CobaltMaghrebV1, Pmc, Corpus, bibRecord, 000043

Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea

Identifieur interne : 000043 ( Pmc/Corpus ); précédent : 000042; suivant : 000044

Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea

Auteurs : Jae-Hwan Kim ; Eiseul Kim ; Chang-Gyeom Kim ; Dong-Won Choo ; Hae-Yeong Kim

Source :

Genome Announcements [ 2169-8287 ] ; 2016.

RBID : PMC:4866855

Abstract

This report describes the 2,032,158-bp draft genome sequence of Lactobacillus sakei (L. sakei) strain FBL1, isolated from mukeunji purchased at the Gwangju World Kimchi Culture Festival in 2012, South Korea. The total draft genome size was 2,032,158 bp with a G+C content of 41.2%.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866855

DOI: 10.1128/genomeA.00365-16
PubMed: 27174278
PubMed Central: 4866855

Links to Exploration step

PMC:4866855

Le document en format XML

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 Strain FBL1, a Probiotic Bacterium Isolated from <italic>Mukeunji</italic>
, a Long-Fermented Kimchi, in South Korea</title>
<author><name sortKey="Kim, Jae Hwan" sort="Kim, Jae Hwan" uniqKey="Kim J" first="Jae-Hwan" last="Kim">Jae-Hwan Kim</name>
<affiliation><nlm:aff id="aff1"><addr-line>Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea</addr-line>
</nlm:aff>
</affiliation>
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<author><name sortKey="Kim, Eiseul" sort="Kim, Eiseul" uniqKey="Kim E" first="Eiseul" last="Kim">Eiseul Kim</name>
<affiliation><nlm:aff id="aff1"><addr-line>Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kim, Chang Gyeom" sort="Kim, Chang Gyeom" uniqKey="Kim C" first="Chang-Gyeom" last="Kim">Chang-Gyeom Kim</name>
<affiliation><nlm:aff id="aff2"><addr-line>Department of Bioinformatics and Biosystems, Korea Polytechnics, Seongnam, Republic of Korea</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Choo, Dong Won" sort="Choo, Dong Won" uniqKey="Choo D" first="Dong-Won" last="Choo">Dong-Won Choo</name>
<affiliation><nlm:aff id="aff2"><addr-line>Department of Bioinformatics and Biosystems, Korea Polytechnics, Seongnam, Republic of Korea</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kim, Hae Yeong" sort="Kim, Hae Yeong" uniqKey="Kim H" first="Hae-Yeong" last="Kim">Hae-Yeong Kim</name>
<affiliation><nlm:aff id="aff1"><addr-line>Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea</addr-line>
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 Strain FBL1, a Probiotic Bacterium Isolated from <italic>Mukeunji</italic>
, a Long-Fermented Kimchi, in South Korea</title>
<author><name sortKey="Kim, Jae Hwan" sort="Kim, Jae Hwan" uniqKey="Kim J" first="Jae-Hwan" last="Kim">Jae-Hwan Kim</name>
<affiliation><nlm:aff id="aff1"><addr-line>Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea</addr-line>
</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kim, Eiseul" sort="Kim, Eiseul" uniqKey="Kim E" first="Eiseul" last="Kim">Eiseul Kim</name>
<affiliation><nlm:aff id="aff1"><addr-line>Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea</addr-line>
</nlm:aff>
</affiliation>
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<author><name sortKey="Kim, Chang Gyeom" sort="Kim, Chang Gyeom" uniqKey="Kim C" first="Chang-Gyeom" last="Kim">Chang-Gyeom Kim</name>
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<author><name sortKey="Choo, Dong Won" sort="Choo, Dong Won" uniqKey="Choo D" first="Dong-Won" last="Choo">Dong-Won Choo</name>
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</affiliation>
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<author><name sortKey="Kim, Hae Yeong" sort="Kim, Hae Yeong" uniqKey="Kim H" first="Hae-Yeong" last="Kim">Hae-Yeong Kim</name>
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<front><div type="abstract" xml:lang="en"><p>This report describes the 2,032,158-bp draft genome sequence of <italic>Lactobacillus sakei</italic>
 (<italic>L. sakei</italic>
) strain FBL1, isolated from <italic>mukeunji</italic>
 purchased at the Gwangju World Kimchi Culture Festival in 2012, South Korea. The total draft genome size was 2,032,158 bp with a G+C content of 41.2%.</p>
</div>
</front>
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<pmc article-type="brief-report"><pmc-dir>properties open_access</pmc-dir>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id>
<journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id>
<journal-id journal-id-type="hwp">ga</journal-id>
<journal-id journal-id-type="pmc">ga</journal-id>
<journal-id journal-id-type="publisher-id">GA</journal-id>
<journal-title-group><journal-title>Genome Announcements</journal-title>
</journal-title-group>
<issn pub-type="epub">2169-8287</issn>
<publisher><publisher-name>American Society for Microbiology</publisher-name>
<publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27174278</article-id>
<article-id pub-id-type="pmc">4866855</article-id>
<article-id pub-id-type="publisher-id">genomeA00365-16</article-id>
<article-id pub-id-type="doi">10.1128/genomeA.00365-16</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Prokaryotes</subject>
</subj-group>
</article-categories>
<title-group><article-title>Draft Genome Sequence of <italic>Lactobacillus sakei</italic>
 Strain FBL1, a Probiotic Bacterium Isolated from <italic>Mukeunji</italic>
, a Long-Fermented Kimchi, in South Korea</article-title>
<alt-title alt-title-type="running-head">Genome Announcement</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Kim</surname>
<given-names>Jae-Hwan</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kim</surname>
<given-names>Eiseul</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kim</surname>
<given-names>Chang-Gyeom</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Choo</surname>
<given-names>Dong-Won</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Kim</surname>
<given-names>Hae-Yeong</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<aff id="aff1"><label>a</label>
<addr-line>Institute of Life Sciences and Resources, Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea</addr-line>
</aff>
<aff id="aff2"><label>b</label>
<addr-line>Department of Bioinformatics and Biosystems, Korea Polytechnics, Seongnam, Republic of Korea</addr-line>
</aff>
</contrib-group>
<author-notes><corresp id="cor1">Address correspondence to Hae-Yeong Kim, <email>hykim@khu.ac.kr</email>
.</corresp>
</author-notes>
<pub-date pub-type="epub"><day>12</day>
<month>5</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><season>May-Jun</season>
<year>2016</year>
</pub-date>
<volume>4</volume>
<issue>3</issue>
<elocation-id>e00365-16</elocation-id>
<history><date date-type="received"><day>20</day>
<month>3</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>22</day>
<month>3</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2016 Kim et al.</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Kim et al.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license</ext-link>
.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:href="jga003163857001.pdf"></self-uri>
<abstract><p>This report describes the 2,032,158-bp draft genome sequence of <italic>Lactobacillus sakei</italic>
 (<italic>L. sakei</italic>
) strain FBL1, isolated from <italic>mukeunji</italic>
 purchased at the Gwangju World Kimchi Culture Festival in 2012, South Korea. The total draft genome size was 2,032,158 bp with a G+C content of 41.2%.</p>
</abstract>
<funding-group><funding-statement>This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.</funding-statement>
</funding-group>
<counts><fig-count count="0"></fig-count>
<table-count count="0"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="5"></ref-count>
<page-count count="1"></page-count>
<word-count count="836"></word-count>
</counts>
<custom-meta-group><custom-meta><meta-name>cover-date</meta-name>
<meta-value>May/June 2016</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
<body><sec id="h0.0"><title>GENOME ANNOUNCEMENT</title>
<p><italic>Lactobacillus sakei</italic>
 (<italic>L. sakei</italic>
) is a facultative heterofermentative and Gram-positive anaerobic lactic acid bacterium (LAB). This bacterium, originally described in rice alcohol or sake, is commonly found in fresh meat and fish and is used as a starter culture (<xref rid="B1" ref-type="bibr">1</xref>
). The complete genome sequence of <italic>L. sakei</italic>
 23K (GenBank accession no. CR936503.1) was reported in 2005 (<xref rid="B2" ref-type="bibr">2</xref>
). It consists of the circular chromosome containing 1,884,661 bp and 1,883 protein coding genes.</p>
<p>The genome sequence of <italic>L. sakei</italic>
 strain FBL1 with bile acid tolerance, isolated from <italic>mukeunji</italic>
, a long-fermented kimchi (<xref rid="B3" ref-type="bibr">3</xref>
), was analyzed in this study. <italic>L. sakei</italic>
 FBL1 was isolated from commercial <italic>mukeunji</italic>
 and showed 99% identity with the <italic>L. sakei</italic>
 strain DGH5 (KF469177.2) 16S rRNA gene. Comparative genomic analysis revealed 84% similarity with <italic>L. sakei</italic>
 23K.</p>
<p>Genomic DNA was extracted with the G-spin genomic extraction kit (Intron Biotechnology Co., Republic of Korea) and quality was evaluated by the Agilent 2100 bioanalyzer with the high-sensitivity DNA kit. Draft genome sequencing was performed using an Ion Torrent Personal Genome Machine (PGM) system (Life Technologies, Germany) and a 318 semiconductor chip with 400-bp sequencing reads. A total of 4,048,495 reads, with an average read length of 320 bp, were generated. Reference-based assembly was carried out using SPAdes version 3.1.0, with <italic>L. sakei</italic>
 23K as the reference genome. Assembly of the reads resulted in 44 contigs (≥500 bp, 541 to 287,097 bp, <italic>N</italic>
<sub>50</sub>
 length 116,042 bp). The total draft genome size was 2,005,160 bp with a G+C content of 41.0%. A total of 1,972 coding sequences, 76 RNA genes, and 296 subsystems were revealed by the RAST server (<xref rid="B4" ref-type="bibr">4</xref>
, <xref rid="B5" ref-type="bibr">5</xref>
). The genome includes the production of a colicin V synthesis protein, adhesion and multidrug resistance efflux pumps, as well as those containing resistance genes, beta-lactam antibiotics, bile salt (choloylglycine hydrolase), and fluoroquinolones. Compared to the <italic>L. sakei</italic>
 23-K genome, about 32 genes are missing. Importantly, phage proteins, choline binding protein, beta-galactosidase, phosphotransferase systems, and cobalt-zinc-cadmium resistance protein existed in <italic>L. sakei</italic>
 strain FBL1.</p>
<sec id="s1"><title>Nucleotide sequence accession numbers.</title>
<p>This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/LSFF00000000">LSFF00000000</ext-link>
. The version described in this paper is the first version, LSFF01000000.</p>
</sec>
</sec>
</body>
<back><fn-group><fn fn-type="other"><p><bold>Citation</bold>
 Kim J-H, Kim E, Kim C-G, Choo D-W, Kim H-Y. 2016. Draft genome sequence of <italic>Lactobacillus sakei</italic>
 strain FBL1, a probiotic bacterium isolated from <italic>mukeunji</italic>
, a long-fermented kimchi, in South Korea. Genome Announc 4(3):e00365-16. doi:10.1128/genomeA.00365-16.</p>
</fn>
</fn-group>
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</record>

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Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea

Draft Genome Sequence of Lactobacillus sakei Strain FBL1, a Probiotic Bacterium Isolated from Mukeunji, a Long-Fermented Kimchi, in South Korea

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