Open access
22 October 2015

Draft Genome Sequence of Yellow Pigmented Jeotgalibacillus alimentarius JY-13T, the First Halophile Strain of the Genus Jeotgalibacillus


Jeotgalibacillus alimentarius JY-13T (=KCCM 80002T = JCM 10872T) is a moderate halophile. In 2001, this was the first strain of the newly proposed Jeotgalibacillus genus. The draft genome of J. alimentarius was found to consist of 32 contigs (N50, 315,125 bp) with a total size of 3,364,745 bp. This genome information will be helpful for studies on pigmentation as well as applications for this bacterium.


Several halophilic bacteria such as Jeotgalibacillus alimentarius (1), Psychrobacter jeotgali (2), Methylobacterium jeotgali (3), and Jeotgalicoccus halotolerans (4) have been isolated from jeotgal, a traditional Korean food (5). Some of these isolated bacteria can be used for various purposes, including antimicrobial agents (6) and fermentation starters (7). J. alimentarius has not been examined for its potential applications, despite the fact that this bacterium was the earliest described strain of the genus Jeotgalibacillus. This bacterium required NaCl to grow, and the cells are capable of tolerating up to 20% (wt/vol) salt (1). The cell exhibits a yellow pigmentation. Pigmentations in marine bacteria are often associated with the bacteria's self-defense against harsh environmental conditions (8). Since synthetically derived pigments may be toxic, carcinogenic, or teratogenic (9), harnessing pigments from microbial resources has received increasing attention. Microbial carotenoids are pigments that are important in various applications (10). Recently, the genome sequences of J. malaysiensis (11), J. soli (12), and J. campisalis (13) were reported. In this study, we determined the genome sequence of J. alimentarius and examined the pigment formation pathway in this strain.
J. alimentarius genomic DNA was extracted using a DNeasy tissue kit (Qiagen, Hilden, Germany). Genome sequencing was conducted using an Illumina MiSeq sequencer (Illumina, Inc., San Diego, CA, USA). Reads were assembled using SPAdes (14) into 32 contigs with an N50 contig size of 315,125 bp. Similarity searches were conducted against several databases (CatFam, IMG-er, COG, NCBI RefSeq, and SEED). Gene prediction was conducted using Glimmer version 3.02 (Delcher et al., 1999), tRNA prediction by tRNASCAN-SE (15), and rRNA prediction by HMMER (16). The genome was 3,364,745 bp in length, with a G+C content of 43.13%. The genome was predicted to include 3,536 open reading frames, 7 rRNA genes, and 74 tRNA genes.
Generally, the formation of carotenoids in bacteria involves several steps: (1) an early reaction due to mevalonic acid to geranylgeranyl pyrophosphate; (2) phytoene formation; (3) desaturation; (4) cyclization; and (5) modifications (17). Eleven genes that are crucial for the first three steps of carotenoid formation are present in the J. alimentarius genome. These 11 key carotenoid-biosynthesis genes encode for an isopentenyl diphosphate isomerase, a geranylgeranyl pyrophosphate synthase, two phytoene synthases, four phytoene dehydrogenases, a fatty acid desaturase, and a glycosyltransferase. These enzymes showed about 48.5 to 98% similarities to various Bacillus spp., suggesting that pigmentation of J. alimentarius may be similar to that in most bacilli. Guo et al. (18) have performed extensive studies on phytoene dehydrogenase and concluded that this enzyme is important in the transformation of colorless carotenoid into colored compounds. The four phytoene dehydrogenase enzymes are responsible for the pigmentation of J. alimentarius.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number JXRQ00000000. The version described in this paper is the first version, JXRQ00000000.1.


This project was financially supported by the University of Malaya-Ministry of Higher Education High Impact Research (UM-MOHE HIR) grant UM C/625/1/HIR/MOHE/CHAN/01 (no. A-000001-50001) and UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/14/1 (no. H-50001-A000027), awarded to K.-G.C. K.M.G. and A.S.Y. are grateful for Universiti Teknologi Malaysia grant 06H31 and a UTM Zamalah Scholarship.


Yoon JH, Weiss N, Lee KC, Lee IS, Kang KH, Park YH. 2001. Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with l-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983. As Marinibacillus marinus gen. nov., comb. nov. Int J Syst Evol Microbiol 51:2087–2093.
Yoon J-H, Kang KH, Park Y-H. 2003. Psychrobacter jeotgali sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 53:449–454.
Aslam Z, Lee CS, Kim K-H, Im W-T, Ten LN, Lee S-T. 2007. Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 57:566–571.
Yoon J-H, Lee K-C, Weiss N, Kang KH, Park Y-H. 2003. Jeotgalicoccus halotolerans gen. nov., sp. nov. and Jeotgalicoccus psychrophilus sp. nov., isolated from the traditional Korean fermented seafood jeotgal. Int J Syst Evol Microbiol 53:595–602.
Yoon JH, Kang SS, Lee KC, Kho YH, Choi SH, Kang KH, Park YH. 2001. Bacillus jeotgali sp. nov., isolated from jeotgal, Korean traditional fermented seafood. Int J Syst Evol Microbiol 51:1087–1092.
Mah J, Chang Y, Hwang H. 2008. Paenibacillus tyraminigenes sp. nov. isolated from Myeolchi-jeotgal, a traditional Korean salted and fermented anchovy. Int J Food Microbiol 127:209–214.
Guan L, Cho KH, Lee J. 2011. Analysis of the cultivable bacterial community in jeotgal, a Korean salted and fermented seafood, and identification of its dominant bacteria. Food Microbiol 28:101–113.
Soliev AB, Hosokawa K, Enomoto K. 2011. Bioactive pigments from marine bacteria: applications and physiological roles. Evid Based Complement Alternat Med 2011:1–17.
Johnson E, Schroeder W. 1996. Microbial carotenoids, downstream processing biosurfactants carotenoids. Heidelberg 53:119–178.
Kirti K, Amita S, Priti S, Mukesh Kumar A, Jyoti S. 2014. Colorful world of microbes: carotenoids and their applications. Adv Biol 2014:1–13.
Goh KM, Chan K, Yaakop AS, Ee R. 2015. Complete genome of Jeotgalibacillus malaysiensis D5T consisting of a chromosome and a circular megaplasmid. J Biotechnol 204:13–14.
Goh KM, Chan K-G, Yaakop AS, Chan CS, Ee R, Tan W-S, Gan HM. 2015. Draft genome sequence of Jeotgalibacillus soli DSM 23228, a bacterium isolated from alkaline sandy soil. Genome Announc 3(3):512–515.
Yaakop AS, Chan K-G, Gan HM, Goh KM. 2015. Draft genome of Jeotgalibacillus campisalis SF-57T, a moderate halophilic bacterium isolated from marine saltern. Mar Genomics 23:59–60.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.
Lowe TM, Eddy SR. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964.
Finn RD, Clements J, Eddy SR. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–W37.
Fraser PD, Linden H, Sandmann G. 1993. Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli. Biochem J 291:687–692.
Guo W, Liu Y, Yan X, Liu M, Tang H, Liu Z, Zhang L. 2015. Cloning and characterization of a phytoene dehydrogenase gene from marine yeast Rhodosporidium diobovatum. Antonie van Leeuwenhoek 107:1017–1027.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 529 October 2015
eLocator: 10.1128/genomea.01224-15


Received: 6 September 2015
Accepted: 11 September 2015
Published online: 22 October 2015



Amira Suriaty Yaakop
Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
Faculty of Science, Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
Han Ming Gan
Monash School of Science, Monash University Sunway Campus, Petaling Jaya, Selangor, Malaysia
Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia


Address correspondence to Kian Mau Goh, [email protected].

Metrics & Citations



  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.


If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media






Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy