Biosynthetic Gene Cluster Mining and In Vitro Evaluation of the Antimicrobial and Cytotoxic Potential of Xenorhabdus thuongxuanensis

Xenorhabdus species are prolific producers of diverse bioactive natural products. However, the genomic characteristics, biosynthetic potential, and biological activities of Xenorhabdus thuongxuanensis remain poorly characterized. This study aimed to characterize the genomic features and biosynthetic potential of X. thuongxuanensis strains KLK17.5 and KLK18.1 through comparative genomic analyses and to evaluate the antibacterial, antifungal, and cytotoxic activities of their crude extracts. Both strains had genome sizes and GC contents comparable to those of other Xenorhabdus species, with average nucleotide identity (ANI) values of 96–98% supporting their classification as X. thuongxuanensis. Functional annotation identified genes involved in secondary metabolism, while antiSMASH predicted diverse biosynthetic regions showing similarity to known BGCs, including those associated with holomycin, putrebactin, avaroferrin, and aryl polyenes. The crude extracts exhibited antibacterial activity against several antibiotic-resistant bacteria with minimum inhibitory concentration (MIC) values ranging from 0.2 to 6.25 mg/mL. They also inhibited Candida albicans and Cryptococcus neoformans, with inhibition zones ranging from 7.5 to 12 mm and from 10 to 42.5 mm, respectively. The crude extract from KLK18.1 exhibited cytotoxicity against HepG2 cells, with an IC50 value of 10.85 µg/mL. These findings expand the current knowledge of the genomic, biosynthetic, and biological potential of X. thuongxuanensis and provide a basis for future characterization of its BGC-associated metabolites.