Open Access

Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106)

  • Ben Temperton,
  • , Simon Thomas,
  • , Karen Tait
  • , Helen Parry
  • , Matt Emery
  • , Mike Allen
  • , John Quinn
  • , John MacGrath
  • and Jack Gilbert, ,

DOI: 10.4056/sigs.1654066

Received: 29 April 2011

Published: 29 April 2011


Vibrio tubiashii NCIMB 1337 is a major and increasingly prevalent pathogen of bivalve mollusks, and shares a close phylogenetic relationship with both V. orientalis and V. coralliilyticus. It is a Gram-negative, curved rod-shaped bacterium, originally isolated from a moribund juvenile oyster, and is both oxidase and catalase positive. It is capable of growth under both aerobic and anaerobic conditions. Here we describe the features of this organism, together with the draft genome and annotation. The genome is 5,353,266 bp long, consisting of two chromosomes, and contains 4,864 protein-coding and 86 RNA genes.


The genus Vibrio is both numerous and ubiquitous within marine environments, with Vibrio species harbored within many diverse marine organisms, such as mollusks, shrimps, fishes, cephalopods and corals [1]. Comparative genome analysis has revealed a huge genetic diversity within this genus, which is driven by mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g. the acquisition of bacteriophages, pathogenicity islands, and super-integrons), the combination of which presumably stimulates genetic and functional diversity and allows this group to colonize a wide variety of ecological niches and hosts [1,2].

Vibrio tubiashii was first described as three strains of Vibrio anguillarum by Tubiash et al [3] in 1965. The organisms were isolated from bivalve mollusks during an outbreak of bacillary necrosis in Milford, Connecticut, and deposited in the American Type Culture Collection as ATCC 19105, 19106 and 19109. These three strains were further elucidated and formally named as V. tubiashii by Hada et al [4] in 1984. Subsequently, several virulence factors have been identified [5,6] and the organism is increasingly implicated in major disease outbreaks in bivalve mollusks [1].

V. tubiashii is closely related to the proposed coral pathogen V. coralliilyticus, as well as V. orientalis, a bacterium associated with penaeid shrimps [7]. Indeed, V. coralliilyticus was initially designated as a V. tubiashii strain [8,9] due to their close similarity.

Classification and features

Vibrio tubiashii 1337 belongs to the Gammaproteobacteria and are contained within the family, Vibrionaceae [Table 1]. Cells of Vibrio tubiashii are Gram-negative curved-rods of approximately 0.5 by 1.5 µm, which are motile in liquid media by means of a single sheathed, polar flagellum [3,4] These cells are facultative anaerobes, [3,4,22]. It is catalase and oxidase positive, capable of splitting indole from tryptophan, and can use glucose, xylose, mannitol, rhamnose, sucrose, arabinose and acetate as sole carbon sources, and has β-galactosidase activity, despite an apparent inability to ferment lactose. V. tubiashii is capable of dissimilatory nitrate and nitrite reduction under anaerobic conditions, can use organic phosphorus during phosphate limitation, and can utilize 2-aminoethylphosphonate as a sole phosphorus source.

Table 1

Classification and general features of V. tubiashii according to the MIGS recommendations

     MIGS ID



     Evidence code

     Domain Bacteria

     TAS [10]

     Phylum Proteobacteria

     TAS [11]

     Class Gammaproteobacteria

     TAS [12,13]

    Current classification

     Order Vibrionales

     TAS [14]

     Family Vibrionaceae

     TAS [15,16]

     Genus Vibrio

     TAS [15,17-19]

     Species Vibrio tubiashii NCIMB 1337

     TAS [4]

    Gram stain



    Cell shape

     Curved rods (vibroid)



     motile via single polar flagellum





    Temperature range

     Mesophile 12-30oC


    Optimum temperature



     MIGS 6.3


     Slightly halophylic, optimum 1-3% NaCl



    Oxygen requirement

     Aerobic/ facultative anaerobic


    Carbon source

     Highly diverse


    Energy source

     Highly diverse




     Marine invertebrates

     TAS [20]


    Biotic relationship


     TAS [3]


    Biosafety level


     TAS [4]


     Moribund juvenile oyster (Crassostrea virginica)

     TAS [3,4]


    Geographical location

     Milford, Connecticut, USA

     TAS [3]


    Sample collection time


     TAS [3]

     MIGS 4.1


     41.22 N

     TAS [3]

     MIGS 4.2


     -73.06 W

     TAS [3]

     MIGS 4.3


     Not reported

     MIGS 4.4



     TAS [3]

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); 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 [21]. If the evidence code is IDA, then the property was directly observed, for a live isolate by one of the authors, or an expert or reputable institution mentioned in the acknowledgements.

V. tubiashii has an absolute requirement for sodium and chloride ions, and is incapable of growth on media containing less than 0.5% W/V NaCl. The temperature optimum for growth is 25oC, but growth does occur in the range of 12-30oC. The organism is killed at 37oC. V. tubiashii has a biphasic pH response and grows optimally at both pH 8.0 and 6.5, but displays weakened growth at pH 7.0 and 7.5. The bacterium shows rapid growth on marine broth and produces buff colored, opaque, irregular, slightly convex colonies on marine agar, and yellow colonies, characteristic of the Vibrionaceae, on Thiosulfate-Citrate-Bile-Sucrose Agar (TCBS).

Growth conditions and DNA isolation

Vibrio tubiashii NCIMB 1337 (ATCC19106) was grown in marine broth (seawater + 1 gl-1 yeast extract and 0.5 gl-1 tryptone) at 25oC for 24 hours. DNA was extracted using the Qiagen DNAeasy blood and tissue kit, without modification of the manufacturer’s protocol.

Genome sequencing and annotation

Genome sequencing

The genome was sequenced using the Illumina sequencing platform. All general aspects of library construction and sequencing performed at the NERC Biomolecular analysis facility can be found on the NBAF website [23]. SOLEXA Illumina reads were assembled using VELVET Large Newbler contigs that were broken into 4,074 overlapping fragments of 1,000 bp and entered into the assembly as pseudo-reads. The sequences were assigned quality scores based on consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. The error rate of the completed genome sequence is less than 1 in 100,000. Overall sequencing provided 131 × coverage of the genome.

Genome annotation

Genes were identified using the RAST server The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. The tRNAScanSE tool [24] was used to find tRNA genes, whereas ribosomal RNAs were found by using BLASTn against the ribosomal RNA databases. The RNA components of the protein secretion complex and the RNaseP were identified by searching the genome for the corresponding Rfam profiles using INFERNAL [25]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG) platform developed by the Joint Genome Institute, Walnut Creek, CA, USA [26,27].

Genome project information

This organism was selected for sequencing on the basis of its increasing impact as a bivalve pathogen, and was funded by i-G Peninsula. The genome project is deposited in the IMG database and the complete genome sequence in GenBank (CP001643). Sequencing, finishing and annotation were performed by the GenePool Team at NERC Biomolecular Analysis Facility (NBAF) Edinburgh. A summary of the project information is shown in Table 2.

Table 2

Project information





     Finishing quality



     Libraries used



     Sequencing platforms

      Illumina SOLEXA GAIIx


     Fold coverage






     Gene calling method


     Genome Database release


     Genbank ID


     Genbank Date of Release

      December 12, 2010

     GOLD ID


Genomic properties

The genome was assembled into 335 contigs and includes two circular chromosomes combining to give a total size of 5,353,266 bp (44.84% GC content). A total of 4,950 genes were predicted, 4,864 of which are protein-coding genes. 74.22% of protein coding genes were assigned to a putative function with the remaining annotated as hypothetical proteins. 658 protein coding genes belong to paralogous families in this genome corresponding to a gene content redundancy of 13.29%. The properties and the statistics of the genome are summarized in Tables 3-5.

Table 3

Summary of genome*


    Size (Mb)

    Chromosome 1


    Chromosome 2


* Two chromosomes with no plasmids. Approximate chromosome size estimated by Pulse field gel electrophoresis

Table 5

Number of genes associated with the 25 general COG functional categories












     RNA processing and modification








     Replication, recombination and repair




     Chromatin structure and dynamics




     Cell cycle control, mitosis and chromosome partitioning


     Nuclear structure




     Defense mechanisms




     Signal transduction mechanisms




     Cell wall/membrane biogenesis




     Cell motility




     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




     Function unknown




     Not in COGs

a) The total is based on the total number of protein coding genes in the annotated genome.

Table 4

Nucleotide content and gene count levels of the genome



    % of totala

     Size (bp)



     G+C content (bp)



     Coding region (bp)



     Total genesb



     RNA genes



     Protein-coding genes



     Genes in paralog clusters



     Genes assigned to COGs



     Genes with signal peptides



     Genes with transmembrane helices



     Paralogous groups



a)The total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome.

b)Also includes 54 pseudogenes and 5 other genes.

Genomic comparison

Based on COG I.D the Vibrio tubiashii genome shows most similarity to the genome of V coralliilyticus (R2 = 0.96) and to V. orientalis (R2 = 0.94), while showing less similarity to V. shilonii (R2= 0.86) [Table 6]. This is in contrast to the 16S-based analysis shown in Figure 1. However, it should be noted that 16S rRNA analysis often poorly discriminates vibrios due to low sequence heterogeneity in the 16S gene [28].

Table 6

Comparison of the genome of Vibrio tubiashii NCIMB 1337 with other sequenced Vibrios

Genome Name

   Vibrio coralliilyticus ATCC BAA-450

    Vibrio orientalis CIP 102891

   Vibrio shilonii AK1

   Vibrio tubiashii NCIMB 1337











w/ Func Pred





w/ Func Pred %










Enzymes %






























Pfam %










TIGRfam %





Signal peptide





Signal peptide %










TransMb Perc





Pfam Clusters





COG Clusters





TIGRfam Clusters





GC Perc










Figure 1

Phylogenetic tree highlighting the position of V. tubiashii NCIMB 1337 relative to other Vibrio strains. The tree was inferred from 1,159 aligned characters of the 16S rRNA gene sequence under the neighborhood joining criterion. Numbers above the branches are support values from 1,000 bootstrap replicates if greater than 60%.

Regulatory systems

The Vibrio tubiashii NCIMB 1337 genome contains multiple quorum sensing systems, most notably a luxM/N system which has two adjacent copies of the luxN gene. In addition, there is a luxS/PQ system, with the lux P and Q gene appearing consecutively. There is also a cqsA/S system. It is probable that these three systems converge on the phospho-relay transfer system encoded by the luxO/luxU/hapR genes. There are two additional lux genes (LuxT and LuxZ). The genome also contains the rpoN gene encoding for the sigma-54 factor, which may indicate the presence of the two-component phosphorylation-dephosphorylation cascade described in V. harveyi [29] (note: Vibrio harveyi is also known as Lucibacterium harveyi and Beneckea harveyi.)

Antibiotic resistance

There are six separate genes encoding for putative β-lactamases within the genome, but only two have homology at the protein levels with any know Vibrio β-lactamases. There is also a multi-antibiotic resistance protein MarC, associated with an operon containing a variety of multidrug resistance proteins. This operon is controlled by a MerR type transcriptional regulator, which is often associated with antibiotic resistance [30], and may account for the kanamycin resistance observed in this strain by the authors.



We wish to thank i-G Peninsula (Prospect Place, the Hoe, Plymouth, Devon, UK) for providing funding for this project, and NBAF Edinburgh for performing the sequencing.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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