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Front. Microbiol. | doi: 10.3389/fmicb.2018.00865

Commentary: Genome sequence of Vibrio parahaemolyticus VP152 Strain Isolated from Penaeus indicus in Malaysia

  • 1School of Medicine, Deakin University, Australia
  • 2Monash University Malaysia, Malaysia
  • 3School of Life and Environmental Sciences, Deakin University, Australia

Vibrio parahaemolyticus is a marine gram negative bacterium that has been gaining significant attention in the shrimp aquaculture industry given its direct association with early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND) in shrimps (Soto-Rodriguez et al., 2015). Despite its significant threat to the industry, the genomic representation of shrimp-associated V. parahaemolyticus isolated from Malaysia or South East Asia in general is relatively low (Kondo et al., 2014; Yang et al., 2014; Foo et al., 2017). Letchumanan and colleagues recently reported the draft genome of V. parahaemolyticus VP152 isolated from a banana prawn in Malaysia (Letchumanan et al., 2016b). Strain VP152 was sequenced on the Illumina MiSeq and its whole genome sequence was deposited in DDBJ/EMBL/GenBank under the accession number and Bioproject ID of LCUL01000000 and PRJNA281142, respectively.
The G+C content for strain VP152 was reported to be 53.4%, a value that is substantially higher in other V. parahaemolyticus accessions (Kondo et al., 2014; Yang et al., 2014; Foo et al., 2017). A similarity search of house-keeping genes coded in the genome of strain VP152 showed best hits to members of the genus Citrobacter (data not shown). A subsequent phylogenomic analysis using PhyloPhlAN (Segata et al., 2013) clustered strain VP152 with members of the genus Citrobacter with strong SH-like local branch support (Figure 1A). In addition, similar to several Citrobacter strains, when searched against the complete genome of V. parahaemolyticus ATCC 17802T, strain VP152 displayed low nucleotide homology to the V. parahaemolyticus reference genome (Figure 1B) (Alikhan et al., 2011). It is also worth noting that V. parahaemolyticus strain VP103 deposited in DDBJ/EMBL/GenBank under the accession number LBDB01000000 reported by the same group in a different data report (Letchumanan et al., 2016a) also showed the same phylogenomic affiliation to the genus Citrobacter instead of Vibrio.
Furthermore, a search in the NCBI bioproject database revealed that C. amalonaticus YG6 and C. amalonaticus YG8 with the Bioproject IDs of PRJNA292629 and PRJNA292637, respectively, were also sequenced by the same institute. This observation in addition to the monophyletic clustering of strains VP103 and VP152 with the two Citrobacter strains suggest potential sample mislabelling or barcode index misassignment during library preparation or sequencing.
Unfortunately, the authors did not describe any methodology associated with genome-based in-silico bacterial species validation in the data report to allow us to reproduce the identification of strain VP152 to the species V. parahaemolyticus. Given that the genome analysis of V. parahaemolyticus strain VP152 was based on the genome of a distantly related genus e.g. Citrobacter, it is unlikely that the biology interpretation in addition to the genome sequence reported in this study will be useful to the genomic study of V. parahaemolyticus or more generally the genus Vibrio.

Figure legends
Figure 1. Potential misidentification of strain VP152 to the genus Vibrio as revealed by phylogenomic analysis and whole genome nucleotide comparison with V. parahaemolyticus ATCC 17802T. (A) Maximum likelihood tree constructed from the concatenated alignment of 400 universal proteins. The tree was rooted with members of the genus Novosphingobium as the outgroup. Node values indicate SH-like local branch support as implemented in FastTree2 and scale bar indicates the number of amino acid changes per site. (B) Whole genome comparisons of various Vibrio and Citrobacter strains against the complete genome of V. parahaemolyticus ATCC 17802T. Homologous regions (BLASTN with an E-value cut-off of 1E-7) were colored based on their percentage identity and strain label.
Author Contributions
HMG , TA and CZYY performed data analysis. HMG wrote the manuscript and all authors proofread the manuscript.
Conflict of Interest Statement
The authors declare that the research was performed in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.



References:
Alikhan, N.-F., Petty, N.K., Ben Zakour, N.L., and Beatson, S.A. (2011). BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12, 402-402. doi: 10.1186/1471-2164-12-402.
Foo, S.M., Eng, W.W.H., Lee, Y.P., Gui, K., and Gan, H.M. (2017). New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing. Genome Announcements 5(19), e00302-00317. doi: 10.1128/genomeA.00302-17.
Kondo, H., Tinwongger, S., Proespraiwong, P., Mavichak, R., Unajak, S., Nozaki, R., et al. (2014). Draft Genome Sequences of Six Strains of Vibrio parahaemolyticus Isolated from Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease Shrimp in Thailand. Genome Announcements 2(2), e00221-00214. doi: 10.1128/genomeA.00221-14.
Letchumanan, V., Ser, H.-L., Chan, K.-G., Goh, B.-H., and Lee, L.-H. (2016a). Genome Sequence of Vibrio parahaemolyticus VP103 Strain Isolated from Shrimp in Malaysia. Frontiers in Microbiology 7, 1496. doi: 10.3389/fmicb.2016.01496.
Letchumanan, V., Ser, H.-L., Tan, W.-S., Ab Mutalib, N.-S., Goh, B.-H., Chan, K.-G., et al. (2016b). Genome Sequence of Vibrio parahaemolyticus VP152 Strain Isolated from Penaeus indicus in Malaysia. Frontiers in Microbiology 7, 1410. doi: 10.3389/fmicb.2016.01410.
Segata, N., Börnigen, D., Morgan, X.C., and Huttenhower, C. (2013). PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature communications 4, 2304-2304. doi: 10.1038/ncomms3304.
Soto-Rodriguez, S.A., Gomez-Gil, B., Lozano-Olvera, R., Betancourt-Lozano, M., and Morales-Covarrubias, M.S. (2015). Field and Experimental Evidence of Vibrio parahaemolyticus as the Causative Agent of Acute Hepatopancreatic Necrosis Disease of Cultured Shrimp (Litopenaeus vannamei) in Northwestern Mexico. Applied and Environmental Microbiology 81(5), 1689-1699. doi: 10.1128/aem.03610-14.
Yang, Y.-T., Chen, I.T., Lee, C.-T., Chen, C.-Y., Lin, S.-S., Hor, L.-I., et al. (2014). Draft Genome Sequences of Four Strains of Vibrio parahaemolyticus, Three of Which Cause Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease in Shrimp in China and Thailand. Genome Announcements 2(5), e00816-00814. doi: 10.1128/genomeA.00816-14.

Keywords: Vibrio parahaemolyticus, Taxonomy, Genomics, shrimp, South East Asia

Received: 08 Aug 2017; Accepted: 13 Apr 2018.

Edited by:

Javier Carballo, University of Vigo, Spain

Reviewed by:

Adrian Canizalez-Roman, School of Medicine, Autonomous University of Sinaloa, Mexico
Elvira Barroso, Universidad Autonoma de Madrid, Spain
Luigi Orrù, Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Italy  

Copyright: © 2018 Allnutt, Yan and Gan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Han Ming Gan, Deakin University, School of Life and Environmental Sciences, Pidgons Road, Geelong, 3220, Victoria, Australia, han.gan@deakin.edu.au