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

Terlouw,Barbara R.1; Blin,Kai2; Navarro-Muñoz,Jorge C.1,3; Avalon,Nicole E.4; Chevrette,Marc G.5; Egbert,Susan6; Lee,Sanghoon7; Meijer,David1; Recchia,Michael J.J.7; Reitz,Zachary L.1; van Santen,Jeffrey A.7,8; Selem-Mojica,Nelly9; Tørring,Thomas10; Zaroubi,Liana7; Alanjary,Mohammad1; Aleti,Gajender11; Aguilar,César12; Al-Salihi,Suhad A.A.13; Augustijn,Hannah E.1,14; Avelar-Rivas,J. Abraham15; Avitia-Domínguez,Luis A.14,15; Barona-Gómez,Francisco14,15; Bernaldo-Agüero,Jordan16; Bielinski,Vincent A.17; Biermann,Friederike1,18,19; Booth,Thomas J.2,20; Carrion Bravo,Victor J.14,21,22; Castelo-Branco,Raquel23,24; Chagas,Fernanda O.25; Cruz-Morales,Pablo2; Du,Chao14; Duncan,Katherine R.26; Gavriilidou,Athina27,28; Gayrard,Damien29; Gutiérrez-García,Karina30; Haslinger,Kristina31; Helfrich,Eric J.N.18,19; van der Hooft,Justin J.J.1,32; Jati,Afif P.33; Kalkreuter,Edward34; Kalyvas,Nikolaos3; Kang,Kyo Bin35; Kautsar,Satria34; Kim,Wonyong36; Kunjapur,Aditya M.37; Li,Yong Xin38; Lin,Geng Min39; Loureiro,Catarina40; Louwen,Joris J.R.1; Louwen,Nico L.L.1; Lund,George41; Parra,Jonathan42,43,44; Philmus,Benjamin45; Pourmohsenin,Bita27,28; Pronk,Lotte J.U.1; Rego,Adriana23,46; Rex,Devasahayam Arokia Balaya47; Robinson,Serina48; Rosas-Becerra,L. Rodrigo14,15; Roxborough,Eve T.49; Schorn,Michelle A.40; Scobie,Darren J.26; Singh,Kumar Saurabh1; Sokolova,Nika31; Tang,Xiaoyu50; Udwary,Daniel51; Vigneshwari,Aruna52; Vind,Kristiina53,54; Vromans,Sophie P.J.M.1; Waschulin,Valentin55; Williams,Sam E.56; Winter,Jaclyn M.57; Witte,Thomas E.58; Xie,Huali1,59; Yang,Dong60; Yu,Jingwei61; Zdouc,Mitja1; Zhong,Zheng40; Collemare,Jérôme3; Linington,Roger G.7; Weber,Tilmann2; Medema,Marnix H.1,14
Corresponding AuthorWeber,Tilmann; Medema,Marnix H.
Publication Years
Source Title

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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Funding Project
Horizon 2020[101000392] ; Horizon 2020[101000794] ; National Institutes of Health[1R01AI155694] ; National Research Foundation of Korea[2020R1C1C1004046] ; National Research Foundation of Korea[2022R1C1C2004118] ; National Science Foundation[2032243] ; Deutsche Forschungsgemeinschaft[398967434-TRR 261] ; Consejo Tamaulipeco de Ciencia y Tecnología[735867] ; Consejo Tamaulipeco de Ciencia y Tecnología[757173] ; Horizon 2020[765147] ; Horizon 2020[893122] ; European Research Council[948770] ; Biotechnology and Biological Sciences Research Council[BB/R022054/1] ; Biotechnology and Biological Sciences Research Council[BB/W013959/1] ; U.S. Department of Energy[DE-AC02-05CH11231] ; Danmarks Grundforskningsfond[DNRF137] ; Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro[E-26/211.314/2019] ; National Institutes of Health[F32AT011475] ; National Institutes of Health[GM134688] ; Horizon 2020[MSCA-IF-EF-ST-897121] ; Novo Nordisk Fonden[NNF16OC0021746] ; Novo Nordisk Fonden[NNF20CC0035580] ; Fundação para a Ciência e a Tecnologia[SFRH/BD/136367/2018] ; Fundação para a Ciência e a Tecnologia[SFRH/BD/140567/2018] ; National Institutes of Health[U24AT010811] ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek[VI.Veni.202.130]
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Scopus EID
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Citation statistics
Cited Times [WOS]:1
Document TypeJournal Article
DepartmentSUSTech-Peking University National Institute of Plants and Food
1.Bioinformatics Group,Wageningen University,Wageningen,Droevendaalsesteeg,6708 PB,Netherlands
2.Novo Nordisk Foundation Center for Biosustainability,Technical University of Denmark,Kgs. Lyngby,Denmark
3.Westerdijk Fungal Biodiversity Institute,Utrecht,Uppsalalaan 8,3584 CT,Netherlands
4.Scripps Institution of Oceanography,University of California San Diego,9500 Gilman Drive, La Jolla,92093-0212,United States
5.Department of Microbiology and Cell Science,University of Florida,Gainesville,32611,United States
6.Department of Chemistry,University of Manitoba,Winnipeg,66 Chancellors Cir,R3T 2N2,Canada
7.Department of Chemistry,Simon Fraser University,Burnaby,8888 University Drive,V5A 1S6,Canada
8.Unnatural Products,Santa Cruz,2161 Delaware Ave. Suite A,95060,United States
9.Centro de Ciencias Matemáticas UNAM,Morelia,Mexico
10.Department of Biological and Chemical Engineering,Aarhus University,Denmark
11.Food and Animal Sciences,Department of Agricultural and Environmental Sciences,Tennessee State University,Nashville,37209,United States
12.Department of Chemistry,Purdue University,West Lafayette,United States
13.Department of Applied Sciences,University of Technology,Iraq
14.Institute of Biology,Leiden University,Leiden,Sylviusweg 72,2333BE,Netherlands
15.Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada,Irapuato,Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, Gto.,CP 36824,Mexico
16.Departamento de Microbiología Molecular,Instituto de Biotecnología,Universidad Nacional Autónoma de México,Cuernavaca,Morelos,Mexico
17.Synthetic Biology and Bioenergy Group,J. Craig Venter Institute,La Jolla,92037,United States
18.Institute of Molecular Bio Science,Goethe-University Frankfurt,Frankfurt am Main,D-60438,Germany
19.LOEWE Center for Translational Biodiversity Genomics (TBG),Frankfurt am Main,Senckenberganlage 25,60325,Germany
20.School of Molecular Sciences,University of Western Australia,Perth,Australia
21.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
22.Department of Microbial Ecology,Netherlands Institute of Ecology (NIOO-KNAW),Wageningen,Netherlands
23.Interdisciplinary Centre of Marine and Environmental Research (CIIMAR),University of Porto,Portugal
24.Faculty of Sciences,University of Porto,Porto,4150-179,Portugal
25.Instituto de Pesquisas de Produtos Naturais Walter Mors,Universidade Federal do Rio de Janeiro,Rio de Janeiro,RJ,21941-599,Brazil
26.University of Strathclyde,Strathclyde Institute of Pharmacy and Biomedical Sciences,Glasgow,141 Cathedral Street,G4 ORE,United Kingdom
27.Translational Genome Mining for Natural Products,Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT),University of Tübingen,Tübingen,Germany
28.Interfaculty Institute for Biomedical Informatics (IBMI),University of Tübingen,Tübingen,Germany
29.Department of Molecular Microbiology,John Innes Centre,Norwich,Norwich Research Park,NR4 7UH,United Kingdom
30.Department of Embryology,Carnegie Institution for Science,Baltimore,3520 San Martin Drive,21218,United States
31.Department of Chemical and Pharmaceutical Biology,Groningen Research Institute of Pharmacy,University of Groningen,Groningen,Antonius Deusinglaan 1,9713 AV,Netherlands
32.Department of Biochemistry,University of Johannesburg,Johannesburg,Auckland Park,2006,South Africa
33.Indonesian Society of Bioinformatics And Biodiversity,Indonesia
34.Department of Chemistry,University of Florida Scripps Biomedical Research,Jupiter,110 Scripps Way,33458,United States
35.College of Pharmacy,Sookmyung Women’s University,Seoul,South Korea
36.Korean Lichen Research Institute,Sunchon National Universtiy,Suncheon,South Korea
37.Department of Chemical and Biomolecular Engineering,University of Delaware,Newark,19716,United States
38.Department of Chemistry,University of Hong Kong,Hong Kong,Pokfulam Road,Hong Kong
39.Department of Biological Engineering,Massachusetts Institute of Technology,Cambridge,United States
40.Laboratory of Microbiology,Wageningen University,Wageningen,Stippeneng 4,6708WE,Netherlands
41.Sustainable Soils and Crops,Rothamsted Research,Harpenden,Hertfordshire,United Kingdom
42.Instituto de Investigaciones Farmacéuticas (INIFAR),Facultad de Farmacia,Universidad de Costa Rica,San José,11501-2060,Costa Rica
43.Centro de Investigaciones en Productos Naturales (CIPRONA),Universidad de Costa Rica,San José,11501-2060,Costa Rica
44.Centro Nacional de Innovaciones Biotecnológicas (CENIBiot),CeNAT-CONARE,San José,1174-1200,Costa Rica
45.Department of Pharmaceutical Sciences,Oregon State University,United States
46.Institute of Biomedical Sciences Abel Salazar (ICBAS),University of Porto,Portugal
47.Centre for Integrative Omics Data Science,Yenepoya (Deemed to be University),Mangalore,575018,India
48.Department of Environmental Microbiology,Eawag: Swiss Federal Institute for Aquatic Science and Technology,Dübendorf,Überlandstrasse 133,CH-8600,Switzerland
49.School of Chemistry,University of Nottingham,Nottingham,University Park,NG7 2RD,United Kingdom
50.Institute of Chemical Biology,Shenzhen Bay Laboratory,Shenzhen,518132,China
51.DOE Joint Genome Institute,Lawrence Berkeley National Lab,Berkeley,United States
52.Department of Microbiology,University of Szeged,Hungary
53.Host-Microbe Interactomics Group,Wageningen University,Wageningen,6708 WD,Netherlands
54.NAICONS Srl,Milan,20139,Italy
55.School of Life Sciences,University of Warwick,Coventry,CV4 7AL,United Kingdom
56.School of Biochemistry,University of Bristol,Bristol,University Walk,BS8 1TD,United Kingdom
57.Department of Medicinal Chemistry,University of Utah,Salt Lake City,84112,United States
58.Department of Chemistry and Biomolecular Sciences,University of Ottawa,Ottawa,Canada
59.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
60.Department of Chemistry,Natural Products Discovery Center,UF Scripps Biomedical Research,University of Florida,Jupiter,33458,United States
61.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
Recommended Citation
GB/T 7714
Terlouw,Barbara R.,Blin,Kai,Navarro-Muñoz,Jorge C.,et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters[J]. Nucleic Acids Research,2023,51(D1):D603-D610.
Terlouw,Barbara R..,Blin,Kai.,Navarro-Muñoz,Jorge C..,Avalon,Nicole E..,Chevrette,Marc G..,...&Medema,Marnix H..(2023).MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.Nucleic Acids Research,51(D1),D603-D610.
Terlouw,Barbara R.,et al."MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters".Nucleic Acids Research 51.D1(2023):D603-D610.
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