Extended Data Fig. 9: Whole genome transcriptional analyses of several additional B. thetaiotaomicron strain and phage combinations.
Whole genome transcriptional analyses of several additional B. thetaiotaomicron strain and phage combinations. a, Infection of the cps1 strain with ARB25, revealing a post-infection response that is largely characterized by increased expression of S-layer/OmpA proteins. b, Infection of wild-type B. thetaiotaomicron with SJC01, revealing that, as with ARB25/wild-type, the bacteria survive phage infection by mostly altering CPS expression. Expression of the non-permissive CPS3 is prominently increased. c, Infection of acapsular B. thetaiotaomicron with SJC01, revealing that in the absence of CPS survival is mostly promoted by increased S-layer/OmpA expression and expression of a phase-variable restriction enzyme system. Transcript abundance values in panels a-c were compared between live and HK treatments to generate fold change (x axis), which is plotted against the adjusted P value (EdgeR) for each gene that was generated using an exact test adapted for overdispersed data55 (n = 3 biological replicates for each panel, peformed with similar results). Please see Supplementary Tables 5-7 for actual adjusted P values for panels (a-c). d, Gene schematic of the phase-variable restriction enzyme system (top) and a lipoprotein contain locus (bottom) that is different from the 8 S-layer loci also revealed in this study. The inverted repeat sequence that was determined to mediate recombination in each locus is shown. e, PCR analysis of the restriction enzyme system and additional lipoprotein promoter orientations with primers designed to detect phase variation from off to on states. Amplicons were sequenced to confirm the re-orientation to the on orientation (not shown). Experiment was performed once. f, Global transcriptional responses of wild-type B. thetaiotaomicron in the ceca of mice after 72 d of co-existence with ARB25. Note that shifts in CPS expression are mostly characterized by increases in permissive CPS, which may be dictated by growth in vivo selecting for these capsules or against the non-permissive CPS3. Correspondingly, wild-type shows increased expression of some but not all S-layer/OmpA systems and the phase-variable restriction enzyme. g, Global transcriptional responses of acapsular B. thetaiotaomicron in the ceca of mice after 72 d of co-existence with ARB25. In the absence of CPS, surviving bacteria show increased expression of only a subset of the identified S-layer/OmpA proteins, with BT1826 expressed most dominantly, along with the BT0291-94 locus and expression of the restriction enzyme system. Experiments in panels f-g are the results of 3 separate biological replicates, statistical tests are identical to those described in panels (a-c). The dashed lines in panels a,b,c,f,g represent the adjusted P value cutoff (≥0.01) that was used to establish significance, which was generated using an exact test adapted for overdispersed data55.
