Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species

Abstract

Roseburiaspecies are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genusRoseburiahave examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genusRoseburiawith respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content amongRoseburiaspecies and strains was most significant for cofactor biosynthesis. Unlike all other species ofRoseburiathat we analysed,Roseburia inulinivoransstrains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities inR. intestinalisstrains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of theRoseburiaspp. genomes may influencein vivogut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology ofRoseburiaspp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.