Development of the genetic toolkit identifies capsular polysaccharides as a competitive colonization factor in Ruminococcus gnavus

Ruminococcus gnavus is a commensal bacterium in the human gut associated with various diseases, and its abundance often increases in the intestines of patients with active inflammatory bowel disease (IBD). However, the genetic factors that establish gut colonization and virulence remain elusive due to the lack of a system for genetic modification. This study develops several genetic tools, including a shuttle vector, an inducible promoter, fluorescent proteins, and gene disruption or deletion systems in R. gnavus to identify the genes involved in R. gnavus colonization. Using these genetic tools, we found the respective sortase enzymes necessary for both cell wall localization of the superantigens and capsular polysaccharide (CPS) production in R. gnavus ATCC 29149. We identified the putative new gene cluster responsible for CPS production in the adjacent region of the sortase gene and confirmed that CPS production is crucial for competitive fitness during colonization in germ-free mouse intestines and that CPS production is inversely correlated with the inflammatory activity of R. gnavus . Furthermore, CPS cluster-possessing strains tended to be more prevalent in healthy human isolates compared to those from Crohn’s disease patients. This implies that CPS production is involved in their inflammatory activities and pathogenesis of intestinal diseases such as IBD. We highlight the potential of precise gene modification systems to identify the genetic factors that facilitate intestinal colonization and pathogenesis in gut bacteria.