Skip to main content

Advertisement

SpringerLink
Log in

Capnocytophaga endodontalis sp. nov., Isolated from a Human Refractory Periapical Abscess

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A novel Gram-negative, capnophilic, fusiform bacterium, designated strain ChDC OS43T, was isolated from a human refractory periapical abscess in the left mandibular second molar and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene sequence revealed that the strain belongs to the genus Capnocytophaga, as it showed sequence similarities to Capnocytophaga ochracea ATCC 27872T (96.30%) and C. sputigena ATCC 33612T (96.16%). The prevalent fatty acids of strain ChDC OS43T were isoC15:0 (57.54%), C16:0 (5.93%), C16:0 3OH (5.72%), and C18:1 cis 9 (4.41%). The complete genome of strain ChDC OS43T was 3,412,686 bp, and the G+C content was 38.2 mol%. The average nucleotide identity (ANI) value between strain ChDC OS43T and C. ochracea ATCC 27872T or C. sputigena ATCC 33612T was >92.01%. The genome-to-genome distance (GGD) value between strain ChDC OS43T and C. ochracea ATCC 27872T or C. sputigena ATCC 33612T was 32.0 and 45.7%, respectively. Based on the results of phenotypic, chemotaxonomic, and phylogenetic analysis, strain ChDC OS43T (= KCOM 1579T = KCTC 5562T = KCCM 42841T = JCM 32133T) should be classified as the type strain of a novel species of genus Capnocytophaga, for which the name Capnocytophaga endodontalis sp. nov. is proposed.

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.

Fig. 1

Similar content being viewed by others

References

  1. 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 

  2. Cho E, Park SN, Shin Y, Lim YK, Paek J, Kim HK, Hwang CH, Jo E, Jin D, Chang YH, Kook JK (2015) Peptoniphilus mikwangii sp. nov., isolated from a clinical specimen of human origin. Curr Microbiol 70:260–266. https://doi.org/10.1007/s00284-014-0712-7

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  4. Handal T, Olsen I, Walker CB, Caugant DA (2005) Detection and characterization of beta-lactamase genes in subgingival bacteria from patients with refractory periodontitis. FEMS Microbiol Lett 242:319–324. https://doi.org/10.1016/j.femsle.2004.11.023

    Article  CAS  PubMed  Google Scholar 

  5. 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 

  6. Kook JK, Kim MK, Kim SG (2006) Microbiological findings in refractory periapical abscess caused by endodontic treatment failure: a case report. Hosp Dent Oral-Maxillofac Surg 18:29–31

    Google Scholar 

  7. Leadbetter ER, Holt SC, Socransky SS (1979) Capnocytophaga: new genus of gram-negative gliding bacteria. I. General characteristics, taxonomic considerations and significance. Arch Microbiol 122:9–16. https://doi.org/10.1007/BF00408040

    Article  CAS  PubMed  Google Scholar 

  8. London J, Celesk RA, Kagermeier A, Johnson JL (1985) Emended description of Capnocytophaga gingivalis. Int J Syst Bacteriol 35:369–370. https://doi.org/10.1099/00207713-35-3-369

    Article  Google Scholar 

  9. Lopez E, Raymond J, Patkai J, El Ayoubi M, Schmitz T, Moriette G, Jarreau PH (2010) Capnocytophaga species and preterm birth: case series and review of the literature. Clin Microbiol Infect 16:1539–1543. https://doi.org/10.1111/j.1469-0691.2009.03151.x

    Article  CAS  PubMed  Google Scholar 

  10. Piau C, Arvieux C, Bonnaure-Mallet M, Jolivet-Gougeon A (2013) Capnocytophaga spp. involvement in bone infections: a review. Int J Antimicrob Agents 41:509–515. https://doi.org/10.1016/j.ijantimicag.2013.03.001

    Article  CAS  PubMed  Google Scholar 

  11. Renzi F, Dol M, Raymackers A, Manfredi P, Cornelis GR (2015) Only a subset of C. canimorsus strains is dangerous for humans. Emerg Microbes Infect 4:e48. https://doi.org/10.1038/emi.2015.48. (Erratum in: Emerg Microbes Infect (2016) 5:e29)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. 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 

  13. Socransky SS, Holt SC, Leadbetter ER, Tanner ACR, Savitt E, Hammond BF (1979) Capnocytophaga: new genus of gram-negative gliding bacteria. III. Physiological characterization. Arch Microbiol 122:9–16. https://doi.org/10.1007/BF00408042

    Article  PubMed  Google Scholar 

  14. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849. https://doi.org/10.1099/00207713-44-4-846

    Article  CAS  Google Scholar 

  15. 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 

  16. 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 

  17. Yamamoto T, Kajiura S, Hirai Y, Watanabe T (1994) Capnocytophaga haemolytica sp. nov. and Capnocytophaga granulosa sp. nov., from human dental plaque. Int J Syst Bacteriol 44:324–329. https://doi.org/10.1099/00207713-44-2-324

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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 (2017M3A9B8065844) and in part by the KRIBB Research Initiative Program funded by the Ministry of Science, ICT, and Future Planning (2013M3A9A5076603).

Author information

Author notes

    Authors and Affiliations

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

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

    2. Oral Biology Research Institute, Chosun University, Gwangju, Republic of Korea

      Joong-Ki Kook

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

      Jayoung Paek, Yeseul Shin & Young-Hyo Chang

    4. Vitabio, Inc., Daejeon, Republic of Korea

      Hongik Kim

    5. Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea

      Si Hyun Kim

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

      Jeong Hwan Shin

    Authors
    1. Eojin Jo
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Soon-Nang Park
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Yun Kyong Lim
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Jayoung Paek
      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. Hongik Kim
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Si Hyun Kim
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Jeong Hwan Shin
      View author publications

      You can also search for this author in PubMed Google Scholar

    9. Young-Hyo Chang
      View author publications

      You can also search for this author in PubMed Google Scholar

    10. Joong-Ki Kook
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding authors

    Correspondence to Jeong Hwan Shin, Young-Hyo Chang or Joong-Ki Kook.

    Ethics declarations

    Conflict of interest

    The authors declare that they have no conflicts of interest.

    Additional information

    Eojin Jo and Soon-Nang Park have contributed equally to this study.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material 1 (DOCX 50 KB)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Jo, E., Park, SN., Lim, Y.K. et al. Capnocytophaga endodontalis sp. nov., Isolated from a Human Refractory Periapical Abscess. Curr Microbiol 75, 420–425 (2018). https://doi.org/10.1007/s00284-017-1397-5

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s00284-017-1397-5

    Search

    Navigation