In-depth sequence analysis of highly-conserved pyrH gene to study distributions of oral treponemes in periodontal disease versus health

Background: More than 75 species/species-level phylotypes of oral treponeme bacteria inhabit the oral cavity. However, their respective genomic compositions and clinical distributions remain poorly understood. Objectives: To compare distributions of phylogroup 1 and 2 oral treponemes in subjects with various periodontal health conditions, via sequence analysis of a highly-conserved treponeme ‘housekeeping’ gene. Methods: Subgingival plaque samples were collected from Chinese subjects with chronic periodontitis (n=5), aggressive periodontitis (n=4), gingivitis (n=5), and healthy controls (n=4). Samples were analyzed by a PCR/plasmid clone sequencing-based approach, using primer sets targeting the pyrH gene. Data was analyzed using various computational/bioinformatic approaches. Results: 1,227 quality-filtered pyrH gene sequences were obtained (mean 66.2±9.6 sequences per subject), which were assigned to 33 ‘pyrH genotypes’ (97% identity cut-off). 538 pyrH sequences (17 pyrH genotypes) corresponded to phylogroup 1 treponemes (including ‘T. vincentii’, Treponema medium, and ‘Treponema sinensis’ taxa). 689 pyrH sequences (16 pyrH genotypes) corresponded to phylogroup 2 taxa. Correlations between pyrH genotype distributions and disease status were complex. One pyrH genotype, which was phylogenetically-related to T. denticola GM-1/MS25 strains, was highly prevalent: being detected in 17/18 subjects. Conclusions: Both healthy and periodontally-diseased subjects harbor multiple genetic lineages corresponding to the same treponeme species/phylotype within their subgingival niches.