Genome mining and phylogenomics reveal diverse biosynthetic gene clusters in desert Actinobacteria

Antimicrobial resistance is a growing global health threat, heightening the need for new bioactive compounds from underexplored microbial niches. Desert ecosystems are increasingly recognized as reservoirs of metabolically versatile Actinobacteria that encode diverse biosynthetic pathways. In this study, we investigated Actinobacteria isolated from the underexplored Sinai Desert in Egypt using phylogenomics and genome-mining approaches. Genomes belonging to Streptomyces , Micromonospora and Actinoplanes were assembled and analysed for biosynthetic potential. Mining of these genomes revealed a broad repertoire of putative non-ribosomal peptide synthetase and polyketide synthase biosynthetic gene clusters (BGCs), including several divergent clusters with low predicted similarity to characterized references. These putatively divergent BGCs are likely to represent biosynthetic pathways with uncharacterized chemical products that could be explored by further experimental and chemical validation. The high diversity and divergence of BGCs in these desert strains could reflect ecological adaptation to harsh conditions and highlight their potential as a source of distinct antimicrobial and antitumour metabolites. Overall, this work underscores desert Actinobacteria as valuable candidates for future natural product discovery and synthetic biology applications.