Community coexistence and stability: insights from a mediator-explicit model of microbial interactions

Communities of interacting microbes impact our health and environment. For example, microbes in our gut microbiota can collectively (but not as individual species) confer resistance against pathogen colonization. How species form a community is thus an important question for maintaining or manipulating human-associated communities for improved health outcomes.

We formulate and experimentally constrain a model that explicitly incorporates chemical compounds (e.g. metabolites or waste-products) that can mediate microbial interactions. In a continuous-growth setting where resources are supplied (similar to a bioreactor or gut microbiota), our model highlights facilitation and self-restraint as interactions that contribute to coexistence. We show that when interactions are strong, coexistence and stability are determined primarily by the topology of facilitation and inhibition influences and not the strengths of influences. Importantly, we show that consumption of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest.