A Comparison of Methods for Computer Taxonomy

Abstract

StrMMARYThe systematic relationships among 54 strains of bacteria, representing principally the genera Achromobacter, Aerobacter, Alcaligenes, Eschmichia, Mima, Pseudomonas, Serratia and Streptococcus, were examined by computer methods. Seventy-one properties of these organisms were determined, and the resulting data scored in different ways (according to various proposed techniques) before being submitted to an appropriate computer program for calculation of similarity (S) values. These comparative studies indicated that better division of organisms into mutually similar groups can be achieved when data about properties which may have several alternative expressions are handled in the manner proposed by Beers & Lockhart (1962). The number of comparisons which contribute to individual similarity values should be held constant by adequate treatment of quantitative data and by adoption of scoring methods which permit comparisons between ' negative ' properties. It may be useful to employ distance (D = log,l/S) rather than similarity as the primary measure of relationships among groups of organisms.

Numerical Survey of Some Bacterial Taxa

“…Serratia and Shigella seem to form distinct generic groups (3b and 3c). A similarly distinct Serratia subgroup was reported by Beers et al (1962). Although some studies (e.g., Beers et al, 1962;Lockhart and Hartman, 1963) have indicated a separation between strains of Escherichia and Enterobacter, these two genera seem in this study to combine with Erwinia and Salmonella into a single, rather diffuse cluster (group 3a) within the enterobacteria.…”

“…A similarly distinct Serratia subgroup was reported by Beers et al (1962). Although some studies (e.g., Beers et al, 1962;Lockhart and Hartman, 1963) have indicated a separation between strains of Escherichia and Enterobacter, these two genera seem in this study to combine with Erwinia and Salmonella into a single, rather diffuse cluster (group 3a) within the enterobacteria. Erwinia amylovora, the type species of its genus, bears little similarity to other enterobacteria, an observation confirmed with several strains of E. amylovora during a more detailed study of the genus Erwinia (Koenig and Lockhart, unpublished data).…”

“…It was excluded from the enterobacteria in the study by Sneath and Cowan (1958), and their data show less similarity among species of Proteus than would be expected within a genus. Lysenko and Sneath (1959) and Beers et al (1962) found that Proteus joined the family only at quite low levels of similarity. The results of Colwell and Liston (1961a) indicate that the type species, P. vulgaris, has little similarity to strains of Escherichia and Aerobacter, and Sueoka (1961) reported that the deoxyribonucleic acid base ratio of P. vulgaris is significantly different from those found for other enterobacteria.…”

Numerical Taxonomy of Clostridium botulinum and Clostridium sporogenes Strains, and Their Susceptibilities to Induced Lysins and to Mitomycin C

“…As presented in Table 2, 70 characters of a bacterial strain were examined, and the resulting 143 features scored were analyzed in a computer NEAC 2230 (Nippon Electric Co.). All methods to determine the characters as well as similarity values (S value) between two strains were previously described by Nakamura and Nishida [15,16] ; data were coded following the procedure III described by Beers et al [2] and sorted by the single linkage method of Sneath [21]. To study spore formation, bacteria from the liver infusion broth were grown on BHI agar for 2 days at 37 C under an anaerobic condition.…”

Properties of Bacteria Isolated from Deep-Sea Sediments

“…Since the application of computer analysis of taxonomic data for the bacteria was first proposed by Sneath (28), many investigators have made use of Adansonian principles to describe and classify bacteria. Various authors have examined the techniques and have proposed modifications of the methods for Adansonian classification (1, 2,27,30). Adansonian principles were first applied to marine microorganisms by Colwell and Liston '(5), and other investigators have since similarly studied the marine bacteria (9,11,21).…”