Challenges and triumphs to genomics-based natural product discovery

  • Paul R. Jensen
  • Krystle L. Chavarria
  • William Fenical
  • Bradley S. Moore
  • Nadine Ziemert


Genome sequencing is rapidly changing the field of natural products research by providing opportunities to assess the biosynthetic potential of strains prior to chemical analysis or biological testing. Ready access to sequence data is driving the development of new bioinformatic tools and methods to identify the products of silent or cryptic pathways. While genome mining has fast become a useful approach to natural product discovery, it has also become clear that identifying pathways of interest is much easier than finding the associated products. This has led to bottlenecks in the discovery process that must be overcome for the potential of genomics-based natural product discovery to be fully realized. In this perspective, we address some of these challenges in the context of our work with the marine actinomycete genus Salinispora, which is proving to be a useful model with which to apply genome mining as an approach to natural product discovery.


Genomics Natural product biosynthesis Genome mining Salinispora 



PJ and WF acknowledge financial support from the National Institutes of Health (NIH R37 CA 044848 and RO1-GM086261) and the Fogerty Center International Cooperative Biodiversity Groups program (grant U01-TW007401-01). PJ, WF, and BSM acknowledge support from the NIH (grant R01-GM085770).


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Copyright information

© Society for Industrial Microbiology and Biotechnology 2013

Authors and Affiliations

  • Paul R. Jensen
    • 1
  • Krystle L. Chavarria
    • 1
  • William Fenical
    • 1
  • Bradley S. Moore
    • 1
  • Nadine Ziemert
    • 1
  1. 1.Scripps Institution of OceanographyUniversity of California, San DiegoLa JollaUSA

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