Probabilistic Identification of Species Free

Abstract

Summary: The character state data for clusters defined at the 83% simple matching coefficient () similarity level in a previous phenetic classification were used to construct a probabilistic identification matrix for species. The 24 phena included consisted of 10 clusters containing from 2 to 17 strains and 14 single-member clusters. Characters most diagnostic for the clusters were selected from the 185 used in the classification, using previously developed computer programs for determination of character separation indices (CHARSEP) and selection of group diagnostic properties (DIACHAR). The resulting matrix consisted of 41 characters x 24 phena, and identification scores, provided by a program for the identification of unknowns against an identification matrix (MATIDEN), were used for its evaluation. Cluster overlap, calculated by a program for determination of overlap between groups in a matrix (OVERMAT), was generally very small, and the best identification scores possible for most typical examples of each group (MOSTTYP program) were very satisfactory. Input of test data for randomly selected cluster representatives resulted in correct identifications with good scores for the three coefficients provided by the MATIDEN program.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-131-7-1681
1985-07-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/131/7/mic-131-7-1681.html?itemId=/content/journal/micro/10.1099/00221287-131-7-1681&mimeType=html&fmt=ahah

References

  1. Baldacci E. 1958; Developments in the classification of actinomycetes. Giornale di microbiologia 6:10–27
    [Google Scholar]
  2. Baldacci E., Locci R. 1974; Genus II. Streptoverticillium Baldacci 1958, 15 emend, mut. char. Baldacci, Farina and Locci 1966, 168. In Bergey’s Manual of Determinative Bacteriology 8th edn, pp 829–842 Edited by Buchanan R. E., Gibbons N. E. Baltimore: Williams & Wilkins;
    [Google Scholar]
  3. Baldacci E., Farina G., Locci R. 1966; Emendation of the genus Streptoverticillium Baldacci (1958) and revision of some species. Giornale di microbiologia 14:153–171
    [Google Scholar]
  4. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. Journal of General Microbiology 100:221–230
    [Google Scholar]
  5. Cross T., Attwell R. W., Locci R. 1973; Fine structure of the spore sheath in Streptoverticillium species. Journal of General Microbiology 75:421–424
    [Google Scholar]
  6. Farina G., Locci R. 1966; Contribution to the study of Streptoverticillium. Description of a new species (Streptoverticillium baldacci sp. nov.) and examination of previously illustrated species. Giornale di microbiologia 14:33–52
    [Google Scholar]
  7. Goodfellow M. 1971; Numerical taxonomy of some nocardioform bacteria. Journal of General Microbiology 69:33–80
    [Google Scholar]
  8. Gordon R. E. 1968; The taxonomy of soil bacteria. In The Ecology of Soil Bacteria pp 293–321 Edited by Gray T. R. G., Parkinson D. Liverpool: Liverpool University Press;
    [Google Scholar]
  9. Hill L. R. 1974; Theoretical aspects of numerical identification. International Journal of Systematic Bacteriology 24:494–499
    [Google Scholar]
  10. Kroppenstedt R. M., Korn-Wendisch F., Fowler V. J., Stackebrandt E. 1981; Biochemical and molecular genetic evidence for a transfer of Actinoplanes armeniacus into the family Streptomyceteae . Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene (Abteilung I, Originate C) 2:254–262
    [Google Scholar]
  11. Kuryolwicz W., Pasziewicz A., Woźnicka W., Kurzatowski W., Szulga T. 1975; Classification of Streptomyces by different numerical methods. Postepy higieny i medycyny doswiadczalnej 29:281–355
    [Google Scholar]
  12. Küster E., Williams S. T. 1964; Production of hydrogen sulphide by streptomycetes and methods for its detection. Applied Microbiology 12:46–52
    [Google Scholar]
  13. Kutzner H. J. 1976 Methoden zur Untersuchung von Streptomycen und einigen anderen Actinomyceten Darmstadt: Teilsammlung Darmstadt am Institut für Mikrobiologie der Technischen Hochschule.;
    [Google Scholar]
  14. Lechevalier M. P., Lechevalier H. A. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. International Journal of Systematic Bacteriology 20:435–443
    [Google Scholar]
  15. Lechevalier M. P., de Biévre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochemical Systematics and Ecology 5:249–260
    [Google Scholar]
  16. Lechevalier M. P., Stern A. E., Lechevalier H. A. 1981; Phospholipids in the taxonomy of actinomycetes. Zentralblatt für Bakteriologie, Mikrobiologie und Hygiene (Abteilung I, Supplement 11)111–116
    [Google Scholar]
  17. Locci R., Petrolini B. B. 1970; Morphology and development of Streptoverticillium species as examined by scanning electron microscopy. Giornale di microbiologia 18:69–76
    [Google Scholar]
  18. Locci R., Baldacci E., Petrolini B. B. 1969; The genus Streptoverticillium. A taxonomic study. Giornale di microbiologia 17:1–60
    [Google Scholar]
  19. Locci R., Rogers J., Sardi P., Schofield G. M. 1981; A preliminary numerical study on named species of the genus Streptoverticillium . Annali di Microbiologia 31:115–121
    [Google Scholar]
  20. Minnikin D. E., O’Donnell A. G. 1984; Actinomycete envelope lipid and peptidoglycan composition. In The Biology of the Actinomycetes pp 335–388 Edited by Goodfellow M., Mordarski M., Williams S. T. London: Academic Press;
    [Google Scholar]
  21. Prauser H. 1976; Host–phage relationships in nocardioform organisms. In The Biology of the Nocardiae pp 266–284 Edited by Goodfellow M., Brownell G. H., Serrano J. A. London: Academic Press;
    [Google Scholar]
  22. Pridham T. G., Tresner H. D. 1974; Streptomyces Waksman and Henrici 1943. In Bergey’s Manual of Determinative Bacteriology 8th edn, pp 747–829 Edited by Buchanan R. E., Gibbons N. E. Baltimore: Williams & Wilkins;
    [Google Scholar]
  23. Shirling E. B., Gotlieb D. 1966; Methods for characterisation of Streptomyces species. International Journal of Systematic Bacteriology 16:313–340
    [Google Scholar]
  24. Sierra G. 1957; A simple method for the detection of lipolytic activity of microorganisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 23:15–22
    [Google Scholar]
  25. Skerman V. B. D., McGowan V., &Sneath P. H. A. 1980; Approved lists of bacterial names. International Journal of Systematic Bacteriology 30:225–420
    [Google Scholar]
  26. Sneath P. H. A. 1974; Test reproducibility in relation to identification. International Journal of Systematic Bacteriology 24:508–523
    [Google Scholar]
  27. Sneath P. H. A. 1979a; Basic program for identification of an unknown with presence–absence data against an identification matrix of percent positive characters. Computers and Geosciences 5:195–213
    [Google Scholar]
  28. Sneath P. H. A. 1979b; Basic program for character separation indices from an identification matrix of percent positive characters. Computers and Geosciences 5:349–357
    [Google Scholar]
  29. Sneath P. H. A. 1980a; Basic program for the most diagnostic properties of groups from an identification matrix of percent positive characters. Computers and Geosciences 6:21–26
    [Google Scholar]
  30. Sneath P. H. A. 1980b; Basic program for determining the best identification scores possible for the most typical example when compared with an identification matrix of percent positive characters. Computers and Geosciences 6:27–34
    [Google Scholar]
  31. Sneath P. H. A. 1980c; Basic program for determining overlap between groups in an identification matrix of percent positive characters. Computers and Geosciences 6:267–278
    [Google Scholar]
  32. Sneath P. H. A., Sokal R. R. 1973 Numerical Taxonomy. The Principles and Practice of Numerical Classification San Francisco: W. H. Freeman.;
    [Google Scholar]
  33. Tresner H. D., Backus E. J. 1963; System of color wheels for streptomycete taxonomy. Applied Microbiology 11:335–338
    [Google Scholar]
  34. Vickers J. C., Williams S. T., Ross G. W. 1984; A taxonomic approach to selective isolation of streptomycetes from soil. In Biological, Biochemical and Biomedical Aspects of Actinomycetes pp 553–561 Edited by Ortiz-Ortiz L., Bojalil L. F., Yakoleff V. Orlando: Academic Press;
    [Google Scholar]
  35. Wellington E. M. H., Williams S. T. 1981; Host ranges of phage isolated to Streptomyces and other genera. Zentralblatt für Bakteriologie, Mikrobiologie und Hygiene, (Abteilung I, Supplement 11)93–98
    [Google Scholar]
  36. Willcox W. R., Lapage S. P., Bascomb S., Curtis M. A. 1973; Identification of bacteria by computer: theory and programming. Journal of General Microbiology 77:317–330
    [Google Scholar]
  37. Williams S. T. 1967; Sensitivity of streptomycetes to antibiotics as a taxonomic character. Journal of General Microbiology 46:151–160
    [Google Scholar]
  38. Williams S. T., Goodfellow M., Alderson G., Wellington E. M. H., Sneath P. H. A., Sackin M. J. 1983a; Numerical classification of Streptomyces and related genera. Journal of General Microbiology 129:1743–1813
    [Google Scholar]
  39. Williams S. T., Goodfellow M., Wellington E. M. H., Vickers J. C., Alderson G., Sneath P. H. A., Sackin M. J., Mortimer A. M. 1983b; A probability matrix for identification of some streptomycetes. Journal of General Microbiology 129:1815–1830
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-131-7-1681
Loading
/content/journal/micro/10.1099/00221287-131-7-1681
Loading

Data & Media loading...

Most cited Most Cited RSS feed