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

Publication dates
Authors	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.
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 Publication	2025
Journal	Nucleic Acids Research
Journal citation	53 (D1), p. D678–D690
Digital Object Identifier (DOI)	https://doi.org/10.1093/nar/gkae1115
Open access	Published as ‘gold’ (paid) open access
Funder	Biotechnology and Biological Sciences Research Council
Funder project or code	Growing Health [ISP]
	Growing Health (WP2) - bio-inspired solutions for healthier agroecosystems: Understanding soil environments
Publisher's version	gkae1115.pdf
Output status	Published
Online	06 Jan 2025
Publication process dates
Accepted	10 Dec 2024
Publisher	Oxford University Press (OUP)
ISSN	0305-1048

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

Download files as zip

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Related outputs

Geographic bioprospection of maize rhizoplane-associated bacteria for consortia construction and impact on plant growth and nutrient uptake under low P availability

Community standards and future opportunities for synthetic communities in plant–microbiota research

Stacked mutations in wheat homologues of rice SEMI-DWARF1 confer a novel semi-dwarf phenotype

The potato rhizosphere microbiota correlated to the yield of three different regions in Korea

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

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10x Metagenomics

Land management legacy affects abundance and function of the acdS gene in wheat root associated pseudomonads

MIBiG 2.0: a repository for biosynthetic gene clusters of known function