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

Author(s)Terlouw, Barbara R.
Author(s)Blin, Kai
Author(s)Navarro-Muñoz, Jorge C.
Author(s)Avalon, Nicole E.
Author(s)Chevrette, Marc G.
Author(s)Egbert, Susan
Author(s)Lee, Sanghoon
Author(s)Meijer, David
Author(s)Recchia, Michael J. J.
Author(s)Reitz, Zachary L.
Author(s)van Santen, Jeffrey A.
Author(s)Selem-Mojica, Nelly
Author(s)Tørring, Thomas
Author(s)Zaroubi, Liana
Author(s)Alanjary, Mohammad
Author(s)Aleti, Gajender
Author(s)Aguilar, César
Author(s)Al-Salihi, Suhad A. A.
Author(s)Augustijn, Hannah E.
Author(s)Avelar-Rivas, J. Abraham
Author(s)Avitia-Domínguez, Luis A.
Author(s)Barona-Gómez, Francisco
Author(s)Bernaldo-Agüero, Jordan
Author(s)Bielinski, Vincent A.
Author(s)Biermann, Friederike
Author(s)Booth, Thomas J.
Author(s)Carrion Bravo, Victor J.
Author(s)Castelo-Branco, Raquel
Author(s)Chagas, Fernanda O.
Author(s)Cruz-Morales, Pablo
Author(s)Du, Chao
Author(s)Duncan, Katherine R.
Author(s)Gavriilidou, Athina
Author(s)Gayrard, Damien
Author(s)Gutiérrez-García, Karina
Author(s)Haslinger, Kristina
Author(s)Helfrich, Eric J. N.
Author(s)van der Hooft, Justin J. J.
Author(s)Jati, Afif P.
Author(s)Kalkreuter, Edward
Author(s)Kalyvas, Nikolaos
Author(s)Kang, Kyo Bin
Author(s)Kautsar, Satria
Author(s)Kim, Wonyong
Author(s)Kunjapur, Aditya M.
Author(s)Li, Yong-Xin
Author(s)Lin, Geng-Min
Author(s)Loureiro, Catarina
Author(s)Louwen, Joris J. R.
Author(s)Louwen, Nico L. L.
Author(s)Lund, George
Author(s)Parra, Jonathan
Author(s)Philmus, Benjamin
Author(s)Pourmohsenin, Bita
Author(s)Pronk, Lotte J. U.
Author(s)Rego, Adriana
Author(s)Rex, Devasahayam Arokia Balaya
Author(s)Robinson, Serina
Author(s)Rosas-Becerra, L. Rodrigo
Author(s)Roxborough, Eve T.
Author(s)Schorn, Michelle A.
Author(s)Scobie, Darren J.
Author(s)Singh, Kumar Saurabh
Author(s)Sokolova, Nika
Author(s)Tang, Xiaoyu
Author(s)Udwary, Daniel
Author(s)Vigneshwari, Aruna
Author(s)Vind, Kristiina
Author(s)Vromans, Sophie P. J. M. Vromans
Author(s)Waschulin, Valentin
Author(s)Williams, Sam E.
Author(s)Winter, Jaclyn M.
Author(s)Witte, Thomas E.
Author(s)Xie, Huali
Author(s)Yang, Dong
Author(s)Yu, Jingwei
Author(s)Zdouc, Mitja
Author(s)Zhong, Zheng
Author(s)Collemare, Jérôme
Author(s)Linington, Roger G.
Author(s)Weber, Tilmann
Author(s)Medema, Marnix H.
Date Accessioned2023-01-24T16:36:07Z
Date Available2023-01-24T16:36:07Z
Publication Date0022-11-18
DescriptionThis article was originally published in Nucleic Acids Research. The version of record is available at: https://doi.org/10.1093/nar/gkac1049
AbstractWith 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/.
SponsorERC Starting Grant [948770-DECIPHER to M.H.M.]; Novo Nordisk Foundation [NNF20CC0035580, NNF16OC0021746 to T.W]; Danish National Research Foundation [DNRF137 to T.W]; National Center for Complementary and Integrative Health (NCCIH) of the National Institutes of Health [U24AT010811 to R.L. and F32AT011475 to N.E.A]; Natural Sciences and Engineering Council of Canada Discovery grant [to R.L.]; Netherlands Organization for Scientific Research (NWO) Veni Science Grant [VI.Veni.202.130 to M.A]; European Union Horizon 2020 projects CARTNET [765147], SECRETed [101000794] and MARBLES [101000392]; Horizon 2020 Marie Skłodowska-Curie Actions [893122 to K.H.]; Horizon 2020 Marie Sklodowska-Curie Individual Fellowship [MSCA-IF-EF-ST-897121 to M.A.S.]; U.S. Department of Energy [DE-AC02-05CH11231]; University of Strathclyde PhD Research Excellence Award [to D.S.]; Consejo Nacional de Ciencia y Tecnología (CONACyT) [757173 to L.R.R.-B.]; Portuguese Science and Technology Foundation (FCT) fellowship [SFRH/BD/140567/2018 to A.R.]; U.S. National Science Foundation [CBET-2032243 to A.M.K]; National Research Foundation of Korea [NRF-2022R1C1C2004118 and NRF-2020R1C1C1004046]; National Institutes of Health [GM134688 to E.K. and 1R01AI155694 to J.M.W.]; Netherlands eScience Center (NLeSC) Accelerating Scientific Discoveries Grant [ASDI.2017.030 to J.J.J.v.d.H.]; Deutsche Forschungsgemeinschaft [398967434-TRR 261]; UKRI Biotechnology and Biological Sciences Research Council [BBSRC; BB/R022054/1 and BB/W013959/1]; UK government Department for Environment, Food and Rural Affairs [project DEEPEND: deep ocean resources and biodiscovery]; Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro [E-26/211.314/2019]; Fundaçao para a Ciencia e Tecnologia (FCT) fellowship [SFRH/BD/136367/2018 to R.C.B.]; German Chemical Industry scholarship [to F.B.]; Cooperative Research Centres Projects scheme [CRCPFIVE000119 to T.J.B.]; Consejo Nacional de Ciencia y Tecnología (CONACyT) [735867 to J.B-A.]; Natural Sciences and Engineering Council of Canada PGSD fellowship [to L.Z.]; Natural Sciences and Engineering Council of Canada PGSD fellowship [to M.R.]; Odo van Vloten foundation [to J.N.-M.]; LOEWE Center for Translational Biodiversity Genomics (LOEWE TBG), Funds of the Chemical Industry Germany; Rothamsted Science Initiatives Catalyst Award scheme grant ‘Microbial natural product discovery pipeline for next generation fungicides’. Funding for open access charge: European Research Council. Conflict of interest statement. J.J.J.vdH. is a member of the Scientific Advisory Board of NAICONS Srl., Milano, Italy. A.M.K. is a co-founder of Nitro Biosciences, Inc. M.H.M. is on the scientific advisory board of Hexagon Bio and co-founder of Design Pharmaceuticals.
CitationTerlouw, Barbara R, Kai Blin, Jorge C Navarro-Muñoz, Nicole E Avalon, Marc G Chevrette, Susan Egbert, Sanghoon Lee, et al. “MIBiG 3.0: A Community-Driven Effort to Annotate Experimentally Validated Biosynthetic Gene Clusters.” Nucleic Acids Research 51, no. D1 (January 6, 2023): D603–10. https://doi.org/10.1093/nar/gkac1049.
PublisherNucleic Acids Research
TitleMIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
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