Comparative genomics studies provide insights into the taxonomic classification and secondary metabolic potential of five bioactiveStreptomycesspecies isolated from the North-Western Himalaya

Abstract

AbstractThe linear genome of genusStreptomycesmembers has the potential to encode diverse and novel biosynthetic gene clusters of invaluable antimicrobial and therapeutic significance. The use of limited taxonomic markers makes the precise identification of these miracle microbes very challenging. In the ongoing omics era, genome sequencing andin-silicoanalysis of these potential antibiotic producers provide deeper insights into their taxonomy, functional capabilities, and potential for antibiotic production. Here this study presents a multifaceted approach for proper taxonomic identification and genomic and bioinformatic analysis of five bioactiveStreptomycesspecies collected from different sampling sites in the high-altitude oligotrophic North-Western Himalaya, Kashmir, India. We used polyphasic taxonomic classification approaches, such as phylogenetic markers (16S rDNA and gyrase B), average nucleotide identity (ANI) estimation, and digital DNA-DNA hybridization (dDDH), which revealed accurate taxonomic placement of fiveStreptomycesspecies, named as,Streptomyces violarusASQP_29,S. rhizosphaerihabitansASQP_78,S. fulvoviolaceusASQP_80,S. mirabilisASQP_98, andS. thajiwasiensisASQP_92. Amongst these, one notable finding is the discovery of a novel species proposed asStreptomyces thajiwasiensissp. nov. ASQP_92. In addition, our study presents the first genome announcement report and analysis forS. rhizosphaerihabitansASQP_78. Genomic annotation highlighted the presence of an exceptionally high number of poorly characterized genes and hypothetical proteins, indicating their potential for undiscovered biotechnological applications. Clusters of orthologous groups (COG) and gene ontology (GO) analysis provided insights into their varied functional roles in metabolism, signaling, information storage and secondary metabolite biosynthesis. Domain-based functional characterization further detailed their involvement in various biological processes particularly in antibiotic biosynthesis, transport, and resistance. Biosynthetic gene clusters (BGC) analysis demonstrated their diverse metabolite biosynthetic capabilities and identified both unique and conserved BGCs emphasizing the species-specific roles in bioactive metabolite production and the potential of orphan BGCs in novel drug discovery.Graphical abstract:Genomic analysis and taxonomic affiliations of five bioactiveStreptomycesspecies isolated from high altitudes of the North Western Himalaya