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

A - Papers appearing in refereed journals

Terlouw, B. R., Blin, K., Navarro-Munoz, J. C., Avalon, N. E., Chevrette, M. G., Egbert, S., Meijer, D., Recchia, M. J. J., Reitz, Z. L., Santen, J. A. V., Selem-Mojica, N., Torring, T., Zaroubi, L., Alanjary, M., Aleti, G., Aguilar, C., Al-Salihi, S. A. A., Augustijn, H. E., Avelar-Rivas, J. A., Avitia-Domınguez, L. A., Barona-Gomez, F., Bernaldo-Aguero, J., Bielinski, V. A., Biermann, F., Booth, T. J., Bravo, V. J. C., Castelo-Branco, R., Chagas, F. O., Cruz-Morales, P., Du, C., Duncan, K. R., Gavriilidou, A., Gayrard, D., Gutierrez-Garcıa, K., Haslinger, K., Helfrich, E. J. N., Hooft, J. J. V. D., Jati, A. P., Kalkreuter, E., Kalyvas, N., Kang, K. B., Kautsar, S., Kim, W., Kunjapur, A. M., Lee, W-S., Li, Y., Lin, G., Loureiro, C., Louwen, J. J. R., Louwen, N. L., Lund, G., Parra, J., Philmus, B., Pourmohsenin, B., Pronk, L. J. U., Rego, A., Rex, D. A. B., Robinson, S., Rosas-Becerra, L. R., Roxborough, E. T., Schorn, M. A., Scobie, D. J., Sing, K. S., Sokolova, N., Tang, X., Udwary, D., Vigneshwari, A., Vind, K., Vromans, S. P. J. M., Waschulin, V., Williams, S. E., Winter, J. M., Witte, T. E., Yang, H. X. D., Yu, J., Zdouc, M., Zhong, Z., Collemare, J., Linington, R. G., Weber, T. and Medema, M. H. 2023. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Research. 51 (D1), pp. D606-D610. https://doi.org/10.1093/nar/gkac1049

AuthorsTerlouw, B. R., Blin, K., Navarro-Munoz, J. C., Avalon, N. E., Chevrette, M. G., Egbert, S., Meijer, D., Recchia, M. J. J., Reitz, Z. L., Santen, J. A. V., Selem-Mojica, N., Torring, T., Zaroubi, L., Alanjary, M., Aleti, G., Aguilar, C., Al-Salihi, S. A. A., Augustijn, H. E., Avelar-Rivas, J. A., Avitia-Domınguez, L. A., Barona-Gomez, F., Bernaldo-Aguero, J., Bielinski, V. A., Biermann, F., Booth, T. J., Bravo, V. J. C., Castelo-Branco, R., Chagas, F. O., Cruz-Morales, P., Du, C., Duncan, K. R., Gavriilidou, A., Gayrard, D., Gutierrez-Garcıa, K., Haslinger, K., Helfrich, E. J. N., Hooft, J. J. V. D., Jati, A. P., Kalkreuter, E., Kalyvas, N., Kang, K. B., Kautsar, S., Kim, W., Kunjapur, A. M., Lee, W-S., Li, Y., Lin, G., Loureiro, C., Louwen, J. J. R., Louwen, N. L., Lund, G., Parra, J., Philmus, B., Pourmohsenin, B., Pronk, L. J. U., Rego, A., Rex, D. A. B., Robinson, S., Rosas-Becerra, L. R., Roxborough, E. T., Schorn, M. A., Scobie, D. J., Sing, K. S., Sokolova, N., Tang, X., Udwary, D., Vigneshwari, A., Vind, K., Vromans, S. P. J. M., Waschulin, V., Williams, S. E., Winter, J. M., Witte, T. E., Yang, H. X. D., Yu, J., Zdouc, M., Zhong, Z., Collemare, J., Linington, R. G., Weber, T. and Medema, M. H.
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 upto-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/

Year of Publication2023
JournalNucleic Acids Research
Journal citation51 (D1), pp. D606-D610
Digital Object Identifier (DOI)https://doi.org/10.1093/nar/gkac1049
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeBB/R022054/1
BB/W013959/1
Publisher's version
Output statusPublished
Publication dates
Online18 Nov 2022
Publication process dates
Accepted21 Oct 2022
PublisherOxford University Press (OUP)
ISSN0305-1048

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