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MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

  • Mitja M. Zdouc
  • , Kai Blin
  • , Nico L.L. Louwen
  • , Jorge Navarro
  • , Catarina Loureiro
  • , Chantal D. Bader
  • , Constance B. Bailey
  • , Lena Barra
  • , Thomas J. Booth
  • , Kenan A.J. Bozhüyük
  • , José D.D. Cediel-Becerra
  • , Zachary Charlop-Powers
  • , Marc G. Chevrette
  • , Yit Heng Chooi
  • , Paul M. D’Agostino
  • , Tristan de Rond
  • , Elena Del Pup
  • , Katherine R. Duncan
  • , Wenjia Gu
  • , Novriyandi Hanif
  • Eric J.N. Helfrich, Matthew Jenner, Yohei Katsuyama, Aleksandra Korenskaia, Daniel Krug, Vincent Libis, George A. Lund, Shrikant Mantri, Kalindi D. Morgan, Charlotte Owen, Chin Soon Phan, Benjamin Philmus, Zachary L. Reitz, Serina L. Robinson, Kumar Saurabh Singh, Robin Teufel, Yaojun Tong, Fidele Tugizimana, Dana Ulanova, Jaclyn M. Winter, César Aguilar, Daniel Y. Akiyama, Suhad A.A. Al-Salihi, Mohammad Alanjary, Fabrizio Alberti, Gajender Aleti, Shumukh A. Alharthi, Mariela Y. Arias Rojo, Amr A. Arishi, Hannah E. Augustijn, Nicole E. Avalon, J. Abraham Avelar-Rivas, Kyle K. Axt, Hellen B. Barbieri, Julio Cesar J. Barbosa, Lucas Gabriel Barboza Segato, Susanna E. Barrett, Martin Baunach, Christine Beemelmanns, Dardan Beqaj, Tim Berger, Jordan Bernaldo-Agüero, Sandra M. Bettenbühl, Vincent A. Bielinski, Friederike Biermann, Ricardo M. Borges, Rainer Borriss, Milena Breitenbach, Kevin M. Bretscher, Michael W. Brigham, Larissa Buedenbender, Brodie W. Bulcock, Carolina Cano-Prieto, João Capela, Victor J. Carrion, Riley S. Carter, Raquel Castelo-Branco, Gabriel Castro-Falcón, Fernanda O. Chagas, Esteban Charria-Girón, Ayesha Ahmed Chaudhri, Vasvi Chaudhry, Hyukjae Choi, Yukyung Choi, Roya Choupannejad, Jakub Chromy, Melinda S. Chue Donahey, Jérôme Collemare, Jack A. Connolly, Kaitlin E. Creamer, Max Crüsemann, Andres Arredondo Cruz, Andres Cumsille, Jean Felix Dallery, Luis Caleb Damas-Ramos, Tito Damiani, Martinus de Kruijff, Belén Delgado Martín, Gerardo Della Sala, Jelle Dillen, Drew T. Doering, Shravan R. Dommaraju, Suhan Durusu, Susan Egbert, Mark Ellerhorst, Baptiste Faussurier, Artem Fetter, Marc Feuermann, David P. Fewer, Jonathan Foldi, Andri Frediansyah, Erin A. Garza, Athina Gavriilidou, Andrea Gentile, Jennifer Gerke, Hans Gerstmans, Juan Pablo Gomez-Escribano, Luz A. González-Salazar, Natalie E. Grayson, Claudio Greco, Juan E. Gris Gomez, Sebastian Guerra, Shaday Guerrero Flores, Alexey Gurevich, Karina Gutiérrez-García, Lauren Hart, Kristina Haslinger, Beibei He, Teo Hebra, Jethro L. Hemmann, Hindra Hindra, Lars Höing, Darren C. Holland, Jonathan E. Holme, Therese Horch, Pavlo Hrab, Jie Hu, Thanh Hau Huynh, Ji Yeon Hwang, Riccardo Iacovelli, Dumitrita Iftime, Marianna Iorio, Sidharth Jayachandran, Eunah Jeong, Jiayi Jing, Jung J. Jung, Yuya Kakumu, Edward Kalkreuter, Kyo Bin Kang, Sangwook Kang, Wonyong Kim, Geum Jin Kim, Hyunwoo Kim, Hyun Uk Kim, Martin Klapper, Robert A. Koetsier, Cassandra Kollten, Ákos T. Kovács, Yelyzaveta Kriukova, Noel Kubach, Aditya M. Kunjapur, Aleksandra K. Kushnareva, Andreja Kust, Jessica Lamber, Martin Larralde, Niels J. Larsen, Adrien P. Launay, Ngoc Thao Hien Le, Sarah Lebeer, Byung Tae Lee, Kyungha Lee, Katherine L. Lev, Shu Ming Li, Yong Xin Li, Cuauhtémoc Licona-Cassani, Annette Lien, Jing Liu, Julius Adam V. Lopez, Nataliia V. Machushynets, Marla I. Macias, Taifo Mahmud, Matiss Maleckis, Añadir Maharai Martinez-Martinez, Yvonne Mast, Marina F. Maximo, Christina M. McBride, Rose M. McLellan, Khyati Mehta Bhatt, Chrats Melkonian, Aske Merrild, Mikko Metsä-Ketelä, Douglas A. Mitchell, Alison V. Müller, Giang Son Nguyen, Hera T. Nguyen, Timo H.J. Niedermeyer, Julia H. O’Hare, Adam Ossowicki, Bohdan O. Ostash, Hiroshi Otani, Leo Padva, Sunaina Paliyal, Xinya Pan, Mohit Panghal, Dana S. Parade, Jiyoon Park, Jonathan Parra, Marcos Pedraza Rubio, Huong T. Pham, Sacha J. Pidot, Jörn Piel, Bita Pourmohsenin, Malik Rakhmanov, Sangeetha Ramesh, Michelle H. Rasmussen, Adriana Rego, Raphael Reher, Andrew J. Rice, Augustin Rigolet, Adriana Romero-Otero, Luis Rodrigo Rosas-Becerra, Pablo Y. Rosiles, Adriano Rutz, Byeol Ryu, Libby Ann Sahadeo, Murrel Saldanha, Luca Salvi, Eduardo Sánchez-Carvajal, Christian Santos-Medellin, Nicolau Sbaraini, Sydney M. Schoellhorn, Clemens Schumm, Ludek Sehnal, Nelly Selem, Anjali D. Shah, Tania K. Shishido, Simon Sieber, Velina Silviani, Garima Singh, Hemant Singh, Nika Sokolova, Eva C. Sonnenschein, Margherita Sosio, Sven T. Sowa, Karin Steffen, Evi Stegmann, Alena B. Streiff, Alena Strüder, Frank Surup, Tiziana Svenningsen, Douglas Sweeney, Judit Szenei, Azat Tagirdzhanov, Bin Tan, Matthew J. Tarnowski, Barbara R. Terlouw, Thomas Rey, Nicola U. Thome, Laura Rosina Torres Ortega, Thomas Tørring, Marla Trindade, Andrew W. Truman, Marie Tvilum, Daniel W. Udwary, Christoph Ulbricht, Lisa Vader, Gilles P. van Wezel, Max Walmsley, Randika Warnasinghe, Heiner G. Weddeling, Angus N.M. Weir, Katherine Williams, Sam E. Williams, Thomas E. Witte, Steffaney M. Wood Rocca, Keith Yamada, Dong Yang, Dongsoo Yang, Jingwei Yu, Zhenyi Zhou, Nadine Ziemert, Lukas Zimmer, Alina Zimmermann, Christian Zimmermann, Justin J.J. van der Hooft, Roger G. Linington, Tilmann Weber, Marnix H. Medema
  • Wageningen University & Research
  • Technical University of Denmark
  • Helmholtz Centre for Infection Research
  • The University of Sydney
  • University of Konstanz
  • Myria Biosciences AG
  • University of Florida
  • Ginkgo Bioworks
  • University of Western Australia
  • Technische Universität Dresden
  • The University of Auckland
  • Newcastle University
  • Sutro Biopharma
  • Institut Pertanian Bogor
  • Goethe University Frankfurt
  • LOEWE Center for Translational Biodiversity Genomics (TBG)
  • Senckenberg Gesellschaft für Naturforschung
  • University of Warwick
  • The University of Tokyo
  • University of Tübingen
  • Saarland University
  • Université Paris Cité
  • Translational Genome Mining for Natural Products
  • Rothamsted Research
  • National Agri-Food and Biomanufacturing Institute
  • Regional Centre for Biotechnology
  • University of Northern British Columbia
  • Norwich Research Park
  • Latvian Institute of Organic Synthesis
  • Oregon State University
  • University of California at Santa Barbara
  • Swiss Federal Institute of Aquatic Science and Technology
  • Utrecht University
  • University of Exeter
  • University of Basel
  • Shanghai Jiao Tong University
  • University of Johannesburg
  • Omnia Holdings Ltd
  • Kochi University
  • University of Utah
  • Instituto Tecnologico de Estudios Superiores de Monterrey
  • Purdue University
  • Universidade Estadual de Campinas
  • University of Technology- Iraq
  • Tennessee State University
  • Swansea University
  • Universidad Nacional Autónoma de México
  • King Saud University
  • Leiden University
  • University of California at San Diego
  • Instituto Politécnico Nacional
  • University of Manitoba
  • University of Illinois at Urbana-Champaign
  • University of Bonn
  • University of Marburg
  • Universidad Nacional Mayor de San Marcos
  • Universidade Federal do Rio de Janeiro
  • Humboldt University of Berlin
  • University of Greifswald
  • Campus Universitario de Teatinos
  • Royal Netherlands Academy of Arts and Sciences
  • University of Leeds
  • University of A Coruna
  • University of Minho
  • University of Málaga
  • University of Porto
  • Technical University of Braunschweig
  • Yeungnam University
  • Sookmyung Women's University
  • Centraalbureau voor Schimmelcultures
  • University of Manchester
  • Innovative Genomics Institute
  • University of California at Berkeley
  • Université Paris-Saclay
  • Czech Academy of Sciences
  • Stazione Zoologica Anton Dohrn Napoli
  • University of Antwerp
  • University of Bayreuth
  • Swiss Institute of Bioinformatics
  • University of Helsinki
  • National Research and Innovation Agency Republic of Indonesia
  • J. Craig Venter Institute
  • Naicons S.r.l.
  • University of Parma
  • Leibniz University Hannover
  • Flanders Institute for Biotechnology
  • KU Leuven
  • German Collection of Microorganisms and Cell Cultures
  • Carnegie Institution of Washington
  • University of Michigan, Ann Arbor
  • University of Groningen
  • The University of Hong Kong
  • Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute
  • McMaster University
  • SINTEF
  • Corteva Agriscience
  • Seoul National University
  • National Institutes of Health
  • VTT Technical Research Centre of Finland Ltd.
  • Florida State University
  • Chonnam National University
  • Dongguk University
  • Korea Advanced Institute of Science and Technology
  • University of Delaware
  • Endogenomiks
  • U-MaMi Centre of Excellence
  • De La Salle University
  • De La Salle University-Manila
  • University of Strathclyde
  • Victoria University of Wellington
  • Aarhus University
  • University of Turku
  • Free University of Berlin
  • Ivan Franko National University of L'viv
  • German-Ukrainian Core of Excellence in Natural Products Research (CENtR)
  • Lawrence Berkeley National Laboratory
  • University of Costa Rica
  • CeNAT-CONARE
  • University of Melbourne
  • Swiss Federal Institute of Technology Zurich
  • University of California at Davis
  • Universidad Técnica Federico Santa Maria
  • University of North Texas
  • Masaryk University
  • University of Bristol
  • University of Zurich
  • University of Padua
  • Vanderbilt University
  • Partner Site Tübingen
  • De Sangosse
  • CNRS
  • University of the Western Cape
  • United States Department of Energy
  • Rosalind Franklin Institute
  • University of the West of England
  • University of Ottawa
  • Korea University
  • Southern University of Science and Technology
  • Zhejiang University of Technology
  • TU Wien
  • Simon Fraser University

Research output: Contribution to journalArticlepeer-review

163 Scopus citations

Abstract

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

Original languageEnglish
Pages (from-to)D678-D690
JournalNucleic Acids Research
Volume53
Issue numberD1
DOIs
StatePublished - 6 Jan 2025

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