Comparative genomic analyses identify the Vibrio harveyi genome sequenced strains BAA‐1116 and HY01 as Vibrio campbellii

Abstract

Summary Three notable members of the Harveyi clade, Vibrio harveyi , Vibrio alginolyticus and Vibrio parahaemolyticus , are best known as marine pathogens of commercial and medical import. In spite of this fact, the discrimination of Harveyi clade members remains difficult due to genetic and phenotypic similarities, and this has led to misidentifications and inaccurate estimations of a species' involvement in certain environments. To begin to understand the underlying genetics that complicate species level discrimination, we compared the genomes of Harveyi clade members isolated from different environments (seawater, shrimp, corals, oysters, finfish, humans) using microarray‐based comparative genomic hybridization (CGH) and multilocus sequence analyses (MLSA). Surprisingly, we found that the only two V. harveyi strains that have had their genomes sequenced (strains BAA‐1116 and HY01) have themselves been misidentified. Instead of belonging to the species harveyi , they are actually members of the species campbellii . In total, 28% of the strains tested were found to be misidentified and 42% of these appear to comprise a novel species. Taken together, our findings correct a number of species misidentifications while validating the ability of both CGH and MLSA to distinguish closely related members of the Harveyi clade.

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References 37

1. 1.

   Austin B, Austin D, Sutherland R, Thompson F, Swings J. Pathogenicity of vibrios to rainbow trout (Oncorhynchus mykiss, Walbaum) and Artemia nauplii. Environ Microbiol. 2005;7:1488-1495.

   Not in our library10.1111/j.1462-2920.2005.00847.x

2. 2.

   Bassler BL, Greenberg EP, Stevens AM. Cross-species induction of luminescence in the quorum-sensing bacterium Vibrio harveyi. J Bacteriol. 1997;179:4043-4045.

   Not in our library10.1128/jb.179.12.4043-4045.1997

3. 3.

   Baumann P, Baumann L, Bang SS, Wollkalis MJ. Reevaluation of the taxonomy of Vibrio, Beneckea, and Photobacterium: abolition of the genus Beneckea. Curr Microbiol. 1980;4:127-132.

   Not in our library

4. 4.

   Bryant TN, Lee JV, West PA, Colwell RR. A probability matrix for the identification of species of Vibrio and related genera. J Appl Bacteriol. 1986;61:469-480.

   Not in our library10.1111/j.1365-2672.1986.tb04309.x

5. 5.

   Cano-Gomez A, Bourne DG, Hall MR, Owens L, Hoj L. Molecular identification, typing and tracking of Vibrio harveyi in aquaculture systems: current methods and future prospects. Aquaculture. 2009;287:1-10.

   Not in our library

6. 6.

   Cervino JM, Thompson FL, Gomez-Gil B, Lorence EA, Goreau TJ, Hayes RL, et al. The Vibrio core group induces yellow band disease in Caribbean and Indo-Pacific reef-building corals. J Appl Microbiol. 2008;105:1658-1671.

   Not in our library10.1111/j.1365-2672.2008.03871.x

7. 7.

   Defoirdt T, Verstraete W, Bossier P. Luminescence, virulence and quorum sensing signal production by pathogenic Vibrio campbellii and Vibrio harveyi isolates. J Appl Microbiol. 2008;104:1480-1487.

   Not in our library10.1111/j.1365-2672.2007.03672.x

8. 8.

   Dorsch M, Lane D, Stackebrandt E. Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences. Int J Syst Bacteriol. 1992;42:58-63.

   Not in our library10.1099/00207713-42-1-58

9. 9.

   Faruque SM, Mekalanos JJ. Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol. 2003;11:505-510.

   Not in our library10.1016/j.tim.2003.09.003

10. 10.

    Gauger EJ, Gomez-Chiarri M. 16S ribosomal DNA sequencing confirms the synonymy of Vibrio harveyi and V. carchariae. Dis Aquat Organ. 2002;52:39-46.

    Not in our library10.3354/dao052039

11. 11.
    Bioconductor: open software development for computational biology and bioinformatics · 2004

    No notice
12. 12.

    Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, et al. Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol. 2005;3:733-739.

    Not in our library10.1038/nrmicro1236

13. 13.

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

    Not in our library10.1099/ijs.0.02430-0

14. 14.

    Gomez-Gil B, Soto-Rodriguez S, Garcia-Gasca A, Roque A, Vazquez-Juarez R, Thompson FL, Swings J. Molecular identification of Vibrio harveyi-related isolates associated with diseased aquatic organisms. Microbiology. 2004;150:1769-1777.

    Not in our library10.1099/mic.0.26797-0

15. 15.

    Hastings JW, Weber K, Friedland J, Eberhard A, Mitchell GW, Gunsalus A. Structurally distinct bacterial luciferases. Biochemistry. 1969;8:4681-4689.

    Not in our library10.1021/bi00840a004

16. 16.

    Henke JM, Bassler BL. Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J Bacteriol. 2004;186:6902-6914.

    Not in our library10.1128/jb.186.20.6902-6914.2004

17. 17.

    Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL. The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell. 2004;118:69-82.

    Not in our library10.1016/j.cell.2004.06.009

18. 18.
    Quantifying the Integration of Quorum-Sensing Signals with Single-Cell Resolution · 2009

    No notice
19. 19.

    Milton DL. Quorum sensing in vibrios: complexity for diversification. Int J Med Microbiol. 2006;296:61-71.

    Not in our library10.1016/j.ijmm.2006.01.044

20. 20.

    Nealson KH, Platt T, Hastings JW. Cellular control of the synthesis and activity of the bacterial luminescent system. J Bacteriol. 1970;104:313-322.

    Not in our library10.1128/jb.104.1.313-322.1970

21. 21.

    O'Brien CH, Sizemore RK. Distribution of the luminous bacterium Beneckea harveyi in a semitropical estuarine environment. Appl Environ Microbiol. 1979;38:928-933.

    Not in our library10.1128/aem.38.5.928-933.1979

22. 22.

    Pascual J, Macian MC, Arahal DR, Garay E, Pujalte MJ. Multilocus sequence analysis of the central clade of the genus Vibrio by using 16S rRNA, recA, pyrH, rpoD, gyrB, rctB, and toxR genes. Int J Syst Evol Microbiol. 2009.

    Not in our library10.1099/ijs.0.010702-0

23. 23.

    Pedersen K, Verdonck L, Austin B, Austin DA, Blanch AR, Grimont PAD, et al. Taxonomic evidence that Vibrio carchariae Grimes et al. 1985 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981. Int J Syst Bacteriol. 1998;48:749-758.

    Not in our library

24. 24.

    Rattanama P, Srinitiwarawong K, Thompson JR, Pomwised R, Supamattaya K, Vuddhakul V. Shrimp pathogenicity, hemolysis, and the presence of hemolysin and TTSS genes in Vibrio harveyi isolated from Thailand. Dis Aquat Organ. 2009;86:113-122.

    Not in our library10.3354/dao02119

25. 25.

    Reichelt JL, Baumann P. Taxonomy of the marine, luminous bacteria. Arch Microbiol. 1973;94:283-330.

    Not in our library

26. 26.

    Reichelt JL, Baumann P, Baumann L. Study of genetic relationships among marine species of the genera Beneckea and Photobacterium by means of in vitro DNA/DNA hybridization. Arch Microbiol. 1976;110:101-120.

    Not in our library10.1007/bf00416975

27. 27.

    Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I. The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol. 2007;5:355-362.

    Not in our library10.1038/nrmicro1635

28. 28.

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

    Not in our library10.1128/jb.00693-07

29. 29.

    Thompson CC, Thompson FL, Vicente AC. Identification of Vibrio cholerae and Vibrio mimicus by multilocus sequence analysis (MLSA). Int J Syst Evol Microbiol. 2008;58:617-621.

    Not in our library10.1099/ijs.0.65461-0

30. 30.

    Thompson FL, Hoste B, Vandemeulebroecke K, Swings J. Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism. Syst Appl Microbiol. 2001;24:520-538.

    Not in our library10.1078/0723-2020-00067

31. 31.

    Thompson FL, Hoste B, Vandemeulebroecke K, Engelbeen K, Denys R, Swings J. Vibrio trachuri Iwamoto et al. 1995 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981. Int J Syst Evol Microbiol. 2002;52:973-976.

    Not in our library10.1099/00207713-52-3-973

32. 32.

    Thompson FL, Iida T, Swings J. Biodiversity of Vibrios. Microbiol Mol Biol Rev. 2004;68:403-431.

    Not in our library10.1128/mmbr.68.3.403-431.2004

33. 33.

    Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S, Hoste B, et al. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol. 2005;71:5107-5115.

    Not in our library10.1128/aem.71.9.5107-5115.2005

34. 34.

    Thompson FL, Gomez-Gil B, Vasconcelos AT, Sawabe T. Multilocus sequence analysis reveals that Vibrio harveyi and V. campbellii are distinct species. Appl Environ Microbiol. 2007;73:4279-4285.

    Not in our library10.1128/aem.00020-07

35. 35.

    Tu KC, Bassler BL. Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev. 2007;21:221-233.

    Not in our library10.1101/gad.1502407

36. 36.

    Waters CM, Bassler BL. The Vibrio harveyi quorum-sensing system uses shared regulatory components to discriminate between multiple autoinducers. Genes Dev. 2006;20:2754-2767.

    Not in our library10.1101/gad.1466506

37. 37.

    Yoshizawa S, Wada M, Kita-Tsukamoto K, Ikemoto E, Yokota A, Kogure K. Vibrio azureus sp. nov., a luminous marine bacterium isolated from seawater. Int J Syst Evol Microbiol. 2009;59:1645-1649.

    Not in our library10.1099/ijs.0.004283-0

Cited by papers we hold 2

• Diversity in Natural Transformation Frequencies and Regulation across <italic toggle="yes">Vibrio</italic> Species · 2019
  Not checked
• Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. · 2013
  No notice

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