Overcoming toxicity: why boom-and-bust cycles are good for non-antagonistic microbes

Microbial community stability and composition are heavily influenced by antagonistic interactions. While the ability to eliminate rivals gives antagonistic microbes a competitive edge, it usually comes with a fitness cost. As a result, many microbes only produce toxins or engage in antagonistic behavior in response to specific signals like quorum sensing molecules or environmental stressors. In lab experiments, antagonistic microbes typically outcompete sensitive ones, which raises the question of why both antagonistic and non-antagonistic microbes coexist in natural settings and host microbiomes. In this study, we combine theoretical models with experiments involving killer strains of Saccharomyces cerevisiae to show that boom-and-bust dynamics driven by periodic dilutions can benefit non-antagonistic microbes that do not bear the cost of toxin production. Furthermore, using control theory, we establish limits on competitive performance and identify optimal strategies for regulating toxin production in different boom-and-bust scenarios, where population dilutions occur either in a predictable or random manner over time. Our findings offer a new perspective on the coexistence of antagonistic and non-antagonistic microbes in fluctuating environments.