- Short genome report
- Open Access
An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T
© The Author(s). 2016
- Received: 7 October 2015
- Accepted: 31 August 2016
- Published: 8 September 2016
Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1T is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1T. The genome comprised 2,748,608 bp with a G + C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.
- Carnobacterium inhibens subsp. inhibens strain K1T
The genus Carnobacterium was proposed in 1987 to encompass a group of closely related bacteria originally classified as unusual species of Lactobacillus [1, 2]. The genus Carnobacterium includes heterofermentative, facultatively anaerobic, psychrotolerant, either motile or non-motile, Gram-positive rod-shaped lactic acid bacteria that produce mostly L-lactic acid by fermentation from glucose . At present the genus contains 11 species with validly published names, which can be roughly divided into two groups. As the genus name implies, most Carnobacterium species ( Carnobacterium divergens , Carnobacterium gallinarum , Carnobacterium inhibens , Carnobacterium jeotgali , Carnobacterium maltaromaticum , Carnobacterium mobile , Carnobacterium viridans ) belong to a group that were originally isolated from biological sources such as living fish or foods derived from animal sources . A second group of Carnobacterium spp. has been isolated from cold, low-nutrient environments such as Antarctic ice lakes ( C. funditum , C. alterfunditum , C. iners ) [5, 6] or Arctic permafrost ( C. pleistocenium , C. inhibens subsp. gilichinskyi ) [7, 8]. Owing to an upsurge in investigations involving Carnobacterium strains isolated from novel environments, at present genome sequences have been published for the following Carnobacterium environmental strains: Carnobacterium sp. 17–4 isolated from permanently cold sea water ; C. maltaromaticum strain ATCC 35586 isolated from a diseased salmon ; C. maltaromaticum strain LMA 28 isolated from ripened soft cheese ; and C. inhibens subsp. gilichinskyi isolated from Siberian permafrost [8, 12]. However, to date only one published report of a genome sequence from a type strain of Carnobacterium has appeared, from C. jeotgali strain MS3T isolated from salt-fermented shrimp . As part of a larger project to determine the genome sequences of all type strains of the genus Carnobacterium , the present study determined the classification and features of Carnobacterium inhibens subsp. inhibens strain K1T  as well as its genome sequence and gene annotations.
Classification and features
Carnobacterium inhibens subsp. inhibens strain K1T ( = DSM 13024T = JCM 16168T ) is the type strain of the species C. inhibens [8, 14]. The strain was isolated from the intestine of an Atlantic salmon . The species epithet was derived from the Latin verb inhibeo, meaning “to inhibit”, referring to the growth-inhibitory activity that the bacterium shows . Recent discovery of C. inhibens strain WN1359 from Siberian permafrost  prompted a re-examination of strains K1T and WN1359, resulting in the proposal to rename the K1T type strain as C. inhibens subsp. inhibens and the permafrost isolate C. inhibens subsp. gilichinskyi .
Classification and general features of Carnobacterium inhibens strain K1T according to the MIGS recommendations published by the Genome Standards Consortium 
Species: Carnobacterium inhibens
Subspecies: Carnobacterium inhibens subsp. inhibens
Type strain: K1T (DSM 13024)
pH range; Optimum
Gastrointestinal tract of fish (Atlantic salmon)
Grows at 0–6 % NaCl (w/v)
Facultative anaerobe; grows better in absence of O2
Below ocean surface
Genome project history
Carnobacterium inhibens subsp. inhibens strain K1T genome sequencing project details
Improved High-Quality Draft
Gene calling method
Genbank Date of Release
16 August 2015
Source material identifier
Growth conditions and genomic DNA preparation
Strain K1T was grown to stationary phase by incubation for 36 h at 20 °C in TSY medium without shaking . DNA was isolated from 100 mL of culture using a CTAB bacterial genomic DNA isolation method following the protocol recommended by JGI . DNA fragment size and quality was confirmed by agarose gel electrophoresis and DNA was quantified by fluorometry (Qubit fluorometer, Invitrogen).
Genome sequencing and assembly
The draft genome of Carnobacterium inhibens K1 was generated at the DOE Joint genome Institute using the Pacific Biosciences sequencing technology . A PacBio SMRTbell™ library was constructed and sequenced on the PacBio RS platform, which generated 252,358 filtered sub-reads totaling 752.5 Mbp. All general aspects of library construction and sequencing performed at the JGI can be found at (http://www.jgi.doe.gov). The raw reads were assembled using HGAP (version: 2.1.1) . The final draft assembly contained six contigs in six scaffolds, totaling 2.7 Mbp in size. The input read coverage was 273.1 ×.
The assembled sequence was annotated using the JGI prokaryotic annotation pipeline  and was further reviewed using the Integrated Microbial Genomes – Expert Review platform . Genes were identified using Prodigal , followed by a round of manual curation using GenePRIMP  for finished genomes and Draft genomes in fewer than 10 scaffolds. The predicted CDSs were translated and used to search the National Center for Biotechnology Information nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool  was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA . Other non–coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL . Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes platform  developed by the Joint Genome Institute, Walnut Creek, CA, USA.
% of Total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, Cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Carnobacterium inhibens is widely distributed in the environment, having been isolated from Atlantic salmon [14, 30], biogas slurry , a medicinal plant , and Siberian permafrost [8, 15]. In this communication we report an improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T ( = DSM 13024T = JCM 16168T ). Genome analysis of this strain demonstrated a single presumed chromosome and at least five putative extrachromosomal elements.
This work was conducted as part of the Community Sequencing Program (CSP-1165) under the auspices of the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
WN supplied DNA and background information for this project and contributed to the assembly of the manuscript with CLD, AC, and NK. NS coordinated the project and all other authors were involved in either sequencing the genome and/or editing the paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Collins MD, Farrow JAE, Phillips BA, Ferusu S, Jones D. Classification of Lactobacillus divergens, Lactobacillus piscicola, and some catalase-negative, asporogenous, rod-shaped bacteria from poultry in a new genus, Carnobacterium. Int J Syst Bacteriol. 1987;37:310–6.View ArticleGoogle Scholar
- Schillinger U, Holzapfel WH. The genus Carnobacteriumm. In: Wood BJB, Holzapfel WH, editors. The Genera of Lactic Acid Bacteria. Volume 2. Springer Science+Business Dordrecht; 1995. p. 307–26.Google Scholar
- Hammes WP, Hertel C. The genera Lactobacillus and Carnobacterium. In: Dworkin M, Falkow S, Rosenberg E, Schliefer K-H, Staeckebrandt E, editors. The Prokaryotes. Volume 4. 3rd ed. Singapore: Springer; 2006. p. 320–403.View ArticleGoogle Scholar
- Leisner JJ, Laursen BG, Prevost H, Drider D, Dalgaard P. Carnobacterium: positive and negative effects in the environment and in foods. FEMS Microbiol Rev. 2007;31:592–613.View ArticlePubMedPubMed CentralGoogle Scholar
- Franzmann PD, Höpfel P, Weiss N, Tindall BJ. Psychrotrophic, lactic acid-producing bacteria from anoxic waters in Ace Lake, Antarctica: Carnobacterium funditum sp. nov. and Carnobacterium alterfunditum sp. nov. Arch Microbiol. 1991;156:255–62.View ArticlePubMedGoogle Scholar
- Snauwaert I, Hoste B, De Bruyne K, Peeters K, De Vuyst L, Willems A, Vandamme P. Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond. Int J Syst Evol Microbiol. 2013;63:1370–5.View ArticlePubMedGoogle Scholar
- Pikuta EV, Marsic D, Bej A, Tang J, Krader P, Hoover RB. Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska. Int J Syst Evol Microbiol. 2005;55:473–8.View ArticlePubMedGoogle Scholar
- Nicholson WL, Zhalnina K, Oliveira RR, Triplett EW. Proposal to rename Carnobacterium inhibens to Carnobacterium inhibens subsp. inhibens subsp. nov., and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a novel psychrotolerant bacterium isolated from Siberian permafrost. Int J Syst Evol Microbiol. 2015;65:556–61.View ArticlePubMedGoogle Scholar
- Voget S, Klippel B, Daniel R, Antranikian G. Complete genome sequence of Carnobacterium sp. 17–4. J Bacteriol. 2011;193:3403–4.View ArticlePubMedPubMed CentralGoogle Scholar
- Leisner JJ, Hansen MA, Larsen MH, Hansen L, Ingmer H, Sorensen SJ. The genome sequence of the lactic acid bacterium, Carnobacterium maltaromaticum ATCC 35586 encodes potential virulence factors. Int J Food Microbiol. 2012;152:107–15.View ArticlePubMedGoogle Scholar
- Cailliez-Grimal C, Chaillou S, Anba-Mondoloni J, Loux V, Afzal MI, Rahman A, Kergourlya G, Champomier-Vergès MC, Zagorec M, Dalgaard P, et al. Complete chromosome sequence of Carnobacterium maltaromaticum LMA 28. Genome Announc. 2013;1. doi: 10.1128/genomeA.00115-12.Google Scholar
- Leonard MT, Panayotova N, Farmerie WG, Triplett EW, Nicholson WL. Complete genome sequence of Carnobacterium gilichinskyi strain WN1359 (DSM 27470). Genome Announc. 2013;1. doi: 10.1128/genomeA.00985-13.Google Scholar
- Whon TW, Hyun D-W, Nam Y-D, Kim MS, Song E-J, Jang YK, Jung ES, Shin N-R, Oh JS, Kim PS, et al. Genomic and phenotypic analyses of Carnobacterium jeotgali strain MS3T, a lactate producing candidate biopreservative bacterium isolated from salt-fermented shrimp. FEMS Microbiol Lett. 2015;362(10). doi:10.1093/femsle/fnv058.
- Jöborn A, Dorsch M, Olsson JC, Westerdahl A, Kjelleberg S. Carnobacterium inhibens sp. nov., isolated from the intestine of Atlantic salmon (Salmo salar). Int J Syst Bacteriol. 1999;49:1891–8.View ArticlePubMedGoogle Scholar
- Nicholson WL, Krivushin K, Gilichinsky D, Schuerger AC. Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars. Proc Natl Acad Sci U S A. 2013;110:666–71.View ArticlePubMedGoogle Scholar
- Benardini JN, Sawyer J, Venkateswaran K, Nicholson WL. Spore UV and acceleration resistance of endolithic Bacillus pumilus and Bacillus subtilis isolates obtained from Sonoran desert basalt: implications for lithopanspermia. Astrobiology. 2003;3:709–17.View ArticlePubMedGoogle Scholar
- Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.View ArticlePubMedPubMed CentralGoogle Scholar
- Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta) genome project classification. Nucleic Acids Res. 2015;43:D1099–106.View ArticlePubMedGoogle Scholar
- Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133–8.View ArticlePubMedGoogle Scholar
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.View ArticlePubMedPubMed CentralGoogle Scholar
- DOE Joint Genome Institute user home. http://www.jgi.doe.gov.
- Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10:563–9.View ArticlePubMedGoogle Scholar
- The Integrated Microbial Genomes (IMG) platform. http://img.jgi.doe.gov.
- Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271–8.View ArticlePubMedGoogle Scholar
- Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.View ArticlePubMedPubMed CentralGoogle Scholar
- Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010;7:455–7.View ArticlePubMedGoogle Scholar
- Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.View ArticlePubMedPubMed CentralGoogle Scholar
- Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–96.View ArticlePubMedPubMed CentralGoogle Scholar
- INFERNAL: Inference of RNA alignments. http://eddylab.org/infernal/. Accessed 6 Sept 2016.
- Ringo E, Sperstad S, Kraugerud OF, Krogdahl A. Use of 16S rRNA gene sequencing analysis to characterize culturable intestinal bacteria in Atlantic salmon (Salmo salar) fed diets with cellulose or non-starch polysaccharides from soy. Aquac Res. 2008;39:1087–100.View ArticleGoogle Scholar
- Feng N, Hao WH, Lei HX, Wei XH. Carnobacterium inhibens isolated from biogas slurry of Tianzhu county of Gansu province. In: National Center for Biotechnology Information (NCBI), August 10, 2013 edition. 2013.Google Scholar
- Bibi F. Isolation of antagonistic bacteria from medicinal plant. In: June 28, 2015 edition. National Center for Biotechnology Information (NCBI). 2015.Google Scholar
- Coordinators NR. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2014;42:D7–D17.View ArticleGoogle Scholar
- Gibbons NE, Murray RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol. 1978;28:1.View ArticleGoogle Scholar
- Editor L. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol. 2010;60:469-72.Google Scholar
- Ludwig W, Schleifer K-H, Whitman WB. Class I. Bacilli class nov. Bergey’s Manual Syst Bacteriol. 2009;3:19-20.Google Scholar
- Ludwig W, Schleifer K-H, Whitman WB. Order II. Lactobacillales ord. nov. Bergey’s Manual Syst Bacteriol. 2009;3:464.Google Scholar
- Ludwig W, Schleifer K-H, Whitman WB. Family III. Carnobacteriaceae fam. nov. Bergey’s Manual of Syst Bacteriol. 2009;3:549.Google Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.View ArticlePubMedPubMed CentralGoogle Scholar