An antimicrobial thiopeptide producing novel actinomycetes sp. nov., isolated from subsurface soil of arable land.

An antimicrobial producing Gram-positive, aerobic, nonmotile, and filamentous actinobacterial strain SKN60 was isolated from soil The isolate exhibited 99.3% and 99.0% identity with ATCC 31255 and TRM 44457, respectively, in 16S rRNA gene sequence analysis. However, the genome sequence displayed maximum ANI (88.45%) and AAI (85.61%) with TRM 44457. Similarly, the dDDH showed 33.7% identity with TRM 44457. It formed a cluster with TRM 44457 and ATCC 31255 in phylogenomic tree. Cell wall analysis revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine as major polar lipids and diaminopimelic acid as diagnostic diamino acid. Major fatty acids were iso-C, anteiso-C, and iso-C. The G+C content was found to be 72.3 mol%. Genome sequence analysis using antiSMASH database showed occurrence of a thiopeptide biosynthesis gene cluster with 94% similarity to berninamycin from UC5144. The mass of 1146 Da is identical with berninamycin. But subtle differences observed in leader peptide sequence of thiopeptide and berninamycin. Notably, is not validly reported and thus SKN60 is the only strain containing berninamycin BGC as no other phylogenetic relative had it. Additionally, strain SKN60 differed in phenotypic and genetic characteristics with all phylogenetic relatives of the genus . Therefore, it is proposed as a novel species with the name sp. nov. strain SKN60 (=MTCC 13163; = JCM 35768).