Open access
20 August 2015

Draft Genome Sequence of Veillonella tobetsuensis ATCC BAA-2400T Isolated from Human Tongue Biofilm


Here, we report the draft genome sequence of Veillonella tobetsuensis ATCC-BAA 2400T. This bacterium has the remarkable ability to form oral biofilms. The genome is predicted to encode the necessary enzymes involved in the pathway that facilitates the conversion of lactate to propionate.


The genus Veillonella consists of small, obligate anaerobic, Gram-negative cocci isolated from human oral cavities (1, 2). Veillonella species cannot catabolize sugars and instead rely on the fermentation of organic acids, such as lactate derived from Streptococcus spp., for the fermentation of sugars to propionic and acetic acids (3, 4). Additionally, Veillonella species demonstrate similar resistance to various antimicrobials, such as streptomycin, vancomycin, and tetracycline (5, 6), and were recently found to be resistant to penicillin and ampicillin (7).
Veillonella tobetsuensis was isolated from human tongue biofilm and established as a novel Veillonella species in 2013 (8). V. tobetsuensis has frequently been isolated from patients with periodontal diseases and in healthy individuals (9, 10). Additionally, it has the remarkable ability to form oral biofilms with Streptococcus species (11).
The draft genome of V. tobetsuensis ATCC BAA-2400T was sequenced using Illumina HiSeq 2500 with sequencing runs for paired-end sequences. The bacterial DNA libraries were prepared using phenol-chloroform extraction and ethanol precipitation, as previously described (12). The genome was assembled into 49 contigs, ranging in size from 189 to 426,788 bp, using a sequence assembler for very short reads (Velvet version 1.2.08) and a de novo assembler designed to assemble high-throughput data (Platanus version 1.2.1) (13, 14). A synteny comparison with the genome was done using the closely related species Veillonella parvula DSM 2008 (accession no. NC_013520). Gene prediction was performed using Rapid Annotations using Subsystems Technology (RAST) ( (15). The genes in the ATCC BAA-2400T genome were assigned to Clusters of Orthologous Groups (COG) (16) categories, using BLASTp comparison with the COG database (, with an alignment E value cutoff of 10-3. Hokkaido System Science (Sapporo, Japan) performed the sequencing runs and read assembly libraries.
The draft genome sequence of ATCC BAA-2400T was 2,161,277 bp, with a G+C content of 38.5% and 500-fold genome coverage. The genome sequence contained 1,913 coding sequences, 48 tRNAs, and 3 ribosomal RNAs. A large fraction of the protein-coding genes were assigned to functions in energy production and conversion and encompassed most of the genes known to be required for the conversion of lactate to propionate. This pathway was completely encoded in the ATCC BAA-2400T genome and includes the characteristic methylmalonyl-coenzyme A (CoA) decarboxylase that generates a transmembrane electrochemical (Na+) gradient (17). This pathway is a critical component of the metabolic relationship of the oral cavity in which Veillonella is proposed to generate energy from the fermentation of lactate-producing bacteria, such as Streptococcus species (18). This system may largely contribute to the formation of biofilms with Streptococcus species (19).

Nucleotide sequence accession numbers.

This draft genome sequence of V. tobetsuensis ATCC BAA-2400T has been deposited at DDBJ/EMBL/GenBank under the accession numbers BBXI01000001 through BBXI01000049 (49 entries). The version described in this paper is the first version.


This study was supported in part by grants-in-aid from the Japan Society for the Promotion of Science (JSPS) Fellows (15J30007), Scientific Research from KAKENHI (grant 26462793), and the 2014–2015 Research Project of the Research Institute of Personalized Health Sciences, Health Sciences University of Hokkaido.


Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. 2005. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43:5721–5732.
Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87:1016–1020.
Ng SK, Hamilton IR. 1971. Lactate metabolism by Veillonella parvula. J Bacteriol 105:999–1005.
Delwiche EA, Pestka JJ, Tortorello ML. 1985. The veillonellae: Gram-negative cocci with a unique physiology. Annu Rev Microbiol 39:175–193.
Rogosa M. 1984. Anaerobic Gram-negative cocci, p 680–685. In Krieg NR, Holt JG, (ed), Bergey's manual of systematic bacteriology, vol 1. Williams & Wilkins, Baltimore, MD.
Williams BL, Osterberg SK, Jorgensen J. 1979. Subgingival microflora of periodontal patients on tetracycline therapy. J Clin Periodontol 6:210–221.
Ready D, Bedi R, Mullany P, Wilson M. 2012. Penicillin and amoxicillin resistance in oral Veillonella spp. Int J Antimicrob Agents 40:188–189.
Mashima I, Kamaguchi A, Miyakawa H, Nakazawa F. 2013. Veillonella tobetsuensis sp. nov., an anaerobic, Gram-negative coccus isolated from human tongue biofilms. Int J Syst Evol Microbiol 63:1443–1449.
Mashima I, Nakazawa F. 2013. Identification of Veillonella tobetsuensis in tongue biofilm by using a species-specific primer pair. Anaerobe 22:77–81.
Mashima I, Fujita M, Nakatsuka Y, Kado T, Furuichi Y, Herastuti S, Nakazawa F. 2015. The distribution and frequency of Veillonella spp. associated with chronic periodontal diseases. Int J Curr Microbiol Appl Sci 4:150–160.
Mashima I, Nakazawa F. 2014. The influence of oral Veillonella species on biofilm formed by Streptococcus species. Anaerobe 28:54–61.
Marmur J. 1961. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218.
Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829.
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T. 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24:1384–1395.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28.
Hilpert W, Dimroth P. 1991. On the mechanism of sodium ion translocation by methylmalonyl-CoA decarboxylase from Veillonella alcalescens. Eur J Biochem 195:79–86.
Van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M. 2013. Draft genome sequence of Veillonella parvula HSIVP1, isolated from the human small intestine. Genome Announc 1(6):e00977-13.
Mashima I, Nakazawa F. 2015. Interaction between Streptococcus spp. and Veillonella tobetsuensis in the early stages of oral biofilm formation. J Bacteriol 197:2104–2111.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 427 August 2015
eLocator: 10.1128/genomea.00808-15


Received: 11 June 2015
Accepted: 15 July 2015
Published online: 20 August 2015



Izumi Mashima
Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
Department of Oral Microbiology, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
Futoshi Nakazawa
Department of Oral Microbiology, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan


Address correspondence to Futoshi Nakazawa, [email protected].

Metrics & Citations


Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy