Phylogenetic relationships and clonal abundance of the 110 Treponeme OTUs identified in this study. Figure components (from left to right). (A) 16S rRNA gene phylogenetic tree of the 110 identified treponeme OTUs and one outgroup species (Treponema primitia ZAS2) shown in an ultrametric form. The tree was constructed using a Neighbour-joining (NJ) method with 500 bootstrap replicates. Bootstrap values ≥50 are shown at branch points. (B) Clonal abundance of each treponeme OTU (i.e. number of 16S rRNA plasmid clones obtained from each subject that correspond to an individual OTU), represented using grey-scale shaded boxes. Scale values are shown at the base of the figure. 1–10: subject number in each cohort; TP: total clonal abundance of OTUs obtained from the periodontitis group; TH: total clonal abundance of OTUs obtained from the periodontitis-free control group; T: total clonal abundance of OTUs obtained from both subject groups; (C) Statistically-significant differences in the clonal abundance of respective OTUs detected within the periodontitis and periodontitis-free subject groups (Mann–Whitney U test, * = p < 0.05, ** = p < 0.01), Strain names in parentheses are representative reference strains belonging to the respective OTUs. (D) Group 1 – Group 7 = oral treponeme phylogroups 1–7.