Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level (original) (raw)

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.

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A Correction to this paper has been published: https://doi.org/10.1007/s00284-020-02133-w

A Correction to this paper has been published: https://doi.org/10.1007/s00284-021-02680-w

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Authors and Affiliations

  1. Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
    Joong-Ki Kook, Soon-Nang Park, Yun Kyong Lim, Eugene Cho & Eojin Jo
  2. Oral Biology Research Institute, Chosun University, Gwangju, Republic of Korea
    Joong-Ki Kook
  3. Macrogen Inc., Seoul, Republic of Korea
    Hansung Roh
  4. ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
    Yeseul Shin, Jayoung Paek & Young-Hyo Chang
  5. Department of Dental Hygiene, Chunnam Techno University, Gokseong-gun, Chunnam, Republic of Korea
    Hwa-Sook Kim
  6. Vitabio, Inc., Daejeon, Republic of Korea
    Hongik Kim
  7. Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
    Jeong Hwan Shin

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  1. Joong-Ki Kook
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  2. Soon-Nang Park
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Kook, JK., Park, SN., Lim, Y.K. et al. Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level.Curr Microbiol 74, 1137–1147 (2017). https://doi.org/10.1007/s00284-017-1296-9

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