{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T22:47:07Z","timestamp":1786229227583,"version":"3.56.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,30]],"date-time":"2021-11-30T00:00:00Z","timestamp":1638230400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970635"],"award-info":[{"award-number":["31970635"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["2017-I2M-3-017"],"award-info":[{"award-number":["2017-I2M-3-017"]}]},{"name":"National Scientific Data Sharing Platform for Population and Health"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The virulence factor database (VFDB, http:\/\/www.mgc.ac.cn\/VFs\/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over\u00a0100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide.<\/jats:p>","DOI":"10.1093\/nar\/gkab1107","type":"journal-article","created":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T19:11:51Z","timestamp":1634843511000},"page":"D912-D917","source":"Crossref","is-referenced-by-count":1668,"title":["VFDB 2022: a general classification scheme for bacterial virulence factors"],"prefix":"10.1093","volume":"50","author":[{"given":"Bo","family":"Liu","sequence":"first","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Zheng","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyu","family":"Zhou","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lihong","family":"Chen","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8826-5198","authenticated-orcid":false,"given":"Jian","family":"Yang","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,30]]},"reference":[{"key":"2022010507312448600_B1","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1093\/femsre\/fuv029","article-title":"Targeted imaging of bacterial infections: advances, hurdles and hopes","volume":"39","author":"van\u00a0Oosten","year":"2015","journal-title":"FEMS Microbiol. Rev."},{"key":"2022010507312448600_B2","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B3","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/nm.4517","article-title":"Current understanding of the human microbiome","volume":"24","author":"Gilbert","year":"2018","journal-title":"Nat. Med."},{"key":"2022010507312448600_B4","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/s41579-019-0265-7","article-title":"Soil microbiomes and climate change","volume":"18","author":"Jansson","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"2022010507312448600_B5","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature11209","article-title":"A framework for human microbiome research","volume":"486","author":"Human\u00a0Microbiome\u00a0Project","year":"2012","journal-title":"Nature"},{"key":"2022010507312448600_B6","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: hierarchical and refined dataset for big data analysis\u201310 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B7","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1111\/j.1365-2958.1991.tb00761.x","article-title":"Structure and function of periplasmic chaperone-like proteins involved in the biosynthesis of K88 and K99 fimbriae in enterotoxigenic Escherichia coli","volume":"5","author":"Bakker","year":"1991","journal-title":"Mol. Microbiol."},{"key":"2022010507312448600_B8","doi-asserted-by":"crossref","first-page":"D274","DOI":"10.1093\/nar\/gkaa1018","article-title":"COG database update: focus on microbial diversity, model organisms, and widespread pathogens","volume":"49","author":"Galperin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B9","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gkaa1113","article-title":"The Gene Ontology resource: enriching a GOld mine","volume":"49","author":"Gene Ontology, C.","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B10","doi-asserted-by":"crossref","first-page":"D693","DOI":"10.1093\/nar\/gky999","article-title":"Victors: a web-based knowledge base of virulence factors in human and animal pathogens","volume":"47","author":"Sayers","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B11","doi-asserted-by":"crossref","first-page":"D539","DOI":"10.1093\/nar\/gkm951","article-title":"VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics","volume":"36","author":"Yang","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B12","doi-asserted-by":"crossref","first-page":"D641","DOI":"10.1093\/nar\/gkr989","article-title":"VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors","volume":"40","author":"Chen","year":"2012","journal-title":"NucleicAcids Res."},{"key":"2022010507312448600_B13","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1016\/j.bej.2009.11.014","article-title":"Bacterial adhesion: from mechanism to control","volume":"48","author":"Hori","year":"2010","journal-title":"Biochem. Eng. J."},{"key":"2022010507312448600_B14","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.VMBF-0012-2015","article-title":"Bacterial secretion systems: an overview","volume":"4","author":"Green","year":"2016","journal-title":"Microbiol. Spectrum"},{"key":"2022010507312448600_B15","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/j.celrep.2019.08.096","article-title":"Genome-wide identification and characterization of a superfamily of bacterial extracellular contractile injection systems","volume":"29","author":"Chen","year":"2019","journal-title":"Cell Rep."},{"key":"2022010507312448600_B16","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.toxicon.2017.10.016","article-title":"Exotoxins and endotoxins: inducers of inflammatory cytokines","volume":"149","author":"Cavaillon","year":"2018","journal-title":"Toxicon"},{"key":"2022010507312448600_B17","first-page":"126","article-title":"Drugs from bugs\u2019: bacterial effector proteins as promising biological (immune-) therapeutics","author":"Ruter","year":"2014"},{"key":"2022010507312448600_B18","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.tim.2018.12.012","article-title":"Nutrition and bipartite metabolism of intracellular pathogens","volume":"27","author":"Best","year":"2019","journal-title":"Trends Microbiol."},{"key":"2022010507312448600_B19","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1111\/j.1574-6968.2000.tb08958.x","article-title":"Hyaluronidases of Gram-positive bacteria","volume":"183","author":"Hynes","year":"2000","journal-title":"FEMS Microbiol. Lett."},{"key":"2022010507312448600_B20","first-page":"185","article-title":"Strategies to block bacterial pathogenesis by interference with motility and chemotaxis","volume":"398","author":"Erhardt","year":"2016","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"2022010507312448600_B21","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.mib.2014.02.008","article-title":"Biofilm dispersion and quorum sensing","volume":"18","author":"Solano","year":"2014","journal-title":"Curr. Opin. Microbiol."},{"key":"2022010507312448600_B22","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.VMBF-0007-2015","article-title":"Stress responses, adaptation, and virulence of bacterial pathogens during host gastrointestinal colonization","volume":"4","author":"Flint","year":"2016","journal-title":"Microbiol. Spectrum"},{"key":"2022010507312448600_B23","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1128\/CMR.00059-12","article-title":"Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world?","volume":"26","author":"Beceiro","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"2022010507312448600_B24","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1039\/D0MO00032A","article-title":"Identifying the targets and functions of N-linked protein glycosylation in Campylobacter jejuni","volume":"16","author":"Cain","year":"2020","journal-title":"Molecular omics"},{"key":"2022010507312448600_B25","doi-asserted-by":"crossref","first-page":"178","DOI":"10.3109\/07853890109002075","article-title":"Virulence gene regulation in Salmonella enterica","volume":"33","author":"Clements","year":"2001","journal-title":"Ann. Med."},{"key":"2022010507312448600_B26","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/bioinformatics\/bti054","article-title":"Circular genome visualization and exploration using CGView","volume":"21","author":"Stothard","year":"2005","journal-title":"Bioinformatics"},{"key":"2022010507312448600_B27","doi-asserted-by":"crossref","first-page":"e1009102","DOI":"10.1371\/journal.ppat.1009102","article-title":"Genome-wide dissection reveals diverse pathogenic roles of bacterial Tc toxins","volume":"17","author":"Song","year":"2021","journal-title":"PLoS Pathog."},{"key":"2022010507312448600_B28","doi-asserted-by":"crossref","first-page":"3693","DOI":"10.1093\/bioinformatics\/btaa230","article-title":"Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors","volume":"36","author":"Zheng","year":"2020","journal-title":"Bioinformatics"},{"key":"2022010507312448600_B29","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022010507312448600_B30","doi-asserted-by":"crossref","first-page":"e12988","DOI":"10.1111\/cmi.12988","article-title":"Listeriolysin O: a phagosome-specific cytolysin revisited","volume":"21","author":"Nguyen","year":"2019","journal-title":"Cell. Microbiol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D912\/42057657\/gkab1107.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D912\/42057657\/gkab1107.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T07:47:10Z","timestamp":1641368830000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D912\/6446532"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,30]]},"references-count":30,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,11,30]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab1107","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,11,30]]}}}