Research

Our research covers the whole microbial natural product discovery process. It spans tool development for metabolomics and genomics data mining, data analysis, wet-lab investigation, compound isolation, and biological characterization. We also provide our expertise via reviews and perspective/opinion articles.

The overarching approach to our research is focused towards the FAIR principles, emphasizing transparency, reproducibility, and rigor.

All

2026

New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome

Stephen A. Jackson, Pavlo Hrab, Mitja M. Zdouc, David J. Clarke, Alan D.W. Dobson

Microbial Genomics  ·  12 Jan 2026  ·  doi:10.1099/mgen.0.001602

2025

Paired-omics-based exploration and characterization of biosynthetic diversity in lichenized fungi

Garima Singh, Maonian Xu, Mitja Zdouc, Anna Pasinato, Susan Egbert, …, Jordan R. Hoffman, Christoph Scheidegger, Imke Schmitt, Francesco Dal Grande, Marnix H. Medema

Microbial Genomics  ·  17 Dec 2025  ·  doi:10.1099/mgen.0.001569

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Kai Blin, Catarina Loureiro, Nico L L Louwen, Jorge C Navarro-Muñoz, Hans Gerstmans, …, Drew T Doering, Justin J J van der Hooft, Tilmann Weber, Marnix H Medema, Mitja M Zdouc

Briefings in Bioinformatics  ·  01 Nov 2025  ·  doi:10.1093/bib/bbaf659

Charting the biosynthetic landscape of hybrid polyketide-nonribosomal peptide-specialized lipids

Fatima El Arnouki Belhaji, Dries De Ruysscher, Giel Vanreppelen, Laura-Lynn Huybrechts, Mohammad M. Alanjary, …, Patrick Van Dijck, Marnix H. Medema, Angus Weir, Eveline Lescrinier, Joleen Masschelein

bioRxiv  ·  24 Oct 2025  ·  doi:10.1101/2025.10.24.682833

Preprint

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

Adriano Rutz, Daniel Probst, César Aguilar, Daniel Y Akiyama, Fabrizio Alberti, …, Tilmann Weber, Kai Blin, Justin J J van der Hooft, Marnix H Medema, Mitja M Zdouc

Nucleic Acids Research  ·  26 Sep 2025  ·  doi:10.1093/nar/gkaf969

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

Adriano Rutz, Daniel Probst, César Aguilar, Daniel Y. Akiyama, Fabrizio Alberti, …, Tilmann Weber, Kai Blin, Justin J. J. van der Hooft, Marnix H. Medema, Mitja M. Zdouc

chemRxiv  ·  20 Aug 2025  ·  doi:10.26434/chemrxiv-2024-78mtl-v2

Preprint

Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset

Joelle Houriet, Preston K. Manwill, Armando Alcázar Magaña, Victoria M. Anderson, Mehdi A. Beniddir, …, Amélie Perez, Justin J. J. van der Hooft, Mitja M. Zdouc, Roger G. Linington, Nadja B. Cech

Analytical Chemistry  ·  22 Jul 2025  ·  doi:10.1021/acs.analchem.4c05577

Olive mill solid waste induces beneficial mushroom-specialized metabolite diversity revealed by computational metabolomics strategies

Soliman Khatib, Idan Pereman, Elizabeth Kostanda, Mitja M. Zdouc, Nirit Ezov, Ron Schweitzer, Justin J. J. van der Hooft

Metabolomics  ·  26 Apr 2025  ·  doi:10.1007/s11306-025-02257-9

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

Kai Blin, Simon Shaw, Lisa Vader, Judit Szenei, Zachary L Reitz, …, Christophe Corre, Marc G Chevrette, Gilles P van Wezel, Marnix H Medema, Tilmann Weber

Nucleic Acids Research  ·  25 Apr 2025  ·  doi:10.1093/nar/gkaf334

Paired-omics-based exploration and characterisation of biosynthetic diversity in lichenized fungi

Garima Singh, Maonian Xu, Mitja Zdouc, Anna Pasinato, Jorge C. Navarro-Muñoz, …, Jordan R Hoffman, Christoph Scheidegger, Imke Schmitt, Francesco Dal Grande, Marnix H. Medema

ResearchSquare  ·  14 Mar 2025  ·  doi:10.21203/rs.3.rs-6073935/v1

Preprint

Non-targeted metabolomics-based molecular networking enables the chemical characterization of Rumex sanguineus, a wild edible plant

Valentina Ramundi, Mitja M. Zdouc, Enrica Donati, Justin J. J. van der Hooft, Sara Cimini, Laura Righetti

Metabolomics  ·  24 Jan 2025  ·  doi:10.1007/s11306-024-02210-2

2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Mitja M Zdouc, Kai Blin, Nico L L Louwen, Jorge Navarro, Catarina Loureiro, …, Christian Zimmermann, Justin J J van der Hooft, Roger G Linington, Tilmann Weber, Marnix H Medema

Nucleic Acids Research  ·  09 Dec 2024  ·  doi:10.1093/nar/gkae1115

Non-targeted metabolomics-based molecular networking enables the chemical characterization of Rumex sanguineus

Valentina Ramundi, Mitja M. Zdouc, Enrica Donati, Justin J.J. van der Hooft, Sara Cimini, Laura Righetti

chemRxiv  ·  09 Jul 2024  ·  doi:10.26434/chemrxiv-2024-03ls0

Preprint

The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis

Mitja M. Zdouc, David Meijer, Friederike Biermann, Jonathan Holme, Aleksandra Korenskaia, …, Justin J. J. van der Hooft, Tilmann Weber, Nadine Ziemert, Kai Blin, Marnix H. Medema

chemRxiv  ·  09 Apr 2024  ·  doi:10.26434/chemrxiv-2024-78mtl

Preprint

Olive mill solid waste induces beneficial mushroom-specialized metabolite diversity revealed by computational metabolomics strategies

Soliman Khatib, Idan Pereman, Elizabeth Kostanda, Mitja M. Zdouc, Nirit Ezov, Ron Schweitzer, Justin J. J. van der Hooft

bioRxiv  ·  09 Feb 2024  ·  doi:10.1101/2024.02.09.579616

Preprint

2023

Metabolome-guided genome mining of RiPP natural products

Mitja M. Zdouc, Justin J.J. van der Hooft, Marnix H. Medema

Trends in Pharmacological Sciences  ·  01 Aug 2023  ·  doi:10.1016/j.tips.2023.06.004

2022

FERMO: a Dashboard for Automated Prioritization of Molecular Features from Mass Spectral Data

Mitja M. Zdouc, Hannah E. Augustijn, Nataliia V. Machushynets, Lina M. Bayona, Sylvia Soldatou, …, Sarah Casu, Marcel Jaspars, Gilles P. van Wezel, Marnix H. Medema, Justin J. J. van der Hooft

bioRxiv  ·  22 Dec 2022  ·  doi:10.1101/2022.12.21.521422

Preprint

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

Barbara R Terlouw, Kai Blin, Jorge C Navarro-Muñoz, Nicole E Avalon, Marc G Chevrette, …, Zheng Zhong, Jérôme Collemare, Roger G Linington, Tilmann Weber, Marnix H Medema

Nucleic Acids Research  ·  18 Nov 2022  ·  doi:10.1093/nar/gkac1049

2021

Feature-Based Molecular Networking for the Targeted Identification of G_q-Inhibiting FR900359 Derivatives

Wiebke Hanke, Julian Patt, Judith Alenfelder, Jan H. Voss, Mitja M. Zdouc, …, Raphael Reher, Christa E. Müller, Evi Kostenis, Max Crüsemann, Gabriele M. König

Journal of Natural Products  ·  01 Jul 2021  ·  doi:10.1021/acs.jnatprod.1c00194

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters

Mitja M. Zdouc, Mohammad M. Alanjary, Guadalupe S. Zarazúa, Sonia I. Maffioli, Max Crüsemann, Marnix H. Medema, Stefano Donadio, Margherita Sosio

Cell Chemical Biology  ·  01 May 2021  ·  doi:10.1016/j.chembiol.2020.11.009

Blocks in the pseudouridimycin pathway unlock hidden metabolites in the Streptomyces producer strain

Marianna Iorio, Sahar Davatgarbenam, Stefania Serina, Paolo Criscenzo, Mitja M. Zdouc, Matteo Simone, Sonia I. Maffioli, Richard H. Ebright, Stefano Donadio, Margherita Sosio

Scientific Reports  ·  12 Mar 2021  ·  doi:10.1038/s41598-021-84833-2

Effective approaches to discover new microbial metabolites in a large strain library

Mitja M Zdouc, Marianna Iorio, Kristiina Vind, Matteo Simone, Stefania Serina, …, Guadalupe S Zarazúa, Max Crüsemann, Sonia I Maffioli, Margherita Sosio, Stefano Donadio

Journal of Industrial Microbiology and Biotechnology  ·  18 Feb 2021  ·  doi:10.1093/jimb/kuab017

Planomonospora : A Metabolomics Perspective on an Underexplored Actinobacteria Genus

Mitja M. Zdouc, Marianna Iorio, Sonia I. Maffioli, Max Crüsemann, Stefano Donadio, Margherita Sosio

Journal of Natural Products  ·  26 Jan 2021  ·  doi:10.1021/acs.jnatprod.0c00807

2020

A biaryl-linked tripeptide from Planomonospora leads to widespread class of minimal RiPP gene clusters

Mitja M. Zdouc, Mohammad M. Alanjary, Guadalupe S. Zarazúa, Sonia I. Maffioli, Max Crüsemann, Marnix H. Medema, Stefano Donadio, Margherita Sosio

bioRxiv  ·  21 Jul 2020  ·  doi:10.1101/2020.07.21.214643

Preprint

Planomonospora : a Metabolomics Perspective on an Underexplored Actinobacteria Genus

Mitja M. Zdouc, Marianna Iorio, Sonia I. Maffioli, Max Crüsemann, Stefano Donadio, Margherita Sosio

bioRxiv  ·  19 Jul 2020  ·  doi:10.1101/2020.07.19.210815

Preprint

2018

Docking study with biological validation on bacterial enzyme MurD

Mitja Zdouc, Julia Schink, Samo Lešnik, Kaja Rožman, Janez Konc, Dušanka Janežič, Stanislav Gobec

Chemical Data Collections  ·  01 Mar 2018  ·  doi:10.1016/j.cdc.2018.02.003

2016

Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction

Tanja Štular, Samo Lešnik, Kaja Rožman, Julia Schink, Mitja Zdouc, …, Michael Schroeder, Thierry Langer, Stanislav Gobec, Dušanka Janežič, Janez Konc

Journal of Medicinal Chemistry  ·  12 Dec 2016  ·  doi:10.1021/acs.jmedchem.6b01277

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