Numerical phenetic classification of clinically significant aerobic sporoactinomycetes and related organisms

Clinically significant aerobic sporoactinomycetes, notably agents of mycetoma, were examined for a balanced set of unit characters and the resultant data analysed using standard numerical taxonomic procedures. All save two of the one hundred and seventy three tested strains were assigned to three multimembered cluster-groups, which encompassed sixteen major (4–7 strains), ten minor (2–3 strains) and forty single membered clusters, in an analysis based on the simple matching coefficient and unweighted pair group method with arithmetic averages algorithm. The three cluster-groups were equated with the genus Actinomadura (including Actinocorallia and Streptomyces somaliensis strains), and the genera Nocardiopsis and Streptomyces, and Thermobifida and Thermomonospora, respectively. In a corresponding principal co-ordinates analysis four multimembered groups corresponding to the genera Actinomadura, Nocardiopsis, Streptomyces, and Thermobifida and Thermomonospora were recognised. The causal agents of actinomycetoma were not only assigned to established taxa, notably, to Actinomadura latina, Actinomadura madurae, Actinomadura pelletieri and Streptomyces somaliensis, but also to additional centres of taxonomic variation which were equated with the rank of species. Most of the streptomycetes isolated from clinical material were assigned to clusters equated with the species Streptomyces albus and Streptomyces anulatus. The numerical taxonomic data were used to generate a frequency matrix designed to facilitate the identification of clinically significant Actinomadura, Nocardiopsis and Streptomyces strains to the species level; rapid enzyme tests accounted for eleven out of the twenty-one diagnostic tests. This revised version was published online in June 2006 with corrections to the Cover Date.     

Numerical and chemical classification ofStreptosporangium and some related actinomycetes

One hundred and seventeen streptosporangia from soil were compared with marker strains of the familyStreptosporangiaceae for many phenotypic properties. The data were examined using the Jaccard, pattern and simple matching coefficients with clustering achieved using average, complete and single linkage algorithms. Particular confidence was placed in the product of the pattern, average linkage analysis given the sharp definition of aggregate groups and clusters and a combination of low test error and high cophenetic correlation values. The test strains were assigned to five aggregate groups that were equated with the generaStreptosporangium (group A),Microbispora (group B),Planobispora andPlanomonospora (Group C),Kutzneria (neéStreptosporangium viridogriseum (group D), andMicrotetraspora (group E). The streptosporangia, both isolates and marker strains, were assigned to 5 major, 7 minor and 18 single membered clusters. Representative streptosporangia examined for chemical markers were characterised by the presence ofmeso-diaminopimelic acid in whole-organism hydrolysates, complex mixtures of straight- and branched chain fatty acids, di- and tetrahydrogenated menaquinones as predominant isoprenologues, and complex polar lipid patterns containing diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and uncharacterised components. The chemical and numerical data support the taxonomic integrity of the validly described species ofStreptosporangium and suggest that the genus is markedly underspeciated.     

Numerical Analysis of the Taxonomy of Nocardiae and Rhodococci

The genera Nocardia and Rhodococcus were clearly differentiated in the present study. Eleven characteristics were shown to be useful for differentiation between these two genera. Nocardia asteroides sunsu stricto previously defined by Tsukamura was divided into two taxa. One contained the type strain and was considered to retain the name Nocardia asteroides in a new sense. Another was named in the present study as Nocardia nova sp. nov. Tsukamura. The type strain of this species is ATCC 33726. The following seven characters were useful for differentiating N. nova from newly defined N. asteroides: 1) arylsulfatase activity after 14 days; 2) catalase activity (semiquantitative); 3) β-esterase activity; 4) pyrazinamidase activity; 5) utilization of citrate as a sole source of carbon; 6) utilization of 2,3-butylene glycol as a sole carbon source; and 7) resistance to 5-fluorouracil (20 μg/ml). The name Nocardia farcinica for Tsukamura's Kyoto-I group should be rejected. This taxon has been named Nocardia paratuberculosis sp. nov. Tsukamura. The type strain is ATCC 23826. Three new species of the genus Rhodococcus were proposed: Rhodococcus aichiensis sp. nov. Tsukamura (type strain, ATCC 33611); Rhodococcus chubuensis sp. nov. Tsukamura (type strain, ATCC 33609); Rhodococcus obuensis sp. nov. Tsukamura (type strain, ATCC 33610).     

Numerical classification of Rhodococcus equi and related actinomycetes

Eighty-three strains received as Corynebacterium or Rhodococcus equi and marker cultures of Corynebacterium and Rhodococcus species were subjected to numerical phenetic analyses using 112 unit characters. The data were examined using the simple matching ( S _SM) and Jaccard ( S _J) coefficients and clustering was achieved using the average linkage algorithm. Cluster composition was not markedly affected by the coefficient used or by test error, estimated at 2.9%. Most of the strains received as R. (C.) equi formed a distinct and homogeneous cluster in the aggregate Rhodococcus taxon, the strains of which were sharply separated from marker cultures of C. pseudotuberculosis and C. renale. The taxon R. equi was redescribed and Nocardia calcarea Metcalf & Brown reduced to a subjective synonym of R. erythropolis (Gray & Thornton) Goodfellow & Alderson.     

Numerical classification of species of Vibrio and related genera

Data from 1091 strains of the family Vibrionaceae collected in five different studies have been merged into a single data matrix and analysed in a taxonomic study. A set of 142 characters was selected to compare these data. Seventy-nine characters were common to all studies, but data for the other 63 characters were incomplete. Cultures of 90 strains, examined in more than one of the original studies, were used to estimate test error and inter-study variability. The data from these replicate strains also allowed the problem of merging data from different studies to be assessed. Taxonomic resemblance was estimated on the basis of 111 characters using the S_SM coefficient and UPGMA clustering. A taxonomic analysis based on 999 strains, which included most of the major species of the family Vibrionaceae, gave 59 clusters and 44 unclustered strains. A table of properties of these phenons was produced. The results showed that data obtained from studies carried out at different times and in different locations, but using standard techniques, could be combined and used to provide useful taxonomic information.     

Molecular classification of living organisms

Recent studies in molecular evolution have generated strong conflicts in opinion as to how world living organisms should be classified. The traditional classification of life into five kingdoms has been challenged by the molecular analysis carried out mostly on rRNA sequences, which supported the division of the extant living organisms into three major groups: Archaebacteria, Eubacteria, and Eukaryota. As to the problem of placing the root of the tree of life, the analysis carried out on a few genes has provided discrepant results. In order to measure the genetic distances between species, we have carried out an evolutionary analysis of the glutamine synthetase genes, which previously have been revealed to be good molecular clocks, and of the small and large rRNA genes. All data demonstrate that archaebacteria are more closely related to eubacteria than to eukaryota, thus supporting the classical division of living organisms into two main superkingdoms, Prokaryota and Eukaryota.Abbreviations Mya million years ago - GS glutamine synthetase - Isu large subunit - ssu small subunit - SMC Stationary Markov clock Correspondence to: G. Pesole     

Species-specificity of DNA trimer densities in chromosomes and their use in the classification of closely related organisms

16S rDNA sequences are conventionally used for classification of organisms. However, the use of these sequences is sometimes not successful, especially for closely related species. For better classification of these organisms, several methods that are genome sequence-based have been developed. Sequence alignment-based methods are tedious and time-consuming, as they need conserved coding sequences to be identified and deduced prior to sequence alignment. Likewise, method that relies on gene function needs genes to be assessed for function similarity. Other alignment-free methods, which are based on particular genome sequence properties, so far have been complex and not species-specific enough for classification of organisms below genus level. The present study found that the ratios of DNA trimer frequencies to chromosomal length were species-specific. Density of a trimer in a chromosomal sequence was defined as the average frequency of the trimer per 1 kbp. The species-specificity of trimer densities in chromosomes of many closely related bacteria was compared in parallel with 16S rDNA sequences in these same bacteria. The results of these comparisons indicate that trimer densities in chromosomes can be used to simply and efficiently classify the organisms below genus level.     

An electron microscope study of the cell surface ofCytophaga johnsonii and some observations on related organisms

The cell surface of a non-fruiting myxobacterium,Cytophaga johnsonii, was investigated by electron optical techniques. Negative staining revealed an irregularly undulating surface topography and the presence of strands of material arising from the cells. Replicas of freeze-dried cells and thin sections confirmed the uneven nature of the surface and showed that, in contrast to eubacteria, the cell was surrounded by an envelope of amorphous, electron-translucent material contained within a crenated, outer, unit membrane. This material could be extruded as long strands. It is considered that this envelope of material represents the slime layer of the organism.The appearance of the slime layer at various stages in the growth of the organism was followed by negative staining and the image of the organism presented by negative staining was compared to that given byMyxococcus xanthus andFlavobacterium aquatile.     

Electrophoretic patterns of cell wall protein as a criterion for the identification and classification of Corynebacteria

Electrophoretic patterns of cell wall protein of three industrial strains, that were used for production of lysin, and eight collection strains from the genus Corynevacterium were studied to analyze their similarity as well as to estimate an opportunity of using this parameter as an additional criterion for identification and classification of corynebacteria. Similarity coefficient of cell wall overall and main protein electrophoretic patterns were determined by a specially created computer program. Electrophoretic analysis showed that every specie had an individual protein profile. There were determined biopolymers common for the specie, genus and individual among the overall majors and minors. The obtained results showed, that the patterns of main proteins were more conservative and informative in comparison with those ones of overall proteins. The definition of similarity coefficient by the main protein patterns has correlated with the protein profile characteristics of every analyzed strain, and it managed to distribute them into the separate groups. The similarity coefficient of preparations by the main protein patterns allows to separate one specie or a strain from another, and that gives us a chance to claim that this parameter could be used as an additional criterion for differentiation and referring the corynebacteria to a certain taxonomic group.     

Numerical classification and identification of Bacillus sphaericus including some strains pathogenic for mosquito larvae

Ninety-one strains of Bacillus sphaericus, including representatives of all the established DNA homology groups, related round-spored and oval-spored species, and six strains pathogenic for mosquito larvae, were examined for 155 characters. Numerical analyses (Jaccard coefficient/average linkage clustering) based on the 88 variable features revealed 14 clusters at the 79% similarity level that contained more than one strain and 17 single member clusters. All insect pathogenic strains were recovered in a single cluster and the classification was in accord with an established classification based on DNA sequence homology. Two frequency matrices for probabilistic identification were constructed and tested. A comprehensive matrix comprising 14 mesophilic, round-spored taxa and 27 tests gave good results for identification of hypothetical median organisms, cluster overlap and identifications of representative strains (based on data generated in the classification study). Reference strains for the 14 taxa and eight additional insect pathogenic strains were examined for the 27 tests and were correctly identified with high scores using this matrix. A second matrix comprising seven taxa and 13 tests also performed well in the theoretical evaluation and correctly identified the reference strains and insect pathogenic strains.     

Comparative cytology,evolution and classification of the green algae with some consideration of the origin of other organisms with chlorophylls A and B

The Botanical Review -     

Numerical taxonomy of some leuconostocs and related bacteria isolated from Scotch whisky distilleries

Forty-six presumptive Leuconostoc strains and 13 lactobacilli isolated from malt and grain whisky fermentations together with 14 reference strains of Leuconostoc and Lactobacillus were examined for 99 characters. Data were analysed using a variety of similarity coefficients and clustering algorithms. Two aggregate clusters representing Leuconostoc and Lactobacillus were consistently recovered. Many of the presumptive leuconostocs from whisky fermentations were identified as Leuc. mesenteroides. A second large cluster of strains could not be positively identified. Although recovered within the Leuconostoc aggregate cluster, some of these strains hydrolysed arginine, a characteristic of lactobacilli. The study demonstrates a more diverse flora of lactic acid bacteria existing in the distillery fermentation than had been previously recognized.     

Numerical taxonomy and laboratory identification of Actinomyces and Arachnia and some related bacteria.

A numerical taxonomic study was made on 49 facultative anaerobic Gram-positive filamentous and/or diphtheroidal organisms isolated from dental plaques, carious dentin and faeces, together with 63 reference strains belonging to the genera Actinomyces, Arachnia, Bifidobacterium, Actinobacterium, Propionibacterium, Eubacterium and Lactobacillus. They were examined for 90 unit characters covering a wide range of tests and properties. The data were subjected to computer analysis in which the simple matching coefficient (SSM) and the similarity index (SJ) were calculated, and the results of single linkage techniques and an unweighted average linkage cluster analysis technique were compared. The strains fell into six major groups (phena). The Actinomyces strains were recovered in two phena; the first contained Actinomyces israelii and the other facultative anaerobic Actinomyces, including subclusters equal to taxospecies of A. odontolyticus and A. viscosus/A. naeslundii, while the other phenon corresponded to the genera Arachnia, Actinobacterium, Bifidobacterium and Propionibacterium. The groups of Arachnia and Actinobacterium each contained one species, representing taxospecies of Arachnia propionica and Actinobacterium meyerii. Taxonomic criteria, both constant and discriminative, were selected to form a diagnostic table useful for laboratory identification of this group of organisms. Immunofluorescence supported the numerical data.