Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies - PubMed (original) (raw)

doi: 10.1128/JCM.01631-09. Epub 2009 Dec 2.

Dae-Sil Lee, Young-Hyo Chang, Min Jung Kim, Sukhoon Koh, Joongsu Kim, Jin-Hyo Seong, Soo Keun Song, Hwan Seon Shin, Jae-Beum Son, Min Young Jung, Soon-Nang Park, So Young Yoo, Ki Woon Cho, Dong-Kie Kim, Seonghoon Moon, Dooil Kim, Yongseok Choi, Byung-Ock Kim, Hyun-Seon Jang, Chun Sung Kim, Chan Kim, Son-Jin Choe, Joong-Ki Kook

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Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies

Hwa-Sook Kim et al. J Clin Microbiol. 2010 Feb.

Abstract

Fusobacterium nucleatum is classified into five subspecies that inhabit the human oral cavity (F. nucleatum subsp. nucleatum, F. nucleatum subsp. polymorphum, F. nucleatum subsp. fusiforme, F. nucleatum subsp. vincentii, and F. nucleatum subsp. animalis) based on several phenotypic characteristics and DNA-DNA hybridization patterns. However, the methods for detecting or discriminating the clinical isolates of F. nucleatum at the subspecies levels are laborious, expensive, and time-consuming. Therefore, in this study, the nucleotide sequences of the RNA polymerase beta-subunit gene (rpoB) and zinc protease gene were analyzed to discriminate the subspecies of F. nucleatum. The partial sequences of rpoB (approximately 2,419 bp), the zinc protease gene (878 bp), and 16S rRNA genes (approximately 1,500 bp) of the type strains of five subspecies, 28 clinical isolates of F. nucleatum, and 10 strains of F. periodonticum (as a control group) were determined and analyzed. The phylogenetic data showed that the rpoB and zinc protease gene sequences clearly delineated the subspecies of F. nucleatum and provided higher resolution than the 16S rRNA gene sequences in this respect. According to the phylogenetic analysis of rpoB and the zinc protease gene, F. nucleatum subsp. vincentii and F. nucleatum subsp. fusiforme might be classified into a single subspecies. Five clinical isolates could be delineated as a new subspecies of F. nucleatum. The results suggest that rpoB and the zinc protease gene are efficient targets for the discrimination and taxonomic analysis of the subspecies of F. nucleatum.

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Figures

FIG. 1.

FIG. 1.

Phylogenetic trees based on the partial nucleotide sequences of (A) 16S rRNA genes (about 1.5 kb), (B) rpoB (about 2,419 bp out of 3,555 bp), and (C) the zinc protease gene (878 bp out of 1,227 bp) of type strains and clinical isolates of Fusobacterium nucleatum and Fusobacterium periodonticum. The resulting tree topology was evaluated by bootstrap analyses of the neighbor-joining tree based on 1,000 resamplings.

FIG. 1.

FIG. 1.

Phylogenetic trees based on the partial nucleotide sequences of (A) 16S rRNA genes (about 1.5 kb), (B) rpoB (about 2,419 bp out of 3,555 bp), and (C) the zinc protease gene (878 bp out of 1,227 bp) of type strains and clinical isolates of Fusobacterium nucleatum and Fusobacterium periodonticum. The resulting tree topology was evaluated by bootstrap analyses of the neighbor-joining tree based on 1,000 resamplings.

FIG. 1.

FIG. 1.

Phylogenetic trees based on the partial nucleotide sequences of (A) 16S rRNA genes (about 1.5 kb), (B) rpoB (about 2,419 bp out of 3,555 bp), and (C) the zinc protease gene (878 bp out of 1,227 bp) of type strains and clinical isolates of Fusobacterium nucleatum and Fusobacterium periodonticum. The resulting tree topology was evaluated by bootstrap analyses of the neighbor-joining tree based on 1,000 resamplings.

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