Veillonella spp. are commonly isolated from carious sites but are indistinguishable at the species level by biochemical methods. Analysis of the 16S rRNA gene is the preferred method for differentiating between Veillonella spp. However, the level of sequence divergence between certain species is quite low, with intra-chromosomal variation between the four 16S rRNA copies in some strains reported to exceed those between species. This suggests that 16S rRNA–based methods are unsuitable for the identification of Veillonella spp. Objectives: To determine whether the highly conserved genes, rpoB, dnaK and gyrB are better gene markers than the 16S rRNA gene for the differentiation of Veillonella spp. obtained from clinical sources. Methods: Partial regions of the rpoB (655 bp), dnaK (717 bp) and gyrB (764 bp) genes and the near full-length 16S rRNA (1497 bp) gene were amplified by PCR from Veillonella strains isolated from carious dentin of extracted teeth and sequenced. The obtained sequences were aligned and subjected to phylogenetic analysis using MEGA2. Results: For taxonomic purposes, the level of interspecies divergence should be much greater than intraspecies. Phylogenetic analysis showed that all three conserved genes studied had greater discriminatory power than the 16S rRNA gene in differentiating between Veillonella strains. Of these, the rpoB gene showed the highest level of interspecies but the lowest intraspecies diversity. Conclusion: For the differentiation of Veillonella species, the data from this study indicate that the rpoB gene is a more useful identification marker than the 16S rRNA gene. This study was supported by NIDCR #R01 DE015272-07.

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