Fig. 1.

Phylogenetic trees of species and phylotypes identified from clones compared with the HOMD. The trees were created from full 16S rRNA reference sequences although it is recognized that use of 500-bp data from study clones could have created a different, but less accurate, treeing topography. Taxa in trees include identifications at >0.1 mean percent positive taxa by subject. A total of 139 taxa were identified. Numbers of children with taxa detected are in the table to the right of each tree. Species or phylotypes that differed in detection frequencies are noted at ∗ p ≤ 0.05, ∗∗ p ≤ 0.01, ∗∗∗ p ≤ 0.001, by χ² analysis, or Fishers exact test. a Phylogenetic tree of 51 taxa in Proteobacteria, Bacteroidetes and Actinobacteria detected in severe caries and caries-free children, with positions of Clostridia and Bacillus as phylogenetic references. The tree includes 28 taxa of Proteobacteria, 15 taxa of Bacteroidetes, 1 Treponema species, 5 Actinobacteria and 2 Leptotrichia taxa. b Phylogenetic tree of 49 taxa in the Clostridia branch of Firmicutes, which includes the Gram-negative Veillonella and Selenomonas genera, detected in severe ECC and caries-free children. This group comprises several named and unnamed taxa, including the Centipeda species. c Phylogenetic tree of 38 taxa in the Bacillus branch of Firmicutes detected in severe caries and caries-free children. The tree includes 29 Streptococcus species, comprising 10 unnamed species, 2 Gemella, 2 Granulicatella and 4 Lactobacillus species.