Abstract
Here, we present the complete genome sequence of Actinomyces naeslundii strain ATCC 27039, isolated from an abdominal wound abscess. This strain is genetically transformable and will thus provide valuable information related to its crucial role in oral multispecies biofilm development.
GENOME ANNOUNCEMENT
It is well known that Actinomyces spp. are common bacteria in the normal flora of the mouth, and that they play an important role in the development of oral biofilm as one of the initial colonizers of tooth surfaces (1–3). Actinomyces spp. have been implicated in the dental caries process as acidogenic bacteria and could also be causative bacteria that make inroads to deeper tissues via traumatic wounds and surgical operations in both immunocompetent and immunocompromised individuals (4–6). Recently, the next-generation sequencing analysis of oral samples revealed that Actinomyces spp., especially A. naeslundii and A. oris, are core members of the healthy oral microbiome (7–12). Standard genetic engineering techniques are now applicable to A. oris (13, 14). On the other hand, there is no information regarding the gene modification system on A. naeslundii; therefore, we examined the transformability of several oral A. naeslundii strains and confirmed that strain ATCC 27039 was genetically tractable. The aim of the present study is to determine the full-genome sequence of A. naeslundii ATCC 27039.
Total bacterial DNA of strain ATCC 27039 was extracted from an overnight culture using a Nucleo spin tissue kit (Macherey-Nagel). A 20-kb SMRTbell library was prepared, and the genome was sequenced using the PacBio RS II system (Pacific Biosciences) on a single-molecule real-time (SMRT) cell using PacBio P6-C4 chemistry.
The de novo assembly of 153,093 reads with a mean length of 5,172 bp was completed using the hierarchical genome assembly process (HGAP) algorithm in SMRT Analysis software version 2.3 (15) and revealed a single contig approximately 3.04 Mb in length with an average coverage of 217.96×; the assembly was manually edited to circularize the overlapping ends of the genome. The final genome sequence is 3,040,449 bp in size and has a G+C content of 68.4%. The genome was then annotated using RAST version 2.0 (16), which successfully identified 3,229 coding sequences, as well as 60 RNA sequences. Of these, 43% of the annotated coding sequences fell within 318 subsystems available in the RAST database. The annotated data set presented here is expected to augment future study of this organism and provide resources for genetic manipulation.
Accession number(s).
The genome sequence of A. naeslundii ATCC 27039 has been deposited in the DDBJ/EMBL/GenBank database under accession number AP017894.
ACKNOWLEDGMENTS
We thank Hisako Sakanaka for technical assistance and the Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, for next-generation DNA sequencing analysis by PacBio.
This work was partly supported by KAKENHI (Grant-in-Aid for Scientific Research [C] 16K11469, 16K11876, 16K11573, and 26861552), by the Japan Society for the Promotion of Science (JSPS), and by an Oral Implant Research Grant (16-03) from Osaka Dental University.
Footnotes
Citation Mashimo C, Yamane K, Yamanaka T, Maruyama H, Wang P-L, Komasa S, Okazaki J, Nambu T. 2016. Genome sequence of Actinomyces naeslundii strain ATCC 27039, isolated from an abdominal wound abscess. Genome Announc 4(6):e01443-16. doi:10.1128/genomeA.01443-16.
REFERENCES
- 1.Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. 2010. The human oral microbiome. J Bacteriol 192:5002–5017. doi: 10.1128/JB.00542-10. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Dige I, Raarup MK, Nyengaard JR, Kilian M, Nyvad B. 2009. Actinomyces naeslundii in initial dental biofilm formation. Microbiology 155:2116–2126. doi: 10.1099/mic.0.027706-0. [DOI] [PubMed] [Google Scholar]
- 3.Zijnge V, van Leeuwen MB, Degener JE, Abbas F, Thurnheer T, Gmür R, Harmsen HJ. 2010. Oral biofilm architecture on natural teeth. PLoS One 5:e9321. doi: 10.1371/journal.pone.0009321. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Takahashi N, Nyvad B. 2016. Ecological hypothesis of dentin and root caries. Caries Res 50:422–431. doi: 10.1159/000447309. [DOI] [PubMed] [Google Scholar]
- 5.Könönen E, Wade WG. 2015. Actinomyces and related organisms in human infections. Clin Microbiol Rev 28:419–442. doi: 10.1128/CMR.00100-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Valour F, Sénéchal A, Dupieux C, Karsenty J, Lustig S, Breton P, Gleizal A, Boussel L, Laurent F, Braun E, Chidiac C, Ader F, Ferry T. 2014. Actinomycosis: etiology, clinical features, diagnosis, treatment, and management. Infect Drug Resist 7:183–197. doi: 10.2147/IDR.S39601. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, Gamonal J, Diaz PI. 2013. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J 7:1016–1025. doi: 10.1038/ismej.2012.174. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA. 2010. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J 4:962–974. doi: 10.1038/ismej.2010.30. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Zaura E, Keijser BJ, Huse SM, Crielaard W. 2009. Defining the healthy “core microbiome” of oral microbial communities. BMC Microbiol 9:259. doi: 10.1186/1471-2180-9-259. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Duran-Pinedo AE, Frias-Lopez J. 2015. Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect 17:505–516. doi: 10.1016/j.micinf.2015.03.014. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Sarkonen N, Könönen E, Summanen P, Kanervo A, Takala A, Jousimies-Somer H. 2000. Oral colonization with Actinomyces species in infants by two years of age. J Dent Res 79:864–867. doi: 10.1177/00220345000790031301. [DOI] [PubMed] [Google Scholar]
- 12.Kolenbrander PE, Palmer RJ Jr, Periasamy S, Jakubovics NS. 2010. Oral multispecies biofilm development and the key role of cell-cell distance. Nat Rev Microbiol 8:471–480. doi: 10.1038/nrmicro2381. [DOI] [PubMed] [Google Scholar]
- 13.Mishra A, Wu C, Yang J, Cisar JO, Das A, Ton-That H. 2010. The Actinomyces oris type 2 fimbrial shaft FimA mediates co-aggregation with oral streptococci, adherence to red blood cells and biofilm development. Mol Microbiol 77:841–854. doi: 10.1111/j.1365-2958.2010.07252.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Wu C, Ton-That H. 2010. Allelic exchange in Actinomyces oris with mCherry fluorescence counterselection. Appl Environ Microbiol 76:5987–5989. doi: 10.1128/AEM.00811-10. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 16.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. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]