Probabilistic identification of streptomycetes using miniaturized physiological tests

Abstract

A frequency matrix of positive results for phena defined in a previous phenetic classification was constructed. A total of 329 physiological characters from 782 strains was taken as the basis for this identification matrix. The minimum number of diagnostic characters for the matrix was selected using computer programs for calculation of different separation indices (CHARSEP) and selection of group diagnostic properties (DIACHAR). The resulting matrix consisted of 52 phena versus 50 characters. Overlap of phena was found to be relatively small (OVERMAT program). Identification scores for the most typical hypothetical organism of each phenon was satisfactory (MOSTTYP program). The matrix was evaluated theoretically and practically (MATIDEN program). For members of major clusters and subclusters, e.g. Streptomyces albidoflavus, S. halstedii, S. griseus, S. fradiae, S. rimosus and S. albus, identification scores were high. Organisms of phena containing only small numbers of strains could be identified correctly, but with lower accuracy. The identification rate of the matrix (Willcox probability > 0.90) in the theoretical evaluation was 84.39%, and in the practical evaluation 78.12%.

The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus

“…A low correlation is observed between the protein profiles and the numerical phenotypic data provided by Williams et al (1989) and Ka$ mpfer & Kroppenstedt (1991). We expected that taxa sharing high DNA-DNA hybridization values would group within the same phenotypic cluster.…”

“…The aim of this study was to screen for synonymous taxa in a representative subset of the genus Streptomyces, using SDS-PAGE of whole-cell proteins, and to compare the data with these of Williams et al (1989) and Ka$ mpfer & Kroppenstedt (1991). It has been shown that under highly standardized cultivation conditions, SDS-PAGE of whole-cell proteins is an excellent and generally applicable method for defining relationships at the species level among large numbers of strains (Vandamme et al, 1996 ;Descheemaeker et al, 1994).…”

“…An extensive species reduction was proposed, and probability matrices were created to identify isolates (Williams et al, 1989). Ka$ mpfer & Kroppenstedt (1991) updated the classification system of Williams et al (1983) by extending the numbers of phenotypic traits and by including more taxa.…”

Identification ofstreptomycesisolated from environmental soil samples using rapid enzyme data

“…Compared with such conventional tests micromethods have the advantage of speed and simplicity and only require the use of 7-amino-4-methylcoumarin and 4-methylumbelliferone-linked derivatives for the detection of specific enzymes. It is clear from this and earlier studies (Goodfellow et al, 1990;Kampfer & Kroppenstedt, 1991) that actinomycete species have biochemical profiles that contain information of taxonomic value. In the present study the excellent agreement found between the results of the qualitative and quantitative studies was especially encouraging as they show that automated data acquisition systems can be used to determine the full potential of fluorogenic probes in streptomycete systematics.…”

Actinomycetes as plant pathogens

“…The majority of the pathogenic isolates were assigned to S. violaceus (57%) and S. griseus (22%), and some were allocated to S. exfoliatus, S. rochei and to single-member clusters. Reference strains of S. scabies and S. acidiscabies, obtained from R. Loria, were similarly recovered in different clusters and subclusters, though for some of them the probabilistic identification, carried out according to the scheme of K~impfert and Kroppenstedt [1991], was admittedly ambiguous. The authors conclude that 'it appears likely that genes required for pathogenicity are spread by mobilization elements among different Streptomyces species within their natural habitat'.…”