1887

Abstract

Vibrios are ubiquitous in the aquatic environment and can be found in association with animal or plant hosts. The range of ecological relationships includes pathogenic and mutualistic associations. To gain a better understanding of the ecology of these microbes, it is important to determine their phenotypic features. However, the traditional phenotypic characterization of vibrios has been expensive, time-consuming and restricted in scope to a limited number of features. In addition, most of the commercial systems applied for phenotypic characterization cannot characterize the broad spectrum of environmental strains. A reliable and possible alternative is to obtain phenotypic information directly from whole genome sequences. The aim of the present study was to evaluate the usefulness of whole genome sequences as a source of phenotypic information. We performed a comparison of the vibrio phenotypes obtained from the literature with the phenotypes obtained from whole genome sequences. We observed a significant correlation between the previously published phenotypic data and the phenotypic data retrieved from whole genome sequences of vibrios. Analysis of 26 vibrio genomes revealed that all genes coding for the specific proteins involved in the metabolic pathways responsible for positive phenotypes of the 14 diagnostic features (Voges–Proskauer reaction, indole production, arginine dihydrolase, ornithine decarboxylase, utilization of -inositol, sucrose and -leucine, and fermentation of -mannitol, -sorbitol, -arabinose, trehalose, cellobiose, -mannose and -galactose) were found in the majority of the vibrios genomes. Vibrio species that were negative for a given phenotype revealed the absence of all or several genes involved in the respective biochemical pathways, indicating the utility of this approach to characterize the phenotypes of vibrios. The absence of the global regulation and regulatory proteins in the genome indicated a non-vibrio phenotype. Whole genome sequences represent an important source for the phenotypic identification of vibrios.

Funding
This study was supported by the:
  • CNPq
  • CAPES
  • FAPERJ
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/content/journal/ijsem/10.1099/ijs.0.057927-0
2014-02-01
2024-12-01
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References

  1. Alice A. F., Crosa J. H. ( 2012 ). The TonB3 system in the human pathogen Vibrio vulnificus is under the control of the global regulators Lrp and cyclic AMP receptor protein. . J Bacteriol 194, 18971911. [View Article] [PubMed]
    [Google Scholar]
  2. Alsina M., Blanch A. R. ( 1994 ). A set of keys for biochemical identification of environmental Vibrio species. . J Appl Bacteriol 76, 7985. [View Article] [PubMed]
    [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403410.[PubMed] [CrossRef]
    [Google Scholar]
  4. Auch A. F., 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 Genomic Sci 2, 117134. [View Article] [PubMed]
    [Google Scholar]
  5. Aziz R. K., Bartels D., Best A. A., DeJongh M., Disz T., Edwards R. A., Formsma K., Gerdes S., Glass E. M. & other authors ( 2008 ). The RAST Server: rapid annotations using subsystems technology. . BMC Genomics 9, 75. [View Article] [PubMed]
    [Google Scholar]
  6. Drews G. ( 2000 ). The roots of microbiology and the influence of Ferdinand Cohn on microbiology of the 19th century. . FEMS Microbiol Rev 24, 225249. [View Article] [PubMed]
    [Google Scholar]
  7. Farmer J. J., Hickman-Brenner F. W. ( 2006 ). The Genera Vibrio and Photobacterium. , 6: 508563 In: The Prokaryotes. A Handbook on the Biology of Bacteria: Proteobacteria: Gamma Subclass , , 3rd edn.. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. . Berlin:: Springer;.
    [Google Scholar]
  8. Garza D. R., Thompson C. C., Loureiro E. C. B., Dutilh B. E., Inada D. T., Junior E. C. S., Cardoso J. F., Nunes M. R. T., de Lima C. P. S. & other authors ( 2012 ). Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic. . PLoS ONE 7, e37283. [View Article] [PubMed]
    [Google Scholar]
  9. Gottesman S. ( 1984 ). Bacterial regulation: global regulatory networks. . Annu Rev Genet 18, 415441. [View Article] [PubMed]
    [Google Scholar]
  10. Hunt D. E., David L. A., Gevers D., Preheim S. P., Alm E. J., Polz M. F. ( 2008 ). Resource partitioning and sympatric differentiation among closely related bacterioplankton. . Science 320, 10811085. [View Article] [PubMed]
    [Google Scholar]
  11. Konstantinidis K. T., Stackebrandt E. ( 2013 ). Defining Taxonomic Ranks. . 229. In The Prokaryotes (4th edition): Prokaryotic Biology and Symbiotic Associations. , 4th edn.. Edited by Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., Thompson F. L. . New York:: Springer;.
    [Google Scholar]
  12. Lo Scrudato M., Blokesch M. ( 2013 ). A transcriptional regulator linking quorum sensing and chitin induction to render Vibrio cholerae naturally transformable. . Nucleic Acids Res 41, 36443658. [View Article] [PubMed]
    [Google Scholar]
  13. Martínez-Antonio A., Collado-Vides J. ( 2003 ). Identifying global regulators in transcriptional regulatory networks in bacteria. . Curr Opin Microbiol 6, 482489. [View Article] [PubMed]
    [Google Scholar]
  14. Moreira A. P. B., Pereira N. Jr, Thompson F. L. ( 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, 23792383. [View Article] [PubMed]
    [Google Scholar]
  15. Noguerola I., Blanch A. R. ( 2008 ). Identification of Vibrio spp. with a set of dichotomous keys. . J Appl Microbiol 105, 175185. [View Article] [PubMed]
    [Google Scholar]
  16. Preheim S. P., Timberlake S., Polz M. F. ( 2011 ). Merging taxonomy with ecological population prediction in a case study of Vibrionaceae . . Appl Environ Microbiol 77, 71957206. [View Article] [PubMed]
    [Google Scholar]
  17. Silveira A. C. G., Robertson K. L., Lin B., Wang Z., Vora G. J., Vasconcelos A. T. R., Thompson F. L. ( 2010 ). Identification of non-coding RNAs in environmental vibrios. . Microbiology 156, 24522458. [View Article] [PubMed]
    [Google Scholar]
  18. Thompson F. L., Iida T., Swings J. ( 2004 ). Biodiversity of vibrios. . Microbiol Mol Biol Rev 68, 403431. [View Article] [PubMed]
    [Google Scholar]
  19. Thompson F. L., Gevers D., Thompson C. C., Dawyndt P., Naser S., Hoste B., Munn C. B., Swings J. ( 2005 ). Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. . Appl Environ Microbiol 71, 51075115. [View Article] [PubMed]
    [Google Scholar]
  20. Thompson C. C., Vicente A. C. P., Souza R. C., Vasconcelos A. T. R., Vesth T., Alves N. Jr, Ussery D. W., Iida T., Thompson F. L. ( 2009 ). Genomic taxonomy of vibrios. . BMC Evol Biol 9, 258. [View Article] [PubMed]
    [Google Scholar]
  21. Thompson C. C., Vieira N. M., Vicente A. C. P., Thompson F. L. ( 2011 ). Towards a genome based taxonomy of Mycoplasmas. . Infect Genet Evol 11, 17981804. [View Article] [PubMed]
    [Google Scholar]
  22. Thompson C. C., Emmel V. E., Fonseca E. L., Marin M. A., Vicente A. C. ( 2013a ). Streptococcal taxonomy based on genome sequence analyses. . F1000 Res 2, 19.[PubMed]
    [Google Scholar]
  23. Thompson C. C., Silva G. G. Z., Vieira N. M., Edwards R., Vicente A. C. P., Thompson F. L. ( 2013b ). Genomic taxonomy of the genus Prochlorococcus . . Microb Ecol 66, 752762. [View Article] [PubMed]
    [Google Scholar]
  24. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. ( 1996 ). Polyphasic taxonomy, a consensus approach to bacterial systematics. . Microbiol Rev 60, 407438.[PubMed]
    [Google Scholar]
  25. Willems A., Doignon-Bourcier F., Goris J., Coopman R., de Lajudie P., De Vos P., Gillis M. ( 2001 ). DNA-DNA hybridization study of Bradyrhizobium strains. . Int J Syst Evol Microbiol 51, 13151322.[PubMed]
    [Google Scholar]
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