Analysis of a phase variable restriction modification system of the human gut symbiont Bacteroides fragilis

We characterize a phase-variable Type I restriction modification (R-M) system of Bacteroides fragilis. Reversible DNA inversions within this R-M locus leads to the generation of eight distinct specificity proteins with different recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. Transcriptome analysis of each of the locked specificity mutants from both in vitro and in vivo grown bacteria have different transcriptional profiles, likely creating different phenotypic populations, one of which was confirmed.