Metabolomics Tools Assisting Classic Screening Methods in Discovering New Antibiotics from Mangrove Actinomycetia in Leizhou Peninsula

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Abstract
Mangrove actinomycetia are considered one of the promising sources for discovering novel biologically active compounds. Traditional bioactivity- and/or taxonomy-based methods are inefficient and usually result in the re-discovery of known metabolites. Thus, improving selection efficiency among strain candidates is of interest especially in the early stage of the antibiotic discovery program. In this study, an integrated strategy of combining phylogenetic data and bioactivity tests with a metabolomics-based dereplication approach was applied to fast track the selection process. A total of 521 actinomycetial strains affiliated to 40 genera in 23 families were isolated from 13 different mangrove soil samples by the culture-dependent method. A total of 179 strains affiliated to 40 different genera with a unique colony morphology were selected to evaluate antibacterial activity against 12 indicator bacteria. Of the 179 tested isolates, 47 showed activities against at least one of the tested pathogens. Analysis of 23 out of 47 active isolates using UPLC-HRMS-PCA revealed six outliers. Further analysis using the OPLS-DA model identified five compounds from two outliers contributing to the bioactivity against drug-sensitive A. baumannii. Molecular networking was used to determine the relationship of significant metabolites in six outliers and to find their potentially new congeners. Finally, two Streptomyces strains (M22, H37) producing potentially new compounds were rapidly prioritized on the basis of their distinct chemistry profiles, dereplication results, and antibacterial activities, as well as taxonomical information. Two new trioxacarcins with keto-reduced trioxacarcinose B, gutingimycin B (16) and trioxacarcin G (20), together with known gutingimycin (12), were isolated from the scale-up fermentation broth of Streptomyces sp. M22. Our study demonstrated that metabolomics tools could greatly assist classic antibiotic discovery methods in strain prioritization to improve efficiency in discovering novel antibiotics from those highly productive and rich diversity ecosystems.
Funding Information
  • the CAMS Innovation Fund for Medical Sciences (CAMS 2017-I2M-B&R-08, CAMS 2017-I2M-1-012)
  • National Natural Science Foundation of China (81803411, 82011530051)
  • Sino-Hungarian Bilateral S&T Cooperation Projects from 2019 to 2020 (Chinese Project: 8–11; Hungarian project: 2018–2.1.14-TÉT-CN-2018–00021)
  • The Science and Technology Program of Guangdong Province (2019B090905011)
  • he Public Service Platform of South China Sea for R&D Marine Biomedicine Resources (2017C8A)
  • the Guangdong University Youth Innovation Talent Project (2020KQNCX023)
  • the Scientific Research Fund of Guangdong Medical University (GDMUM202002)
  • PUMC Doctoral Innovation Fund Project (2018-1007-16)

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