DOE OSTI · 2481018
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
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/.
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[Institute for Molecular Bio Science, Goethe University Frankfurt , Max-von-Laue Strasse 9, 60438 Frankfurt am Main,; LOEWE Center for Translational Biodiversity Genomics (TBG) , Senckenberganlage 25, 60325 Frankfurt am Main,; Senckenberg Society for Nature Research , Senckenberganlage 25, 60325 Frankfurt am Main,], Jenner, Matthew [Department of Chemistry, University of Warwick , Gibbet Hill Rd, Coventry , CV4 7AL ,; Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick , Gibbet Hill Rd, Coventry , CV4 7AL ,], Katsuyama, Yohei [Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo , 1-1-1, Yayoi, Bunkyo-ku, Tokyo , 113-8657 ,; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo , 1-1-1, Yayoi, Bunkyo-ku, Tokyo , 113-8657 ,], Korenskaia, Aleksandra [Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen , Sand 14, 72076 Tübingen,], Krug, Daniel [Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1 , 66123 Saarbrücken,; Saarland University, Campus E8.1 , 66123 Saarbrücken,; Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) , Inhoffenstr. 7, 38124 Braunschweig ,], Libis, Vincent [Université Paris Cité - Inserm Unit 1284 , 75015 Paris ,; Translational Genome Mining for Natural Products, Generare Bioscience , 75011 Paris , Île-de-France,], Lund, George A [Sustainable Soils and Crops, Rothamsted Research , West Common, Harpenden , Hertfordshire , AL5 2JQ ,], Mantri, Shrikant [Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI) , Sector 81, S.A.S. 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Matthews Ave, Urbana , IL 61801 ,; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign , 1206 W. Gregory Drive, Urbana , IL 61801 ,], Baunach, Martin [Institute of Pharmaceutical Biology, University of Bonn , Nussallee 6, 53115 Bonn ,], Beemelmanns, Christine [Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1 , 66123 Saarbrücken,; Saarland University, Campus E8.1 , 66123 Saarbrücken,], Beqaj, Dardan [Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen , Auf der Morgenstelle 28, 72076 , Tübingen,], Berger, Tim [Institute of Pharmaceutical Biology and Biotechnology, University of Marburg , Robert-Koch-Str. 4, 35037 Marburg ,], Bernaldo-Agüero, Jordan [Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 , Chamilpa, 62210 Cuernavaca , Morelos ,; Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos , Av. 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Carlos Chagas Filho, 373 - Bloco H - Cidade Universitária, Rio de Janeiro - RJ, 21941 -599,], Borriss, Rainer [Department of Biology, Humboldt University Berlin , Invaliden-Str. 42, 10115 Berlin ,; Institute of Marine Biotechnology (IMaB), University of Greifswald ,Walter-Rathenau-Str. 49A, 17489 Greifswald ,], Breitenbach, Milena [Institute for Molecular Bio Science, Goethe University Frankfurt , Max-von-Laue Strasse 9, 60438 Frankfurt am Main,; LOEWE Center for Translational Biodiversity Genomics (TBG) , Senckenberganlage 25, 60325 Frankfurt am Main,], Bretscher, Kevin M [Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden ,; Department of Crop Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Campus Universitario de Teatinos , 29010 , Málaga,; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Droevendaalsesteeg 10 6708 PB Wageningen ,], Brigham, Michael W [School of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Leeds , 6 Clarendon Way, Woodhouse, Leeds , LS2 3AA ,], Buedenbender, Larissa [CICA – Centro Interdisciplinar de Química e Bioloxía, Universidade da Coruña, As Carballeiras, s/n, Campus de Elviña , 15071 A Coruña,], Bulcock, Brodie W [School of Molecular Sciences, University of Western Australia , 35 Stirling Highway, Perth 6009 ,], Cano-Prieto, Carolina [The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Building 220, Søltofts Plads, 2800 Kongens Lyngby,], Capela, João [Centre of Biological Engineering, University of Minho , 4710-057 , Braga ,], Carrion, Victor J [Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden ,; Department of Crop Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Campus Universitario de Teatinos , 29010 , Málaga,; Department of Microbiology, Faculty of Science, Campus Universitario de Teatinos s/n, University of Málaga , 29010 Málaga,], Carter, Riley S [Department of Chemistry, University of Illinois Urbana-Champaign , 600 S. Matthews Ave, Urbana , IL 61801 ,; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign , 1206 W. Gregory Drive, Urbana , IL 61801 ,], Castelo-Branco, Raquel [Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto , 4450-208 Matosinhos ,], Castro-Falcón, Gabriel [Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , 9500 Gilman Drive, La Jolla , CA 92093-0212 ,], Chagas, Fernanda O [Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro , CCS - Av. Carlos Chagas Filho, 373 - Bloco H - Cidade Universitária, Rio de Janeiro - RJ, 21941 -599,], Charria-Girón, Esteban [Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI) , Inhoffenstr. 7, 38124 Braunschweig ,; Institute of Microbiology, Technische Universität Braunschweig , Spielmannstraße 7, 38106 Braunschweig ,], Chaudhri, Ayesha Ahmed [Institute for Molecular Bio Science, Goethe University Frankfurt , Max-von-Laue Strasse 9, 60438 Frankfurt am Main,; LOEWE Center for Translational Biodiversity Genomics (TBG) , Senckenberganlage 25, 60325 Frankfurt am Main,], Chaudhry, Vasvi [Microbial Interactions in Plant Ecosystems, IMIT/ZMBP, Eberhard Karls University of Tübingen , 72076 Tübingen,], Choi, Hyukjae [College of Pharmacy, Yeungnam University , 280 Daehak-ro Gyeongsan-Si, Gyeongsangbuk-do 38541 ,; Research Institute of Cell Culture, Yeungnam University , 280 Daehak-ro Gyeongsan-Si, Gyeongsangbuk-do 38541 ,], Choi, Yukyung [College of Pharmacy and Drug Information Research Institute, Sookmyung Women's University , 100 Cheongpa-ro 47 gil, Seoul 04310 ,], Choupannejad, Roya [Fungal Natural Products, Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584CT Utrecht ,], Chromy, Jakub [Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester , 131 Princess Street, Manchester M1 7DN ,], Donahey, Melinda S Chue [Department of Microbiology and Cell Science, University of Florida , 1355 Museum Drive, Gainesville , Florida , 32611 ,] (ORCID:0000000235657737), Collemare, Jérôme [Fungal Natural Products, Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584CT Utrecht ,], Connolly, Jack A [Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester , 131 Princess Street, Manchester M1 7DN ,], Creamer, Kaitlin E [Innovative Genomics Institute, University of California Berkeley , 2151 Berkeley Way, Berkeley , CA 94720 ,; Department of Earth and Planetary Science, University of California , 307 McCone Hall Berkeley, CA 94720-4767 ,], Crüsemann, Max [Institute of Pharmaceutical Biology, University of Bonn , Nussallee 6, 53115 Bonn ,], Cruz, Andres Arredondo [Escuela Nacional de Estudios Superiores Unidad Leon, Universidad Nacional Autonoma de Mexico , Blv. UNAM # 2011 , Predio El Saucillo y, Comunidad de los Tepetates, El Potrero, 37684 León de los Aldama, Gto.,], Cumsille, Andres [Department of Microbiology and Cell Science, University of Florida , 1355 Museum Drive, Gainesville , Florida , 32611 ,], Dallery, Jean-Felix [Université Paris-Saclay , INRAE, UR BIOGER, 22 place de l’Agronomie, 91120 Palaiseau ,], Damas-Ramos, Luis Caleb [The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Building 220, Søltofts Plads, 2800 Kongens Lyngby,], Damiani, Tito [IOCB Prague, Czech Academy of Science , Flemingovo náměstí 542/2, 160 00 Praha 6,], de Kruijff, Martinus [Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1 , 66123 Saarbrücken,], Martín, Belén Delgado [Department of Microbiology, Faculty of Science, Campus Universitario de Teatinos s/n, University of Málaga , 29010 Málaga,], Sala, Gerardo Della [Department of Ecosustainable Marine Biotechnology , Stazione Zoologica Anton Dohrn, Giardini del Molosiglio, Via A.F. Acton 55, 80133 Naples ,], Dillen, Jelle [Department of Bioscience Engineering, Research Group Laboratory of Applied Microbiology and Biotechnology, University of Antwerp , Groenenborgerlaan 171, 2020 Antwerp,]. 2024-12-09. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. https://doi.org/10.1093/nar%2Fgkae1115
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