Numerical taxonomy of some non-saccharolytic and saccharolytic Bacteroides species

Various Bacteroides spp. were examined by physiological tests, presence of specific enzymes, antibiotic sensitivity, menaquinone composition and a few miscellaneous tests. The data matrix containing 58 strains and 55 unit characters was examined using Gower's similarity coefficients (SG) and included matching negative character states and multistate characters. The highly saccharolytic strains were separated from the less saccharolytic and non-fermentative strains at the 55% similarity level; while at the slightly higher level of 63% strains of Capnocytophaga (formerly Bact. ochraceus) were recovered as a compact phenon distinct from other saccharolytic species. The phenogram was divided into 6 clusters at 72% similarity level. Most of the 'Bact. fragilis group' of species clustered in one phenon while Bact. melaninogenicus ssp. melaninogenicus, Bact. bivius and a new species, Bact. denticola, formed another group. Another phenon comprised the saccharolytic non-pigmented species closely related to Bact. oralis such as Bact. buccalis and Bact. pentosaceus. The less saccharolytic strains of Bact. melaninogenicus ssp. intemedius and Bact. disiens were recovered in a distinct phenon. The low affinity (less than 55% similarity) between the two subspecies of Bact. melaninogenicus emphasised the need for reclassifying these taxa into separate species. The non-fermentative and very weakly saccharolytic strains formed good taxospecies. The separation of this cluster into three subclusters is in excellent agreement with chemotaxonomic data now available.     

Numerical taxonomy of some species of hypoxylon

Numerical analysis has resulted in a division of the coloured and non-coloured species ofHypoxylon. It is suggested that the coloured papillate species e.g.H. multiforme are more closely related toH. fragiforme and members of the Hypoxylon section than to non-coloured papillate species as indicated in the current classification of the genus.The relationships betweenHypoxylon, Daldinia andRosellinia are discussed.     

Numerical taxonomy of Bacteroides and other genera of Gram-negative anaerobic rods.

A numerical taxonomy was performed on 157 cultures (141 different strains) of species of Bacteroides, Polyphyromonas, Prevotella [not Prevotella (Labroue, 1976)] and Fusobacterium. Isolates were each tested for 111 phenotypic characters which included possession of constitutive enzymes, fermentation of specific carbohydrates, gas chromatographic analysis of metabolic end-products and of cellular carboxylic acid composition. Computation of similarity coefficients was followed by a single-linkage cluster analysis. At the 94% similarity level, the following groupings at genus level were apparent: (1) Bacteroides ureolyticus; (2) Fusobacterium mortiferum, F. necrogenes, F. necrophorum, F. nucleatum and F. varium; (3) B. caccae, B. distasonis, B. eggerthii, B. fragilis, B. merdae, B. ovatus, B stercoris, B. thetaiotaomicron, B. uniformus and B. vulgatus; (4) B. splanchnicus; (5) Porphyromonas asaccharolytica; (6) B. bivius (Prevotella bivia); (7) B. disiens (P. disiens); (8) B. intermedius (P. intermedia);and (9) B. melaninogenicus (P. melaninogenica). Single isolates of B. ruminicola (P. ruminicola), B. denticola (P. denticola) and B. capillosus did not cluster with other strains.     

Numerical taxonomy of some charophytes in Iran

Morphological characters of 10 species of Chara from different localities in northern, western and central Iran have been analyzed, with Nitella hyalina and Tolypella glomerata as outgroups. Phenetic and cladistics analyses of populations belonging to the 10 Chara species were undertaken to reveal their inter‐population morphological variation and inter‐specific relationships. Clustering was based on 54 characters (41 qualitative and 13 quantitative). This produced two major clusters, grouping Chara crassicauliss, C. vulgaris var. longibracteata, C. vulgaris var. vulgaris and C. contraria separate from C. grovesii, C. gymnophylla var. gymnophylla, C. gymnophylla var. rohlenae, C. kirghisorum and C. tomentosa. A smaller cluster of C. socotrensioides, C. fibrosa and Chara sp. was separate from these two clusters. A factor analysis identified the most variable morphological characters as type of cortification, prescence and length of the spine cells, stipulode length, type of branchlet cortication, bract cells length, placement of the gametangia, character of end segment, length of branchlet and internode, development of posterior bract cells, oogonia length and width, oospore length, width and length/width ratio, fossa breath, and number of striae.     

Numerical taxonomy of alpha-amylase producing Bacillus species

A total of 134 alpha-amylase producing Bacillus isolates and 21 reference strains were divided into 12 groups according to their similarities (% SSM). Phenotypic characteristics determined by the API 20E and API 50CHB galleries, other biochemical tests and morphological characteristics were used for the numerical analysis. The API Computer Service identified 45% of the isolates. The amylase yields of 16 alpha-amylase hyperproducing (AHP) isolates were compared with those of seven amylolytic reference and type strains. The AHP isolates were related to Bacillus subtilis, B. licheniformis and 'B. amyloliquefaciens'.     

Fermentation of L-aspartate by a saccharolytic strain of Bacteroides melaninogenicus.

Resting cells of Bacteroides melaninogenicus fermented L-[14C]aspartate as a single substrate. The 14C-labeled products included succinate, acetate, CO2, oxaloacetate, formate, malate, glycine, alanine, and fumarate in the relative percentages 68, 15, 9.9, 2.7, 1.8, 1.0, 0.7, 0.5, and 0.06, respectively, based on the total counts per minute of the L-[14C]aspartate fermented. Ammonia was produced in high amounts, indicating that 96% of the L-aspartate fermented was deaminated. These data suggest that L-aspartate is mainly being reduced through a number of intermediate reactions involving enzymes of the tricarboxylic acid cycle to succinate. L-[14C]asparagine was also fermented by resting cells of B. melaninogenicus to form L-aspartate, which was subsequently, but less actively, fermented.     

Fermentation of L-aspartate by a saccharolytic strain of Bacteroides melaninogenicus.

Resting cells of Bacteroides melaninogenicus fermented L-[14C]aspartate as a single substrate. The 14C-labeled products included succinate, acetate, CO2, oxaloacetate, formate, malate, glycine, alanine, and fumarate in the relative percentages 68, 15, 9.9, 2.7, 1.8, 1.0, 0.7, 0.5, and 0.06, respectively, based on the total counts per minute of the L-[14C]aspartate fermented. Ammonia was produced in high amounts, indicating that 96% of the L-aspartate fermented was deaminated. These data suggest that L-aspartate is mainly being reduced through a number of intermediate reactions involving enzymes of the tricarboxylic acid cycle to succinate. L-[14C]asparagine was also fermented by resting cells of B. melaninogenicus to form L-aspartate, which was subsequently, but less actively, fermented.     

Numerical taxonomy of α-amylase producing Bacillus species

A total of 134 α-amylase producing Bacillus isolates and 21 reference strains were divided into 12 groups according to their similarities (% S_SM). Phenotypic characteristics determined by the API 20E and API 50CHB galleries, other biochemical tests and morphological characteristics were used for the numerical analysis. The API Computer Service identified 45% of the isolates. The amylase yields of 16 α-amylase hyperproducing (AHP) isolates were compared with those of seven amylolytic reference and type strains. The AHP isolates were related to Bacillus subtilis, B. licheniformis and 'B. amyloliquefaciens' .     

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.     

Numerical taxonomy of Streptococcus

A numerical taxonomic study of strains of Streptococcus, together with representatives of allied genera, showed 28 reasonably distinct phenons. The major areas, with their phenons, were: (a) enterococcal species group (S. faecalis, S. faecium, 'S. avium' and a proposed new species 'S. gallinarum'); (b) paraviridans species group (S. bovis, S. equinus, S. salivarius, 'S. casseliflavus', S. mutans, S. raffinolactis and an unidentified Oral Group I); (c) lactic species group (S. lactis including S. cremoris); (d) thermophilic species group (S. thermophilus); (e) viridans species group (S. mitis, S. sanguis, a proposed new species 'S. oralis' and 'S. milleri'); (f) pyogenic species group (S. agalactiae, S. pyogenes, S. equi, 'S. equisimilis' including 'S. zooepidemicus, and a cluster of Lancefield Group B strains of human origin); (g) parapyogenic species group (S. uberis, 'S. dysgalactiae', and a cluster of strains of Lancefield Groups R, S and T). Species of Aerococcus, Gemella, Leuconostoc and Pediococcus are very closely related to the streptococci.     

Numerical taxonomy of some taxa of the genus Fucus in the Iberian Peninsula

A study of morphological variation patterns in three Iberian Fucus species has been carried out. Data on 36 features from 113 specimens have been studied by numerical methods (PCA, discriminant analysis and ANOVA).The PCA ordination displayed a continuous trend of variation in the following Fucus species: F. ceranoides, F. vesiculosus and F. spiralis. However, no obvious morphological discontinuities have been observed. In addition, three varieties of F. spiralis and five of F. vesiculosus have been identified.At the varietal level discriminant functions could be used for identifying 93–100% of the individuals within F. vesiculosus and 72–91% of F. spiralis.The most discriminating diagnostic character appeared to be the midrib size, as detected by ANOVA procedures.Some qualitative characters, such as presence of vesicles, dioecious-monoecious character and receptacle edge shape, frond and receptacle shape, have been also important for discriminating specific and infraspecific taxa.A nomenclatural discussion of varietal taxa is also included.