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1. BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.

Author

Bağcı C, Nuhamunada M, Goyat H, Ladanyi C, Sehnal L, Blin K, Kautsar SA, Tagirdzhanov A, Gurevich A, Mantri S, von Mering C, Udwary D, Medema MH, Weber T, and Ziemert N

Subjects
Databases, Genetic, Bacteria genetics, Bacteria metabolism, Bacteria classification, Metagenomics methods, Metagenome genetics, Biosynthetic Pathways genetics, Secondary Metabolism genetics, Software, Genome, Bacterial genetics, Internet, Multigene Family
Abstract

Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2025
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2. MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.

Author

Zdouc MM, Blin K, Louwen NLL, Navarro J, Loureiro C, Bader CD, Bailey CB, Barra L, Booth TJ, Bozhüyük KAJ, Cediel-Becerra JDD, Charlop-Powers Z, Chevrette MG, Chooi YH, D'Agostino PM, de Rond T, Del Pup E, Duncan KR, Gu W, Hanif N, Helfrich EJN, Jenner M, Katsuyama Y, Korenskaia A, Krug D, Libis V, Lund GA, Mantri S, Morgan KD, Owen C, Phan CS, Philmus B, Reitz ZL, Robinson SL, Singh KS, Teufel R, Tong Y, Tugizimana F, Ulanova D, Winter JM, Aguilar C, Akiyama DY, Al-Salihi SAA, Alanjary M, Alberti F, Aleti G, Alharthi SA, Rojo MYA, Arishi AA, Augustijn HE, Avalon NE, Avelar-Rivas JA, Axt KK, Barbieri HB, Barbosa JCJ, Barboza Segato LG, Barrett SE, Baunach M, Beemelmanns C, Beqaj D, Berger T, Bernaldo-Agüero J, Bettenbühl SM, Bielinski VA, Biermann F, Borges RM, Borriss R, Breitenbach M, Bretscher KM, Brigham MW, Buedenbender L, Bulcock BW, Cano-Prieto C, Capela J, Carrion VJ, Carter RS, Castelo-Branco R, Castro-Falcón G, Chagas FO, Charria-Girón E, Chaudhri AA, Chaudhry V, Choi H, Choi Y, Choupannejad R, Chromy J, Donahey MSC, Collemare J, Connolly JA, Creamer KE, Crüsemann M, Cruz AA, Cumsille A, Dallery JF, Damas-Ramos LC, Damiani T, de Kruijff M, Martín BD, Sala GD, Dillen J, Doering DT, Dommaraju SR, Durusu S, Egbert S, Ellerhorst M, Faussurier B, Fetter A, Feuermann M, Fewer DP, Foldi J, Frediansyah A, Garza EA, Gavriilidou A, Gentile A, Gerke J, Gerstmans H, Gomez-Escribano JP, González-Salazar LA, Grayson NE, Greco C, Gomez JEG, Guerra S, Flores SG, Gurevich A, Gutiérrez-García K, Hart L, Haslinger K, He B, Hebra T, Hemmann JL, Hindra H, Höing L, Holland DC, Holme JE, Horch T, Hrab P, Hu J, Huynh TH, Hwang JY, Iacovelli R, Iftime D, Iorio M, Jayachandran S, Jeong E, Jing J, Jung JJ, Kakumu Y, Kalkreuter E, Kang KB, Kang S, Kim W, Kim GJ, Kim H, Kim HU, Klapper M, Koetsier RA, Kollten C, Kovács ÁT, Kriukova Y, Kubach N, Kunjapur AM, Kushnareva AK, Kust A, Lamber J, Larralde M, Larsen NJ, Launay AP, Le NT, Lebeer S, Lee BT, Lee K, Lev KL, Li SM, Li YX, Licona-Cassani C, Lien A, Liu J, Lopez JAV, Machushynets NV, Macias MI, Mahmud T, Maleckis M, Martinez-Martinez AM, Mast Y, Maximo MF, McBride CM, McLellan RM, Bhatt KM, Melkonian C, Merrild A, Metsä-Ketelä M, Mitchell DA, Müller AV, Nguyen GS, Nguyen HT, Niedermeyer THJ, O'Hare JH, Ossowicki A, Ostash BO, Otani H, Padva L, Paliyal S, Pan X, Panghal M, Parade DS, Park J, Parra J, Rubio MP, Pham HT, Pidot SJ, Piel J, Pourmohsenin B, Rakhmanov M, Ramesh S, Rasmussen MH, Rego A, Reher R, Rice AJ, Rigolet A, Romero-Otero A, Rosas-Becerra LR, Rosiles PY, Rutz A, Ryu B, Sahadeo LA, Saldanha M, Salvi L, Sánchez-Carvajal E, Santos-Medellin C, Sbaraini N, Schoellhorn SM, Schumm C, Sehnal L, Selem N, Shah AD, Shishido TK, Sieber S, Silviani V, Singh G, Singh H, Sokolova N, Sonnenschein EC, Sosio M, Sowa ST, Steffen K, Stegmann E, Streiff AB, Strüder A, Surup F, Svenningsen T, Sweeney D, Szenei J, Tagirdzhanov A, Tan B, Tarnowski MJ, Terlouw BR, Rey T, Thome NU, Torres Ortega LR, Tørring T, Trindade M, Truman AW, Tvilum M, Udwary DW, Ulbricht C, Vader L, van Wezel GP, Walmsley M, Warnasinghe R, Weddeling HG, Weir ANM, Williams K, Williams SE, Witte TE, Rocca SMW, Yamada K, Yang D, Yang D, Yu J, Zhou Z, Ziemert N, Zimmer L, Zimmermann A, Zimmermann C, van der Hooft JJJ, Linington RG, Weber T, and Medema MH

Subjects
Biosynthetic Pathways genetics, Molecular Sequence Annotation, Biological Products metabolism, Biological Products chemistry, Data Curation, Multigene Family, Databases, Genetic
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 broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2025
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