Genome analysis of Bacteroides by pulsed-field gel electrophoresis: chromosome sizes and restriction patterns

The chromosomal DNAs of nine strains of seven Bacteroides species including B. fragilis, the type species of the genus Bacteroides, were digested with rare-cutting restriction enzymes I-Ceu I, Not I, and Asc I and analysed by pulsed-field gel electrophoresis. The genome sizes of B. fragilis, B. distasonis, B. eggerthii, B. ovatus, B. thetaiotaomicron, B. uniformis, and B. vulgatus were determined to be 5.3, 4.8, 4.4, 6.9, 4.8, 4.6, and 5.1 Mbp, respectively. B. distasonis and B. vulgatus, and also B. uniformis and B. eggerthii, showed similar I-Ceu I restriction profiles. I-Ceu I cut B. uniformis and B. eggerthii genomes into four, B. ovatus into five, B. fragilis and B. thetaiotaomicron into six, and B. distasonis and B. vulgatus into seven fragments. On the basis of genome size, restriction profile, and I-Ceu I fragment number, a phylogenetic tree of the Bacteroides species was proposed. This was in overall agreement with the previous phylogenetic tree obtained by 16S rRNA data, with the exceptions of B. distasonis and B. ovatus.