Resource competition predicts assembly of in vitro gut bacterial communities

Abstract

Members of microbial communities interact via a plethora of mechanisms, including resource competition, cross-feeding, and pH modulation. However, the relative contributions of these mechanisms to community dynamics remain uncharacterized. Here, we develop a framework to distinguish the effects of resource competition from other interaction mechanisms by integrating data from growth measurements in spent media, synthetic community assembly, and metabolomics with consumer-resource models. When applied to human gut commensals, our framework revealed that resource competition alone could explain most pairwise interactions. The resource-competition landscape inferred from metabolomic profiles of individual species predicted assembly compositions, demonstrating that resource competition is a dominant driver of in vitro community assembly. Moreover, the identification and incorporation of interactions other than resource competition, including pH-mediated effects and cross-feeding, improved model predictions. Our work provides an experimental and modeling framework to characterize and quantify interspecies interactions in vitro that should advance mechanistically principled engineering of microbial communities.