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

2022; Oxford University Press; Volume: 51; Issue: D1 Linguagem: Inglês

10.1093/nar/gkac1049

1362-4962

Barbara R. Terlouw, Kai Blin, Jorge C. Navarro-Muñoz, Nicole E. Avalon, Marc G. Chevrette, Susan Egbert, Sang Hyeon Lee, David Meijer, Michael J. J. Recchia, Zachary L. Reitz, Jeffrey A. van Santen, Nelly Sélem‐Mójica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A. A. Al-Salihi, Hannah E. Augustijn, J. Abraham Avelar‐Rivas, Luis A Avitia-Domínguez, Francisco Barona‐Gómez, Jordan Bernaldo-Agüero, Vincent A. Bielinski, Friederike Biermann, Thomas Booth, Víctor J. Carrión, Raquel Castelo‐Branco, Fernanda O. Chagas, Pablo Cruz‐Morales, Chao Du, Katherine Duncan, Athina Gavriilidou, Damien Gayrard, Karina Gutiérrez-García, Kristina Haslinger, Eric J. N. Helfrich, Justin J. J. van der Hooft, AFIF PRANAYA JATI, Edward Kalkreuter, Nikolaos Kalyvas, Kyo Bin Kang, Satria A. Kautsar, Wonyong Kim, Aditya M. Kunjapur, Yong‐Xin Li, Geng-Min Lin, Catarina Loureiro, Joris J. R. Louwen, Nico L L Louwen, George Lund, Jonathan Parra, Benjamin Philmus, Bita Pourmohsenin, Lotte J. U. Pronk, Adriana Rego, Rex Devasahayam Arokia Balaya, Serina L. Robinson, Luis Rodrigo Rosas-Becerra, Eve Tallulah Roxborough, Michelle Schorn, Darren J Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel W. Udwary, Aruna Vigneshwari, Kristiina Vind, Sophie P. J. M. Vromans, Valentin Waschulin, Sam E. Williams, Jaclyn M. Winter, Thomas E. Witte, Huali Xie, Dong Yang, Jingwei Yu, Mitja M. Zdouc, Zheng Zhong, Jérôme Collemare, Roger G. Linington, Tilmann Weber, Marnix H. Medema,

Microbial Metabolism and Applications

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/.