The Treponema vincentii LA-1 (ATCC 35580) and Treponema pallidum subsp. pallidum SS14 reference strains were selected as outgroups, using complete genomes obtained from GenBank under Accession numbers NZ_ACYH00000000 and NC_010741, respectively.

Acknowledgments We are grateful to Dr. Chris Wyss, Dr. Barry McBride and Dr. E. Peter Greenberg for providing us with reference strains and clinical isolates. RMW acknowledges financial buy Metformin support from the University of Hong Kong through the Infection and Immunology Strategic Research Theme and a Seed Funding grant (#200911159092); and the Research Grants Council of Hong Kong, via a General Research Fund (GRF) grant (#781911). YCFS and GJDS are supported by the Duke–NUS Signature Research Program funded by the Agency for Science, Technology MDV3100 cost and Research, and the Ministry of Health, Singapore. Electronic supplementary material Additional file 1: Table summarizing G + C content (%) for the eight genes selected for sequence analysis within the 20 Treponema denticola strains. (PDF 8 KB) Additional file 2: Table summarizing details

of the flaA , recA , pyrH , ppnK , dnaN , era and radC gene homologues present in Treponema pallidum SS14 and Treponema vincentii LA-1 (ATCC 35580). (PDF 8 KB) Additional file 3: Table summarizing the optimal models and parameter values for the individual gene and concatenated flaA

 −  recA  −  pyrH  −  ppnK  −  dnaN  −  era − radC gene datasets analyzed in this study. (PDF 8 KB) Additional file 4: Maximum likelihood (ML) phylogenetic trees obtained for the individual 16S rRNA, flaA , recA , pyrH , ppnK , dnaN , era and radC gene datasets. (PDF 341 KB) D-malate dehydrogenase References 1. Darveau RP: Periodontitis: a polymicrobial disruption of host homeostasis. Nat Rev Microbiol 2010,8(7):481–490.PubMedCrossRef 2. Loesche WJ, Grossman NS: Periodontal disease as a specific, albeit chronic, infection: diagnosis and treatment. Clin Microbiol Rev 2001,14(4):727–752.PubMedCrossRef 3. Pihlstrom BL, Michalowicz BS, Johnson NW: Periodontal diseases. Lancet 2005,366(9499):1809–1820.PubMedCrossRef 4. Petersen PE, Ogawa H: Strengthening the prevention of periodontal disease: the WHO approach. J Periodontol 2005,76(12):2187–2193.PubMedCrossRef 5. Socransky SS, Haffajee AD: Periodontal microbial ecology. Periodontol 2000 2005, 38:135–187.PubMedCrossRef 6. Ellen RP, Galimanas VB: Spirochetes at the forefront of periodontal infections. Periodontol 2000 2005, 38:13–32.PubMedCrossRef 7. Sela MN: Role of Treponema denticola in periodontal diseases. Crit Rev Oral Biol Med 2001,12(5):399–413.PubMedCrossRef 8.