Skip to main content

Vibrio mexicanus sp. nov., isolated from a cultured oyster Crassostrea corteziensis

Antonie van Leeuwenhoek volume 108, pages 355–364 (2015)Cite this article

Abstract

A bacterial strain was taxonomically characterised by means of a genomic approach comprising 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), the DNA G+C content, whole genome analyses (ANI and GGDC) and phenotypic characterisation. The strain CAIM 1540T was isolated from a cultured oyster Crassostrea corteziensis in La Cruz, Sinaloa state, México. The isolate was found to be catalase and oxidase positive, cells were observed to be motile, O/129-sensitive and facultatively anaerobic. The almost-complete 16S rRNA gene sequence placed this strain within the genus Vibrio; the closest related species were found to be Vibrio aestivus, Vibrio marisflavi, Vibrio maritimus and Vibrio variabilis with similarity values of 99.02, 97.05, 96.70, and 96.59 % respectively. MLSA of four housekeeping genes (ftsZ, gapA, recA, and topA) was performed with the closely related species. A draft genome sequence of strain CAIM 1540T was obtained. The DNA G+C content of this strain was determined to be 43.7 mol%.The ANI values with V. aestivus were 89.6 % (ANIb), 90.6 % (ANIm) and a GGDC value of 39.5 ± 2.5 % was obtained; with V. marisflavi the genomic similarities were 71.5 % (ANIb), 85.5 % (ANIm) and 20.2 ± 2.3 % (GGDC); with V. maritimus 72.6 % (ANIb), 85.7 % (ANIm) and 22.0 ± 2.0 % (GGDC); and with V. variabilis 72.6 % (ANIb), 85.8 % (ANIm) and 21.6 ± 1.6 % (GGDC). These ANI and GGDC values are below the threshold for the delimitation of prokaryotic species, i.e. 95–96 and 70 %, respectively. Phenotypic characters also showed differences with the closest related species analysed. The results presented here support the description of a novel species, for which the name Vibrio mexicanus sp. nov. is proposed, with strain CAIM 1540T (= CECT 8828T, = DSM 100338T) as the type strain. In addition, we found that the recently described species Vibrio thalassae and Vibrio madracius might be a single species because the values of ANIb 95.8 %, ANIm 96.6 % and GGDC 70.2 ± 2.9 % are above the accepted species thresholds.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

Abbreviations

ANI:

Average nucleotide identity

GGDC:

Genome-to-genome distance calculator

MLSA:

Multilocus sequence analysis

References

  • Amaral GRS, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME, Thompson FL, Thompson CC (2014) Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 64:357–365

    Article  CAS  PubMed  Google Scholar 

  • Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genom Sci 2:117–134

    Article  Google Scholar 

  • Austin B, Austin DA (1999) Bacterial fish pathogens: disease of farmed and wild fish, 3rd edn. Springer, Berlin

    Google Scholar 

  • Cano-Gomez A, Goulden EF, Owens L, Høj L (2010) Vibrio owensii sp. nov., isolated from cultured crustaceans in Australia. FEMS Microbiol Lett 302:175–181

    Article  CAS  PubMed  Google Scholar 

  • Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A, De Vos P, Thompson FL (2011) Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum. Int J Syst Evol Microbiol 61:3009–3015

  • Dieguez AL, Beaz-Hidalgo R, Cleenwerck I, Balboa S, de Vos P, Romalde JL (2011) Vibrio atlanticus sp. nov. and Vibrio artabrorum sp. nov., isolated from the clams Ruditapes philippinarum and Ruditapes decussates. Int J Syst Evol Microbiol 61:2406–2411

    Article  PubMed  Google Scholar 

  • Gomez-Gil B, RoqueA TurnbullJF, Tron-Mayen L (1998) Species of Vibrio isolated from hepatopancreas, hemolymph and digestive tract of a population of healthy juvenile Penaeus vannamei. Aquaculture 163:1–9

    Article  Google Scholar 

  • Gomez-Gil B, Thompson FL, Thompson CC, Swings J (2003) Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis. Int J Syst Evol Microbiol 53:239–243

    Article  CAS  PubMed  Google Scholar 

  • González-Castillo A, Balboa S, Romalde JL, Gomez-Gil B (2014) Vibrio crosai sp. nov., isolated from a cultured oyster Crassostrea gigas. Antonie Van Leeuwenhoek 106:457–463

    Article  PubMed  Google Scholar 

  • Henz S, Huson D, Auch AF, Nieselt-Struwe K, Schuster S (2005) Whole-genomeprokaryotic phylogeny. Bioinformatics 21(10):2329–2335

    Article  CAS  PubMed  Google Scholar 

  • Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23(2):254–267

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Lucena T, Ruvira MA, Arahal DR, Macián MC, Pujalte MJ (2012) Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. Syst Appl Microbiol 35:427–431

    Article  CAS  PubMed  Google Scholar 

  • MacFaddin JF (1993) Pruebas bioquímicas para la identificación de bacterias de importancia clínica (translation by Médica Panamericana SA). Williams & Wilkins, Baltimore

    Google Scholar 

  • Macián MC, Ludwig W, Aznar R, Grimont P, Schleifer KH, Garay E, Pujalte MJ (2001) Vibrio lentus sp. nov., isolated from Mediterranean oysters. Int J Syst Evol Microbiol 51:1449–1456

    Article  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Alexander AF, Hans-Peter K, Markus K (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • Moreira AP, Pereira N Jr, Thompson FL (2011) Usefulness of a real-time PCR platform for G+C content and DNA–DNA hybridization estimations in vibrios. Int J Syst Evol Microbiol 61:2379–2383

    Article  CAS  PubMed  Google Scholar 

  • Moreira AP, Duytschaever G, Tonon LAC, Dias GM, Mesquita M, Cnockaert M, Francini-Filho RB, DeVos P, Thompson CC, Thompson FL (2014) Vibrio madracius sp. nov. isolated from Madracisdecactis (Scleractinia) in St. Peter & St. Paul Archipelago, Mid-Atlantic Ridge, Brazil. Curr Microbiol 69(4):405–411

  • Noguerola I, Blanch AR (2008) Identification of Vibrio spp. with a set of dichotomous keys. J Appl Microbiol 105:175–185

    Article  CAS  PubMed  Google Scholar 

  • Oren A, Garrity GM (2014) List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 64:3603–3606

    Article  Google Scholar 

  • Oren A, Garrity GM (2015) List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 65:1–4

    Article  Google Scholar 

  • Pascual J, Macián MC, Arahal DR, Garay E, Pujalte MJ (2010) Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int J Syst Evol Microbiol 60:154–165

    Article  CAS  PubMed  Google Scholar 

  • Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and IlluminaMiSeq sequencers. BMC Genom 13(1):341

    Article  CAS  Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Microbial ID Inc, Newark

    Google Scholar 

  • Sawabe T, Kita-Tsukamoto K, Thompson FL (2007) Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189:7932–7936

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sawabe T, Ogura Y, Matsumura Y, Feng G, Rohul Amin AKM, Mino S, Nakagawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R, Thompson FL, Gomez-Gil B, Christen R, Maruyama F, Kurokawa K, Hayashi T (2013) Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 4:(414)1–14

  • Sheu S-Y, Jiang S-R, Chen CA, Wang JT, Chen WM (2011) Vibrio stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata. Int J Syst Evol Microbiol 61:2180–2185

    Article  CAS  PubMed  Google Scholar 

  • Soto-Rodriguez SA, Gomez-Gil B, Lozano-Olvera R, Betancourt-Lozano M, Morales-Covarrubias MS (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. Appl Environ Microbiol 81:1689–1699

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tarazona E, LucenaT Arahal DR, Macián MC, Ruvira MA, Pujalte MJ (2014) Multilocus sequence analysis of putative Vibrio mediterranei strains and description of Vibrio thalassae sp. nov. Syst Appl Microbiol 37:320–328

    Article  CAS  PubMed  Google Scholar 

  • Thompson FL, Swings J (2006) Taxonomy of the vibrios. In: Thompson FL, Austin B, Swings J (eds) The biology of vibrios. American Society for Microbiology, Washington, pp 29–43

    Chapter  Google Scholar 

  • Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL (2015) Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 197:359–370

    Article  CAS  PubMed  Google Scholar 

  • Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL (2013) Microbial genomic taxonomy. BMC Genom 14:913

    Article  Google Scholar 

  • Tran L, Nunan L, Redman RM, Mohney LL, Pantoja CR, Fitzsimmons K, Lightner DV (2013) Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp. Dis Aquat Organ 105:45–55

    Article  PubMed  Google Scholar 

  • Wang H, Liu J, Wang Y, Zhang X-H (2011) Vibrio marisflavi sp. nov., isolated from sea water. Int J Syst Evol Microbiol 61:568–573

    Article  CAS  PubMed  Google Scholar 

  • Yoshizawa S, Wada M, Yokota A, Kogure K (2010) Vibrio sagamiensis sp. nov., luminous marine bacteria isolated from sea water. J Gen Appl Microbiol 56:499–507

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was partially funded by CONACYT project CB-2009-01 132328 and Grant AGL–2010–18438 from the Ministerio de Ciencia e Innovación (Spain).

Author information

Authors and Affiliations

  1. CIAD, A.C., Mazatlán Unit for Aquaculture, AP. 711, 82000, Mazatlán, Sinaloa, Mexico

    Adrián González-Castillo, Julissa Enciso-Ibarrra, M. Carmen Bolán-Mejia & Bruno Gomez-Gil

  2. Departamento de Microbiología y Parasitología, CIBUS, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain

    Sabela Balboa, Aide Lasa & Jesús L. Romalde

  3. Instituto Tecnológico de Tepic, Av. Tecnológico 2595, 63175, Tepic, Nayarit, Mexico

    Hector Cabanillas-Beltrán

Authors
  1. Adrián González-Castillo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Julissa Enciso-Ibarrra
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Carmen Bolán-Mejia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sabela Balboa
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Aide Lasa
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jesús L. Romalde
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hector Cabanillas-Beltrán
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bruno Gomez-Gil
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bruno Gomez-Gil.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 978 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

González-Castillo, A., Enciso-Ibarrra, J., Bolán-Mejia, M.C. et al. Vibrio mexicanus sp. nov., isolated from a cultured oyster Crassostrea corteziensis . Antonie van Leeuwenhoek 108, 355–364 (2015). https://doi.org/10.1007/s10482-015-0488-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-015-0488-1

Keywords

  • Vibrio mexicanus
  • Vibrio naceae
  • Vibrio aestivus
  • Vibrio marisflavi