1887

Abstract

Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 representatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA–DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species , , or , while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the family .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63136-0
2005-01-01
2019-12-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/1/ijs550057.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63136-0&mimeType=html&fmt=ahah

References

  1. Anderberg, M. R. ( 1973; ). Cluster Analysis for Applications. New York: Academic Press.
  2. Arias, C. R., Verdonck, L., Swings, J., Garay, E. & Aznar, R. ( 1997; ). Intraspecific differentiation of Vibrio vulnificus biotypes by amplified fragment length polymorphism and ribotyping. Appl Environ Microbiol 63, 2600–2606.
    [Google Scholar]
  3. Austin, B., Dawyndt, P., Gyllenberg, M., Koski, T., Lund, T., Swings, J. & Thompson, F. L. ( 2004; ). Sliding window discretization: a new method for multiple band matching of bacterial genotyping fingerprints. Bull Math Biol 66, 1575–1596.[CrossRef]
    [Google Scholar]
  4. Ben-Haim, Y., Thompson, F. L., Thompson, C. C., Cnockaert, M. C., Hoste, B., Swings, J. & Rosenberg, E. ( 2003; ). Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis. Int J Syst Evol Microbiol 53, 309–315.[CrossRef]
    [Google Scholar]
  5. Buchanan, R. E. ( 1925; ). General Systematic Bacteriology. Baltimore: Williams & Wilkins.
  6. Cover, T. M. & Thomas, J. A. ( 1991; ). Elements of Information Theory. New York: Wiley.
  7. Dice, L. R. ( 1945; ). Measures of the amount of ecological association between species. Ecology 26, 297–302.[CrossRef]
    [Google Scholar]
  8. Gomez-Gil, B., Thompson, F. L., Thompson, C. C. & Swings, J. ( 2003; ). Vibrio pacinii sp. nov., from cultured aquatic organisms. Int J Syst Evol Microbiol 53, 1569–1573.[CrossRef]
    [Google Scholar]
  9. Gyllenberg, M., Koski, T. & Verlaan, M. ( 1997a; ). Classification of binary vectors by stochastic complexity. J Multivariate Anal 63, 47–72.[CrossRef]
    [Google Scholar]
  10. Gyllenberg, H. G., Gyllenberg, M., Koski, T., Lund, T., Schindler, J. & Verlaan, M. ( 1997b; ). Classification of Enterobacteriaceae by minimization of stochastic complexity. Microbiology 143, 721–732.[CrossRef]
    [Google Scholar]
  11. Gyllenberg, H. G., Gyllenberg, M., Koski, T. & Lund, T. ( 1998; ). Stochastic complexity as a taxonomic tool. Comput Methods Programs Biomed 56, 11–22.[CrossRef]
    [Google Scholar]
  12. Gyllenberg, H. G., Gyllenberg, M., Koski, T., Lund, T. & Schindler, J. ( 1999; ). Enterobacteriaceae taxonomy approached by minimization of stochastic complexity. Quantitative Microbiol 1, 157–170.[CrossRef]
    [Google Scholar]
  13. Gyllenberg, M., Koski, T. & Lund, T. ( 2001; ). BinClass: a software package for classifying binary vectors. User's guide. TUCS Technical Report 411 http://www.tucs.fi/publications/techreports/TR411.php.
    [Google Scholar]
  14. Gyllenberg, M., Dawyndt, P., Koski, T., Lund, T., Thompson, F., Austin, B. & Swings, J. ( 2002; ). New methods for the analysis of binarized BIOLOG GN data of Vibrio species: minimization of stochastic complexity and cumulative classification. Syst Appl Microbiol 25, 403–415.[CrossRef]
    [Google Scholar]
  15. Janssen, P., Coopman, R., Huys, G., Swings, J., Bleeker, M., Vos, P., Zabeau, M. & Kersters, K. ( 1996; ). Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142, 1881–1893.[CrossRef]
    [Google Scholar]
  16. Liston, J., Wiebe, W. J. & Colwell, R. R. ( 1963; ). Quantitative approach to the study of bacterial species. J Bacteriol 85, 1061–1070.
    [Google Scholar]
  17. Mácian, M. C., Garay, E., Gonzalez-Candelas, F., Pujalte, M. J. & Aznar, R. ( 2000; ). Ribotyping of Vibrio populations associated with cultured oysters (Ostrea edulis). Syst Appl Microbiol 23, 409–417.[CrossRef]
    [Google Scholar]
  18. Priest, F. & Austin, B. ( 1993; ). Modern Bacterial Taxonomy, 2nd edn. London: Chapman & Hall.
  19. Sawabe, T., Thompson, F. L., Heyrman, J. & 7 other authors ( 2002; ). Fluorescent amplified fragment length polymorphism and repetitive extragenic palindrome-PCR fingerprinting reveal host-specific genetic diversity of Vibrio halioticoli-like strains isolated from the gut of japanese Abalone. Appl Environ Microbiol 68, 4140–4144.[CrossRef]
    [Google Scholar]
  20. Sawabe, T., Hayashi, K., Moriwaki, J., Thompson, F. L., Swings, J. & Christen, R. ( 2004; ). Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. isolated from the gut of Japanese abalones. Syst Appl Microbiol 27, 527–534.[CrossRef]
    [Google Scholar]
  21. Schiewe, M. H., Trust, T. J. & Crosa, J. H. ( 1981; ). Vibrio ordalii sp. nov.: a causative agent of vibriosis in fish. Curr Microbiol 6, 343–348.[CrossRef]
    [Google Scholar]
  22. Sneath, P. H. A. ( 1984; ). Bacterial Nomenclature. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 19–23. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  23. Sneath, P. H. A. & Sokal, R. R. ( 1973; ). Numerical Taxonomy: the Principles and Practice of Numerical Classification. San Francisco: W. H. Freeman.
  24. Thompson, F. L., Hoste, B., Vandemeulebroecke, K. & Swings, J. ( 2001; ). Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism. Syst Appl Microbiol 24, 520–538.[CrossRef]
    [Google Scholar]
  25. Thompson, F. L., Hoste, B., Thompson, C. C., Goris, J., Gomez-Gil, B., Huys, L. & Swings, J. ( 2002; ). Enterovibrio norvegicus gen. nov., sp. nov., isolated from the gut of turbot (Scophthalmus maximus) larvae: a new member of the family Vibrionaceae. Int J Syst Evol Microbiol 52, 2015–2022.[CrossRef]
    [Google Scholar]
  26. Thompson, F. L., Thompson, C. C., Hoste, B., Vandemeulebroecke, K., Gullian, M. & Swings, J. ( 2003a; ). Vibrio fortis sp. nov. and Vibrio hepatarius sp. nov., isolated from aquatic animals and the marine environment. Int J Syst Evol Microbiol 53, 1495–1501.[CrossRef]
    [Google Scholar]
  27. Thompson, F. L., Thompson, C. C. & Swings, J. ( 2003b; ). Vibrio tasmaniensis sp. nov., isolated from atlantic salmon (Salmo salar L.). Syst Appl Microbiol 26, 65–69.[CrossRef]
    [Google Scholar]
  28. Thompson, F. L., Thompson, C. C., Li, Y., Gomez-Gil, B., Vandenberghe, J. & Swings, J. ( 2003c; ). Vibrio kanaloae sp. nov, Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals. Int J Syst Evol Microbiol 53, 753–759.[CrossRef]
    [Google Scholar]
  29. Thompson, F. L., Li, Y., Gomez-Gil, B. & 8 other authors ( 2003d; ). Vibrio neptunius sp. nov., Vibrio brasiliensis sp. nov. and Vibrio xuii sp. nov., isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps). Int J Syst Evol Microbiol 53, 245–252.[CrossRef]
    [Google Scholar]
  30. Vandenberghe, J., Verdonck, L., Robles-Arozarena, R. & 7 other authors ( 1999; ). Vibrios associated with Litopenaeus vannamei larvae, postlarvae, broodstock and hatchery probionts. Appl Environ Microbiol 65, 2592–2597.
    [Google Scholar]
  31. Ward, J. H. ( 1963; ). Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58, 236–244.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63136-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63136-0
Loading

Data & Media loading...

Supplements

An example of a stochastic-complexity-minimizing dendrogram(PDF file, 85KB) for the fAFLP dataset of and the source code and a user manual for the BinClass software package(ZIP file, 989KB) are available to download.

PDF

An example of a stochastic-complexity-minimizing dendrogram(PDF file, 85KB) for the fAFLP dataset of and the source code and a user manual for the BinClass software package(ZIP file, 989KB) are available to download.

ARCHIVE

Most Cited This Month

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