Abstract
The coexistence of diverse microbial communities despite the common presence of antimicrobial weapons presents a fundamental puzzle in ecology. To address this issue, we investigate the role of antibiotic-mediated interactions in driving microbial diversity using methods from graph theory and theoretical ecology. Our exhaustive analysis of small interaction graphs involving antibiotic production, resistance, and degradation reveals that two factors together determine whether an interaction pattern can support coexistence or not: a certain producer-sensitive-degrader (PSD) motif is critical, and a form of cyclicity between the action of different antibiotics is necessary. Using individual-based simulations, we also explore the role of the PSD motif in spatially structured populations and demonstrate that community coexistence is robust over a wide range of antibiotic and degrader diffusivities. Our findings provide a deeper understanding of the interaction patterns that drive diversity in complex microbial communities. Specifically, we emphasize how antagonism does not preclude biodiversity. These results offer clear pathways for cultivating synthetic microbial consortia, enabling the design of more effective strategies for manipulating microbial communities.