A computational framework to interpret the chemical language of the microbiome

Project Information

DECIPHER

Grant agreement ID: 948770

DOI

10.3030/948770

Project closed

EC signature date 20 October 2020

Start date 1 December 2020

End date 30 November 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 965,00

EU contribution

€ 1 499 965,00

Coordinated by

WAGENINGEN UNIVERSITY
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (25)

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Author(s): Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG, Egbert S, Lee S, Meijer D, Recchia MJJ, Reitz ZL, van Santen JA, Selem-Mojica N, Tørring T, Zaroubi L, Alanjary M, Aleti G, Aguilar C, Al-Salihi SAA, Augustijn HE, Avelar-Rivas JA, Avitia-Domínguez LA, Barona-Gómez F, Bernaldo-Agüero J, Bielinski VA, Biermann F, Booth TJ, Carrion Bravo VJ, Castelo-Branco R, Chagas FO, Cruz-Morales
Published in: Nucleic Acids Research, 2023, Page(s) D603-D610, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac1049

Harnessing regulatory networks in Actinobacteria for natural product discovery

Author(s): Hannah E Augustijn, Anna M Roseboom, Marnix H Medema, Gilles P van Wezel
Published in: Journal of Industrial Microbiology and Biotechnology, Issue 51, 2025, ISSN 1367-5435
Publisher: Springer Verlag
DOI: 10.1093/jimb/kuae011

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota

Author(s): Victòria Pascal Andreu; Hannah E. Augustijn; Lianmin Chen; Alexandra Zhernakova; Jingyuan Fu; Michael A. Fischbach; Dylan Dodd; Marnix H. Medema
Published in: ISSN=10870156;TITLE=Nature Biotechnology, Issue 1, 2023, ISSN 1546-1696
Publisher: Springer Nature
DOI: 10.1038/s41587-023-01675-1

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota

Author(s): Yijun Zhu, Hannah E. Augustijn, Victòria Pascal Andreu, Arjan Draisma, Gilles P. van Wezel, Dylan Dodd, Michael A. Fischbach, Marnix H. Medema
Published in: Journal of Molecular Biology, 2026, Page(s) 169567, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2025.169567

CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer

Author(s): David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
Published in: Journal of Cheminformatics, Issue 16, 2024, Page(s) 58, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.26434/chemrxiv-2024-bvxr2

Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis

Author(s): Hannah E. Augustijn, Zachary L. Reitz, Le Zhang, Jeanine A. Boot, Somayah S. Elsayed, Gregory L. Challis, Marnix H. Medema, Gilles P. van Wezel
Published in: PLOS Biology, Issue 23, 2025, Page(s) e3003183, ISSN 1545-7885
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pbio.3003183

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation

Author(s): Kai Blin, Simon Shaw, Lisa Vader, Judit Szenei, Zachary L Reitz, Hannah E Augustijn, José D D Cediel-Becerra, Valérie de Crécy-Lagard, Robert A Koetsier, Sam E Williams, Pablo Cruz-Morales, Sopida Wongwas, Alejandro E Segurado Luchsinger, Friederike Biermann, Aleksandra Korenskaia, Mitja M Zdouc, David Meijer, Barbara R Terlouw, Justin J J van der Hooft, Nadine Ziemert, Eric J N H
Published in: Nucleic Acids Research, Issue 53, 2025, Page(s) W32-W38, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf334

The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more

Author(s): Kai Blin; Simon Shaw; Marnix H Medema; Tilmann Weber
Published in: Crossref, Issue 2, 2023, Page(s) 0305-1048, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad984

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

Author(s): Zachary L. Reitz, Bita Pourmohsenin, Melanie Susman, Emil Thomsen, Daniel Roth, Alison Butler, Nadine Ziemert, Marnix H. Medema
Published in: eLife, 2026, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.1101/2025.07.29.667501

RAIChU: automating the visualisation of natural product biosynthesis

Author(s): Barbara R. Terlouw, Friederike Biermann, Sophie P. J. M. Vromans, Elham Zamani, Eric J. N. Helfrich, Marnix H. Medema
Published in: Journal of Cheminformatics, Issue 16, 2024, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-024-00898-x

LogoMotif: a comprehensive database of transcription factor binding site profiles in Actinobacteria

Author(s): Hannah E. Augustijn, Dimitris Karapliafis, Kristy Joosten, Sébastien Rigali, Gilles P. van Wezel, Marnix H. Medema
Published in: Journal of Molecular Biology, Issue 436, 2024, Page(s) 168558, ISSN 1089-8638
Publisher: Elsevier
DOI: 10.1101/2024.02.28.582527

Biosynfoni: a biosynthesis-informed and interpretable lightweight molecular fingerprint

Author(s): Lucina-May Nollen, David Meijer, Maria Sorokina, Justin J. J. van der Hooft
Published in: Journal of Cheminformatics, Issue 17, 2025, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-025-01081-6

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota.

Author(s): Victòria Pascal Andreu; Jorge Roel-Touris; Dylan Dodd; Michael A. Fischbach; Marnix H. Medema
Published in: urn:issn:03051048, Issue 1, 2021, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab353

Taxonomic and metabolic diversity of Actinobacteria isolated from faeces of a 28,000-year-old mammoth

Author(s): Doris A. van Bergeijk, Hannah E. Augustijn, Somayah S. Elsayed, Joost Willemse, Victor J. Carrión, Mia Urem, Lena V. Grigoreva, Maksim Y. Cheprasov, Semyon Grigoriev, Bas Wintermans, Andries E. Budding, Herman P. Spaink, Marnix H. Medema, Gilles P. van Wezel
Published in: Environmental Microbiology, 2026, ISSN 1462-2920
Publisher: Wiley
DOI: 10.1101/2022.12.22.521380

improving cluster detection and comparison capabilities

Author(s): Kai Blin; Simon Shaw; Alexander M. Kloosterman; Zach Charlop-Powers; Gilles P. van Wezel; Marnix H. Medema; Marnix H. Medema; Tilmann Weber
Published in: TITLE=Nucleic Acids Research, Issue 1, 2021, Page(s) W29-W35, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab335

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Author(s): Arjan Draisma, Catarina Loureiro, Nico L. L. Louwen, Satria A. Kautsar, Jorge C. Navarro-Muñoz, Drew T. Doering, Nigel J. Mouncey & Marnix H. Medema
Published in: Nature Communications, 2026, ISSN 2041-1723
Publisher: Nature Publishing Group

Genome mining strategies for metallophore discovery.

Author(s): Zachary L Reitz; Marnix H Medema
Published in: urn:issn:09581669, Issue 1, 2022, Page(s) 102757, ISSN 1879-0429
Publisher: Elsevier
DOI: 10.1016/j.copbio.2022.102757

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

Author(s): Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T
Published in: Nucleic Acids Research, 2023, Page(s) W46-W50, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad344

MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis

Author(s): Adriano Rutz, Daniel Probst, César Aguilar, Daniel Y Akiyama, Fabrizio Alberti, Hannah E Augustijn, Nicole E Avalon, Christine Beemelmanns, Hellen Bertoletti Barbieri, Friederike Biermann, Alan J Bridge, Esteban Charria Girón, Russell Cox, Max Crüsemann, Paul M D’Agostino, Marc Feuermann, Jennifer Gerke, Karina Gutiérrez García, Jonathan E Holme, Ji-Yeon Hwang, Riccardo Iacovelli, Júlio C
Published in: Nucleic Acids Research, Issue 54, 2026, Page(s) D635-D642, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaf969

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

Author(s): Athina Gavriilidou; Satria A. Kautsar; Nestor Zaburannyi; Daniel Krug; Rolf Müller; Marnix H. Medema; Nadine Ziemert
Published in: ISSN: 2058-5276, Issue 1, 2022, ISSN 2058-5276
Publisher: Springer Nature
DOI: 10.1038/s41564-022-01110-2

Unleashing the potential of cell painting assays for compound activities and hazards prediction

Author(s): Floriane Odje, David Meijer, Elena von Coburg, Justin J. J. van der Hooft, Sebastian Dunst, Marnix H. Medema, Andrea Volkamer
Published in: Frontiers in Toxicology, Issue 6, 2024, ISSN 2673-3080
Publisher: Frontiers Media SA
DOI: 10.3389/ftox.2024.1401036

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

Author(s): David Meijer, Mehdi A. Beniddir, Connor W. Coley, Yassine M. Mejri, Meltem Öztürk, Justin J. J. van der Hooft, Marnix H. Medema, Adam Skiredj
Published in: Natural Product Reports, Issue 42, 2025, Page(s) 654-662, ISSN 0265-0568
Publisher: Royal Society of Chemistry
DOI: 10.1039/d4np00008k

CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters

Author(s): Matthias van den Belt; Cameron Gilchrist; Thomas J. Booth; Yit-Heng Chooi; Marnix H. Medema; Mohammad Alanjary
Published in: ISSN: 1471-2105, Issue 2, 2023, Page(s) 181, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-023-05311-2

Taxonomic and metabolic diversity of <scp>Actinomycetota</scp> isolated from faeces of a 28,000‐year‐old mammoth

Author(s): Doris A. van Bergeijk, Hannah E. Augustijn, Somayah S. Elsayed, Joost Willemse, Victor J. Carrión, Chao Du, Mia Urem, Lena V. Grigoreva, Maksim Y. Cheprasov, Semyon Grigoriev, Hans Jansen, Bas Wintermans, Andries E. Budding, Herman P. Spaink, Marnix H. Medema, Gilles P. van Wezel
Published in: Environmental Microbiology, Issue 26, 2024, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.16589

Artificial intelligence for natural product drug discovery

Author(s): Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kauts
Published in: Nature Reviews Drug Discovery, 2023, ISSN 1474-1776
Publisher: Nature Publishing Group
DOI: 10.1038/s41573-023-00774-7

Other (2)

Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures

Author(s): Reitz ZL, Butler A, Medema MH
Published in: BioRxiv, 2022
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.12.14.519525

PARAS: high-accuracy machine learning of substrate specificities in nonribosomal peptide synthetases

Author(s): Barbara R. Terlouw, Chuan Huang, David Meijer, José D. D. Cediel-Becerra, Ruolin He, Marlene L. Rothe, Matthew Jenner, Shanshan Zhou, Yu Zhang, Christopher D. Fage, Yuta Tsun- ematsu, Gilles P. van Wezel, Serina L. Robinson, Fabrizio Alberti, Lona M. Alkhalaf, Marc G. Chevrette, Gregory L. Challis and Marnix H. Medema
Published in: 2025
Publisher: BiorXiv, Cold Spring Harbor Laboratory