Complete genome sequencing of Oral Spirochete Treponema sp. OMZ 305

Abstract

Objectives: More than 75 species/species-level phylotypes of bacteria belonging to the genus Treponema inhabit the human oral cavity. However, our understanding of oral treponeme taxonomy and genome biology remains limited. Objective: To sequence the whole genome of the human oral treponeme isolate Treponema sp. OMZ 305, formerly known as ‘Treponema vincentii’ RitzA. Methods: Genomic DNA was purified (Promega, Wizard genomic DNA purification kit) from Treponema sp. OMZ 305 (supplied by Dr. Chris Wyss), cultured anaerobically in TYGVS medium. Whole genome sequencing libraries were prepared and sequenced using both Pacific Biosciences RSII and Illumina Hi-Seq platforms. Raw sequencing reads were trimmed and quality filtered. De novo assembly was performed using PacBio Corrected Reads (PBcR) pipeline. The draft genome was annotated using RASTv2. Results: The PacBio RS II sequencing generated 177,228 filtered subreads, and 986 megabases (Mb), with an average length of 5,567 bases, which provided 329x coverage. The Illumina sequencing generated 9.2 million reads (310x coverage), of which>94% were high quality (>Q30). Genome assembly using the PBcR pipeline resulted in one single contig (2.63 Mb) with G+C content of 45.05%. Preliminary annotation revealed two ribosomal RNA (16S-23S-5S) operons; 49 tRNA genes, and 2,473 coding DNA sequences (CDS). Two putative integrons and one incomplete prophage (8.2kb, 8 CDs, 43.24% GC; similar to Mannheimia phage vB_MhS_1152AP2) were identified. Notably, homologues of the following CDS from Treponema denticola ATCC 35405 were not present: prolyl oligopeptidase (TDE1195), Oligopeptidase B (TDE 2140); Chymotrypsin-like protease complex pcrAB-prtP (TDE0760-61). Two small alarmone synthetase homologues were observed: one homologous to TDE1711, another similar to JO41_10760 from ‘Treponema sinensis’ OMZ 838. Conclusions: Treponema sp. OMZ 305 has a single genome whose size and composition share many similarities with those of other oral treponemes characterized to date. However, it is highly distinct from the ‘T. vincentii’ ATCC 35580 and F0403 genomes.