Chromosomal DNA probes for the identification of Bacteroides species

We compared 22 Bacteroides species by DNA-DNA homology studies using the S1 endonuclease method. None of the currently defined species shared more than 30% DNA homology with any other species examined with the exception of B. buccae and B. capillus (which along with B. pentosaceus are now considered a single species), which shared 86% of their DNA sequences. Two clusters showed weak genetic relationships, with DNA homology greater than 10%. The first cluster included B. coporis, B. disiens, B. bivius, B. intermedius and B. melaninogenicus. The second cluster included B. fragilis, B. eggerthii, B. ovatus, B. thetaiotaomicron and B. uniformis. Five of the oral species, B. asaccharolyticus, B. gingivalis, B. loescheii, B. intermedius and B. melanogenicus, were chosen for study as whole chromosomal probes in dot blot assays. These were tested against 243 clinical strains biochemically identified as Bacteroides species. The DNA probes correctly identified 94% of the clinical strains. DNA probe and biochemical identification was 100% for two of the five species. In contrast, only 86% of the strains biochemically identified as B. intermedius were identified by the DNA probe. The DNA probes gave a species identification to seven strains which could not be biochemically identified.