Unveiling the Biosynthetic Landscape of Endophytic Streptomyces sp. PGLac3x via Growth Optimization and Whole-Genome...

The re-isolation of already known compounds in natural product research is a significant challenge. To address this, genome mining and optimization studies serve as dereplication strategies. This study focused on optimizing the growth and analyzing the genome of endophytic Streptomyces sp. strain PGLac3x isolated from Piper guineense. The growth optimization study assessed mycelium dry weight in mg/100 mL of media. Genomic DNA was extracted and 16S rRNA gene and whole genome sequencing (WGS) were performed via Sanger and Illumina Miseq technologies. Comprehensive genome analysis was conducted using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database, and antibiotic and secondary metabolite analysis shell (antiSMASH) tool version 6.1.1. PGLac3x optimally grew on potato dextrose media at 32 °C, pH 7-8, and 2% salt concentration over 16 days. Based on the 16S rRNA gene blast, PGLac3x is closely related to Streptomyces sampsonii ATCC 25495 ^T (99.31%), Streptomyces albidoflavus NBRC 100770 ^T (99.30%) and Streptomyces champavatii NRRL B-5682 ^T (99.24%). The genome size is 6.96 Mb, with 59 biosynthetic gene clusters (BGCs) and a guanine-cytosine content of 73.46%. The genome contained 6477 coding sequences (CDS), 50 tRNAs, and 3 rRNAs, along with genes for polyketide synthases (T1PKS, T2PKS, T3PKS), terpenes, non-ribosomal peptide synthetases (NRPS), and ribosomally synthesized and post-translationally modified peptides (RiPPs). PGLac3x's phylogenetic distinctiveness and low gene similarity to the BGCs of known compounds suggests its potential to synthesize of distinct compounds. This study unveiled the biosynthetic potential, genetic diversity of secondary metabolites of Streptomyces sp. PGLac3x and provided a fresh insight for the exploration of new bioactive compounds.

The online version contains supplementary material available at 10.1007/s12088-025-01532-6.