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

Abstract

The linear genome of genus Streptomyces members 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 and in-silico analysis 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 bioactive Streptomyces species 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 five Streptomyces species, named as, Streptomyces violarus ASQP_29, S. rhizosphaerihabitans ASQP_78, S. fulvoviolaceus ASQP_80, S. mirabilis ASQP_98, and S. thajiwasiensis ASQP_92. Amongst these, one notable finding is the discovery of a novel species proposed as Streptomyces thajiwasiensis sp. nov. ASQP_92. In addition, our study presents the first genome announcement report and analysis for S. rhizosphaerihabitans ASQP_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. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/596145v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@15ac69corg.highwire.dtl.DTLVardef@a52f89org.highwire.dtl.DTLVardef@d3f8d6org.highwire.dtl.DTLVardef@75cce7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Genomic analysis and taxonomic affiliations of five bioactive Streptomyces species isolated from high altitudes of the North Western Himalaya C_FIG