B. fragilis T1RM specificity sequence

The genomes of gut Bacteroidales strains contain numerous invertible regions. Here, we characterize the Type I restriction modification system. We show that reversible DNA inversions within this R-M locus leads to the generation of eight distinct specificity proteins with different recognition sites. By creating a series of mutants each able to produce only one specificity protein from this region, we characterized the R-M recognition sites of four of these S-proteins using SMRT and MinION sequencing. The four methylation sites occur on average every 815 bp in the bacterial genome, but are almost completely lacking from a 45,990 bp Bacteroides phage. Transcriptome analysis revealed that 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.