{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:51:06Z","timestamp":1760241066921,"version":"build-2065373602"},"reference-count":26,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2019,11,23]],"date-time":"2019-11-23T00:00:00Z","timestamp":1574467200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Agriculture, Food and Rural Affairs (MAFRA) of Korea","award":["918013-04-2-SB010"],"award-info":[{"award-number":["918013-04-2-SB010"]}]},{"DOI":"10.13039\/501100014188","name":"Ministry of Science and ICT, South Korea","doi-asserted-by":"publisher","award":["NRF- 2014M3C9A3063541"],"award-info":[{"award-number":["NRF- 2014M3C9A3063541"]}],"id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.<\/jats:p>","DOI":"10.3390\/pathogens8040261","type":"journal-article","created":{"date-parts":[[2019,11,25]],"date-time":"2019-11-25T03:10:00Z","timestamp":1574651400000},"page":"261","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio cholerae"],"prefix":"10.3390","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7466-8415","authenticated-orcid":false,"given":"YoungJae","family":"Hur","sequence":"first","affiliation":[{"name":"Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mauricio","family":"Chalita","sequence":"additional","affiliation":[{"name":"Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea"},{"name":"ChunLab Inc., Seoul 06725, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sung-min","family":"Ha","sequence":"additional","affiliation":[{"name":"ChunLab Inc., Seoul 06725, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inwoo","family":"Baek","sequence":"additional","affiliation":[{"name":"Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3385-5171","authenticated-orcid":false,"given":"Jongsik","family":"Chun","sequence":"additional","affiliation":[{"name":"ChunLab Inc., Seoul 06725, Korea"},{"name":"Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea"},{"name":"School of Biological Sciences, Seoul National University, Seoul 08826, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,11,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/S0140-6736(03)15328-7","article-title":"Cholera","volume":"363","author":"Sack","year":"2004","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Chapman, C., Henry, M., Bishop-Lilly, K.A., Awosika, J., Briska, A., Ptashkin, R.N., Wagner, T., Rajanna, C., Tsang, H., and Johnson, S.L. (2015). Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 Vibrio cholerae by Whole Genome Mapping Reveals ExtensivePopulation Genetic Diversity. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0120311"},{"key":"ref_3","first-page":"63","article-title":"New strains of Vibrio cholerae O139 in India and Bangladesh: Lessonsfrom the recent epidemics","volume":"11","author":"Rabbani","year":"1993","journal-title":"J. Diarrhoeal Dis. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.mib.2010.08.007","article-title":"Genomic evolution of Vibrio cholerae","volume":"13","author":"Cho","year":"2010","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Hsiao, W.W.L., Ung, K., Aeschliman, D., Bryan, J., Finlay, B.B., and Brinkman, F.S.L. (2005). Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands. PLoS Genet., 1.","DOI":"10.1371\/journal.pgen.0010062"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"15442","DOI":"10.1073\/pnas.0907787106","article-title":"Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae","volume":"106","author":"Chun","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Kaas, R.S., Ngandjio, A., Nzouankeu, A., Siriphap, A., Fonkoua, M.C., Aarestrup, F.M., and Hendriksen, R.S. (2016). The Lake Chad Basin, an Isolated and Persistent Reservoir of Vibrio cholerae O1: A Genomic Insight into the Outbreak in Cameroon, 2010. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0155691"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: Expanded prediction of genomic islands forlarger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"D624","DOI":"10.1093\/nar\/gku985","article-title":"PAIDB v2.0: Exploration and analysis of pathogenicity and resistanceislands","volume":"43","author":"Yoon","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"bav058","DOI":"10.1093\/database\/bav058","article-title":"Pre_GI: A global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes","volume":"2015","author":"Pierneef","year":"2015","journal-title":"Database"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Waack, S., Keller, O., Asper, R., Brodag, T., Damm, C., Fricke, W.F., Surovcik, K., Meinicke, P., and Merkl, R. (2006). Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-142"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Langille, M.G.I., Hsiao, W.W.L., and Brinkman, F.S.L. (2008). Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-329"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1093\/bioinformatics\/btg004","article-title":"IslandPath: Aiding detection of genomic islands in prokaryotes","volume":"19","author":"Hsiao","year":"2003","journal-title":"Bioinformatics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.csbj.2016.05.001","article-title":"Computational methods for predicting genomic islands in microbial genomes","volume":"14","author":"Lu","year":"2016","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1073\/pnas.042667999","article-title":"Comparative genomic analysis of Vibrio cholerae: Genes that correlate with cholera endemic and pandemic disease","volume":"99","author":"Dziejman","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: Multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","article-title":"Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies","volume":"67","author":"Yoon","year":"2017","journal-title":"Int. J. Syst. Evolut. Microbiol."},{"key":"ref_19","first-page":"3691","article-title":"Roary: Rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"bioRxiv"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data","volume":"33","author":"Serra","year":"2016","journal-title":"Mol. Biol. Evolut."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/1748-7188-7-9","article-title":"Maximum Parsimony on Phylogenetic networks","volume":"7","author":"Kannan","year":"2012","journal-title":"Algorithms Mol. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"D286","DOI":"10.1093\/nar\/gkv1248","article-title":"eggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences","volume":"44","author":"Szklarczyk","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/s41586-019-1065-y","article-title":"Structural variation in the gut microbiome associates with host health","volume":"568","author":"Zeevi","year":"2019","journal-title":"Nature"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/8\/4\/261\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:37:01Z","timestamp":1760189821000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/8\/4\/261"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,23]]},"references-count":26,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["pathogens8040261"],"URL":"https:\/\/doi.org\/10.3390\/pathogens8040261","relation":{},"ISSN":["2076-0817"],"issn-type":[{"type":"electronic","value":"2076-0817"}],"subject":[],"published":{"date-parts":[[2019,11,23]]}}}