PCR-Based Identification of Oral Streptococcal Species

Figure 2

Molecular phylogenetic tree of MLSA concatenated sequences for the map, pfl, ppaC, and tuf genes. The evolutionary history was inferred by using the Maximum Likelihood Method based on the Tamura-Nei model [15]. The tree with the highest log likelihood is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Evolutionary analyses were conducted in MEGA7 [16]. The prospective S. oralis isolates (upper portion of the dendrogram from 116-1v-2 to 29-2v-2) appear segregated from the prospective S. mitis isolates (1881-2v-4 to 11-2v-6). Among the prospective S. oralis isolates, 1412-2v-1 (S. intermedius), 510-1v-1 (S. intermedius), 964-1v-4 (uncertain species assignment), 139-1v-1 (S. gordonii), and 29-2v-2 (S. sanguinis) were assigned to species other than S. oralis and map furthest from the S. oralis control. Two prospective S. oralis strains (96-2v-4 and 1881-2v-3) were not included due to poor sequence quality in the regions of alignment.