Whole-genome analysis and biosynthetic gene cluster profiling of Stenotrophomonas sp. ASucR1 isolated from Sof Umer Cave, Ethiopia

Sof Umer Cave is a unique habitat that hosts industrially significant microbes. In this study, Stenotrophomonas sp. ASucR1 was isolated from the cave rock and screened for antimicrobial activity. High-molecular-weight genomic DNA was extracted and subjected to whole-genome sequencing using the Illumina NovaSeq platform. Comprehensive genomic and biosynthetic gene cluster (BGC) profiling were conducted. In vitro tests revealed that Stenotrophomonas sp. ASucR1 exhibited a broad spectrum of antagonistic activity. Functional genome annotation identified diverse biosynthetic gene clusters (BGCs) and metabolic pathways, including genes involved in the synthesis of secondary metabolites. A total of 19 BGCs were identified, several of which showed no matches in the minimum information about a biosynthetic gene cluster (MiBIG) database, indicating the presence of previously uncharacterized bioactive compounds. Single nucleotide polymorphism (SNP) analysis showed that 91.5% of variants were identified within coding regions, with 85.84% being synonymous. Classification of SNPs and insertion-deletion mutations through clusters of orthologous groups (COG) analysis highlighted their association with key biological functions. This study highlights the metabolic versatility and biosynthetic potential of Stenotrophomonas sp. ASucR1, a promising candidate for antimicrobial development and biotechnological applications. The identification of various biosynthetic gene clusters paves the way for exploring bioactive compounds with pharmaceutical significance.