how microbes adapt to novel environments is essential to understanding acute bacterial infection and long-term disease, as genetic architecture underlying the production and maintenance of genetic variation influences a population’s potential for adaptation. In this in-depth analysis of a highly replicated Escherichia coli long-term evolution experiment, we observe rapid diversification into stable subpopulations in response to several environmental variables. This niche separation creates novel genetic backgrounds upon which new traits, such as differential nutrient utilization or antimicrobial resistance, can arise. The observed genetic changes, in a simple and tractable experimental system, mimic events known to occur during bacterial infections.