Open Access

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T

  • Wayne L. Nicholson1Email author,
  • Christina L. Davis1,
  • Nicole Shapiro2,
  • Marcel Huntemann2,
  • Alicia Clum2,
  • T. B. K. Reddy2,
  • Manoj Pillay3,
  • Victor Markowitz3,
  • Neha Varghese2,
  • Amrita Pati2,
  • Natalia Ivanova2,
  • Nikos Kyrpides2, 4 and
  • Tanja Woyke2
Standards in Genomic Sciences201611:65

https://doi.org/10.1186/s40793-016-0193-3

Received: 7 October 2015

Accepted: 31 August 2016

Published: 8 September 2016

Abstract

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.

Keywords

Carnobacterium inhibens subsp. inhibens strain K1T

Introduction

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 [3]. 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 [4]. 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 [9]; C. maltaromaticum strain ATCC 35586 isolated from a diseased salmon [10]; C. maltaromaticum strain LMA 28 isolated from ripened soft cheese [11]; 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 [13]. 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 [8] as well as its genome sequence and gene annotations.

Organism Information

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 [14]. The species epithet was derived from the Latin verb inhibeo, meaning “to inhibit”, referring to the growth-inhibitory activity that the bacterium shows [14]. Recent discovery of C. inhibens strain WN1359 from Siberian permafrost [15] 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 [8].

Carnobacterium inhibens subsp. inhibens strain K1T is a motile Gram-positive rod (Fig. 1). It is a psychrophile that lacks both catalase and oxidase, does not grow on acetate containing media, but grows at pH 9 and in Trypticase Soy Broth containing up to 6 % (w/v) sodium chloride. Strain K1T is facultatively anaerobic and tryptone as a sole source of nutrient promotes growth. The most abundant cellular fatty acid of strain K1T is oleic acid (18:1cis9) [14]. Classification of strain K1T according to the MIGS recommendations published by the Genome Standards Consortium is presented in Table 1.
Fig. 1

Scanning electron micrograph of Carnobacterium inhibens subsp. inhibens strain K1T. Size bar is 1 μm in length

Table 1

Classification and general features of Carnobacterium inhibens strain K1T according to the MIGS recommendations published by the Genome Standards Consortium [20]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain: Bacteria

 

Phylum: Firmicutes

TAS [34]

Class: Bacilli

TAS [35, 36]

Order: Lactobacillales

TAS [35, 37]

Family: Carnobacteriaceae

TAS [35, 38]

Genus: Carnobacterium

TAS [1]

Species: Carnobacterium inhibens

TAS [14]

Subspecies: Carnobacterium inhibens subsp. inhibens

TAS [8]

Type strain: K1T (DSM 13024)

 
 

Gram stain

Positive

TAS [14]

 

Cell shape

Rod

TAS [8, 14]

 

Motility

Motile

TAS [14]

 

Sporulation

Non-spore forming

TAS [8, 14]

 

Temperature range

0–37 °C

TAS [8]

 

Optimum temperature

35 °C

TAS [8]

 

pH range; Optimum

6–9; 8.2

TAS [8]

 

Carbon source

Tryptone,

TAS [14]

MIGS-6

Habitat

Gastrointestinal tract of fish (Atlantic salmon)

TAS [14]

MIGS-6.3

Salinity

Grows at 0–6 % NaCl (w/v)

TAS [8, 14]

MIGS-22

Oxygen requirement

Facultative anaerobe; grows better in absence of O2

TAS [8, 14, 15]

MIGS-15

Biotic relationship

Unknown

 

MIGS-14

Pathogenicity

Unknown

 

MIGS-4

Geographic location

Göteborg, Sweden

 

MIGS-5

Sample collection

Unknown

 

MIGS-4.1

Latitude

Unknown

 

MIGS-4.2

Longitude

Unknown

 

MIGS-4.3

Depth

Unknown

 

MIGS-4.4

Altitude

Below ocean surface

TAS [14]

aEvidence codes - IDA Inferred from Direct Assay, TAS Traceable Author Statement (i.e., a direct report exists in the literature), NAS Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [39]

C. inhibens subsp. inhibens strain K1T [8] was obtained from the German Collection of Microorganisms and Cell Cultures as strain DSM 13024. The strain was sub-cultured once and was stored as a −70 °C frozen glycerol stock in the corresponding author’s strain collection as strain WN1362. DNA isolated from strain WN1362 corresponding to 16S rRNA gene sequences was PCR amplified with universal bacterial primers B27F (5’-GAGTTTGATCMTGGCTCAG-3’) and B1512R (5’-AAGGAGGTGATCCANCCRCA-3’) as described previously [16] and sequenced at the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR). The sequence was compared with those obtained using NCBI BLAST [17] with the default settings (only highly similar sequences). The most frequently occurring genera were Carnobacterium (17 %) and unidentified bacteria (83 %) (100 hits in total). The species with the Max score was Carnobacterium inhibens subsp. inhibens strain K1T (NCBI Reference Sequence NR_036895) with a shared identity of 100.0 %, thus verifying the identity of strain WN1362 with the type strain. An updated 16S rRNA phylogenetic analysis of Carnobacterium spp. isolates including C. inhibens subsp. inhibens strain K1T is presented in Fig. 2 to supplement and expand upon those published previously [8, 14, 15].
Fig. 2

Phylogenetic tree highlighting the position of Carnobacterium inhibens subsp. inhibens strain K1T relative to other type (green boxes) and non-type strains within the genus Carnobacterium. Accession numbers are in parentheses: dbj, Database of Japan; emb, EMBL database; gb, NCBI Genbank. The top 100 hits by NCBI-BLASTN were input into the Distance Tree function at NCBI [33]. Alignments were converted to a distance matrix using the Jukes-Cantor distance correction model and the tree was constructed using the Neighbor-Joining method

Genome sequencing information

Genome project history

This organism was selected for sequencing on the basis of its relevance to environmental issues in phylogenetic diversity, bioenergy, and bioremediation, and is part of the Community Sequencing Program at the U.S. Department of Energy, Joint Genome Institute for projects of relevance to agency missions (http://www.jgi.doe.gov). The project is registered in the Genomes OnLine Database [18] and the permanent draft genome sequence is deposited in GenBank. Draft sequencing and assembly were performed at JGI using state of the art sequencing technology [19]. A summary of the project information is shown in Table 2, which presents the project information and its association with MIGS version 2.0 compliance [20].
Table 2

Carnobacterium inhibens subsp. inhibens strain K1T genome sequencing project details

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved High-Quality Draft

MIGS-28

Libraries used

PacBio

MIGS-29

Sequencing platforms

PacBio

MIGS-31.2

Fold coverage

273.1×

MIGS-30

Assemblers

HGAP v.2.1.1

MIGS-32

Gene calling method

Prodigal 2.5

 

Locus Tag

BR65

 

Genbank ID

JQIV01000006.1

 

Genbank Date of Release

16 August 2015

 

GOLD ID

Gp0042580

 

BIOPROJECT

PRJNA234895

MIGS-13

Source material identifier

DSM 13024T

 

Project relevance

Environmental

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 [8]. DNA was isolated from 100 mL of culture using a CTAB bacterial genomic DNA isolation method following the protocol recommended by JGI [21]. 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 [19]. 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) [22]. The final draft assembly contained six contigs in six scaffolds, totaling 2.7 Mbp in size. The input read coverage was 273.1 ×.

Genome annotation

The assembled sequence was annotated using the JGI prokaryotic annotation pipeline [23] and was further reviewed using the Integrated Microbial Genomes – Expert Review platform [24]. Genes were identified using Prodigal [25], followed by a round of manual curation using GenePRIMP [26] 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 [27] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [28]. 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 [29]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes platform [23] developed by the Joint Genome Institute, Walnut Creek, CA, USA.

Genome properties

The genome includes five smaller contigs, for a total size of 201,043 bp, and one large contig of 2,547,565 bp (34.85 % GC content) (Fig. 3). For the genome, 2737 genes were predicted, 2621 of which are protein-coding genes. Of these, 2151 were assigned to a putative function with the remaining 470 genes annotated as hypothetical proteins. 1838 protein coding genes belong to paralogous families in this genome, corresponding to a gene content redundancy of 67.15 %. The statistics of the genome are summarized in Tables 3 and 4. Examination of the sequence data for the five small contigs revealed a variety of putative genes encoding plasmid functions such as: autonomous replication, mobilization, bacteriocin production and immunity, toxin-antitoxin systems, and Hg or Cd/Co resistance cassettes; therefore it is reasonable to assume that these five small contigs represent plasmids.
Fig. 3

Graphical map of the six scaffolds assembled for the genome of Carnobacterium inhibens K1T, DSM 13024. From top to bottom, the scaffolds are: DSM 13024: DR65DRAFT_scf7180000000016_quiver.6, DSM 13024: DR65DRAFT_deg7180000000011.2, DSM 13024: DR65DRAFT_deg7180000000013.1, DSM 13024: DR65DRAFT_deg7180000000014.3, DSM 13024: DR65DRAFT_scf7180000000017, and DSM 13024: DR65DRAFT_scf7180000000019. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew

Table 3

Genome statistics

Attribute

Value

% of Total

Genome size (bp)

2,748,608

100.00

DNA coding (bp)

2,356,497

85.73

DNA G + C (bp)

957,950

34.85

DNA scaffolds

6

100.00

Total genes

2737

100.00

Protein coding genes

2621

95.76

RNA genes

116

4.24

Pseudo genes

66

2.41

Genes in internal clusters

515

18.82

Genes with function prediction

2151

78.59

Genes assigned to COGs

1900

69.42

Genes with Pfam domains

2196

80.23

Genes with signal peptides

113

4.13

Genes with transmembrane helices

691

25.25

CRISPR repeats

0

0

Table 4

Number of genes associated with general COG functional categories

Code

Value

% age

Description

J

196

9.36

Translation, ribosomal structure and biogenesis

A

25

1.20

RNA processing and modification

K

186

8.89

Transcription

L

101

4.83

Replication, recombination and repair

B

19

0.91

Chromatin structure and dynamics

D

32

1.53

Cell cycle control, Cell division, chromosome partitioning

V

71

3.39

Defense mechanisms

T

78

3.73

Signal transduction mechanisms

M

113

5.40

Cell wall/membrane biogenesis

N

51

2.44

Cell motility

U

22

1.05

Intracellular trafficking and secretion

O

61

2.91

Posttranslational modification, protein turnover, chaperones

C

71

3.39

Energy production and conversion

G

186

8.89

Carbohydrate transport and metabolism

E

163

7.79

Amino acid transport and metabolism

F

96

4.59

Nucleotide transport and metabolism

H

76

3.63

Coenzyme transport and metabolism

I

80

3.82

Lipid transport and metabolism

P

102

4.87

Inorganic ion transport and metabolism

Q

34

1.62

Secondary metabolites biosynthesis, transport and catabolism

R

199

9.51

General function prediction only

S

156

7.45

Function unknown

-

837

30.58

Not in COGs

Conclusion

Carnobacterium inhibens is widely distributed in the environment, having been isolated from Atlantic salmon [14, 30], biogas slurry [31], a medicinal plant [32], 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.

Declarations

Acknowledgments

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.

Authors’ contributions

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.

Competing interests

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.

Authors’ Affiliations

(1)
Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida
(2)
DOE Joint Genome Institute
(3)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(4)
Department of Biological Sciences, Faculty of Science, King Abdulaziz University

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Copyright

© The Author(s). 2016