Volume 78, November 2025, Pages 46-52Author links open overlay panel, , , , AbstractBackground

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 was conducted.

Results

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.

Conclusions

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.

How to cite: Meka AF, Bekele GK, Gebre SG, et al. Whole genome analysis and biosynthetic gene cluster profiling of Stenotrophomonas sp. ASucR1 isolated from Sof Umer Cave, Ethiopia. Electron J Biotechnol 2025;78. https://doi.org/10.1016/j.ejbt.2025.07.004.Keywords

Biosynthetic gene clusters

Secondary metabolites

Stenotrophomonas sp.

Whole-genome sequencing

Data availabilityThe data that have been used are confidential. The sequence data supporting the findings of this study have been submitted to the NCBI Sequence Read Archive (SRA) under accession number PRJNA1198506 (https://www.ncbi.nlm.nih.gov/sra/PRJNA1198506).

© 2025 The Author(s). Published by Elsevier Inc. on behalf of Pontificia Universidad Católica de Valparaíso.