Generalized modeling reveals stabilizing mechanisms in cross-feeding microbial communities

Abstract

Understanding what makes microbial communities stable and able to resist perturbation is a fundamental question in microbial ecology. Theoretical approaches to this problem typically require making strict assumptions about the structure, parameters and functional forms used in models, hindering general insight. Here, we address this problem by developing and analyzing a generalized model of microbial community dynamics, capturing resource-mediated competitive and cross-feeding interactions between populations. The generalized modeling approach allows us to assess the stability of microbial systems across large ensembles of models with variable size, structure and non-linear dynamics. Our analysis shows how community stability is constrained by system size and identifies its key metabolic and dynamical drivers, highlighting the central roles of self-limitation, metabolic efficiency and plasticity. Furthermore, we show how the structure of communities mediates their stability, allowing communities to counteract the destabilizing cross-feeding loops through organization into hierarchical trophic structures. Together, these results provide new insight into the stability of microbial communities and offer a flexible analytical framework for future work to explore the responses of communities to perturbation.