南方科技大学知识苑(SUSTech KC): MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

题名	MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
作者	Terlouw，Barbara R.1; Blin，Kai 2; Navarro-Muñoz，Jorge C.1,3; Avalon，Nicole E.4; Chevrette，Marc G.5; Egbert，Susan 6; Lee，Sanghoon 7; Meijer，David 1; Recchia，Michael J.J.7; Reitz，Zachary L.1; van Santen，Jeffrey A.7,8; Selem-Mojica，Nelly 9; Tørring，Thomas 10; Zaroubi，Liana 7; Alanjary，Mohammad 1; Aleti，Gajender 11; Aguilar，César 12; Al-Salihi，Suhad A.A.13; Augustijn，Hannah E.1,14; Avelar-Rivas，J. Abraham 15; Avitia-Domínguez，Luis A.14,15; Barona-Gómez，Francisco 14,15; Bernaldo-Agüero，Jordan 16; Bielinski，Vincent A.17; Biermann，Friederike 1,18,19; Booth，Thomas J.2,20; Carrion Bravo，Victor J.14,21,22; Castelo-Branco，Raquel 23,24; Chagas，Fernanda O.25; Cruz-Morales，Pablo 2; Du，Chao 14; Duncan，Katherine R.26; Gavriilidou，Athina 27,28; Gayrard，Damien 29; Gutiérrez-García，Karina 30; Haslinger，Kristina 31; Helfrich，Eric J.N.18,19; van der Hooft，Justin J.J.1,32; Jati，Afif P.33; Kalkreuter，Edward 34; Kalyvas，Nikolaos 3; Kang，Kyo Bin 35; Kautsar，Satria 34; Kim，Wonyong 36; Kunjapur，Aditya M.37; Li，Yong Xin 38; Lin，Geng Min 39; Loureiro，Catarina 40; Louwen，Joris J.R.1; Louwen，Nico L.L.1; Lund，George 41; Parra，Jonathan 42,43,44; Philmus，Benjamin 45; Pourmohsenin，Bita 27,28; Pronk，Lotte J.U.1; Rego，Adriana 23,46; Rex，Devasahayam Arokia Balaya 47; Robinson，Serina 48; Rosas-Becerra，L. Rodrigo 14,15; Roxborough，Eve T.49; Schorn，Michelle A.40; Scobie，Darren J.26; Singh，Kumar Saurabh 1; Sokolova，Nika 31; Tang，Xiaoyu 50; Udwary，Daniel 51; Vigneshwari，Aruna 52; Vind，Kristiina 53,54; Vromans，Sophie P.J.M.1; Waschulin，Valentin 55; Williams，Sam E.56; Winter，Jaclyn M.57; Witte，Thomas E.58; Xie，Huali 1,59; Yang，Dong 60; Yu，Jingwei61 ; Zdouc，Mitja 1; Zhong，Zheng 40; Collemare，Jérôme 3; Linington，Roger G.7; Weber，Tilmann 2; Medema，Marnix H.1,14
通讯作者	Weber，Tilmann; Medema，Marnix H.
发表日期	2023-01-06
DOI	10.1093/nar/gkac1049
发表期刊	Nucleic Acids Research 影响因子和分区
ISSN	0305-1048
EISSN	1362-4962
卷号	51 期号:D1页码:D603-D610
摘要	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/.
相关链接	[Scopus记录]
收录类别	SCI
语种	英语
重要成果	ESI高被引
学校署名	其他
资助项目	Horizon 2020[101000392] ; Horizon 2020[101000794] ; National Institutes of Health[1R01AI155694] ; National Research Foundation of Korea[2020R1C1C1004046] ; National Research Foundation of Korea[2022R1C1C2004118] ; National Science Foundation[2032243] ; Deutsche Forschungsgemeinschaft[398967434-TRR 261] ; Consejo Tamaulipeco de Ciencia y Tecnología[735867] ; Consejo Tamaulipeco de Ciencia y Tecnología[757173] ; Horizon 2020[765147] ; Horizon 2020[893122] ; European Research Council[948770] ; Biotechnology and Biological Sciences Research Council[BB/R022054/1] ; Biotechnology and Biological Sciences Research Council[BB/W013959/1] ; U.S. Department of Energy[DE-AC02-05CH11231] ; Danmarks Grundforskningsfond[DNRF137] ; Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro[E-26/211.314/2019] ; National Institutes of Health[F32AT011475] ; National Institutes of Health[GM134688] ; Horizon 2020[MSCA-IF-EF-ST-897121] ; Novo Nordisk Fonden[NNF16OC0021746] ; Novo Nordisk Fonden[NNF20CC0035580] ; Fundação para a Ciência e a Tecnologia[SFRH/BD/136367/2018] ; Fundação para a Ciência e a Tecnologia[SFRH/BD/140567/2018] ; National Institutes of Health[U24AT010811] ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek[VI.Veni.202.130]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000898752800001
出版者	OXFORD UNIV PRESS
ESI学科分类	BIOLOGY & BIOCHEMISTRY
Scopus记录号	2-s2.0-85146851279
来源库	Scopus
引用统计	被引频次[WOS]：149
成果类型	期刊论文
条目标识符	http://sustech.caswiz.com/handle/2SGJ60CL/524311
专题	南方科技大学-北京大学植物与食品联合研究所生命科学学院生命科学学院_生物系
作者单位	1.Bioinformatics Group,Wageningen University,Wageningen,Droevendaalsesteeg,6708 PB,Netherlands 2.Novo Nordisk Foundation Center for Biosustainability,Technical University of Denmark,Kgs. Lyngby,Denmark 3.Westerdijk Fungal Biodiversity Institute,Utrecht,Uppsalalaan 8,3584 CT,Netherlands 4.Scripps Institution of Oceanography,University of California San Diego,9500 Gilman Drive, La Jolla,92093-0212,United States 5.Department of Microbiology and Cell Science,University of Florida,Gainesville,32611,United States 6.Department of Chemistry,University of Manitoba,Winnipeg,66 Chancellors Cir,R3T 2N2,Canada 7.Department of Chemistry,Simon Fraser University,Burnaby,8888 University Drive,V5A 1S6,Canada 8.Unnatural Products,Santa Cruz,2161 Delaware Ave. Suite A,95060,United States 9.Centro de Ciencias Matemáticas UNAM,Morelia,Mexico 10.Department of Biological and Chemical Engineering,Aarhus University,Denmark 11.Food and Animal Sciences,Department of Agricultural and Environmental Sciences,Tennessee State University,Nashville,37209,United States 12.Department of Chemistry,Purdue University,West Lafayette,United States 13.Department of Applied Sciences,University of Technology,Iraq 14.Institute of Biology,Leiden University,Leiden,Sylviusweg 72,2333BE,Netherlands 15.Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada,Irapuato,Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, Gto.,CP 36824,Mexico 16.Departamento de Microbiología Molecular,Instituto de Biotecnología,Universidad Nacional Autónoma de México,Cuernavaca,Morelos,Mexico 17.Synthetic Biology and Bioenergy Group,J. Craig Venter Institute,La Jolla,92037,United States 18.Institute of Molecular Bio Science,Goethe-University Frankfurt,Frankfurt am Main,D-60438,Germany 19.LOEWE Center for Translational Biodiversity Genomics (TBG),Frankfurt am Main,Senckenberganlage 25,60325,Germany 20.School of Molecular Sciences,University of Western Australia,Perth,Australia 21.Departamento de Microbiología,Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’,Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC),Universidad de Málaga,Málaga,Spain 22.Department of Microbial Ecology,Netherlands Institute of Ecology (NIOO-KNAW),Wageningen,Netherlands 23.Interdisciplinary Centre of Marine and Environmental Research (CIIMAR),University of Porto,Portugal 24.Faculty of Sciences,University of Porto,Porto,4150-179,Portugal 25.Instituto de Pesquisas de Produtos Naturais Walter Mors,Universidade Federal do Rio de Janeiro,Rio de Janeiro,RJ,21941-599,Brazil 26.University of Strathclyde,Strathclyde Institute of Pharmacy and Biomedical Sciences,Glasgow,141 Cathedral Street,G4 ORE,United Kingdom 27.Translational Genome Mining for Natural Products,Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT),University of Tübingen,Tübingen,Germany 28.Interfaculty Institute for Biomedical Informatics (IBMI),University of Tübingen,Tübingen,Germany 29.Department of Molecular Microbiology,John Innes Centre,Norwich,Norwich Research Park,NR4 7UH,United Kingdom 30.Department of Embryology,Carnegie Institution for Science,Baltimore,3520 San Martin Drive,21218,United States 31.Department of Chemical and Pharmaceutical Biology,Groningen Research Institute of Pharmacy,University of Groningen,Groningen,Antonius Deusinglaan 1,9713 AV,Netherlands 32.Department of Biochemistry,University of Johannesburg,Johannesburg,Auckland Park,2006,South Africa 33.Indonesian Society of Bioinformatics And Biodiversity,Indonesia 34.Department of Chemistry,University of Florida Scripps Biomedical Research,Jupiter,110 Scripps Way,33458,United States 35.College of Pharmacy,Sookmyung Women’s University,Seoul,South Korea 36.Korean Lichen Research Institute,Sunchon National Universtiy,Suncheon,South Korea 37.Department of Chemical and Biomolecular Engineering,University of Delaware,Newark,19716,United States 38.Department of Chemistry,University of Hong Kong,Hong Kong,Pokfulam Road,Hong Kong 39.Department of Biological Engineering,Massachusetts Institute of Technology,Cambridge,United States 40.Laboratory of Microbiology,Wageningen University,Wageningen,Stippeneng 4,6708WE,Netherlands 41.Sustainable Soils and Crops,Rothamsted Research,Harpenden,Hertfordshire,United Kingdom 42.Instituto de Investigaciones Farmacéuticas (INIFAR),Facultad de Farmacia,Universidad de Costa Rica,San José,11501-2060,Costa Rica 43.Centro de Investigaciones en Productos Naturales (CIPRONA),Universidad de Costa Rica,San José,11501-2060,Costa Rica 44.Centro Nacional de Innovaciones Biotecnológicas (CENIBiot),CeNAT-CONARE,San José,1174-1200,Costa Rica 45.Department of Pharmaceutical Sciences,Oregon State University,United States 46.Institute of Biomedical Sciences Abel Salazar (ICBAS),University of Porto,Portugal 47.Centre for Integrative Omics Data Science,Yenepoya (Deemed to be University),Mangalore,575018,India 48.Department of Environmental Microbiology,Eawag: Swiss Federal Institute for Aquatic Science and Technology,Dübendorf,Überlandstrasse 133,CH-8600,Switzerland 49.School of Chemistry,University of Nottingham,Nottingham,University Park,NG7 2RD,United Kingdom 50.Institute of Chemical Biology,Shenzhen Bay Laboratory,Shenzhen,518132,China 51.DOE Joint Genome Institute,Lawrence Berkeley National Lab,Berkeley,United States 52.Department of Microbiology,University of Szeged,Hungary 53.Host-Microbe Interactomics Group,Wageningen University,Wageningen,6708 WD,Netherlands 54.NAICONS Srl,Milan,20139,Italy 55.School of Life Sciences,University of Warwick,Coventry,CV4 7AL,United Kingdom 56.School of Biochemistry,University of Bristol,Bristol,University Walk,BS8 1TD,United Kingdom 57.Department of Medicinal Chemistry,University of Utah,Salt Lake City,84112,United States 58.Department of Chemistry and Biomolecular Sciences,University of Ottawa,Ottawa,Canada 59.Key laboratory of Detection for Biotoxins,Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute,Chinese Academy of Agricultural Sciences,Wuhan,430061,China 60.Department of Chemistry,Natural Products Discovery Center,UF Scripps Biomedical Research,University of Florida,Jupiter,33458,United States 61.SUSTech-PKU Institute of Plant and Food Science,Department of Biology,School of Life Sciences,Southern University of Science and Technology,Shenzhen,Guangdong,518055,China
推荐引用方式 GB/T 7714	Terlouw，Barbara R.,Blin，Kai,Navarro-Muñoz，Jorge C.,et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters[J]. Nucleic Acids Research,2023,51(D1):D603-D610.
APA	Terlouw，Barbara R..,Blin，Kai.,Navarro-Muñoz，Jorge C..,Avalon，Nicole E..,Chevrette，Marc G..,...&Medema，Marnix H..(2023).MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.Nucleic Acids Research,51(D1),D603-D610.
MLA	Terlouw，Barbara R.,et al."MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters".Nucleic Acids Research 51.D1(2023):D603-D610.