Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level
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Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level Joong-Ki Kook1,2 • Soon-Nang Park1 • Yun Kyong Lim1 • Eugene Cho1 • Eojin Jo1 • Hansung Roh3 • Yeseul Shin4 • Jayoung Paek4 • Hwa-Sook Kim5 Hongik Kim6 • Jeong Hwan Shin7 • Young-Hyo Chang4
•
Received: 24 April 2017 / Accepted: 29 June 2017 Ó Springer Science+Business Media, LLC 2017
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%) Electronic supplementary material The online version of this article (doi:10.1007/s00284-017-1296-9) contains supplementary material, which is available to authorized users. & Joong-Ki Kook [email protected] & Young-Hyo Chang [email protected]
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.
1
Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
2
Oral Biology Research Institute, Chosun University, Gwangju, Republic of Korea
3
Macr
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