Integrating Genome Mining and Untargeted Metabolomics to Uncover the Chemical Diversity of Streptomyces galbus I339, a Strain from the Unique Brazilian Caatinga Biome

Background/Objectives: The escalating antimicrobial resistance crisis underscores the urgent need to explore underexplored ecological niches as reservoirs of novel bioactive compounds. The Brazilian Caatinga, a unique semi-arid biome, represents a promising reservoir for microbial discovery. Methods: In this study, we report the polyphasic characterization of Streptomyces galbus I339, a strain isolated from Caatinga soil. Whole-genome sequencing and phylogenomic analysis confirmed its taxonomic identity. In silico mining of the genome was conducted to assess biosynthetic potential. This genetic promise was experimentally validated through an integrated metabolomic approach, including liquid chromatography-tandem mass spectrometry (LC-MS/MS), nuclear magnetic resonance (NMR) spectroscopy, and gas chromatography-mass spectrometry (GC-MS) profiling. The anti-mycobacterial activity of the crude extract was evaluated against Mycobacterium tuberculosis. Results: The strain S. galbus I339 possesses a 7.55 Mbp genome with a high GC content (73.17%). Genome mining uncovered a remarkable biosynthetic potential, with 45 biosynthetic gene clusters (BGCs) predicted, including those for known antibiotics like actinomycins, as well as numerous orphan clusters. Genome mining uncovered a remarkable biosynthetic potential, with 45 biosynthetic gene clusters (BGCs) predicted, including those for known antibiotics like actinomycins, as well as numerous orphan clusters. Metabolomic analyses confirmed the production of actinomycins and identified abundant diketopiperazines. Furthermore, the crude extract exhibited antimycobacterial activity, with a potent MIC of 0.625 µg/mL. Conclusions: The convergence of genomic and metabolomic data not only validates the expression of a fraction of this strain’s biosynthetic arsenal but also highlights a significant untapped potential, with the majority of BGCs remaining silent under the tested conditions. Our work establishes S. galbus I339 as a compelling candidate for biodiscovery and underscores the value of integrating genomics and metabolomics to unlock the chemical diversity of microbes from extreme environments.