The correlation between the gyrB genetic distance and the digital DNA-DNA hybridization value for the genus Micromonospora and taxonomic studies on Micromonospora cynarae sp. nov

Abstract

An early study on Micromonospora species indicated that a gyrB (DNA gyrase subunit B) genetic distance about 0.014 would equal to the 70% value in DNA hybridization value. However, based on the corresponding relation of gyrB genetic distance and dDDH (digital DNA–DNA hybridization) among 40 type strains of the genus Micromonospora , it was proposed that, when the gyrB genetic distance between a novel Micromonospora strain and a reference strain was less than 0.009, the novel strain should be considered a strain of the same species as the reference strain despite nothingness of such paired strains to date; when the gyrB genetic distance was greater than 0.015, the novel strain could be regarded as a new Micromonospora species; when the gyrB genetic distance was between 0.009 (included) and 0.015 (included), ANI (average nucleotide identity) or dDDH value between strains must be carried out in order to confirm a new species. Based on these results, the taxonomic status of an actinobacterial strain HUAS YX12 T , isolated from the rhizosphere soil of Cynara scolymus , was determined using a polyphasic taxonomic method. Sequence analysis of the 16S rRNA gene indicated that HUAS YX12 T shared the highest 16S rRNA gene sequence similarities with Micromonospora fluminis A38 T (99.7%) and M. tulbaghiae DSM 45142 T (99.4%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HUAS YX12 T is closely related to M. fluminis A38 T . However, phylogenetic trees based on gyrB gene, whole-genome sequences and 120 core gene sequences revealed that the closest phylogenetic neighbor of strain HUAS YX12 T was M. tulbaghiae DSM 45142 T , not M. fluminis A38 T . ANI, dDDH and AAI (average amino acid identity) values between strain HUAS YX12 T and above-mentioned two strains were 91.9–94.4% and 51.0–63.9%, respectively, less than 95–96%, 70% and 95% cut-off points recommended for delineating species. Consequently, based on the phenotypic and genotypic data, it is concluded that strain HUAS YX12 T (= MCCC 1K09226 T = JCM 37023 T ) represents a novel species of the genus Micromonospora , for which the name Micromonospora cynarae sp. nov. is proposed.

The authors' abstract, as published at the source. BMC Microbiology, 2026 · DOI ↗