Genomic and Phenotypic Characterization of Streptomyces marxii sp. nov., Producer of Kinanthraquinone B

Describing novel microbial species opens access to uncharted biosynthetic gene clusters and their associated secondary metabolites, offering fresh opportunities in the search for new antibiotics urgently needed to combat multidrug resistance. In this study, we describe a new species of Streptomyces, S. marxii sp. nov. (type strain VKM Ac-3100), an actinobacterium isolated from soil in the Yaroslavl Region of Russia. Using a polyphasic taxonomic approach that included whole-genome sequencing (WGS), we found that the strain’s average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values relative to its closest relative, S. maoxianensis, were 92.53% and 47.9%, respectively. Both values fell significantly below the species delimitation thresholds. Functional screening using the pDualrep2 dual fluorescent reporter system identified a unique SOS-silent antimicrobial profile characterised by growth inhibition without induction of the SOS response or translation stress. High-resolution mass spectrometry (HRMS) and genomic mining revealed that this activity is linked to the production of kinanthraquinone B ([M+H]+ m/z 275.0550), a rare polycyclic aromatic polyketide. Genomic analysis identified a specialised type II polyketide synthase (T2PKS) biosynthetic gene cluster (BGC) with evidence of acquisition via horizontal gene transfer (HGT). Our findings characterise S. marxii as a promising natural producer of rare catalytic inhibitors of DNA topoisomerases II and IV, offering a scaffold for the development of antibiotics with potentially lower genotoxicity.