Identification and Grouping of Bacteria Numerical Analysis of their Electrophoretic Protein Patterns

Abstract

Improved methods for the identification and grouping of bacteria by polyacrylamide gel electrophoresis of soluble proteins are described. Electrophoretic protein patterns were obtained in rigorously standardized conditions. The results were much more reproducible than any described previously. Some of the factors affecting reproducibility were : growth conditions, time and speed of centrifugation of extracts, and conditions of gel electrophoresis. Protein patterns were compared by computing correlation coefficients from normalized densitometric tracings and clustering the strains by the unweighted average pair group method. As model systems, both Agrobacterium and Zymomonas were used because of differences in the sharpness of the peaks. The method was applied to 42 Agrobacterium strains. The agreement with the results of clustering by either phenotypic tests or DNA : DNA hybridization was excellent. Computerized comparisons of electrophoretic protein patterns can be a fast, easy and powerful tool for classification and identification of bacteria.

Comparison Between Xanthomonas campestris pv. manihotis (ISPP List 1980) and X. campestris pv. cassavae (ISPP List 1980) by Means of Phenotypic, Protein Electrophoretic, DNA Hybridization and Phytopathological Techniques

“…computer-assisted comparisons of normalized protein electrophoregrams were done as previously described (Kersters & De Ley, 1975; Vera Cruz et af., 1984 Ley (1970). DNA :DNA hybridizations.…”

“…Similarities between the strains were calculated with the similarity coefficient SSM of Sokal & Michener (1958) using a modified program of Bonham-Carter (1967). The clustering of the strains was done according to the unweighted average pair-group method (Sneath & Sokal, 1973) with the Clustan 1C program (Wishart, 1978) , 1976 Nigeria, 1978 Rwanda, 1977 Rwanda, 1977 Rwanda, 1977 Rwanda, 1977 Rwanda, 1977 Rwanda, 1977 Rwanda, 1978 Rwanda, 1978 Rwanda, 1978 Malawi, 1951 Tanzania, 1978 Nairobi, Kenya, 1979 Nairobi, Kenya, 1979 computer-assisted comparisons of normalized protein electrophoregrams were done as previously described (Kersters & De Ley, 1975; Vera Cruz et af., 1984 Ley (1970). DNA :DNA hybridizations.…”

Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines

“…These values did not reveal relatedness at the species level for any of these pairs. Strains 1245 T and 1263a T and the type strains of established Cupriavidus species were further compared by SDS-PAGE of whole-cell proteins, a method that has often been proven to differentiate at the species level (Pot et al, 1994;Kersters & De Ley, 1975): indeed, in the genera Ralstonia and Cupriavidus, high protein electrophoretic similarity correlates with a high level of DNA-DNA hybridization (Coenye et al, , 2003aVandamme et al, 1999;Goris et al, 2001;Vandamme & Coenye, 2004). UPGMA cluster analysis of SDS-PAGE protein profiles showed that strain 1245 T and Ralstonia sp.…”

Characterization of Corynebacterium Group JK by Whole-cell Protein Patterns

“…The absorbance traces of the patterns were compared with the correlation coefficient and UPGMA clustering, as was found useful in previous studies (Jackman et af., 1983;Kersters & De Ley, 1975). A computer program in Pascal to do these procedures is available from the corresponding author.…”