Metabolomics for the Discovery of Natural Products from Cyanobacteria

Cyanobacteria are chemically rich microorganisms shown to produce natural products with relevant biotechnological applications. The discovery of natural products has been traditionally based on bioassay-guided approaches. Recently, omics techniques have added new tools to the field of natural product discovery. In this study, we applied mass spectrometry metabolomics to explore the chemistry of cultured cyanobacteria, leading to the discovery of new metabolites. Comparative metabolomics was used to analyze cyanobacterial strains growing in media with different levels of phosphate and nitrate. Among many relevant observations, these experiments revealed a new linear peptide, named scytodecamide, produced in increased amounts by strain Scytonema sp. UIC 10036 under low nitrate and high phosphate conditions. In a second approach, in situ dereplication using the droplet–liquid microjunction–surface sampling probe (droplet probe) coupled with UPLC-UV-HRMS/MS led to the discovery of calothrixamides A and B from strain Calothrix sp. UIC 10520. Calothrixamides and scytodecamide were elucidated by HRMS, MS/MS, and 1D and 2D NMR, along with chemical degradation and derivatization reactions. Calothrixamides are the first functionalized fatty acid amides found in freshwater cyanobacteria and one of the few natural products described from the genus Calothrix. Their discovery inspired the investigation of other Calothrix strains for new natural products. A combination UPLC-HRMS profiling, UPLC-MS/MS, and stable isotope labeling experiments with PCA, molecular networking, and comparative metabolomics led to the identification of known and new natural products in Calothrix strains. This study presented metabolomic strategies that can be incorporated into natural product discovery workflows to select strains and identify new compounds from microbial sources.