{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T14:32:16Z","timestamp":1769178736780,"version":"3.49.0"},"reference-count":46,"publisher":"Oxford University Press (OUP)","funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02\u201305CH11231"],"award-info":[{"award-number":["DE-AC02\u201305CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015911","name":"Joint Genome Institute","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100015911","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100006235","name":"Lawrence Berkeley National Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006235","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Microbial secondary metabolism is a reservoir of bioactive compounds of immense biotechnological and biomedical potential. The biosynthetic machinery responsible for the production of these secondary metabolites (SMs) (also called natural products) is often encoded by collocated groups of genes called biosynthetic gene clusters (BGCs). High-throughput genome sequencing of both isolates and metagenomic samples combined with the development of specialized computational workflows is enabling systematic identification of BGCs and the discovery of novel SMs. In order to advance exploration of microbial secondary metabolism and its diversity, we developed the largest publicly available database of predicted BGCs combined with experimentally verified BGCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https:\/\/img.jgi.doe.gov\/abc-public). Here we describe the first major content update of the IMG-ABC knowledgebase, since its initial release in 2015, refreshing the BGC prediction pipeline with the latest version of antiSMASH (v5) as well as presenting the data in the context of underlying environmental metadata sourced from GOLD (https:\/\/gold.jgi.doe.gov\/). This update has greatly improved the quality and expanded the types of predicted BGCs compared to the previous version.<\/jats:p>","DOI":"10.1093\/nar\/gkz932","type":"journal-article","created":{"date-parts":[[2019,10,10]],"date-time":"2019-10-10T03:36:39Z","timestamp":1570678599000},"source":"Crossref","is-referenced-by-count":39,"title":["IMG-ABC v.5.0: an update to the IMG\/Atlas of Biosynthetic Gene Clusters Knowledgebase"],"prefix":"10.1093","author":[{"given":"Krishnaveni","family":"Palaniappan","sequence":"first","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"I-Min A","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Ken","family":"Chu","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Anna","family":"Ratner","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Rekha","family":"Seshadri","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Nikos C","family":"Kyrpides","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Natalia N","family":"Ivanova","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Nigel J","family":"Mouncey","sequence":"additional","affiliation":[{"name":"Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA"},{"name":"Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,10,29]]},"reference":[{"key":"2019103013364312500_B1","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1039\/C5NP00013K","article-title":"Natural products in soil microbe interactions and evolution","volume":"32","author":"Traxler","year":"2015","journal-title":"Nat. Prod. Rep."},{"key":"2019103013364312500_B2","doi-asserted-by":"crossref","first-page":"1254766","DOI":"10.1126\/science.1254766","article-title":"HUMAN MICROBIOTA. Small molecules from the human microbiota","volume":"349","author":"Donia","year":"2015","journal-title":"Science"},{"key":"2019103013364312500_B3","doi-asserted-by":"crossref","first-page":"e518","DOI":"10.1016\/j.cell.2016.12.021","article-title":"Discovery of reactive microbiota-derived metabolites that inhibit host proteases","volume":"168","author":"Guo","year":"2017","journal-title":"Cell"},{"key":"2019103013364312500_B4","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1016\/j.tim.2016.07.006","article-title":"Natural products and the gene cluster revolution","volume":"24","author":"Jensen","year":"2016","journal-title":"Trends Microbiol."},{"key":"2019103013364312500_B5","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1126\/science.1203980","article-title":"Deciphering the rhizosphere microbiome for disease-suppressive bacteria","volume":"332","author":"Mendes","year":"2011","journal-title":"Science"},{"key":"2019103013364312500_B6","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1039\/B703499G","article-title":"Metabolites from symbiotic bacteria","volume":"26","author":"Piel","year":"2009","journal-title":"Nat. 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Biotechnol."},{"key":"2019103013364312500_B10","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1016\/j.cell.2015.11.031","article-title":"A new golden age of natural products drug discovery","volume":"163","author":"Shen","year":"2015","journal-title":"Cell"},{"key":"2019103013364312500_B11","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/ja.2013.61","article-title":"Specialized microbial metabolites: functions and origins","volume":"66","author":"Davies","year":"2013","journal-title":"J. Antibiot. (Tokyo)."},{"key":"2019103013364312500_B12","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1007\/s10295-016-1815-x","article-title":"Gifted microbes for genome mining and natural product discovery","volume":"44","author":"Baltz","year":"2017","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"2019103013364312500_B13","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/s10295-018-2115-4","article-title":"Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities","volume":"46","author":"Baltz","year":"2018","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"2019103013364312500_B14","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nchembio.2319","article-title":"A new genome-mining tool redefines the lasso peptide biosynthetic landscape","volume":"13","author":"Tietz","year":"2017","journal-title":"Nat. Chem. Biol."},{"key":"2019103013364312500_B15","doi-asserted-by":"crossref","first-page":"78","DOI":"10.3390\/md14040078","article-title":"Next generation sequencing of actinobacteria for the discovery of novel natural products","volume":"14","author":"Gomez-Escribano","year":"2016","journal-title":"Mar. 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Bioinform."},{"key":"2019103013364312500_B20","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.cell.2014.06.034","article-title":"Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters","volume":"158","author":"Cimermancic","year":"2014","journal-title":"Cell"},{"key":"2019103013364312500_B21","doi-asserted-by":"crossref","first-page":"32","DOI":"10.3390\/medicines6010032","article-title":"New approaches to detect biosynthetic gene clusters in the environment","volume":"6","author":"Chen","year":"2019","journal-title":"Medicines"},{"key":"2019103013364312500_B22","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1038\/nchembio.1890","article-title":"Minimum Information about a Biosynthetic Gene cluster","volume":"11","author":"Medema","year":"2015","journal-title":"Nat. Chem. 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