| All animals live in symbiosis. Shaped by eons of co-evolution, host-bacterial associations have developed into prosperous relationships creating mechanisms for mutual benefits to both microbe and host. No better example exists in biology than the astounding numbers of bacteria harbored by the lower gastrointestinal tract of mammals. This community of symbionts establishes a life-long habitat within the distal gut and profoundly impacts host health. Although many recent investigations have led to determination of the microbiota composition, molecular mechanisms mediating establishment and maintenance of the microbial community within the gut is poorly described.;We use gnotobiotic mice to elucidate mechanisms of colonization by Bacteroides, one of the most numerically prominent genera in the intestine. We generate mutant strains of Bacteroides fragilis that lack the ability to express multiple capsular polysaccharides and demonstrate defect in colonization in competition with wild-type strain, suggesting a role for surface sugar architecture during host-symbiont mutualism. Through a functional in vivo genetic screen of colonization, we identify a novel operon from the genome of B. fragilis that is highly conserved among many sequenced intestinal Bacteroides and that mediate a species-specific colonization profile. We have named this genetic locus the commensal colonization factor (ccf). B. fragilis deleted in the ccf genes exhibit colonization defects in both germ-free and complex microbiota harboring mice. The ccf genes of B. fragilis are up-regulated during gut colonization, preferentially at the mucosal surface, supporting an in vivo function. Indeed, deletion of ccf genes leads to reduced mucosal association and a defect in bacterial occupation of colonic crypts of mice. The ability of B. fragilis to repopulate the gut after antibiotic perturbation or gastroenteritis requires expression of ccf, suggesting the niche within colonic crypts represents a colonization reservoir for the gut microbiota following environmental stress. These findings suggest a novel and evolutionarily conserved mechanism for persistent gut colonization by the Bacteroides species. |
