{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1361137045260833408.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1128/aem.02157-10"}},{"identifier":{"@type":"URI","@value":"https://journals.asm.org/doi/pdf/10.1128/AEM.02157-10"}}],"dc:title":[{"@value":"Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>ABSTRACT</jats:title><jats:p>Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:<jats:italic>Leuconostoc</jats:italic>,<jats:italic>Lactobacillus</jats:italic>, and<jats:italic>Weissella</jats:italic>. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the<jats:italic>Leuconostoc mesenteroides</jats:italic>subsp.<jats:italic>mesenteroides</jats:italic>ATCC 8293 and<jats:italic>Lactobacillus sakei</jats:italic>subsp.<jats:italic>sakei</jats:italic>23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to<jats:italic>Leuconostoc mesenteroides</jats:italic>and<jats:italic>Lactobacillus</jats:italic>genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1381137045260833415","@type":"Researcher","foaf:name":[{"@value":"Ji Young Jung"}],"jpcoar:affiliationName":[{"@value":"Schools of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833414","@type":"Researcher","foaf:name":[{"@value":"Se Hee Lee"}],"jpcoar:affiliationName":[{"@value":"Schools of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833412","@type":"Researcher","foaf:name":[{"@value":"Jeong Myeong Kim"}],"jpcoar:affiliationName":[{"@value":"Schools of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833408","@type":"Researcher","foaf:name":[{"@value":"Moon Su Park"}],"jpcoar:affiliationName":[{"@value":"Schools of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833411","@type":"Researcher","foaf:name":[{"@value":"Jin-Woo Bae"}],"jpcoar:affiliationName":[{"@value":"Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833410","@type":"Researcher","foaf:name":[{"@value":"Yoonsoo Hahn"}],"jpcoar:affiliationName":[{"@value":"Schools of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833409","@type":"Researcher","foaf:name":[{"@value":"Eugene L. Madsen"}],"jpcoar:affiliationName":[{"@value":"Department of Microbiology, Cornell University, Ithaca, New York 14853-8101"}]},{"@id":"https://cir.nii.ac.jp/crid/1381137045260833413","@type":"Researcher","foaf:name":[{"@value":"Che Ok Jeon"}],"jpcoar:affiliationName":[{"@value":"Schools of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"00992240"},{"@type":"EISSN","@value":"10985336"}],"prism:publicationName":[{"@value":"Applied and Environmental Microbiology"}],"dc:publisher":[{"@value":"American Society for Microbiology"}],"prism:publicationDate":"2011-04","prism:volume":"77","prism:number":"7","prism:startingPage":"2264","prism:endingPage":"2274"},"reviewed":"false","dc:rights":["https://journals.asm.org/non-commercial-tdm-license"],"url":[{"@id":"https://journals.asm.org/doi/pdf/10.1128/AEM.02157-10"}],"createdAt":"2011-02-12","modifiedAt":"2025-03-02","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360004236779317888","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Phylogenetic placement of metagenomic reads using the minimum evolution principle"}]},{"@id":"https://cir.nii.ac.jp/crid/1360298754893328512","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Environmental factors drive microbial community succession in biofortified wheat Qu and its improvement on the quality of Chinese huangjiu"}]},{"@id":"https://cir.nii.ac.jp/crid/1360567185732155008","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Evaluation of the Dynamics of Microbiological Quality in Lightly Pickled Napa Cabbages During Manufacture"}]},{"@id":"https://cir.nii.ac.jp/crid/1360848661286342528","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identification of Multiple Dehalogenase Genes Involved in Tetrachloroethene-to-Ethene Dechlorination in a<i>Dehalococcoides</i>-Dominated Enrichment Culture"}]},{"@id":"https://cir.nii.ac.jp/crid/1390001204458060032","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Impact of <i>Lactobacillus paracasei</i> HD1.7 as a Starter Culture on Characteristics of Fermented Chinese Cabbage (<i>Brassica rapa</i> var. <i>pekinensis</i>)"}]},{"@id":"https://cir.nii.ac.jp/crid/1390001277344761984","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Dietary intake of probiotic kimchi ameliorated IL-6-driven cancer cachexia"}]},{"@id":"https://cir.nii.ac.jp/crid/1390282679122409728","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Pyrosequencing-based analysis of the bacterial community during fermentation of Alaska pollock <i>sikhae</i>: traditional Korean seafood"},{"@value":"Pyrosequencing-based analysis of the bacterial community during fermentation of Alaska pollock sikhae: traditional Korean seafood"}]},{"@id":"https://cir.nii.ac.jp/crid/1390282679321895680","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond"}]},{"@id":"https://cir.nii.ac.jp/crid/1521699230674882944","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Characterisation of the bacterial community structures of sunki, a traditional unsalted pickle of fermented turnip leaves"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1128/aem.02157-10"},{"@type":"CROSSREF","@value":"10.1186/1471-2164-16-s1-s13_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.1264/jsme2.me16024_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.3164/jcbn.19-10_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.2323/jgam.60.227_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.1016/j.jbiosc.2023.11.008_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.1111/jfs.12195_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.1016/j.jbiosc.2019.11.010_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.1155/2017/9191086_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"},{"@type":"CROSSREF","@value":"10.3136/fstr.22.325_references_DOI_8P2h9KZmfvjn2beSVvLMpuqvTe8"}]}