In vitro metabolic interaction network of a rationally designed nasal microbiota community

Abstract

Mounting evidence suggests that metabolite exchange between microbiota members is a key driver of microbiota composition. However, we still know little about the metabolic interaction networks within many microbiota. To tackle this issue, we developed the porcine nasal consortium (PNC8), which represents the most in vivo abundant genera in the nasal microbiota of healthy piglets, and used it to systematically map the in vitro metabolic interactions between its members. Spent media experiments, exometabolomics, and direct co-cultivation, revealed that most pairwise interactions between PNC8 strains are negative, with co-depletion of sugars acting as a key driver. This prevalence of negative interactions leads to a complex competition hierarchy in which only few strains are able to consistently outcompete all others. Overall, this work provides a valuable resource for studying the nasal microbiota under experimentally tractable in vitro conditions and is a key step toward mapping its metabolic interaction network.