21A variety of cell surface structures, including capsular polysaccharides (CPS), dictate 22interactions between bacteria and their environment including their viruses (bacteriophages). 23Members of the prominent human gut Bacteroidetes characteristically produce several phase-24 variable CPS, but their contributions to bacteriophage interactions are unknown. We used 25 engineered strains of the human symbiont Bacteroides thetaiotaomicron, which differ only in the 26 CPS they express, to isolate bacteriophages from two locations in the United States. Testing each 27 of 71 bacteriophages against a panel of strains that express wild-type phase-variable CPS, one of 28 eight different single CPS, or no CPS at all, revealed that each phage infects only a subset of 29 otherwise isogenic strains. Deletion of infection-permissive CPS from B. thetaiotaomicron was 30 sufficient to abolish infection for several individual bacteriophages, while infection of wild-type 31 B. thetaiotaomicron with either of two different bacteriophages rapidly selected for expression of 32 non-permissive CPS. Surprisingly, acapsular B. thetaiotaomicron also escapes complete killing 33 by these bacteriophages, but surviving bacteria exhibit increased expression of 8 distinct phase-34 variable lipoproteins. When constitutively expressed, one of these lipoproteins promotes 35 resistance to multiple bacteriophages. Finally, both wild-type and acapsular B. thetaiotaomicron 36 were able to separately co-exist with one bacteriophage for over two months in the mouse gut, 37suggesting that phase-variation promotes resistance but also generates sufficient numbers of 38 susceptible revertants to allow bacteriophage persistence. Our results reveal important roles for 39Bacteroides CPS and other cell surface structures that allow these bacteria to persist despite 40 bacteriophage predation and hold important implications for using bacteriophages therapeutically 41 to target gut symbionts. 42 43Bacteroides thetaiotaomicron and Bacteroides fragilis each encode 8 different CPS 14,15 and there 61 is broad genetic diversity of cps loci among different strains within these species (e.g., 47 62 different cps biosynthetic loci were identified in just 14 strains of B. thetaiotaomicron) 8 . In 63Bacteroides, CPS structures appear to surround the entire bacterial cell 16,17 and the cps 64 biosynthetic loci that encode these surface coatings are often under the control of phase variable 65 promoters 8,15,18 . In conjunction with other regulatory mechanisms, phase variable CPS 66 4 expression generates phenotypic heterogeneity within an otherwise isogenic population that may 67 facilitate survival in the face of diverse disturbances 8,15,19,20 . 68 Bacterial viruses or bacteriophages (herein, phages), like the bacteria on which they prey, 69 vary greatly across individual gut microbiomes and are even responsive to host dietary changes 70 and disease states [21][22][23][24][25] . Compared to gut bacteria, far less is understood about the phages of the 71 gut microbi...

SummaryClostridium difficile infection (CDI) is an enteric bacterial disease that is increasing in prevalence worldwide. C. difficile capitalizes on gut inflammation and microbiome dysbiosis to establish infection, with symptoms ranging from watery diarrhea to toxic megacolon. We recently reported that the safe in human clinical drug candidate ebselen (NCT03013400, NCT01452607, NCT00762671, NCT02603081) has biochemical, cell-based and in vivo efficacy against the bacterial toxins of C. difficile. Here, we show that ebselen treatment reduces recurrence rates and decreases colitis in a hamster relapse model of CDI. Furthermore, ebselen treatment does not alter microbiome diversity but promotes its recovery back to that of healthy controls after antibiotic-induced dysbiosis in both healthy and C. difficile-infected mice. This increased microbiome recovery upon ebselen treatment correlates with a decrease in host-derived inflammatory markers suggesting that the anti-inflammatory properties of ebselen, combined with its anti-toxin function, help to mitigate the major clinical challenges of CDI, including recurrence, microbial dysbiosis, and colitis.