Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5

Abstract

Elucidating microorganism genomes holds great promise for the discovery of novel bioactive compounds with diverse applications. In this study, we investigated the complete genome of Xenorhabdus stockiae strain RT25.5, which is recognized for its symbiotic association with entomopathogenic nematodes (EPNs) and its biosynthesis of secondary metabolites relevant to the pharmaceutical industry, agriculture, and ecology. Through high-throughput genome sequencing, assembly, and annotation, followed by advanced bioinformatics analyses, we elucidated the genetic basis of its antimicrobial potential. Our analysis revealed 21 putative biosynthetic gene clusters (BGCs) associated with bioactive compound production. Notably, LC‒MS/MS analysis of the bacterial cultures confirmed the presence of diverse secondary metabolites, which aligned with the in silico predictions. Furthermore, the crude extract of X. stockiae strain RT25.5 exhibited antibacterial activity against 10 pathogenic bacterial isolates, highlighting its potential as a source of novel antimicrobial agents. This study highlights the importance of X. stockiae as a promising candidate for natural product discovery. The integration of genome mining, LC‒MS/MS, and bioassays not only advances our understanding of its biosynthetic capabilities but also paves the way for the development of novel antimicrobial agents. Future research should focus on the isolation and structural characterization of key metabolites, as well as evaluations of their mechanisms of action against multidrug-resistant pathogens.