Genome based analyses reveals the presence of heterotypic synonyms and subspecies in Bacteria and Archaea

Abstract

AbstractTerm heterotypic synonym refers to different names have been associated with different type strains, however from the opinion of a bacteriologist, different names belongs to the same taxon and term subspecies refers to strains and genetically close organisms that were diverging phenotypically. In this study, sequenced and publicly available genomes in the Edgar 2.0 server were carefully analysed and based on high (>98 %) amino acid identity value, synonyms were putatively identified. The 16S rRNA gene sequence of those species were used for the construction of maximum likelihood based phylogenetic trees to infer the genetic closeness or distance by examining the tree topology and clustering of the organisms within clades. They were further subjected to overall genome related indices like digital DNA-DNA hybridization, average nucleotide identity to confirm the presence of synonyms or subspecies with phenotypic data support. The outcome of this polyphasic taxonomic re-analysis was identification of 40 later heterotypic synonyms and 13 subspecies spread over phylum Actinobacteria, Bacteroidetes, Firmicutes, Nitrospirae, Proteobacteria and Thermotogae and in domain Archaea.