Reclassification of Nocardia Species Based on Whole Genome Sequence and Associated Phenotypic Data

J Antibiot (Tokyo). 2018 Jul;71(7):633-641. doi: 10.1038/s41429-018-0043-1. Epub 2018 Apr 4.

Abstract

Type strains of 72 validated Nocardia species were phylogenetically analyzed based on the multilocus sequence analysis (MLSA) concatenated atpD-groL1-groL2-recA-rpoA-secY-sodA-ychF. Furthermore, their similarity based on digital DNA-DNA hybridization (dDDH) was calculated. Nocardia soli, Nocardia cummidelens and Nocardia salmonicida, Nocardia nova and Nocardia elegans, Nocardia exalbida and Nocardia gamkensis, and Nocardia coubleae and Nocardia ignorata formed coherent clades, respectively. Moreover, each set showed over 70% relatedness by dDDH and shared common phenotypic characteristics. Therefore, we propose a reclassification of Nocardia soli and Nocardia cummidelens as a later heterotypic synonym of Nocardia salmonicida, Nocardia elegans as a later heterotypic synonym of Nocardia nova, Nocardia gamkensis as a later heterotypic synonym of Nocardia exalbida, and Nocardia coubleae as a later heterotypic synonym of Nocardia ignorata.

MeSH terms

  • Bacterial Typing Techniques
  • DNA, Bacterial / analysis
  • DNA, Bacterial / genetics
  • Genome, Bacterial / genetics
  • Genotype
  • Multilocus Sequence Typing
  • Nocardia / classification*
  • Nocardia / genetics*
  • Phenotype
  • Phylogeny
  • Whole Genome Sequencing

Substances

  • DNA, Bacterial