Assembly of stool-derived bacterial communities follows "early-bird" resource utilization dynamics

Abstract

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human stool to develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Among these communities, membership was largely determined by the donor stool, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient due to the ability of a few organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that assembly of this community of gut commensals can be explained by nutrient utilization dynamics that provide a predictive framework for manipulating community composition through nutritional perturbations.

Keywords: Enterobacteriaceae; Enterococcaceae; central carbon metabolism; ecology; gut microbiome; metabolism; microbiota; niche overlap; nutrients; resource competition; synthetic communities.