New Insights Into the Threshold Values of Multi-Locus Sequence Analysis, Average Nucleotide Identity and Digital DNA–DNA Hybridization in Delineating Streptomyces Species

Abstract

Multi-locus sequence analysis (MLSA) has been proved to be a useful method for Streptomyces identification and MLSA distance of 0.007 is considered as the boundary value. However, we found that MLSA distance of 0.007 might be insufficient to act as a threshold according to the correlations among average nucleotide identity based on MuMmer ultra-rapid aligning tool (ANIm), digital DNA–DNA hybridization (dDDH) and MLSA from the 80 pairs of Streptomyces species; in addition, a 70% dDDH value did not correspond to a 95∼96% ANIm value but approximately to 96.7% in the genus Streptomyces. Based on our analysis, it was proposed that when the MLSA distance value between a novel Streptomyces and a reference strain was < 0.008, the novel strain could be considered as a heterotypic synonym of the reference strain; when the MLSA distance value was ≥ 0.014, the novel strain could be regarded as a new Streptomyces species; when the MLSA distance value was between 0.008 and 0.014 (not included), the dDDH or ANIm value between a new strain and a reference strain must be calculated in order to determine the taxonomic status of a novel strain. In this context, a 70% dDDH or 96.7% ANIm value could act as the threshold value in delineating Streptomyces species, but if the dDDH or ANIm value was less than but close to 70 or 96.7% cut-off point, the taxonomic status of a novel strain could only be determined by a combination of phenotypic characteristics, chemotaxonomic characteristics and phylogenomic analysis.

Streptomyces solincola sp. nov., isolated from soil in Malaysia

“…The comparative analysis based on 16S rRNA gene sequence similarity of strain T5 T showed highest sequence similarity (99.0 % pairwise similarity) to Streptomyces lichenis LCR6-01 T (LC360144). The MLSA distance between strain T5 T and S. lichenis LCR6-01 T was 0.036 which was above the recommended threshold (≥0.014) for species delineation [25]. Similarly, the strain T5 T and S. lichenis LCR6-01 T gene sequences of gyrB, recA, rpoB and trpB used in MLSA also showed pairwise sequence similarities of 96.6, 95.0, 98.2 and 96.1 %, respectively, which were lower than the recommended threshold for species delineation (gyrB, <99.0 %; recA, <99.5 %; rpoB, <99.6 % trpB, <97.9 %) [26].…”

“…The MLSA distance between strain T5 T and S. lichenis LCR6-01 T was 0.036 which was above the recommended threshold (≥0.014) for species delineation [25]. Similarly, the strain T5 T and S.…”

Synergy between Genome Mining, Metabolomics, and Bioinformatics Uncovers Antibacterial Chlorinated Carbazole Alkaloids and Their Biosynthetic Gene Cluster fromStreptomyces tubbatahanensissp. nov., a Novel Actinomycete Isolated from Sulu Sea, Philippines

“…2B ). In a recent study, a 70% dDDH corresponded to approximately 96.7% and not the 95 to 96% cutoff point in delineating Streptomyces species ( 27 ). These findings suggested that S. tubbatahanensis DSD3025 T is a novel species based on the MLSA, dDDH, and orthoANI values between S. tubbatahanensis DSD3025 T and its closest match, S. diacarni LHW51701 T .…”

Streptomyces longhuiensis sp. nov, a novel species isolated from soil of Lilium brownii in Hunan Province, PR China

“…Meanwhile, the ANI and dDDH values between the whole-genome sequences of strain BH-MK-02 T and S. aureus CGMCC 4.1833 T were 78.1 and 23.2 %, respectively, below the 96.7 and 70 % cut-off points recommended for delineating Streptomyces species [44, 45], suggesting that BH-MK-02 T represents a novel species of the genus Streptomyces . This result was further confirmed by phenotypic differences between strain BH-MK-02 T and S.…”