Skip to main content

Advertisement

SpringerLink
Log in

Streptococcus gwangjuense sp. nov., Isolated from Human Pericoronitis

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A novel facultative anaerobic, Gram-stain-negative coccus, designated strain ChDC B345T, was isolated from human pericoronitis lesion and was characterized by polyphasic taxonomic analysis. The 16S ribosomal RNA gene (16S rDNA) sequence revealed that the strain belonged to the genus Streptococcus. The 16S rDNA sequence of strain ChDC B345T was most closely related to those of  Streptococcus mitis NCTC 12261T (99.5%) and Streptococcus pseudopneumoniae ATCC BAA-960T (99.5%). Complete genome of strain ChDC B345T was 1,972,471 bp in length and the G + C content was 40.2 mol%. Average nucleotide identity values between strain ChDC B345T and S. pseudopneumoniae ATCC BAA-960T or S. mitis NCTC 12261T were 92.17% and 93.63%, respectively. Genome-to-genome distance values between strain ChDC B345T and S. pseudopneumoniae ATCC BAA-960T or S. mitis NCTC 12261T were 47.8% (45.2–50.4%) and 53.0% (51.0–56.4%), respectively. Based on these results, strain ChDC B345T (= KCOM 1679T = JCM 33299T) should be classified as a novel species of genus Streptococcus, for which we propose the name Streptococcus gwangjuense sp. nov.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Arbique JC, Poyart C, Trieu-Cuot P, Quesne G, Carvalho Mda G, Steigerwalt AG, Morey RE, Jackson D, Davidson RJ, Facklam RR (2004) Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 42:4686–4696. https://doi.org/10.1128/JCM.42.10.4686-4696.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Bridge PD, Sneath PHA (1982) Streptococcus gallinarum sp. nov. and Streptococcus oralis sp. nov. Int J Syst Bacteriol 32:410–415

    Article  Google Scholar 

  3. 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. https://doi.org/10.1038/nmeth.2474

    Article  CAS  PubMed  Google Scholar 

  4. Cho E, Park SN, Lim YK, Shin Y, Paek J, Hwang CH, Chang YH, Kook JK (2015) Fusobacterium hwasookii sp. nov., isolated from a human periodontitis lesion. Curr Microbiol 70:169–175. https://doi.org/10.1007/s00284-014-0692-7

    Article  CAS  PubMed  Google Scholar 

  5. Doern CD, Burnham CA (2010) It’s not easy being green: the viridans group streptococci, with a focus on pediatric clinical manifestations. J Clin Microbiol 48:3829–3835. https://doi.org/10.1128/JCM.01563-10

    Article  PubMed  PubMed Central  Google Scholar 

  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  7. Gao XY, Zhi XY, Li HW, Klenk HP, Li WJ (2014) Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups. PLoS ONE 30:e101229. https://doi.org/10.1371/journal.pone.0101229

    Article  CAS  Google Scholar 

  8. Handley P, Coykendall A, Beighton D, Hardie JM, Whiley RA (1991) Streptococcus crista sp. nov., a viridans streptococcus with tufted fibrils, isolated from the human oral cavity and throat. Int J Syst Bacteriol 41:543–547. https://doi.org/10.1099/00207713-41-4-543

    Article  CAS  PubMed  Google Scholar 

  9. Huch M, De Bruyne K, Cleenwerck I, Bub A, Cho GS, Watzl B, Snauwaert I, Franz CM, Vandamme P (2013) Streptococcus rubneri sp. nov., isolated from the human throat. Int J Syst Evol Microbiol 63:4026–4032. https://doi.org/10.1099/ijs.0.048538-0

    Article  CAS  PubMed  Google Scholar 

  10. Jensen A, Scholz CF, Kilian M (2016) Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus. Int J Syst Evol Microbiol 66:4803–4820. https://doi.org/10.1099/ijsem.0.001433

    Article  CAS  PubMed  Google Scholar 

  11. Kawamura Y, Hou XG, Sultana F, Miura H, Ezaki T (1995) Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and hylogenetic relationships among members of the genus Streptococcus. Int J Syst Bacteriol 45:406–408 (Erratum in: Int J Syst Bacteriol (1995) 45:882)

    Article  CAS  PubMed  Google Scholar 

  12. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  13. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  14. Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760

    Article  CAS  PubMed  Google Scholar 

  15. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60

    Article  Google Scholar 

  16. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106

    Article  PubMed  PubMed Central  Google Scholar 

  17. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  18. Scholz CF, Poulsen K, Kilian M (2012) Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies. J Clin Microbiol 50:1968–1973. https://doi.org/10.1128/JCM.00365-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Whiley RA, Fraser HY, Douglas CW, Hardie JM, Williams AM, Collins MD (1990) Streptococcus parasanguis sp. nov., an atypical viridans Streptococcus from human clinical specimens. FEMS Microbiol Lett 56:115–121. https://doi.org/10.1111/j.1574-6968.1990.tb04133

    Article  CAS  PubMed  Google Scholar 

  22. Whiley RA, Hardie JM (2009) Genus I. Streptococcus Rosenbach 1884, 22AL. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 655–711

    Google Scholar 

  23. Willcox MD, Zhu H, Knox KW (2001) Streptococcus australis sp. nov., a novel oral streptococcus. Int J Syst Evol Microbiol 51:1277–1281. https://doi.org/10.1099/00207713-51-4-1277

    Article  CAS  PubMed  Google Scholar 

  24. Zbinden A, Mueller NJ, Tarr PE, Spröer C, Keller PM, Bloemberg GV (2012) Streptococcus tigurinus sp. nov., isolated from blood of patients with endocarditis, meningitis and spondylodiscitis. Int J Syst Evol Microbiol 62:2941–2945. https://doi.org/10.1099/ijs.0.038299-0

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Ministry of Science and ICT (Grant No. 2017M3A9B8065844) and in part by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (Grant No. 2018R1A2B5002239).

Author information

Author notes

  1. Soon-Nang Park and Yun Kyong Lim have contributed equally to this work.

Authors and Affiliations

  1. Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea

    Soon-Nang Park, Yun Kyong Lim & Joong-Ki Kook

  2. Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea

    Jeong Hwan Shin

  3. ABS Research Support Center, KRIBB, Daejeon, Republic of Korea

    Young-Hyo Chang, Yeseul Shin & Jayoung Paek

  4. Vitabio, Inc, Daejeon, Republic of Korea

    Hongik Kim

Authors
  1. Soon-Nang Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yun Kyong Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jeong Hwan Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Young-Hyo Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yeseul Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jayoung Paek
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hongik Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Joong-Ki Kook
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joong-Ki Kook.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

DPD Number: TA00862.

GenBank accession number of 16S rRNA gene for strain ChDC B345T: KF733672.

GenBank accession number of genome for strain ChDC B345T: CP032620.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 42 kb)

284_2019_1687_MOESM2_ESM.pptx

Supplementary material 2—Maximum likelihood (a) and the minimum evolution (b) phylogenetic tree based on 16S rDNA of strain ChDC B345T and type strains of related species. All 16S rDNAs of the strains used in this study were downloaded from GenBank. Stability of phylogenetic trees was assessed using a bootstrap analysis of 1,000 replicates with MEGA version 6.06 [19]. Bars indicate 0.01 (a) or 0.005 (b) changes per nucleotide position (PPTX 95 kb)

284_2019_1687_MOESM3_ESM.pptx

Supplementary material 3—Neighbor-joining phylogenetic tree based on DNA gyrase subunit B gene (gyrB) (a) and RNA polymerase beta-subunit gene (rpoB) (b) of strain ChDC B345T and type strains of related species. The stability of the trees was assessed using bootstrap analysis of 1000 replicates with MEGA version 6.06 [19]. Bars indicate 0.1 (a) or 0.02 (b) changes per nucleotide position (PPTX 97 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Park, SN., Lim, Y.K., Shin, J.H. et al. Streptococcus gwangjuense sp. nov., Isolated from Human Pericoronitis. Curr Microbiol 76, 799–803 (2019). https://doi.org/10.1007/s00284-019-01687-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-019-01687-8

Search

Navigation