Figure 3. Commensal colonization of colonic crypts.

a, Colonization exclusion. Stable colonization of germfree mice with B. fragilis prevents the subsequent colonization by isogenic B. fragilis sister cells, suggesting that the initial population of B. fragilis has occupied all niches available to it and are not subject to forces of random displacement. b, Co-colonization. Stable colonization of germfree mice with B. fragilis does not prevent invasion by another species of Bacteroides, suggesting limited niche overlap between the two species. c, Niche displacement. Stable colonization of germfree mice with a B. fragilis mutant lacking genes for a specialized PUL named commensal colonization factor (CCF) can be disrupted by subsequent colonization by wildtype B. fragilis cells. B. fragilis ccf mutants are defective in their ability to colonize deep within the colonic crypts, which are thought to serve as a microbial reservoir that seeds the gut lumen and promotes long-term colonization of the gut. Figure based on data from ref. ⁴¹.