Comparative genomics and taxonomic characterization of Streptomyces diversicolor sp. nov.: a novel species exhibiting intraspecific genomic divergence and biotechnological potential.

内容摘要

Two actinomycete strains, designated SSUT88AT and SSUT88R, were isolated from distinct soil samples in Nakhon Ratchasima, Thailand. While both belong the genus Streptomyces, they exhibited phenotypic divergence; strain SSUT88AT produced yellowish-white mycelia with potent antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), whereas SSUT88R produced red colonies with limited inhibitory effects. Genomic analyses confirmed the isolates are conspecific, sharing high ANI (99.99%) and dDDH (99.6%) values, yet exhibiting genomic divergence; the 11.2 Mb genome of SSUT88AT exceeded the 8.3 Mb genome of SSUT88R. Comparative genome mining revealed this variation extended to secondary metabolism, as SSUT88AT encoded a more diverse biosynthetic potential. Furthermore, ANI and dDDH values against the closest phylogenomic neighbors were below species thresholds (79.69-87.55% and 25.7-30.2%, respectively), supporting their classification as a novel species. Metagenomic screening using IMNGS and Branchwater revealed a predominantly terrestrial distribution. While the broader lineage appeared ecologically versatile, high-confidence conspecific populations (cANI ≥0.97) were restricted to soil and rhizosphere habitats, with evidence of regional persistence in Thailand. Chemotaxonomic characteristics including ll-diaminopimelic acid, MK-9(H8) and whole-cell sugars contained ribose, mannose, and glucose. The polar lipid profile included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, and an unidentified glycolipid. Major fatty acids included iso-C16:0, anteiso-C15:0, anteiso-C17:0 and iso-C15:0. Based on this polyphasic evidence, strains SSUT88AT and SSUT88R are proposed to represent a novel species, for which the name Streptomyces diversicolor sp. nov. is proposed. The type strain is SSUT88AT (InaCC A1220T = TISTR 10074T). Strain SSUT88R is deposited as InaCC A1221 = TISTR 10075.