title: Multilocus Sequence Analysis of Phylogroup 1 and 2 Oral Treponeme Strains.
abstract: More than 75 "species-level" phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet-uncultivated taxa or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly conserved 16S rRNA, pyrH, recA, and flaA genes. We utilized this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n = 71) of diverse geographical origins. This comprises phylogroup 1 (n = 23) and phylogroup 2 (n = 48) treponeme strains, including all relevant American Type Culture Collection reference strains. The taxonomy of all strains was confirmed or inferred via the analysis of ca. 1,450-bp 16S rRNA gene sequences using a combination of bioinformatic and phylogenetic approaches. Taxonomic and phylogenetic relationships between the respective treponeme strains were further investigated by analyzing individual and concatenated flaA (1,074-nucleotide [nt]), recA (1,377-nt), and pyrH (696-nt) gene sequence data sets. Our data confirmed the species differentiation between Treponema denticola (n = 41) and Treponema putidum (n = 7) strains. Notably, our results clearly supported the differentiation of the 23 phylogroup 1 treponeme strains into five distinct "species-level" phylotypes. These respectively corresponded to "Treponema vincentii" (n = 11), Treponema medium (n = 1), "Treponema sinensis" (Treponema sp. IA; n = 4), Treponema sp. IB (n = 3), and Treponema sp. IC (n = 4). In conclusion, our MLSA-based approach can be used to effectively discriminate oral treponeme taxa, confirm taxonomic assignment, and enable the delineation of species boundaries with high confidence.
  
  
  
  Periodontal diseases are caused by persistent polymicrobial biofilm infections of the gums and underlying tooth-supporting structures and have a complex and variable etiology. Although Treponema denticola is strongly associated with periodontal diseases, the etiological roles of other treponeme species/phylotypes are less well defined. This is due to a paucity of formal species descriptions and a poor understanding of genetic relationships between oral treponeme taxa. Our study directly addresses these issues. It represents one of the most comprehensive analyses of oral treponeme strains performed to date, including isolates from North America, Europe, and Asia. We envisage that our results will greatly facilitate future metagenomic efforts aimed at characterizing the clinical distributions of oral treponeme species/phylotypes, helping investigators to establish a more detailed understanding of their etiological roles in periodontal diseases and other infectious diseases. Our results are also directly relevant to various polymicrobial tissue infections in animals, which also involve treponeme populations.
authors.affiliation: Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China.
authors.forename: Yong-Biao
authors.initials: YB
authors.lastname: Huo
authors.affiliation: Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China.
authors.forename: Yuki
authors.identifier: http://orcid.org/0000-0002-9570-5462
authors.initials: Y
authors.lastname: Chan
authors.affiliation: Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China.
authors.forename: Donnabella C
authors.initials: DC
authors.lastname: Lacap-Bugler
authors.affiliation: Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China.
authors.forename: Sisu
authors.initials: S
authors.lastname: Mo
authors.affiliation: Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
authors.forename: Patrick C Y
authors.initials: PCY
authors.lastname: Woo
authors.affiliation: Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China.
authors.forename: W Keung
authors.initials: WK
authors.lastname: Leung
authors.affiliation: Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Sai Ying Pun, Hong Kong SAR, China rmwatt@hku.hk.
authors.forename: Rory M
authors.identifier: http://orcid.org/0000-0002-8718-1988
authors.initials: RM
authors.lastname: Watt
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D005408:Flagellin / Q000235:genetics; D014644:Genetic Variation; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011938:Rec A Recombinases / Q000235:genetics; D017422:Sequence Analysis, DNA; D014208:Treponema / Q000145:classification / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D005408:Flagellin; C067138:flaA protein, bacteria; D011938:Rec A Recombinases
keywords: DNA sequencing; MLSA; Treponema; bacterial genome; dentistry; infection; oral microbiome; periodontitis; phylogeny; soft tissue infection; spirochete; taxonomy