Microbes perform essential ecosystem functions, from carbon fixation in the ocean to pathogen resistance in the human gut, in communities with thousands of coexisting species. This remarkable diversity contrasts with classical ecological theory, which predicts that the number of coexisting species should be limited by the number of available resources. At the same time, microorganisms evolve rapidly, and evolutionary theory would suggest that the fittest genotypes should dominate; nevertheless, microbial populations maintain extensive genetic variation. Explaining microbial diversity therefore requires a framework that integrates both ecological and evolutionary processes.

Frequency-dependent selection provides such a mechanism. Species and genotypes often modify their own environment—by depleting resources, producing toxic by-products, detoxifying the environment or generating metabolites that benefit competitors—causing their fitness to decline as they become common and promoting coexistence at low frequencies.

I will present theoretical and experimental results showing how metabolic trade-offs enable stable coexistence in simple environments and how growth–resistance trade-offs shape the evolution of antibiotic resistance. Understanding these mechanisms offers new opportunities to predict and steer the evolution of microbial communities.