In silico exploration of biosynthetic gene clusters in marine Streptomyces sp. and Nocardiopsis sp. from the western coast of India: Genome-based profiling using whole genome sequencing

Hithesh Kumar; Santhiya Vijayakumar; Neha Shintre; Vaijayanti Tamhane; Neelima Deshpande; Tushar Joshi; Shalini Mathpal; Anand Anbarasu; Sudha Ramaiah

doi:10.1016/j.jgeb.2025.100483

In silico exploration of biosynthetic gene clusters in marine Streptomyces sp. and Nocardiopsis sp. from the western coast of India: Genome-based profiling using whole genome sequencing

J Genet Eng Biotechnol. 2025 Jun;23(2):100483. doi: 10.1016/j.jgeb.2025.100483. Epub 2025 Mar 25.

Authors

Hithesh Kumar¹, Santhiya Vijayakumar¹, Neha Shintre², Vaijayanti Tamhane³, Neelima Deshpande⁴, Tushar Joshi⁵, Shalini Mathpal¹, Anand Anbarasu⁵, Sudha Ramaiah⁶

Affiliations

¹ Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014 Tamil Nadu, India; Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014 Tamil Nadu, India.
² Content Writer - Biology, JoVE, India.
³ Institute of Bioinformatics & Biotechnology, Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India.
⁴ Abasaheb Garware College, Pune, Maharashtra, India.
⁵ Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014 Tamil Nadu, India; Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014 Tamil Nadu, India.
⁶ Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014 Tamil Nadu, India; Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014 Tamil Nadu, India. Electronic address: sudhaanand@vit.ac.in.

Abstract

Actinomycetes are known for their ability to produce bioactive compounds with significant potency of antibiotics and natural product synthesis. With the growing threat of antimicrobial resistance, effective treatment for many infections has become increasingly challenging. Our study aims to explore the secondary metabolites produced by Actinomycetes isolated from marine sponge samples collected from the west coast of India using in silico approaches. The pre-processed high-throughput Illumina sequencing reads from six Actinomycete genomes showed high quality. Initial BLAST analysis followed by phylogenetic analysis revealed that isolates A01 and A96 closely matched Nocardiopsis sp., while isolates A03, A45, A57, and A90 were closely related to Streptomyces sp. In silico biosynthetic gene clusters (BGC) prediction indicated that Streptomyces sp. A57 had the highest number of BGCs, with 28 clusters identified. All Streptomyces sp. (A03, A45, A57, and A90) were predicted to contain a high number of terpene gene clusters. Ectoine was commonly found in all genomes of Streptomyces sp. and Nocardiopsis sp. Most of the BGCs identified in Actinomycete genomes revealed less similarity to the known BGCs, indicating their potential for producing novel secondary metabolites. The study reveals the genomic potential of the Actinomycetes by providing new insights into the ecological roles and potential applications of marine Actinomycetes, highlighting their promise as candidates for the discovery of new pharmaceuticals. Future investigations could benefit from integrating functional genomics and metabolomics to gain deeper insights into the metabolic pathways governing the biosynthesis of these secondary metabolites.

Keywords: Actinobacteria; Bioactive compounds; Biosynthetic gene clusters; Genome sequencing; Secondary metabolites.