ArticleNucleic acids research2023
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.
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Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 263 papers, 1 of them a synthesis that pooled it.
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263citing papers in PubMed, 1 pooled it
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263 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.Cell host & microbe · 2025Pooled it
- Temporal dynamics of gut biosynthetic gene clusters link persistent colonization and engraftment in fecal microbiota transplantation.Gut microbes · 2026Article
- Fast, flexible gene cluster family delineation with IGUA.Nucleic acids research · 2026Article
- Biosynthetic Gene Cluster Mining and In Vitro Evaluation of the Antimicrobial and Cytotoxic Potential ofBiology · 2026Article
- The Oxytetracycline ProducerInternational journal of molecular sciences · 2026Article
- Genomic signatures of host-range divergence in the generalist Beauveria bassiana and the specialist Beauveria brongniartii.Molecular genetics and genomics : MGG · 2026Article
- Comparative Phylogenomics Reveals Conserved Protoilludene Synthase Neighbourhoods and Unevenly Distributed Biosynthetic Gene Cluster Families in Armillaria.Journal of fungi (Basel, Switzerland) · 2026Article
- Integrated Genome Mining and Bioactivity-Guided Isolation of Antimicrobial Peptides from Bacillus amyloliquefaciens BS4.Probiotics and antimicrobial proteins · 2026Article
- A MarineMarine drugs · 2026Article
- Diverse biosynthetic pathways in Arctic hydrothermal biofilms.Nature communications · 2026Article
- CelluBase: a comprehensive genomic platform for advancing cellulose-producing bacteria.Microbial genomics · 2026Article
- Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.Journal of advanced research · 2026Article
- Genome mining of Trp-anthranilic acid cyclic dipeptides in Aspergillus driven by analysis of NRPS adenylation domains.Archives of microbiology · 2026Article
- Unveiling the Taxonomic Diversity and Unprecedented Biosynthetic Treasure of the Phylum Myxococcota.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Nerpa 2: probabilistic linking of biosynthetic gene clusters to nonribosomal peptides.Bioinformatics (Oxford, England) · 2026Article
- A Machine Learning-Based Genome Mining Approach Reveals Unprecedented Biarylitide Diversity.JACS Au · 2026Article
- The "dark magic mushroom" co-produces amatoxins and psilocybin.bioRxiv : the preprint server for biology · 2026Article
- Opportunistic pathogenicity in fungi can transcend species boundaries.bioRxiv : the preprint server for biology · 2026Article
- DeepAden: an explainable machine learning method for predicting the substrate specificity of nonribosomal peptide synthetases.Nucleic acids research · 2026Article
- Complex multicellularity is linked with expanded specialized metabolite production in microorganisms.Nature microbiology · 2026Article
203 more citing papers are in PubMed but not listed here.
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Authors and funding
82 authors.
Barbara R TerlouwBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-4058-6718
Kai BlinThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.ORCID 0000-0003-3764-6051
Jorge C Navarro-MuñozBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0003-2992-1607
Nicole E AvalonScripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA.ORCID 0000-0003-3588-892X
Marc G ChevretteDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.ORCID 0000-0002-7209-0717
Susan EgbertDepartment of Chemistry, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada.ORCID 0000-0001-5458-1099
Sanghoon LeeDepartment of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.ORCID 0000-0002-1377-3913
David MeijerBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0001-6406-4394
Michael J J RecchiaDepartment of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.ORCID 0000-0002-1450-0941
Zachary L ReitzBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0003-1964-8221
Jeffrey A van SantenDepartment of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.ORCID 0000-0002-5424-804X
Nelly Selem-MojicaCentro de Ciencias Matemáticas UNAM, Morelia, México.ORCID 0000-0003-1697-3862
Thomas TørringDepartment of Biological and Chemical Engineering, Aarhus University, Denmark.ORCID 0000-0001-5257-2121
Liana ZaroubiDepartment of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.ORCID 0000-0001-8218-7216
Mohammad AlanjaryBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0001-8420-1325
Gajender AletiFood and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA.ORCID 0000-0002-1867-9758
César AguilarDepartment of Chemistry, Purdue University, West Lafayette, IN, USA.ORCID 0000-0001-7044-2419
Suhad A A Al-SalihiDepartment of Applied Sciences, University of Technology, Iraq.ORCID 0000-0001-7665-7904
Hannah E AugustijnBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-1862-6699
J Abraham Avelar-RivasLaboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México.
Luis A Avitia-DomínguezInstitute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.ORCID 0000-0002-5902-2410
Francisco Barona-GómezInstitute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.ORCID 0000-0003-1492-9497
Jordan Bernaldo-AgüeroDepartamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.ORCID 0000-0002-7753-5527
Vincent A BielinskiSynthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA.ORCID 0000-0002-8107-8752
Friederike BiermannBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-9152-2562
Thomas J BoothThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.ORCID 0000-0002-6134-1488
Victor J Carrion BravoInstitute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.ORCID 0000-0002-4093-0355
Raquel Castelo-BrancoInterdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal.
Fernanda O ChagasInstituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil.ORCID 0000-0001-9534-3521
Pablo Cruz-MoralesThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.ORCID 0000-0002-6751-8897
Chao DuInstitute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.ORCID 0000-0003-3447-5293
Katherine R DuncanUniversity of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK.ORCID 0000-0002-3670-4849
Athina GavriilidouTranslational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.ORCID 0000-0002-6805-3868
Damien GayrardDepartment of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.ORCID 0000-0002-1447-9548
Karina Gutiérrez-GarcíaDepartment of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA.ORCID 0000-0002-6077-7490
Kristina HaslingerDepartment of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.ORCID 0000-0003-1361-1508
Eric J N HelfrichInstitute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.ORCID 0000-0001-8751-3279
Justin J J van der HooftBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-9340-5511
Afif P JatiIndonesian Society of Bioinformatics And Biodiversity, Indonesia.ORCID 0000-0002-3147-6293
Edward KalkreuterDepartment of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA.ORCID 0000-0002-8241-4455
Nikolaos KalyvasWesterdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.ORCID 0000-0002-5676-1859
Kyo Bin KangCollege of Pharmacy, Sookmyung Women's University, Seoul, South Korea.ORCID 0000-0003-3290-1017
Satria KautsarDepartment of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA.ORCID 0000-0002-9815-511X
Wonyong KimKorean Lichen Research Institute, Sunchon National Universtiy, Suncheon, South Korea.ORCID 0000-0002-9094-8908
Aditya M KunjapurDepartment of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.ORCID 0000-0001-6869-9530
Yong-Xin LiDepartment of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China.ORCID 0000-0003-4422-2302
Geng-Min LinDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0001-8123-0921
Catarina LoureiroLaboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.ORCID 0000-0002-6258-2080
Joris J R LouwenBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0003-4887-9109
Nico L L LouwenBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-4431-5499
George LundSustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, UK.ORCID 0000-0001-9099-3461
Jonathan ParraInstituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, 11501-2060, Costa Rica.ORCID 0000-0001-7273-0406
Benjamin PhilmusDepartment of Pharmaceutical Sciences, Oregon State University, USA.ORCID 0000-0003-2085-0873
Bita PourmohseninTranslational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.ORCID 0000-0002-5754-7221
Lotte J U PronkBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-3083-954X
Adriana RegoInterdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal.ORCID 0000-0001-9647-1197
Devasahayam Arokia Balaya RexCentre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore 575018, India.ORCID 0000-0002-9556-3150
Serina RobinsonDepartment of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.ORCID 0000-0001-6947-7913
L Rodrigo Rosas-BecerraInstitute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.ORCID 0000-0002-4105-1563
Eve T RoxboroughSchool of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.ORCID 0000-0002-4573-1670
Michelle A SchornLaboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.ORCID 0000-0001-8144-6052
Darren J ScobieUniversity of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK.ORCID 0000-0002-9858-9444
Kumar Saurabh SinghBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0001-8352-5897
Nika SokolovaDepartment of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.ORCID 0000-0003-4129-2890
Xiaoyu TangInstitute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China.ORCID 0000-0002-7855-5984
Daniel UdwaryDOE Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA.ORCID 0000-0002-3491-0198
Aruna VigneshwariDepartment of Microbiology, University of Szeged, Hungary.ORCID 0000-0002-8131-1518
Kristiina VindHost-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands.ORCID 0000-0001-6307-1461
Sophie P J M VromansBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-7482-5721
Valentin WaschulinSchool of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK.ORCID 0000-0002-8905-1263
Sam E WilliamsSchool of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK.ORCID 0000-0002-6949-426X
Jaclyn M WinterDepartment of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.ORCID 0000-0001-6273-5377
Thomas E WitteDepartment of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada.ORCID 0000-0002-6385-3655
Huali XieBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-6581-9573
Dong YangDepartment of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA.ORCID 0000-0003-2917-0663
Jingwei YuSUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.ORCID 0000-0003-4268-436X
Mitja ZdoucBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0001-6534-6609
Zheng ZhongLaboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands.ORCID 0000-0002-1262-4115
Jérôme CollemareWesterdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.ORCID 0000-0001-8152-6642
Roger G LiningtonDepartment of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.ORCID 0000-0003-1818-4971
Tilmann WeberThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.ORCID 0000-0002-8260-5120
Marnix H MedemaBioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.ORCID 0000-0002-2191-2821
Funding
NP-MRD: Natural Products Magnetic Resonance DatabaseU24AT010811 · NCCIH · BATTELLE PACIFIC NORTHWEST LABORATORIES · PI CORT, JOHN R · 2020 to 2024
$4.1MGenomics-Assisted Antibiotic Discovery from Unprecedented Microbes of the Great Salt LakeR01AI155694 · NIAID · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI WINTER, JACLYN MARIE · 2021 to 2025
$3.1MA Genomic Approach to Discovering Novel Cathepsin Inhibitors from CyanobacteriaF32AT011475 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AVALON, NICOLE ELIZABETH · 2022 to 2024
$218kCharacterization of the Thioacid Biosynthetic Machinery and Isolation of a Novel Thioacid Enediyne Natural ProductF32GM134688 · NIGMS · UNIVERSITY OF FLORIDA · PI KALKREUTER, ROBERT EDWARD · 2019 to 2021
$192kNCCIH NIH HHS F32 AT011475NCCIH NIH HHS U24 AT010811NIAID NIH HHS R01 AI155694NIGMS NIH HHS F32 GM134688
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/.
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GenomeGenomicsBiosynthetic PathwaysMultigene Family
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