Numerical Classification of Bacteria

Forty five organisms selected from 12 genera of bacteria listed in Bergey’s Manual (1957) were subjected to numerical analysis based on the two different similarity matrices representing the overall similarities of phenetic characters and the similarities of guanine + cytosine contents of DNA molecules.

The classification based on the similarities of GC-contents obtained “lump” taxa, in contrast with the classification based on the overall similarities of phenetic characters.

Rationale of the former classification is briefly discussed.     

Numerical Classification of Bacteria

It has been suggested by Sokal and Sneath that the mathematical techniques used in numerical taxonomy would effectively be applied to elucidate serological (and perhaps phylogenetic) relations among organisms. This excellent idea, however, has hitherto never come into operation. The present paper describes a mathematical method for analyzing the intensities of antigen-antibody reactions between test organisms to make clear their serological relations. Eighteen corynebacteria were examined as a test case, and a brief discussion is presented on the results obtained.     

Numerical Classification of Bacteria

Sixty three organisms selected from 12 genera of bacteria were subjected to numerical analysis. The purpose of this work is to examine the relationships among 38 coryneform bacteria included in the test organisms by two coding methods—Sneath’s and Lockhart’s systems—, and to compare the results with conventional classification. In both cases of codification, five groups and one or two single item(s) were found in the resultant classifications. Different codings brought, however, a few distinct differences in some groups, especially in a group of sporogenic bacilli or lactic-acid bacteria. So far as the present work concerns, the result obtained on Lockhart’s coding rather than that obtained on Sneath’s coding resembled the conventional classification. The taxonomic positions of corynebacteria were quite different from those of the conventional classification, regardless of which coding method was applied.

Though animal corynebacteria have conventionally been considered to occupy the taxonomic position neighboring to genera Arthrobacter and Cellulomonas and regarded to be the nucleus of so-called “coryneform bacteria,’ the present work showed that many of the corynebacteria are akin to certain mycobacteria rather than to the organisms belonging to the above two genera.     

The Properties and Classification of the Predominant Bacteria in Rotten Eggs

A collection of 226 strains of bacteria was assembled from eggs which had rotted on the premises of the producer and from others which had been allowed to rot in the laboratory at 10, 20 or 30°. A majority of the eggs had a mixed infection. All but 8 of the isolates were Gram negative rods. The predominant types were Alcaligenes faecalis, Aeromonas liquefaciens, Proteus vulgaris, Cloaca spp., Citrobacter sp. and Pseudomonas fluorescens. A nonpigmented pseudomonad could not be identified with any of the species included in Pseudomonas.     

Aciduric Proteobacteria isolated from pH 2.9 soil

Acidic (pH 2.9) soil was used as an inoculum to culture heterotrophic bacteria at pH values of 3-4. Four isolates were obtained; on the basis of 16S rDNA sequence, they were shown to be members of the beta- and gamma-Proteobacteria. The three isolates that were most closely related to Burkholderia spp. had simple nutritional requirements and could grow in glucose-mineral salts media; two of these used a broad array of organic substrates. The 16S rDNA sequence of the fourth isolate was most similar (96%) to Frateuria aurantia. The isolates were aciduric rather than acidophilic; their pH ranges for growth were approximately 3.5-8. Unlike many bacteria whose acid tolerance represents the capacity to survive acid exposure, these microorganisms carried out exponential growth at pH<4 and their growth rates at pH 3.9 ranged from 60 to 98% of those found at pH 7. The cell yields on glucose of two strains were identical at pH 4 and pH 7. The acidic soils appeared to contain a very diverse bacterial community as assessed by denaturing gradient gel electrophoresis fingerprinting of PCR amplicons of a portion of the 16S rDNA gene. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-002-0427-1.     

Classification of Bacteria Based on the Biases of Terminal Amino Acid Residues

The frequencies of amino acid residues are known to be biased at both terminal regions of amino acid sequences deduced from bacterial genomic DNA. To investigate whether or not the features of biases of amino acid residues at the terminal regions are related to the bacterial phylogeny, we calculated the normalized amino acid compositions at both terminal regions, and used these compositions to classify 144 bacteria by hierarchical clustering analysis. Our results showed that most of these bacteria were classified into taxonomic classes by the hierarchical clustering analysis that was based on the normalized amino acid compositions at the N-terminal region. Therefore, we concluded that the features of biases of the N-terminal amino acid residues were related to the bacterial phylogeny.