Each person's gut microbiome contains a specific community of microorganisms that normally remains stable for years. However, it can be thrown off balance by factors such as dietary changes, infections or medications. Antibiotics in particular have a strong influence on the microbiome. In response, microorganisms employ various resistance mechanisms, with individual bacterial populations evolving through selection of antibiotic-resistant variants. Yet, the extent and mechanisms of these processes and their impact on the ecology of the microbial community are poorly understood.