Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales.

Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium, and how repeatable and predictable are changes when they occur. Here, we address this knowledge gap by tracking the composition of 87 two- and three-species bacterial communities, with 3–18 replicates each, for ~400 generations. We find that community composition typically changed during evolution, but that the composition of replicate communities remained similar. Furthermore, these changes were predictable in a bottom-up approach—changes in the composition of trios were consistent with those that occurred in pairs during coevolution. Our results demonstrate that simple assembly rules can hold even on evolutionary timescales, suggesting it may be possible to forecast the evolution of microbial communities. Evolution affects microbial community composition, but it is still unknown how commonly compositions change, and how predictable such changes are. Using experimental evolution, Meroz et al. show that compositional changes typically occur within ~400 generations, and are predictable by a bottom-up approach.