Abstract
The taxonomic position of novel bianthraquinone antibiotic producer Streptomyces strain RA-WS2, a soil isolate from Shivalik region of NW Himalayas, India, has been described. The isolate produces Setomimycin as a major secondary metabolite under defined submerged fermentation conditions. 16S rRNA partial gene sequencing of the isolate indicated its closest similarity (99.4%) with Streptomyces cyaneochromogenes, followed by Streptomyces aquilus. However, the morphological characteristics i.e. colony colour, mycelium and spore chain arrangement were found to be close to Streptomyces aquilus. Therefore, a polyphasic approach was used for taxonomic positioning of the isolate. The Whole genome based similarity with 88.4% dDDH value, 98.65% ANI and 96.99% AAI value indicated its closest identity with Streptomyces justiciae. The taxonomic characteristics such as white colony with smooth surface, cylindrical spores arranged in straight chain, diffusible melanin production, high salt tolerance, 16S rRNA gene sequencing and phylogenomic studies, led to the identification of the strain as Streptomyces justiciae RA-WS2. The predicted biosynthetic gene clusters further confirmed the presence of the BGC for setomimycin biosynthesis in Streptomyces justiciae strain RA-WS2.
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Data availability
This whole-genome shotgun project has been deposited at GenBank under the accession number GCF_024508375.2. The raw reads are available in BioProject number PRJNA842579. The Biosample number is SAMN28688843. The version explained in current text is JAMXPJ000000000.2, ranging from JAMXPJ020000001-JAMXPJ020000076.
Abbreviations
- AAI:
-
Average amino-acid identity
- ANI:
-
Average nucleotide identity
- antiSMASH:
-
Antibiotics and secondary metabolite analysis shell
- BGC:
-
Biosynthetic gene cluster
- BLAST:
-
Basic Local Alignment Search Tool
- dDDH:
-
Digital DNA–DNA hybridization
- EtBr:
-
Ethidium bromide
- ISP:
-
International Streptomyces project
- IToL:
-
Interactive Tree of Life
- MEGA:
-
Molecular Evolutionary Genetics Analysis
- NCBI:
-
National Center for Biotechnology Information
- NW Himalayas:
-
North Western Himalayas
- RDP:
-
Ribosomal database project
- PBS:
-
Phosphate buffer saline
- SCA:
-
Starch casein agar
- SEM:
-
Scanning electron microscopy
- SRA:
-
Sequence read archive
- SSY:
-
Starch soyabean meal yeast extract
- STAG:
-
Species tree inference all gene method
- TAE:
-
Tris acetate EDTA
- TYGS:
-
Type strain genome server
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Acknowledgements
The authors are thankful to Director, IIIM for his interest. RSM and DC are thankful to ICMR and UGC for their respective fellowships. The manuscript bears institutional communication number CSIR-IIIM/IPR/00499.
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The authors did not receive financial support for submitted work, RSM and DC are thankful for fellowship from ICMR and UGC respectively.
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RSM performed all the wet lab experiments and wrote original manuscript, DC performed all the bioinformatics analysis and contributed in writing the manuscript, AC conceptualized, supervised, finalized the study and corrected the manuscript.
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Manhas, R.S., Chander, D. & Chaubey, A. Identification and taxonomy of Streptomyces justiciae strain RA-WS2: a novel setomimycin producing actinobacterium. 3 Biotech 13, 47 (2023). https://doi.org/10.1007/s13205-023-03459-5
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DOI: https://doi.org/10.1007/s13205-023-03459-5