Metabolic dependencies drive species co-occurrence in diverse microbial communities

TLDR

Microbial communities inhabit most environments and are shaped by competition and metabolic cooperation, yet the prevalence of metabolic interactions remains largely unknown. We systematically surveyed over 800 communities using genome‑scale metabolic modeling to quantify resource competition and metabolic exchanges. We enumerated flux‑balanced metabolic exchanges within co‑occurring subcommunities, predicting exchanged metabolites such as amino acids and sugars that support group survival under nutrient stress. Our results show that metabolically interdependent groups recur across diverse habitats, indicating metabolic dependencies as a major driver of species co‑occurrence and highlighting cooperative modules in community architecture.

Abstract

Microbial communities populate most environments on earth and play a critical role in ecology and human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated in community assembly. The prevalence of metabolic interactions in microbial communities, however, has remained largely unknown. Here, we systematically survey, by using a genome-scale metabolic modeling approach, the extent of resource competition and metabolic exchanges in over 800 communities. We find that, despite marked resource competition at the level of whole assemblies, microbial communities harbor metabolically interdependent groups that recur across diverse habitats. By enumerating flux-balanced metabolic exchanges in these co-occurring subcommunities we also predict the likely exchanged metabolites, such as amino acids and sugars, that can promote group survival under nutritionally challenging conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence and hint at cooperative groups as recurring modules of microbial community architecture.