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.
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 sequencing information
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.
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