Genome-based taxonomic classification within the family Thermoactinomycetaceae

Int J Syst Evol Microbiol. 2019 Jul;69(7):2028-2036. doi: 10.1099/ijsem.0.003425. Epub 2019 May 8.


The family Thermoactinomycetaceaecomprises 43 validly published species, which were identified by a polyphasic taxonomic study based on molecular phylogenetics, physiological and biochemical characteristics. However, phylogenetic analysis merely based on 16S rRNA gene sequences cannot infer a robust and reliable phylogeny. For disentangling the phylogenetic relationships among members of this family, we used a large collection of genome data and the approach of phylogenomics, to re-examine their taxonomy. The topologies of phylogenomic trees are different from those of the 16S rRNA gene sequences. In addition, based on the average nucleotide identity, digital DNA-DNA hybridization, phenotypic and biochemical characteristics, we found that Laceyella sediminis should be reclassified as a later heterotypic synonym of Laceyella tengchongensis; and reclassified Thermoactinomyces guangxiensis as Paenactinomyces guangxiensis gen. nov., comb. nov.; and establish Novibacillaceae fam. nov. to accommodate the genus Novibacillus as the type genus. In addition, compared to values calculated directly from genome sequences, the genomic DNA G+C contents mentioned in some species descriptions are too imprecise; and the corrected G+C content values have a significantly better fit to the phylogeny. Thus, the corresponding emendations of species descriptions are also proposed. In this paper, phylogenomics has been used to resolve the classification of the family Thermoactinomycetaceae.

Keywords: family Thermoactinomycetaceae; gene content; phylogenomics; supermatrix.

MeSH terms

  • Bacillales / classification*
  • Bacterial Typing Techniques
  • Base Composition
  • DNA, Bacterial / genetics
  • Nucleic Acid Hybridization
  • Peptidoglycan / chemistry
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Vitamin K 2 / analogs & derivatives
  • Vitamin K 2 / chemistry


  • DNA, Bacterial
  • Peptidoglycan
  • RNA, Ribosomal, 16S
  • Vitamin K 2
  • menaquinone 7