MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

A - Papers appearing in refereed journals

Zdouc, M. M., Blin, K., Louwen, N. L., Navarro, J., Loureiro, C., Bader, C. D., Bailey, C. B., Barra, L., Booth, T. J., Bozhuyuk, K. A., Cediel-Becerra, J. D., Charlop-Powers, Z., Chevrette, M. G., Chooi, Y. H., D’Agostino, P. M., Rond, T. D., Pup, E. D., Duncan, K. R., Gu, W., Hanif, N., Helfrich, E. J., Jenner, M., Katsuyama, Y., Korenskaia, A., Krug, D., Libis, V., Lund, G., Mantri, S., Morgan, K. D., Owen, C., Phan, C., Philmus, B., Reitz, Z. L., Robinson, S. L., Singh, K. S., Teufel, R., Tong, Y., Tugizimana, F., Ulanova, D., Winter, J. M., Aguilar, C., Akiyama, D. Y., Al-Salihi, S. A., Alanjary, M., Alberti, F., Aleti, G., Alharthi, S. A., Rojo, M. Y. A., Arishi, A. A., Augustijn, H. E., Avalon, N. E., Avelar-Rivas, J. A., Axt, K. K., Barbieri, H. B., Barbosa, J. C. J., Segato, L. G. B., Barrett, S. E., Baunach, M., Beemelmanns, C., Beqaj, D., Berger, T., Bernaldo-Aguero, J., Bettenbuhl, S. M., Bielinski, V. A., Biermann1, F., Borges, R. M., Borriss, R., Breitenbach, M., Bretscher, K. M., Brigham, M. W., Buedenbender, L., Bulcock, B. W., Cano-Prieto, C., Capela, J., Carrion, V. J., Carter, R. S., Castelo-Branco, R., Castro-Falcon, G., Chagas, F. O., Charria-Giron, E., Chaudhri, A. A., Chaudhry, V., Choi, H., Choi, Y., Choupannejad, R., Chromy, J., Donahey, M. S. C., Collemare, J., Connolly, J. A., Creamer, K. E., Crusemann, M., Cruz, A. A., Cumsille, A., Dallery, J., Damas-Ramos, L. C., Damiani, T., Kruijff, M. D., Martin, B. D., Sala, G. D., Dillen, J., Doering, D. T., Dommaraju, S. R., Durusu, S., Egbert, S., Ellerhorst, M., Faussurier, B., Fetter, A., Feuermann, M., Fewer, D. P., Foldi, J., Frediansyah, A., Garza, E. A., Gavriilidou, A., Gentile, A., Gerke, J., Gerstmans, H., Gomez-Escribano, J. P., Gonzalez-Salazar, L. A., Grayson, N. E., Greco, C., Gomez, J. E. G., Guerra, S., Flores, S. G., Gurevich, A., Gutierrez-Garcia, K., Hart, L., Haslinger, K., He, B., Hebra, T., Hemmann, J. L., Hindra, H., Hoing, L., Holland, D. C., Holme, J. E., Horch, T., Hrab, P., Hu, J., Huynh, T., Hwang, J., Lacovelli, R., Lftime, D., Lorio, M., Jayachandran, S., Jeong, E., Jing, J., Jung, J. J., Kakumu, Y., Kalkreuter, E., Kang, K. B., Kang, S., Kim, W., Kim, G. J., Kim, H., Kim, H. U., Klapper, M., Koetsier, R. A., Kollten, C., Kovacs, A. T., Kriukova, Y., Kubach, N., Kunjapur, A. M., Kushnareva, A. K., Kust, A., Lamber, J., Larralde, M., Larsen, N. J., Launay, A. P., Le, N., Lebeer, S., Lee, B. T., Lee, K., Lev, K. L., Li, S., Li, Y., Licona-Cassani, C., Lien, A., Liu, J., Lopez, J. A. V., Machushynets, N. V., Macias, M. I., Mahmud, T., Maleckis, M., Martinez-Martinez, A. M., Mast, Y., Maximo, M. F., McBride, C. M., McLellan, R. M., Bhatt, K. M., Melkonian, C., Merrild, A., Metsä-Ketela, M., Mitchell, D. A., Müller, A. V., Nguyen, G., Nguyen, H. T., Niedermeyer, T. H. J., O’Hare, J. H., Ossowicki, A., Ostash, B. O., Otani, H., Padva, L., Paliya, S., Pan, X., Panghal, M., Parade, D. S., Park, J., Parra, J., Rubio, M. P., Pham, H. T., Pidot, S. J., Piel, J., Pourmohsenin, B., Rakhmanov, M., Ramesh, S., Rasmussen, M. H., Rego, A., Reher, R., Rice, A. J., Rigolet, A., Romero-Otero, A., Rosas-Becerra, L. R., Rosiles, P. Y., Rutz, A., Ryu, B., Sahadeo, L., Saldanha, M., Salvi, L., Sánchez-Carvajal, E., Santos-Medellin, C., Sbaraini, N., Schoellhorn, S. M., Schumm, C., Sehnal, L., Selem, N., Shah, A. D., Shishido, T. K., Sieber, S., Silviani, V., Singh, G., Singh, H., Sokolova, N., Sonnenschein, E. C., Sosio, M., Sowa, S. T., Steffen, K., Stegmann, E., Streiff, A. B., Strüder, A., Surup, F., Svenningsen, T., Sweeney, D., Szenei, J., Tagirdzhanov, A., Tan, B., Tarnowski, M. J., Terlouw1, B. R., Rey, T., Thome, N. U., Ortega, L. R. T., Torring, T., Trindade, M., Truman, A. W., Tvilum, M., Udwary, D. W., Ulbricht, C., Vader, L., Wezel, G. P. V., Walmsley, M., Warnasinghe, R., Weddeling, H. G., Weir, A. N., Williams, K., Williams, S. E., Witte, T. E., Rocca, S. M. W., Yamada, K., Yang, D., Yang, D., Yu, J., Zhou, Z., Ziemert, N., Zimmer, L., Zimmermann, A., Zimmermann, C., Hooft, J. J. V. D., Linington, R. G., Weber, T. and Medema, M. H. 2025. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration. Nucleic Acids Research. 53 (D1), p. D678–D690. https://doi.org/10.1093/nar/gkae1115

AuthorsZdouc, M. M., Blin, K., Louwen, N. L., Navarro, J., Loureiro, C., Bader, C. D., Bailey, C. B., Barra, L., Booth, T. J., Bozhuyuk, K. A., Cediel-Becerra, J. D., Charlop-Powers, Z., Chevrette, M. G., Chooi, Y. H., D’Agostino, P. M., Rond, T. D., Pup, E. D., Duncan, K. R., Gu, W., Hanif, N., Helfrich, E. J., Jenner, M., Katsuyama, Y., Korenskaia, A., Krug, D., Libis, V., Lund, G., Mantri, S., Morgan, K. D., Owen, C., Phan, C., Philmus, B., Reitz, Z. L., Robinson, S. L., Singh, K. S., Teufel, R., Tong, Y., Tugizimana, F., Ulanova, D., Winter, J. M., Aguilar, C., Akiyama, D. Y., Al-Salihi, S. A., Alanjary, M., Alberti, F., Aleti, G., Alharthi, S. A., Rojo, M. Y. A., Arishi, A. A., Augustijn, H. E., Avalon, N. E., Avelar-Rivas, J. A., Axt, K. K., Barbieri, H. B., Barbosa, J. C. J., Segato, L. G. B., Barrett, S. E., Baunach, M., Beemelmanns, C., Beqaj, D., Berger, T., Bernaldo-Aguero, J., Bettenbuhl, S. M., Bielinski, V. A., Biermann1, F., Borges, R. M., Borriss, R., Breitenbach, M., Bretscher, K. M., Brigham, M. W., Buedenbender, L., Bulcock, B. W., Cano-Prieto, C., Capela, J., Carrion, V. J., Carter, R. S., Castelo-Branco, R., Castro-Falcon, G., Chagas, F. O., Charria-Giron, E., Chaudhri, A. A., Chaudhry, V., Choi, H., Choi, Y., Choupannejad, R., Chromy, J., Donahey, M. S. C., Collemare, J., Connolly, J. A., Creamer, K. E., Crusemann, M., Cruz, A. A., Cumsille, A., Dallery, J., Damas-Ramos, L. C., Damiani, T., Kruijff, M. D., Martin, B. D., Sala, G. D., Dillen, J., Doering, D. T., Dommaraju, S. R., Durusu, S., Egbert, S., Ellerhorst, M., Faussurier, B., Fetter, A., Feuermann, M., Fewer, D. P., Foldi, J., Frediansyah, A., Garza, E. A., Gavriilidou, A., Gentile, A., Gerke, J., Gerstmans, H., Gomez-Escribano, J. P., Gonzalez-Salazar, L. A., Grayson, N. E., Greco, C., Gomez, J. E. G., Guerra, S., Flores, S. G., Gurevich, A., Gutierrez-Garcia, K., Hart, L., Haslinger, K., He, B., Hebra, T., Hemmann, J. L., Hindra, H., Hoing, L., Holland, D. C., Holme, J. E., Horch, T., Hrab, P., Hu, J., Huynh, T., Hwang, J., Lacovelli, R., Lftime, D., Lorio, M., Jayachandran, S., Jeong, E., Jing, J., Jung, J. J., Kakumu, Y., Kalkreuter, E., Kang, K. B., Kang, S., Kim, W., Kim, G. J., Kim, H., Kim, H. U., Klapper, M., Koetsier, R. A., Kollten, C., Kovacs, A. T., Kriukova, Y., Kubach, N., Kunjapur, A. M., Kushnareva, A. K., Kust, A., Lamber, J., Larralde, M., Larsen, N. J., Launay, A. P., Le, N., Lebeer, S., Lee, B. T., Lee, K., Lev, K. L., Li, S., Li, Y., Licona-Cassani, C., Lien, A., Liu, J., Lopez, J. A. V., Machushynets, N. V., Macias, M. I., Mahmud, T., Maleckis, M., Martinez-Martinez, A. M., Mast, Y., Maximo, M. F., McBride, C. M., McLellan, R. M., Bhatt, K. M., Melkonian, C., Merrild, A., Metsä-Ketela, M., Mitchell, D. A., Müller, A. V., Nguyen, G., Nguyen, H. T., Niedermeyer, T. H. J., O’Hare, J. H., Ossowicki, A., Ostash, B. O., Otani, H., Padva, L., Paliya, S., Pan, X., Panghal, M., Parade, D. S., Park, J., Parra, J., Rubio, M. P., Pham, H. T., Pidot, S. J., Piel, J., Pourmohsenin, B., Rakhmanov, M., Ramesh, S., Rasmussen, M. H., Rego, A., Reher, R., Rice, A. J., Rigolet, A., Romero-Otero, A., Rosas-Becerra, L. R., Rosiles, P. Y., Rutz, A., Ryu, B., Sahadeo, L., Saldanha, M., Salvi, L., Sánchez-Carvajal, E., Santos-Medellin, C., Sbaraini, N., Schoellhorn, S. M., Schumm, C., Sehnal, L., Selem, N., Shah, A. D., Shishido, T. K., Sieber, S., Silviani, V., Singh, G., Singh, H., Sokolova, N., Sonnenschein, E. C., Sosio, M., Sowa, S. T., Steffen, K., Stegmann, E., Streiff, A. B., Strüder, A., Surup, F., Svenningsen, T., Sweeney, D., Szenei, J., Tagirdzhanov, A., Tan, B., Tarnowski, M. J., Terlouw1, B. R., Rey, T., Thome, N. U., Ortega, L. R. T., Torring, T., Trindade, M., Truman, A. W., Tvilum, M., Udwary, D. W., Ulbricht, C., Vader, L., Wezel, G. P. V., Walmsley, M., Warnasinghe, R., Weddeling, H. G., Weir, A. N., Williams, K., Williams, S. E., Witte, T. E., Rocca, S. M. W., Yamada, K., Yang, D., Yang, D., Yu, J., Zhou, Z., Ziemert, N., Zimmer, L., Zimmermann, A., Zimmermann, C., Hooft, J. J. V. D., Linington, R. G., Weber, T. and Medema, M. H.
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 broaderinvolvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

Year of Publication2025
JournalNucleic Acids Research
Journal citation53 (D1), p. D678–D690
Digital Object Identifier (DOI)https://doi.org/10.1093/nar/gkae1115
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeGrowing Health [ISP]
Growing Health (WP2) - bio-inspired solutions for healthier agroecosystems: Understanding soil environments
Publisher's version
Output statusPublished
Publication dates
Online06 Jan 2025
Publication process dates
Accepted10 Dec 2024
PublisherOxford University Press (OUP)
ISSN0305-1048

Permalink - https://repository.rothamsted.ac.uk/item/9934z/mibig-4-0-advancing-biosynthetic-gene-cluster-curation-through-global-collaboration

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