Activities
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 BGCs platform
MGnify Biosynthetic Gene Clusters: 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.
Explore the MGnify BGCs platform →
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
Project outputs
EUREMAP is building an integrated, multidisciplinary marine bioprospecting workflow that connects the expertise of its consortium partners — EU-OPENSCREEN, EMBL, EMBRC, and ELIXIR — to accelerate the discovery of novel bioactive natural products from marine organisms. Below is an overview of the project’s key outputs to date.
Demonstrator projects EUREMAP’s demonstrator projects showcase the marine bioprospecting workflow in action, translating consortium capabilities into real-world discovery pipelines:
- Enhancing the Production and Therapeutic Potential of Streptocyclinones for Alzheimer’s Disease — investigating novel streptocyclinones from marine Streptomyces sp. CA-237351, compounds with anti-inflammatory and neuroprotective properties, to explore new therapeutic avenues for neurodegenerative disease.
- Metabolomic Profiling of the Sea Surface Microlayer and Bio-fouling Organisms, with a Focus on Siderophores — exploring an underexplored marine niche for novel siderophores, metabolites with promising applications in medicine, agriculture, and bioremediation.
EUREMAP Data management book
