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Current Microbiology

, Volume 74, Issue 10, pp 1137–1147 | Cite as

Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level

  • Joong-Ki KookEmail author
  • Soon-Nang Park
  • Yun Kyong Lim
  • Eugene Cho
  • Eojin Jo
  • Hansung Roh
  • Yeseul Shin
  • Jayoung Paek
  • Hwa-Sook Kim
  • Hongik Kim
  • Jeong Hwan Shin
  • Young-Hyo ChangEmail author
Article

Abstract

Fusobacterium nucleatum is classified as four subspecies, subsp. nucleatum, polymorphum, vincentii, and animalis, based on DNA–DNA hybridization (DDH) patterns, phenotypic characteristics, and/or multilocus sequence analysis (MLSA). The gold standards for classification of bacterial species are DDH and 16S ribosomal RNA gene (16S rDNA) sequence homology. The thresholds of DDH and 16S rDNA similarity for delineation of bacterial species have been suggested to be >70 and 98.65%, respectively. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis based on genome sequences were recently introduced as a replacement for DDH to delineate bacterial species with ANI (95–96%) and GGD (70%) threshold values. In a previous study, F. hwasookii was classified as a new species based on MLSA and DDH results. 16S rDNA similarity between F. hwasookii type strain and F. nucleatum subspecies type strains was higher than that between F. nucleatum subspecies type strains. Therefore, it is possible that the four F. nucleatum subspecies can be classified as Fusobacterium species. In this study, we performed ANI and GGD analyses using the genome sequences of 36 F. nucleatum, five F. hwasookii, and one Fusobacterium periodonticum strain to determine whether the four F. nucleatum subspecies could be classified as species using OrthoANI and ANI web-based softwares provided by ChunLab and Kostas lab, respectively, and GGD calculator offered by German Collection of Microorganisms and Cell Cultures. ANI values calculated from OrthoANI and ANI calculators between the type strains of F. nucleatum subspecies ranged from 89.80 to 92.97 and from 90.40 to 91.90%, respectively. GGD values between the type strains of F. nucleatum subspecies ranged from 42.3 to 46.0%. ANI and GGD values among strains belonging to the same F. nucleatum subspecies, subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis were >96 and >68.2%, respectively. These results strongly suggest that F. nucleatum subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis should be classified as F. nucleatum, F. polymorphum, F. vincentii, and F. animalis, respectively.

Notes

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

284_2017_1296_MOESM1_ESM.docx (39 kb)
Supplementary material 1 (DOCX 38 kb)

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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  • Joong-Ki Kook
    • 1
    • 2
    Email author
  • Soon-Nang Park
    • 1
  • Yun Kyong Lim
    • 1
  • Eugene Cho
    • 1
  • Eojin Jo
    • 1
  • Hansung Roh
    • 3
  • Yeseul Shin
    • 4
  • Jayoung Paek
    • 4
  • Hwa-Sook Kim
    • 5
  • Hongik Kim
    • 6
  • Jeong Hwan Shin
    • 7
  • Young-Hyo Chang
    • 4
    Email author
  1. 1.Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of DentistryChosun UniversityGwangjuRepublic of Korea
  2. 2.Oral Biology Research InstituteChosun UniversityGwangjuRepublic of Korea
  3. 3.Macrogen Inc.SeoulRepublic of Korea
  4. 4.ABS Research Support CenterKRIBBDaejeonRepublic of Korea
  5. 5.Department of Dental HygieneChunnam Techno UniversityChunnamRepublic of Korea
  6. 6.Vitabio, Inc.DaejeonRepublic of Korea
  7. 7.Department of Laboratory MedicineInje University College of MedicineBusanRepublic of Korea

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