Advertisement

Fusobacterium pseudoperiodonticum sp. nov., Isolated from the Human Oral Cavity

  • Soon-Nang Park
  • Yun Kyong Lim
  • Jeong Hwan Shin
  • Hwa-Sook Kim
  • Eojin Jo
  • Won-Pyo Lee
  • Yeseul Shin
  • Jayoung Paek
  • Young-Hyo Chang
  • Hongik Kim
  • Joong-Ki KookEmail author
Article
  • 24 Downloads

Abstract

In the present study, three strains (ChDC F213T, ChDC F251, and ChDC F267) were classified as novel species of genus Fusobacterium based on average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis and chemotaxonomic characterization. 16S rDNA sequences of strains ChDC F213T, ChDC F251, and ChDC F267 were highly similar to that of F. periodonticum ATCC 33693T (99.6, 99.4, and 99.4%, respectively). ANI and GGD values of the three isolates with F. periodonticum ATCC 33693T ranged from 92.5 to 92.6% and 47.7 to 48.2%, respectively. Considering that threshold of ANI and GGD values for bacterial species discrimination are 95–96% and 70%, respectively, these results indicate that the three isolates represent a novel Fusobacterium species. DNA G + C contents of the three isolates were 28.0 mol% each. Cellular fatty acid analysis of these strains revealed that C14:0, C16:0, and C16:1 ω6c/C16:1 ω7c were major fatty acids. Therefore, these three strains are novel species belonging to genus Fusobacterium. Strain ChDC F213T (= KCOM 1259T = KCTC 5677T = JCM 33009T) is the type strain of a novel species of genus Fusobacterium, for which a name of Fusobacterium pseudoperiodonticum sp. nov. is proposed.

Notes

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 (No. 2017M3A9B8065844) and in part by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (2017R1A2B4004894).

Supplementary material

284_2019_1675_MOESM1_ESM.docx (57 kb)
Supplementary material 1 (DOCX 57 kb)
284_2019_1675_MOESM2_ESM.pptx (83 kb)
Maximum likelihood (A) and the minimum evolution (B) phylogenetic tree based on 16S ribosomal genes of strains. GenBank accession number of 16S rDNA of each strain was written in parenthesis. Stability of phylogenetic trees was assessed by a bootstrap analysis of 1000 replicates using MEGA version 6.06 [15]. Bars indicate 0.002 (A) or 0.002 (B) changes per nucleotide position. Supplementary material 2 (PPTX 83 kb)

References

  1. 1.
    Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134.  https://doi.org/10.4056/sigs.531120 CrossRefGoogle Scholar
  2. 2.
    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 CrossRefGoogle Scholar
  3. 3.
    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 CrossRefGoogle Scholar
  4. 4.
    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 CrossRefGoogle Scholar
  5. 5.
    Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  6. 6.
    Jo E, Park SN, Lim YK, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Chang YH, Kook JK (2018) Capnocytophaga endodontalis sp. nov., isolated from a human refractory periapical abscess. Curr Microbiol 75:420–425.  https://doi.org/10.1007/s00284-017-1397-5 CrossRefGoogle Scholar
  7. 7.
    Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  8. 8.
    Kook JK, Park SN, Lim YK, Cho E, Jo E, Roh H, Shin Y, Paek J, Kim HS, Kim H, Shin JH, Chang YH (2017) Genome-based reclassification of Fusobacterium nucleatum subspecies at the species level. Curr Microbiol 74:1137–1147.  https://doi.org/10.1007/s00284-017-1296-9 CrossRefGoogle Scholar
  9. 9.
    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 CrossRefGoogle Scholar
  10. 10.
    Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 14:60.  https://doi.org/10.1186/1471-2105-14-60 CrossRefGoogle Scholar
  11. 11.
    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 CrossRefGoogle Scholar
  12. 12.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  13. 13.
    Slots J, Potts TV, Mashimo PA (1983) Fusobacterium periodonticum, a new species from the human oral cavity. J Dent Res 62:960–963.  https://doi.org/10.1177/00220345830620090901 CrossRefGoogle Scholar
  14. 14.
    Strauss J, White A, Ambrose C, McDonald J, Allen-Vercoe E (2008) Phenotypic and genotypic analyses of clinical Fusobacterium nucleatum and Fusobacterium periodonticum isolates from the human gut. Anaerobe 14:301–309.  https://doi.org/10.1016/j.anaerobe.2008.12.003 CrossRefGoogle Scholar
  15. 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 CrossRefGoogle Scholar
  16. 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 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Soon-Nang Park
    • 1
  • Yun Kyong Lim
    • 1
  • Jeong Hwan Shin
    • 2
  • Hwa-Sook Kim
    • 3
  • Eojin Jo
    • 1
  • Won-Pyo Lee
    • 1
  • Yeseul Shin
    • 4
  • Jayoung Paek
    • 4
  • Young-Hyo Chang
    • 4
  • Hongik Kim
    • 5
  • Joong-Ki Kook
    • 1
    Email author
  1. 1.Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of DentistryChosun UniversityGwangjuRepublic of Korea
  2. 2.Department of Laboratory MedicineInje University College of MedicineBusanRepublic of Korea
  3. 3.Department of Dental HygieneChunnam Techno UniversityChunnamRepublic of Korea
  4. 4.ABS Research Support Center, KRIBBDaejeonRepublic of Korea
  5. 5.Vitabio, Inc.DaejeonRepublic of Korea

Personalised recommendations