Work Package 2: Fermentation and Extract Library Construction

WP2 will generate non-repetitive and chemically unique annotated microbial extract libraries with small molecules biosynthesised from unique marine microorganisms and heterologous expression of biosynthetic pathways from deep sea metagenomes for the discovery of new chemotherapeutic agents.

Partners will apply their expertise to build a composite extract library of at least 18.000 crude and fractionated microbial extracts. Strains and metagenomes from WP1 will be used, and best practice methods, new tools, technologies and organism-specific media will be employed to grow organisms in order to overcome limited expression of repressed secondary metabolism and produce metabolite-enriched extracts.

The extract library will include crude organism extracts and fractions prepared by fractionation across polarity or molecular size gradients. Extract complexity will be reduced by removing interfering components by SPE. Fractionation will facilitate downstream bioassay and analytical chemistry. New analytical and automation technologies will be used to process extracts into fractions.

In-house applications that measure compound diversity and redundancy among undefined samples from different organisms or organisms cultivated in different ways, developed by some partners, will be improved to enhance capabilities for high-throughput, robust LC-MS analysis and data processing methods. These will allow visualising sample profiles and chemical diversity, measure inter-sample relatedness and redundancy, and recognise when bioactive extracts contain known or unknown molecules that may explain bioactivity. Application of state-of-the-art chemometric methods will quantify the uniqueness, quality, and complexity of the natural product extract and fraction library generated in the project.

The assembly of three extract libraries, one at each of the major screening laboratories, plus a central repository to be used by academic collaborators and European companies will be the main deliverable from this package.

WP leader: Fundación Medina, Fernando Reyes