Agent-Based Simulations Show How Facilitative and Inhibitory Components of Inter-Species Interactions Affect Spatial Structures of Microbial Communities

The spatial structure of multispecies microbial communities often underlies their function. Predicting the structure, however, has been challenging. A limitation of current theories is in their handling of interspecies interactions. While species can exert both facilitative and inhibitory effects on each other, via cross-feeding metabolites, toxins, and competition for resources, current theories lump them into their net effect, sacrificing information shaping spatial structure. Here, we develop agent-based simulations that explicitly incorporate the facilitative and inhibitory interaction components and predict community structures. We let bacterial cells grow and divide, exert repulsive contact-forces, compete for nutrients, and secrete diffusible metabolites and toxins. We find that diverse spatial structures emerge when the components vary even while their net effects remain unaltered. For instance, stronger components increase segregation of species into sectors, helping them avoid toxins. Our simulations elucidate links between the interaction components and the emergent spatial structure, helping better design multispecies communities.