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Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG, Egbert S, Lee S, Meijer D, Recchia MJ, Reitz Z, van Santen J, Selem-Mojica N, Tørring T, Zaroubi L, Alanjary M, Aleti G, Aguilar C, Al-Salihi SA, Augustijn H, Avelar-Rivas J, Avitia-Domínguez L, Barona-Gómez F, Bernaldo-Agüero J, Bielinski VA, Biermann F, Booth T, Carrion Bravo V, Castelo-Branco R, Chagas F, Cruz-Morales P, Du C, Duncan K, Gavriilidou A, Gayrard D, Gutiérrez-García K, Haslinger K, Helfrich EN, van der Hooft JJ, Jati A, Kalkreuter E, Kalyvas N, Kang K, Kautsar S, Kim W, Kunjapur A, Li YX, Lin GM, Loureiro C, Louwen JR, Louwen NL, Lund G, Parra J, Philmus B, Pourmohsenin B, Pronk LU, Rego A, Rex D, Robinson S, Rosas-Becerra L, Roxborough E, Schorn M, Scobie D, Singh K, Sokolova N, Tang X, Udwary D, Vigneshwari A, Vind K, Vromans SJM, Waschulin V, Williams S, Winter J, Witte T, Xie H, Yang D, Yu J, Zdouc M, Zhong Z, Collemare J, Linington R, Weber T, Medema M. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res 2022; 51:D603-D610. [PMID: 36399496 PMCID: PMC9825592 DOI: 10.1093/nar/gkac1049] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 11/19/2022] Open
Abstract
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
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Affiliation(s)
| | | | - Jorge C Navarro-Muñoz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA
| | - Marc G Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Susan Egbert
- Department of Chemistry, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - David Meijer
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Michael J J Recchia
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada,Unnatural Products, 2161 Delaware Ave. Suite A, Santa Cruz, CA 95060, USA
| | | | - Thomas Tørring
- Department of Biological and Chemical Engineering, Aarhus University, Denmark
| | - Liana Zaroubi
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Gajender Aleti
- Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - J Abraham Avelar-Rivas
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Luis A Avitia-Domínguez
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Francisco Barona-Gómez
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Jordan Bernaldo-Agüero
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Thomas J Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark,School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Victor J Carrion Bravo
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal,Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
| | - Fernanda O Chagas
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Pablo Cruz-Morales
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Chao Du
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK
| | - Athina Gavriilidou
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Karina Gutiérrez-García
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Afif P Jati
- Indonesian Society of Bioinformatics And Biodiversity, Indonesia
| | - Edward Kalkreuter
- Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA
| | - Nikolaos Kalyvas
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Satria Kautsar
- Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National Universtiy, Suncheon, South Korea
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China
| | - Geng-Min Lin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Nico L L Louwen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - George Lund
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, 11501-2060, Costa Rica,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica,Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, USA
| | - Bita Pourmohsenin
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Lotte J U Pronk
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | | | - Serina Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - L Rodrigo Rosas-Becerra
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Eve T Roxborough
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Darren J Scobie
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK
| | - Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Nika Sokolova
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | | | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands,NAICONS Srl, 20139 Milan, Italy
| | - Sophie P J M Vromans
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Valentin Waschulin
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E Witte
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Huali Xie
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Key laboratory of Detection for Biotoxins, Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China
| | - Dong Yang
- Department of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | - Jingwei Yu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Mitja Zdouc
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Zheng Zhong
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Tilmann Weber
- Correspondence may also be addressed to Tilmann Weber. Tel: +45 24896132;
| | - Marnix H Medema
- To whom correspondence should be addressed. Tel: +31 317484706;
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