Activities
From marine samples to medicines: EUREMAP’s bioprospecting workflow in action.
Project activities
EUREMAP is an European initiative that integrates leading marine research infrastructures to accelerate the discovery of bioactive compounds from marine organisms. By creating a sustainable and collaborative marine bioprospecting pipeline. This pipeline will comprise a wide range of services spanning the biodiscovery process, from isolating specific molecules to testing their applications in clinical trials. EUREMAP supports bothe academia and industry in advancing innovation in the Blue Bioeconomy.
Our mission is to unlock the potencial of marine biodiversity through genomics, green chemistry, marine natural products research, and FAIR data management. Together, we aim to transform marine resources into solutions for health, biotechnology, and sustainable development.
Phylum-rank evolutionary distributions of Biosynthetic Gene Cluster classes
MGnify biosynthetic gene clusters platform: uncovering nature’s chemical blueprints
Biosynthetic gene clusters (BGCs) are the genetic instructions behind many of the natural products found in marine and other environmental organisms — including antibiotics, pigments, and other bioactive compounds of interest to health and food research. Identifying these clusters at scale, however, has traditionally required significant computational expertise and resources.
To address this, EUREMAP partner MGnify (EMBL-EBI) has developed the MGnify BGCs platform, a dedicated resource for exploring, analysing, and retrieving BGC predictions from metagenomic assemblies. The platform brings together three leading detection tools — antiSMASH, GECCO, and SanntiS — into a single standardised pipeline, making it possible to compare results across studies and identify consensus predictions with greater confidence.
Built for both researchers and non-specialists, MGnify BGCs offers an accessible analytics interface alongside a full API for advanced data queries, opening up a rich dataset of natural product potential to the wider scientific and industry community. It forms part of the broader MGnify resource, which provides automated pipelines for analysing microbiome data and determining the taxonomic and functional diversity of environmental samples.
By making standardised, cross-validated BGC predictions freely available, this partnership directly supports EUREMAP’s mission: unlocking the biosynthetic potential of marine organisms to discover new bioactive compounds for health and food applications.
The biosynthetic classes
TWe group BGCs by the chemestry of the molecule they encode, following the classes used by the MIBiG reference repository. Some clusters combine chemistries; we label these as hybrids. (Class definitions follow Hanson, J.R.(2003), Natural Products: The Secondary Metabolites (Vol. 17), Royal Society of Chemistry; and Kautsar, S.A. et al. (2020) MIBiG 2.0, Nucleic Acids Research, 48(D1), D454-D458.C)
Image: Terpenes used for chiral pool synthesis. (T. Gaich, J. Mulzer 2012)
Composed of isoprene (C5) units derived from isopentenyl pyrophosphate
Nitrogen-containing compounds derived from amino acids (e.g., ornithine, lysine, tyrosine, tryptophan)
Image: (Wang, S., Lin, S., Fang, Q. et al. A ribosomally synthesised and post-translationally modified peptide containing a β-enamino acid and a macrocyclic motif. Nat Commun 13, 5044 (2022).)
Ribosomally synthesised and Post-translationally modified Peptide
Image: The structure of cyclosporine. (D.K. Daley, K.J. Brown, S. Badal, Chapter 20 – Fungal Metabolites, Editor(s): Simone Badal, Rupika Delgoda, Pharmacognosy, Academic Press, 2017, Pages 413-421, ISBN 9780128021040, https://doi.org/10.1016/B978-0-12-802104-0.00020-2. )
Nonribosomal Peptide
Image: Carbohydrates (Girija S. Singh, Chapter Thirteen – Carbohydrate-based antibiotics: Opportunities and challenges, Editor(s): Vinod Kumar Tiwari, Carbohydrates in Drug Discovery and Development, Elsevier, 2020, Pages 523-559, ISBN 9780128166758, https://doi.org/10.1016/B978-0-12-816675-8.00013-0.)
Carbohydrate-based natural products (e.g., aminoglycoside antibiotics)
Image: cyclitols (J.P. Kamerling, 1.01 – Basics Concepts and Nomenclature Recommendations in Carbohydrate Chemistry, Editor(s): Hans Kamerling, Comprehensive Glycoscience, Elsevier, 2007, Pages 1-38, ISBN 9780444519672, https://doi.org/10.1016/B978-044451967-2/00001-5.)
Catch-all class for clusters encoding metabolites outside main classes (e.g. cyclitols, indolocarbazoles, and phosphonates)
Image: Diterpene and triterpene alkaloids. (Brocksom, Timothy & Oliveira, Kleber & Desiderá, André. (2017). The Chemistry of the Sesquiterpene Alkaloids. Journal of the Brazilian Chemical Society. 10.21577/0103-5053.20170049. )
Clusters combining two or more classes; Polyketide + NRP is flagged separately
The datasets collection
- MIBiG 4.0 – experimentally characterised, published BGCs; the reference set of clusters.
- BacDive – marine bacterial genomes from type strains.
- MGnify Marine Genome Catalogues – genomes assembled from marine water-column and sediment metagenomes.
- MGnify Assembles (v5) – assembled contigs from marine-related metagenomes.
BGC prediction and classification
Three detectors (antiSMASH, GECCO, and SanntiS) annotable each dataset. We merge overlapping predictions on the same genomic interval into one integrated BGC. We derive the integrated BGC class by consensus across detectors. Each detector’s class prediction is collapsed to the shared vocabulary above and the calls are pooled. A single agreed class wins outright. A Polyketide + NRP combination is flagged as that specific hybrid. Any other multi-class combination becomes a general hybrid. Clusters with no usable signal default to Other.
Tree calculation
Trees were calculated using the CommonTree tool of the NCBI taxonomy datebase. Synonyms were resolved as directed by the CommonTree tool, and other unresolved taxa removed from the tree (this included many BGCs resolving to Candidatus phyla in Bacteria).
Demonstrator projects
EUREMAP in action
EUREMAP’s demonstrator projects put the consortium’s combined expertise to work on real marine bioprospecting challenges. Eleven partners — spanning Norway, Spain, Belgium, Israel, Italy, Germany, Portugal, France, and the EU-OPENSCREEN, EMBL, EMBRC, and ELIXIR research infrastructures — contribute complementary capabilities to each project: microbial strain collections and cultivation know-how, compound extraction and purification methods, LC-MS and NMR analytical pipelines, and bioinformatic tools for biosynthetic gene cluster prediction and metagenomic analysis. This is paired with a wide range of bioactivity and toxicity assays, including antifouling bioassays, transcriptomic screening for unknown mechanisms of action, and kinase-inhibition and cell-viability assays. By integrating these capabilities into a single workflow, each demonstrator project traces a path from raw marine samples to characterised, potentially bioactive compounds — testing and refining the EUREMAP pipeline as it goes.
Enhancing the production and therapeutic potential of streptocyclinones for alzheimer’s disease
Can the ocean hold the key to new therapies for Alzheimer’s disease? This EUREMAP demonstrator project is exploring exactly that. The project focuses on identifying and characterising additional streptocyclinones — a family of natural products already known for their anti-inflammatory and neuroprotective properties — produced by the marine bacterium Streptomyces sp. CA-237351.
By deepening understanding of their biosynthesis and expanding the known diversity of streptocyclinone variants, the work aims to unlock new therapeutic potential for neurodegenerative disease.
The project reflects EUREMAP’s mission in action: building an integrated, multidisciplinary marine bioprospecting workflow — combining the expertise of EU-OPENSCREEN, EMBL, EMBRC, and ELIXIR — to accelerate the discovery of novel bioactive marine natural products and strengthen the European blue bioeconomy.
Exploring an under-explored marine niche for novel siderophores, metabolites with promising applications in medicine, agriculture, and bioremediation. While the open ocean has already yielded known siderophores, the sea surface microlayer (SSML) and tidal bio-fouling habitats remain largely unstudied. Microbial communities in these niches are exposed to intense UV radiation, fierce nutrient competition, and constant environmental fluctuation — conditions that may drive them to produce distinctive secondary metabolites, making this a promising new frontier for siderophore bioprospecting.
Working from existing marine bacterial strain collections, the demonstrator project team is generating extracts and applying comprehensive metabolomics analysis — including an LC-MS/MS-based post-column metal infusion method — to characterise these metabolomes, identify novel siderophores, and screen for antifouling potential. The demonstrator project reflects EUREMAP’s broader mission: building an integrated, multidisciplinary marine bioprospecting workflow across EU-OPENSCREEN, EMBL, EMBRC, and ELIXIR to accelerate the discovery of novel bioactive marine natural products.
EUREMAP data management
EUREMAP data management book
To help researchers navigate how data are handled across the EUREMAP pipeline, the EUREMAP Data Management Book offers a short, practical guide available on GitHub. Built around ELIXIR’s contribution to the European Open Science Cloud (EOSC), the guide walks through EUREMAP’s data management workflow: from linking every sample and dataset to a project’s BioProject/Study accession, to registering sample metadata in BioSamples, depositing data in the appropriate repository (e.g. EMBL-ENA for sequence data, MetaboLights for metabolomics), and tying it all together under a single BioStudies accession. A quick-start section takes users step by step through open science principles, drafting a Data Management Plan, and submitting through EMBL-EBI’s Webin Portal. Designed to be read in about 20 minutes, it’s a practical companion for anyone submitting data through the EUREMAP Marine Bioprospecting Pipeline.
