Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era

Jade L. L. Teng,Ying Tang,Patrick C. Y. Woo,Susanna K. P. Lau,Feng-Biao Guo,Yi Huang,Samson S. Y. Wong,Wen Wei,Jonathan H. K. Chen

doi:10.3389/fmicb.2016.01137

Abstract

Owing to the highly similar phenotypic profiles, protein spectra and 16S rRNA gene sequences observed between three pairs of Tsukamurella species (Tsukamurella pulmonis/Tsukamurella spongiae, Tsukamurella tyrosinosolvens/Tsukamurella carboxy-divorans, and Tsukamurella pseudospumae/Tsukamurella sunchonensis), we hypothesize that and the six Tsukamurella species may have been misclassified and that there may only be three Tsukamurella species. In this study, we characterized the type strains of these six Tsukamurella species by tradition DNA–DNA hybridization (DDH) and “digital DDH” after genome sequencing to determine their exact taxonomic positions. Traditional DDH showed 81.2 ± 0.6% to 99.7 ± 1.0% DNA–DNA relatedness between the two Tsukamurella species in each of the three pairs, which was above the threshold for same species designation. “Digital DDH” based on Genome-To-Genome Distance Calculator and Average Nucleotide Identity for the three pairs also showed similarity results in the range of 82.3–92.9 and 98.1–99.1%, respectively, in line with results of traditional DDH. Based on these evidence and according to Rules 23a and 42 of the Bacteriological Code, we propose that T. spongiae Olson et al. 2007, should be reclassified as a later heterotypic synonym of T. pulmonis Yassin et al. 1996, T. carboxydivorans Park et al. 2009, as a later heterotypic synonym of T. tyrosinosolvens Yassin et al. 1997, and T. sunchonensis Seong et al. 2008 as a later heterotypic synonym of T. pseudospumae Nam et al. 2004. With the advancement of genome sequencing technologies, classification of bacterial species can be readily achieved by “digital DDH” than traditional DDH.

Highlights

Classification of bacteria is performed on the basis of their phenotypic characteristics, such as the appearance of the bacterium under light microscope after Gram staining, growth requirements, biochemical tests, and chemotaxonomic characteristics
The six strains included in this study were type strains and obtained from four culture collections, with T. pulmonis CCUG 35732T and T. tyrosinosolvens CCUG 38499T obtained from Culture Collection, University of Gothenburg, Sweden (CCUG), T. spongiae DSM 44990T from Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Germany (DSMZ), and T. sunchonensis JCM 15929T, T. pseudospumae JCM 13375T, and T. carboxydivorans JCM 15482T from Japan Collection of Microorganisms (JCM), Japan
The major fatty acids compositions of strains T. pulmonis CCUG 35732T, T. spongiae DSM 44990T, T. tyrosinosolvens CCUG 38499T, T. carboxydivorans JCM 15482T, T. pseudospumae JCM 13375T, and T. sunchonensis JCM 15929T included C16:0, C18:1ω9c, and 10-methyl C18:0, which is typical of members of Tsukamurella (Table 2; Goodfellow and Kumar, 2012)

Summary

Introduction

Classification of bacteria is performed on the basis of their phenotypic characteristics, such as the appearance of the bacterium under light microscope after Gram staining, growth requirements, biochemical tests, and chemotaxonomic characteristics. DDH studies were performed between T. pulmonis CCUG 35732T and T. spongiae DSM 44990T, T. tyrosinosolvens CCUG 38499T and T. carboxydivorans JCM 15482T and T. pseudospumae JCM 13375T and T. sunchonensis JCM 15929T, respectively.

Results

Conclusion