Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

A variety of cell surface structures, including capsular polysaccharides (CPS), dictate the interactions between bacteria and elements of their environment including their viruses (bacteriophages). Members of the prominent human gut Bacteroidetes characteristically produce several phase-variable CPS, which have been demonstrated as key determinants in interacting with the host immune system. However, the contributions of Bacteroidetes CPS to bacteriophage interactions are unknown. We used engineered strains of the human symbiont Bacteroides thetaiotaomicron , which differ only in the CPS they express, to isolate bacteriophages from two locations in the United States. Testing each of 71 bacteriophages against a panel of strains that express wild-type phase-variable CPS, one of eight different single CPS, or no CPS at all, revealed that each infects only a subset of strains. Deletion of infection-permissive CPS from B. thetaiotaomicron was sufficient to abolish infection for several individual bacteriophages. Likewise, infection of wild-type B. thetaiotaomicron with one bacteriophage from this collection selected for a cell population expressing non-permissive CPS. Surprisingly, acapsular B. thetaiotaomicron also escapes complete killing by this bacteriophage, but surviving bacteria increased expression of a family of 9 phase-variable lipoproteins. When constitutively expressed, one of these lipoproteins enhances resistance to this bacteriophage. Our results reveal distinct roles for Bacteroides CPS in mediating bacteriophage susceptibility. Beneath this vanguard protective layer, additional mechanisms exist to protect these bacteria from being eradicated by bacteriophage. Given the diversity of CPS and other phase-variable surface structures encoded by gut-dwelling Bacteroidetes, our results provide important insight into the adaptations that allow these bacteria to persist despite bacteriophage predation and hold important implications for using bacteriophages therapeutically to target gut symbionts.