Phylogeny of Plasmid Strains of S. mutans

Objectives: A 5.6-kb plasmid is found in approximately 3% of isolates of S. mutans from humans. S. mutans is a member of the human indigenous biota and likely co-evolves with its host. Previously, we reported clustering of plasmid strains within racial and familial cohorts. Based on restriction fragment length polymorphism and association with chromosomal mutacin expression, we classified plasmid strains into Group I and Group II. Blacks and Asians harbored the Group I plasmids, Whites harbored Group II, with few exceptions. Because plasmid DNA sequence within groups are 96% homologous, they are presumed to be derived from a common ancestor. Here, we examined plasmid phylogeny and then compared to human racial affiliations. Methods: 31 plasmid strains of S. mutans were collected from humans from 5 continents including Japan, Europe, North and South America, China and Africa. A 611-bp non-coding region (hypervariable region;HVR) was amplified via PCR and sequenced. Sequences were aligned (Clustal W) and phylogenies approximated using similarity (neighbor joining), optimality criteria (maximum parsimony, maximum likelihood) and Bayesian inference. Bootstrap values were estimated from over 100 trees, depending upon the computational intensity. Results: Out of 611-bp, 63 sites were informative. This extensive degree of polymorphism suggests genetic drift rather than selection accounted for diversity in the HVR. Comparison of trees from the various methods yield similar tree architecture. Although terminal node clustering was noted among members of the same racial group, the overall tree topography failed to support major clades in which plasmid sequence and race of host corresponded. Conclusion: We conclude that divergence in plasmid sequences occurred prior to formation of extant racial groupings in humans. Supported by NIDCR grant DE11147.