Antibiotic-mediated interactions underlying microbial diversity

The immense diversity observed in natural microbial communities is surprising in light of the numerous weapons microbes have evolved to inhibit each other’s growth. It is thus imperative to understand which interaction patterns can sustain a biodiverse community when individual species antagonistically affect one another. In this study, we leverage potent methods from theoretical ecology to show how antibiotic-mediated interactions between microbes drive biological diversity. Building on previous experimental and theoretical results, we analyse the dynamics induced by various interaction graphs involving antibiotic production, resistance, and degradation. Previous work has recognised the importance of a particular producer-sensitive-degrader (PSD) motif in the interaction graph. We study this motif in detail and elucidate the mechanistic reason for this importance. Concretely, we give exact rules for coexistence in some simple cases where exhaustive enumeration of the interaction graphs is feasible. More generally, our results suggest that the PSD motif, in combination with a cyclic interaction structure, is sufficient for stable coexistence in well-mixed populations. Using individual-based simulations, we then study the importance of the PSD motif in spatially structured populations. We show that community coexistence is robust for an extensive range of antibiotic and degrader diffusivities. Together, these findings illuminate the interaction patterns that give rise to diversity in complex microbial communities, stressing that antagonism does not imply a lack of diversity and suggesting clear approaches for culturing synthetic microbial consortia.