1887

Abstract

The Orientalis clade has a relevant significance for bivalve aquaculture since it includes the pathogens , subsp. and subsp. . However, the previous taxonomic description of the subspecies of shows some incongruities that should be emended. In the genomic age, the comparison between genome assemblies is the key to clarify the taxonomic position of both subspecies. With this purpose, we have tested the ability of multilocus sequence analysis based on eight housekeeping gene sequences ( , , , , , , and ), different genome-to-genome comparisons, chemotaxonomic features and phenotypic traits to reclassify the subspecies subsp. within the Orientalis clade. This polyphasic approach clearly demonstrated that this subspecies is phylogenetically and phenotypically distinct from and should be elevated to the rank of species as sp. nov. This reclassification allows us to update the Orientalis clade ( , , , , , and sp. nov.) and reconstruct a better phylogeny of the genus . An emended description of is provided. Finally, the proposed novel species is represented by emergent bivalve pathogens [type strain PP-638 (=CECT 8136=DSM 27349), PP2-843 and 07/118 T2] responsible for high mortalities in Spanish and French hatcheries.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001431
2016-11-01
2022-01-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4791.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001431&mimeType=html&fmt=ahah

References

  1. Al-Saari N., Gao F., Rohul A. A., Sato K., Sato K., Mino S., Suda W., Oshima K., Hattori M. et al. 2015; Advanced microbial taxonomy combined with genome-based-approaches reveals that Vibrio astriarenae sp. nov., an agarolytic marine bacterium, forms a new clade in Vibrionaceae. PLoS One 10:e0136279 [View Article][PubMed]
    [Google Scholar]
  2. Bennett J. S., Jolley K. A., Earle S. G., Corton C., Bentley S. D., Parkhill J., Maiden M. C. 2012; A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria. Microbiology 158:1570–1580 [View Article][PubMed]
    [Google Scholar]
  3. Chan J. Z. M., Halachev M. R., Loman N. J., Constantinidou C., Pallen M. J. 2012; Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12:302 [View Article][PubMed]
    [Google Scholar]
  4. Dubert J., Romalde J. L., Prado S., Barja J. L. 2016; Vibrio bivalvicida sp. nov., a novel larval pathogen for bivalve molluscs reared in a hatchery. Syst Appl Microbiol 39:8–13 [View Article][PubMed]
    [Google Scholar]
  5. González-Castillo A., Balboa S., Romalde J. L., Gomez-Gil B. 2014; Vibrio crosai sp. nov., isolated from a cultured oyster Crassostrea gigas. Antonie van Leeuwenhoek 106:457–463 [View Article][PubMed]
    [Google Scholar]
  6. Hada H. S., West P. A., Lee J. V., Stemmler J., Colwell R. R. 1984; Vibrio tubiashii sp. nov., a pathogen of bivalve mollusks. Int J of Syst Bacteriol 34:1–4 [View Article]
    [Google Scholar]
  7. Hoffmann M., Monday S. R., Allard M. W., Strain E. A., Whittaker P., Naum M., McCarthy P. J., Lopez J. V., Fischer M., Brown E. W. 2012; Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea. Int J Syst Evol Microbiol 62:1736–1743 [View Article][PubMed]
    [Google Scholar]
  8. Huson D. H., Bryant D. 2006; Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267 [View Article][PubMed]
    [Google Scholar]
  9. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 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 [View Article][PubMed]
    [Google Scholar]
  10. Konstantinidis K. T., Tiedje J. M. 2005; Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  11. Lee I., Kim Y. O., Park S.-C., Chun J. 2016; OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103 [View Article]
    [Google Scholar]
  12. Li X., Huang Y., Whitman W. B. 2015; The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes. Antonie van Leeuwenhoek 107:241–249 [View Article][PubMed]
    [Google Scholar]
  13. Lin B., Wang Z., Malanoski A. P., O'Grady E. A., Wimpee C. F., Vuddhakul V., Alves N. Jr, Thompsonm F. L., Gomez-Gil B., Vora G. J. 2010; Comparative genomic analyses identify the Vibrio harveyi genome sequenced strains BAA-1116 and HY01 as Vibrio campbellii. Environ Microbiol Rep 2:81–89 [View Article][PubMed]
    [Google Scholar]
  14. Meier-Kolthoff J. P., Klenk H. P., Göker M. 2014; Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356 [View Article][PubMed]
    [Google Scholar]
  15. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60 [View Article][PubMed]
    [Google Scholar]
  16. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelsky A., Pyshkin A., Sirotkin A. et al. 2013; Assembling genomes and mini–metagenomes from highly chimeric reads. In Lecture Notes in Computer Science pp 158–170 Edited by Deng M., Jiang R., Sun F., Zhang X. Berlin, Germany: Springer–Verlag;
    [Google Scholar]
  17. Pearson W. R., Lipman D. J. 1988; Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85:2444–2448 [View Article][PubMed]
    [Google Scholar]
  18. Prado S., Dubert J., Barja J. L. 2015; Characterization of pathogenic vibrios isolated from bivalve hatcheries in Galicia, NW Atlantic coast of Spain. Description of Vibrio tubiashii subsp. europaensis subsp. nov. Syst Appl Microbiol 38:26–29 [View Article][PubMed]
    [Google Scholar]
  19. Richter M., Rosselló-Móra R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  20. Richter M., Rosselló-Móra R., Glöckner F. O., Peplies J. 2016; JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931 [View Article][PubMed]
    [Google Scholar]
  21. Sawabe T., Kita-Tsukamoto K., Thompson F. L. 2007; Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189:7932–7936 [View Article][PubMed]
    [Google Scholar]
  22. Sawabe T., Ogura Y., Matsumura Y., Feng G., Amin A. R., Mino S., Nakagawa S., Sawabe T., Kumar R. et al. 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: doi:10.3389/fmicb. 2013.00414 [View Article][PubMed]
    [Google Scholar]
  23. Stackerbrant E., Ebers J. 2006; Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
    [Google Scholar]
  24. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  25. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  26. Thompson C. C., Vicente A. C., Souza R. C., Vasconcelos A. T., Vesth T., Alves N., Ussery D. W., Iida T., Thompson F. L. 2009; Genomic taxonomy of vibrios. BMC Evol Biol 9:258 [View Article][PubMed]
    [Google Scholar]
  27. Travers M. A., Mersni Achour R., Haffner P., Tourbiez D., Cassone A. L., Morga B., Doghri I., Garcia C., Renault T. et al. 2014; First description of french V. tubiashii strains pathogenic to mollusk: I. characterization of isolates and detection during mortality events. J Invertebr Pathol 123:38–48 [View Article][PubMed]
    [Google Scholar]
  28. Urbanczyk Y., Ogura Y., Hayashi T., Urbanczyk H. 2016; Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida. Int J Syst Evol Microbiol 66:3214–3218 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001431
Loading
/content/journal/ijsem/10.1099/ijsem.0.001431
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error