Bacteroides–Escherichia interactions contribute to colonization resistance against Clostridioides difficile

Abstract Commensal gut bacteria are key contributors to the resilience against pathogen invasion. This is exemplified by the success of faecal microbiota transplantation in treating recurrent Clostridioides difficile infection. Yet, characteristics of communities that can confer colonisation 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 against C. difficile invasion. We challenged this synthetic community as well as faecal-matter-derived communities with antibiotic treatment and C. difficile in a continuous flow bioreactor. Using generalised Lotka-Volterra and genome-scale metabolic modelling, we identified interactions between Escherichia coli and Bacteroides/Phocaeicola sp. as key to the pathogen’s suppression. Metabolomics and targeted validation experiments revealed that fructan-derived fructooligosaccharides, vitamin B3 biosynthesis, and competition for Stickland metabolism precursors causally contribute to suppression across multiple C. difficile strains and donor backgrounds. Analysis of metagenomics data from patient cohorts and clinical trials attested the in vivo relevance of the identified metabolic pathways and the ratio between Bacteroides and Escherichia in successful colonisation resistance. The latter was found to be a stronger discriminator than commonly used alpha diversity metrics. Together, our study uncovers emergent microbial interactions in pathogen resistance with implications for rational design of bacteriotherapies.