Genomic and phenotypic analysis reveals taxonomic and biosynthetic diversity in desert-derived Saccharothrix

Rare actinomycetes represent an underexplored source of bioactive natural products, yet their taxonomic diversity and biosynthetic potential remain incompletely characterized. Here, ten Saccharothrix strains isolated from the Gurbantunggut Desert in Xinjiang, northwestern China, were investigated using phylogenomics, comparative genomics, biosynthetic gene cluster (BGC) mining, and antimicrobial assays. Genome-based analyses identified two lineages that may represent novel species. A total of 413 BGCs were predicted across the ten genomes. Comparative BiG-SCAPE analysis grouped 1,461 BGCs from the ten study strains, reference Saccharothrix genomes, and MIBiG into 735 gene cluster families (GCFs). Only three of the 19 GCFs containing MIBiG reference BGCs also included BGCs from the study strains, indicating limited overlap with characterized BGCs. Antimicrobial activity was detected in 89 of 300 strain–medium–indicator combinations, with positive results more frequent against fungal than bacterial indicators. Notably, the strain with the largest number of predicted BGCs did not exhibit the broadest antimicrobial spectrum. These findings reveal taxonomic and biosynthetic diversity among desert-derived Saccharothrix and provide a basis for prioritizing strains and biosynthetic pathways for further natural product discovery.