Emergent metabolic interactions in resistance toClostridioides difficileinvasion

Abstract

Commensal gut bacteria are key contributors to the resilience against pathogen invasion. This is exemplified by the success of fecal microbiota transplantation in treating recurrentClostridioides difficileinfection. Yet, characteristics of communities that can confer colonization resistance and the underlying mechanisms remain largely unknown. Here we use a synthetic community of 14 commensal gut bacteria to uncover inter-species interactions and metabolic pathways underpinning the emergent resilience againstC. difficileinvasion. We challenged this synthetic community as well as fecal-matter-derived communities with antibiotic treatment andC. difficilein a continuous flow bioreactor. Using generalized Lotka-Volterra and genome-scale metabolic modelling, we identified interactions betweenEscherichia coliandBacteroides/Phocaeicolasp. as key to the pathogen’s suppression. Metabolomics analysis further revealed that fructooligosaccharide metabolism, vitamin B3 biosynthesis, and competition for Stickland metabolism precursors contribute to suppression. Analysis of metagenomics data from patient cohorts and clinical trials attested thein vivorelevance of the identified metabolic pathways and the ratio betweenBacteroidesandEscherichiain successful colonization resistance. The latter was found to be a much stronger discriminator than commonly used alpha diversity metrics. Our study uncovers emergent microbial interactions in pathogen resistance with implications for rational design of bacteriotherapies.