Unweighted Average Linkage Clustering Research Articles

A comparison of the bacterial microflora between coastal sites in Qingdao, P. R. China and Loch Fyne, Scotland

Aerobic, heterotrophic bacteria, recovered from two sites located on the west coast of Scotland, were compared to cultures obtained in a similar way from industrial, aquacultural and clean sites in the vicinity of Qingdao, Shandong, P. R. China. Gram-negative bacterial cultures were examined by BIOLOG-GN, and the data analysed by the simple matching (SSM) and Jaccard coefficients (SJ) and unweighted average linkage clustering using NTSys. The output revealed that 20% of the bacteria, namely, Acinetobacter johnsonii, Aquaspirillum dispar, Pseudomonas spp. (two groups), Sphingobacterium sp., Vibrio, sp., V. campbellii, V. mimicus and V. hollisae, were common between the two geographical locations. However, the study revealed shortcomings with the BIOLOG-GN system for the study of coastal Gram-negative bacteria.

Numerial Taxonomy and DNA-DNA Hybridizations of Aeromonas strains Isolated from Human diarrhoeal Stool, Fish and Environment

Summary A numerical taxonomic study and DNA-DNA hybridizations were performed on seventy-one isolates of Aeromonas collected from children diarrhoeal stool, dead and alive fish Rutilus rutilus, and environment. These isolates were compared with the fifteen type and reference strains of the presently recognized Aeromonas genomic species. Results of the phenotypic tests were analysed by numerical taxonomic techniques, using the simple matching coefficient (SSM) and Jaccard coefficient (SJ), and the unweighted average linkage clustering (UPGMA). At SSM > 85% and SJ > 75% these analyses resolved 6 groups and 9 single strains. DNA-DNA hybridization experiments revealed seven genomic groups among the examined Aeromonas isolates. Clusters were identified as A. hydrophila/A. bestiarum (two groups), A. veronii biotype sobria (two groups), A. caviae/A. medial A. eucrenophila, and A. media. The results obtained with the numerical taxonomy were not in perfect agreement with the DNA-DNA hybridization results and showed genetic heterogeneity of some phena. In some cases strains of one genomic species were found in different clusters or one cluster contained more than one hybridization group (HG). Among isolates of HG 8/10 biovariants were found. Strains of HG 1–3 and of HG 4–6 showed high phenotypic homogeneity. The results of this study emphasise the need to use of molecular methods in addition to phenotypic characteristics for identification of Aeromonas isolates with the genomic species.

Numerical Taxonomy and Biochemical Identification of Fish Associated Motile Aeromonas spp.

Summary Four hundred and thirty-eight Aeromonas, 31 Vibrio and 3 Plesiomonas strains isolated from moribund and healthy fish, water samples and humans, including 36 reference strains, were compared using numerical taxonomy based on 128 unit characters. Data were examined by the simple matching (SSM) and Jaccard (SJ) coefficients, and by unweighted average linkage clustering. As expected, Aeromonas spp. were clearly distinct from those of Vibrio and Plesiomonas. The motile Aeromonas spp., i.e. Aeromonas hydropbila, Aeromonas caviae and Aeromonas veronii biotype sobria formed discrete homogeneous clusters, distinct from the nonmotile species Aeromonas salmonicida. Furthermore, A. caviae was divided into two biotypes with D-mannose fermentation as the most important differentiating characteristic. Of the recently described species, A. veronii biotype veronii (type strain ATCC 35624) was phenotypically closest to A. bydropbila, although from DNA: DNA hybridisation studies it was classified within the A. sobria group. Aeromonas scbubertii (type strain ATCC 43 700) was well defined and formed a single member cluster. The phenotypic boundaries of Aeromonas media (type strain ATCC 33907) and Aeromonas eucrenopbila (type strain CDC 0859-83) were not clear. All the fish isolates (n = 208) were identified, with A. bydropbila predominating (43.8%), followed by A. veronii biotype sobria (26.9%), A. caviae biotype I (16.3 %), A. salmonicida (6.7%), A. sobria (HG7) (2.9 %), A. caviae biotype II (2.4 %), and A. veronii biotype veronii (1 %).

Numerical taxonomic study of thermophilic Bacillus isolated from three geographically separated deep-sea hydrothermal vents

A numerical taxonomic study has been carried out with 80 strains, newly isolated, from three geographically separated deep-sea hydrothermal vents (Mid-Atlantic Ridge, Guaymas Basin and Lau Basin) and eleven thermophilic reference strains representing 11 Bacillus species. The deep-sea isolates were all halotolerant spore-forming rods and grew aerobically above 65°C. Results from unweighted average linkage cluster analysis of a similarity matrix derived from the simple matching coefficient, showed formation of nine major phena, which were defined at the 83% similarity level or above. Seven phena were composed exclusively of strains isolated from the same site (4 from Mid-Atlantic Ridge, 1 from Guaymas Basin and 2 from Lau Basin). The majority of the Lau Basin isolates clustered with 6 of the reference strains in one phenon, while isolates from Mid-Atlantic Ridge and Guaymas Basin were found separated from this phenon at the 69% similarity level. The other reference strains showed less than 69% similarity with the deep-sea isolates.

Numerical taxonomic study of thermophilic Bacillus isolated from three geographically separated deep-sea hydrothermal vents

A numerical taxonomic study has been carried out with 80 strains, newly isolated, from three geographically separated deep-sea hydrothermal vents (Mid-Atlantic Ridge, Guaymas Basin and Lau Basin) and eleven thermophilic reference strains representing 11 Bacillus species. The deep-sea isolates were all halotolerant spore-forming rods and grew aerobically above 65°C. Results from unweighted average linkage cluster analysis of a similarity matrix derived from the simple matching coefficient, showed formation of nine major phena, which were defined at the 83% similarity level or above. Seven phena were composed exclusively of strains isolated from the same site (4 from Mid-Atlantic Ridge, 1 from Guaymas Basin and 2 from Lau Basin). The majority of the Lau Basin isolates clustered with 6 of the reference strains in one phenon, while isolates from Mid-Atlantic Ridge and Guaymas Basin were found separated from this phenon at the 69% similarity level. The other reference strains showed less than 69% similarity with the deep-sea isolates.

Estimation of the Intrinsic Biodiversity among Poly(3-Hydroxyalkanoates) Degrading Streptomycetes using Gas Chromatographic Analysis of Fatty Acids

One hundred and twenty three poly(3-hydroxyalkanoates) degrading streptomycetes (referred to as PHA strains) from soils, composts, natural waters, and some other sources were characterized by gas chromatographic analysis of their methylated cellular fatty acids. They were compared to reference strains of the genera Streptomyces (46 strains) and Streptoverticillium (9 strains) by numerical analysis. Saturated iso - and anteiso -branched fatty acids of between 14 and 18 carbons constituted the major components in the fatty acid profiles of most of the strains. In the dendrogram, obtained by unweighted average linkage clustering of the Euclidean distances Δ, calculated between each pair of fatty acid profiles, all strains were linked at Δ = 43. At Δ = 11, 18 clusters, consisting each of 2 to 63 strains, could be delineated, and 16 strains remained unclustered. The clusters could also be recognized by principal-component analysis, although small overlaps between some clusters were evident. Most clusters could be differentiated from each other by their fatty acid compositions. The PHA strains were scattered over 14 different clusters, 11 of which also contained reference strains, and 9 PHA strains remained unclustered. In addition to the PHA strains, 29 of the 46 reference strains of Streptomyces were also shown to degrade poly(3-hydroxybutyrate) in vitro . Poly(3-hydroxybutyrate-co-10%3-hydroxyvalerate) was degraded in vitro by all 56 PHA strains tested. The study demonstrates the biodiversity of streptomycetes involved in the degradation of poly(3-hydroxyalkanoates) in different habitats. The numerical analysis of fatty acid profiles confirms the homogeneity of the Streptomyces albidoflavus group, and the heterogeneity of the Streptomyces cyaneus and Streptomyces anulatus groups, and supports the reunification of the genera Streptomyces and Streptoverticillium .

Distribution of epiphytic bacteria on olive leaves and the influence of leaf age and sampling time

Mesophilic heterotrophic, aerobic or facultatively anaerobic bacteria that grow on yeast tryptone glucose extract agar were isolated from the surface of olive leaves of 3 or 4 different ages in January, April, July, and October from 1984 to 1989. Unweighted average linkage cluster analysis on either the Jaccard coefficient or the simple matching coefficient recovered 1,701 representative strains in 32 phena defined at the 70% and 80% similarity level, respectively. Of these, 25 were identified to genus or lower level. From the identity of the representative strains, the frequency of occurrence among the phylloplane bacteria over the 6-year period was estimated at 51% forPseudomonas syringae, followed byXanthomonas campestris (6.7%),Erwinia herbicola (6%),Acetobacter aceti (4.7%),Gluconobacter oxydans (4.3%),Pseudomonas fluorescens (3.9%),Bacillus megaterium (3.8%),Leuconostoc mesenteroides subsp.dextranicum (3.1%),Lactobacillus plantarum (2.8%),Curtobacterium plantarum (2.2%),Micrococcus luteus (2.2%),Arthrobacter globiformis (1.4%),Klebsiella planticola (1.2%),Streptococcus faecium (1.2%),Clavibacter sp. (0.98%),Micrococcus sp. (0.82%),Serratia marcescens (0.81%),Bacillus subtilis (0.57%),Cellulomonas flavigena (0.4%),Erwinia sp. (0.37%),Zymomonas mobilis (0.3%),Bacillus sp. (0.29%),Alcaligenes faecalis (0.27%),Erwinia carotovora (0.08%), andPseudomonas aeruginosa (0.04%). Bacterial communities on leaves of a given age at a given time during any one year displayed a very similar structure but differed significantly from those on the leaves of the same age at a different time or on the leaves of a different age at any time during any one year. Communities on the leaves of a given age at a given time of the year were invariably dominated by one or another of only 9 taxa, which accounted for 22 to 98.5% of the isolates from those leaves. The communities on 10- and 13-month-old leaves were invariably made up of fewer taxa than those on younger leaves at the same time of the year.

ISOZYME ANALYSIS OF MATING POPULATIONS OF GONIUM PECTORALE (CHLOROPHYTA)1

ABSTRACTIntraspecific variation among 36 strains of the freshwater alga Gonium pectorale Müller (Chlorophyceae) isolated from three geographically different locations in Tibet, Nepal, and Japan was investigated by isozyme analysis. Variation in isozyme patterns of eight enzyme systems (malate dehydrogenase, glutamate dehydrogenase, tetrazolium oxidase, lactate dehydrogenase, octanol dehydrogenase, xanthine dehydrogenase, phosphoglucomutase, and malic enzyme) of axenic and clonal cultures was revealed by polyacrylamide gel electrophoresis. Unweighted average linkage clustering, based on Jaccard's similarity coefficient, illustrated the high similarity between most strains from Nepal and all strains from the Ryukyu Islands (Japan). However, there was relatively low similarity between strains from Tibet and those from Nepal and Japan. Strains from the Ryukyu Islands (Japan) grouped into two clusters, and most Nepalese strains formed a single cluster, but Tibetan strains were heterogenous.

Taxonomy of Fish Associated Aeromonas spp., with the Description of Aeromonas salmonicida subsp. smithia subsp. nov.

Summary One hundred and eighty Aeromonas strains were compared using numerical taxonomy based on 140 unit characters. Data were examined by the simple matching (S SM ) and Jaccard (S J ) coefficients, and by unweighted average linkage clustering. Representative strains were also examined by DNA : DNA hybridization. The aeromonads formed discrete homogeneous clusters, in which motile organisms, i.e. A. caviae, A. hydrophila and A. sobria were distinct from their non-motile counterparts, namely A. media and A. salmonicida . A new subspecies of A. salmonicida was recognised, for which the name of Aeromonas salmonicida subsp. smithia has been proposed.

Numerical Taxonomy of Red-pigmented Bacteria Isolated from a Lowland River, with the Description of a New Taxon, Rugamonas rubra gen. nov., sp. nov.

Summary: Twenty red-pigmented bacterial strains, isolated from river water, and 15 named reference cultures were analysed using numerical taxonomic procedures. A simplified dendrogram, based on the simple matching coefficient and unweighted average linkage clustering algorithm, showed that the environmental isolates were recovered in two phenetic groups, defined at or above the 89% similarity level. Nine strains were contained in phenon 1, which exhibited the general characteristics of the Pseudomonadaceae, but did not match the descriptions of any of the existing genera within this family. A new genus and species, Rugamonas rubra, is proposed for these isolates. The 11 red-pigmented environmental strains in phenon 2 were identified as Serratia rubidaea. The red pigment of R. rubra contains at least two compounds related to prodigiosin. The major component produced a mass spectrum compatible with its being 6-methoxy-2-methyl-3-heptylprodigeosene (m/e 351). A second component produced a mass spectrum indistinguishable from that of prodigiosin itself (m/e 323).

Amylase and esterase polymorphisms in economically important stored product mites (Acari: Astigmata)

1. 1. Ten populations representing six species of economically important astigmatid mites, Acarus siro (L.), Glycyphagus destructor (Schrank), Glycyphagus domesticus (De Geer), Rhizoglyphus callae (Oudemans), Rhizoglyphus robini Claparede and Tyrophagus longior (Gervais) were investigated for amylase and non-specific esterase polymorphisms using polyacrylamide gel iso-electric focusing. 2. 2. All populations showed multiple enzymic forms for both amylase and esterase. Some differential levels of activity were detected. 3. 3. A simple phenetic technique is given whereby dendrograms of sample affinities can be constructed from densitometric scans of zymograms (using unweighted average linkage cluster analysis on a Gower-type general similarity coefficient). Amylase scans gave a more interpretable clustering than esterase scans. 4. 4. A critical discussion and suggestions for improvement of the technique are given.

Deleya halophila, a New Species of Moderately Halophilic Bacteria

Deleya halophila sp. nov., which was isolated from hypersaline soils, is proposed. Each of 38 isolates, together with 8 reference strains, was examined in 97 phenotypic tests, and the data were analyzed by numerical taxonomy procedures. The 38 isolates formed a distinct group at a 76% similarity value, as determined by an analysis performed with the simple matching coefficient and unweighted average linkage clustering. Characteristically, the isolates were aerobic, gram-negative rods that were motile by one to eight peritrichous flagella. They grew optimally in the presence of 7.5% (wt/vol) marine salts. The distinguishing features of the new species are its salt requirement, biochemical features, and nutritional versatility. The guanine-plus-cytosine content of the deoxyribonucleic acid is 66.7 mol%. The type strain of this species is strain F5-7 (= CCM 3662).

Development of Probability Matrices for Identification of Alaskan Marine Bacteria

Probabilistic identification matrices were developed by using data from 86 phenotypic clusters. In our analyses we used data gathered from 1,119 bacterial strains isolated from Alaskan outer continental shelf regions (320 features per isolate), the Jaccard similarity coefficient, and unweighted average linkage clustering. A normalized probability score (relative likelihood, identification score) based on a modification of the Bayes theorem and the ratio of observed likelihood to best possible relative likelihood were used as identification criteria. Error rates were compared for the proper association of isolates with 86 previously defined phenons by using an inclusive matrix of 61 feature probabilities and a hierarchical scheme containing a primary probability matrix (supermatrix) to indicate the most likely of six secondary probability matrices (submatrices) for detailed identification. The supermatrix-submatrix scheme was superior to the inclusive scheme on the basis of economy of tests and had a comparable error rate.

Genetic variation inSymbiodinium(=Gymnodinium)microadriaticumFreudenthal, and specificity in its symbiosis with marine invertebrates. I. Isoenzyme and soluble protein patterns of axenic cultures ofSymbiodiniummicroadriaticum

Axenically culturedSymbiodinium(=Gymnodinium)microadriaticumFreudenthal, isolated from 40 host individuals (or colonies) representing 17 species in two phyla were resolved into 12 strains, each strain having a unique combination of four isoenzyme patterns as revealed by starch gel electrophoresis. Each individual host appeared to contain an electrophoretically homogeneous population of algae. Each characteristic isoenzyme pattern was maintained after re-isolation of a cross-infecting strain (i. e. a strain that had been experimentally introduced into a host of a species other than that from which it was originally isolated), indicating a genetic basis for the protein patterns observed in each strain. The strains could be separated into three groups after constructing a dendrogram by the unweighted average linkage clustering method based on calculations of similarity coefficients. Soluble protein patterns obtained from the algae were also strainspecific. A dendrogram constructed from data obtained by analysis of protein patterns resolved by a polyacrylamide gel disc electrophoresis was similar to the dendrogram constructed from the data on isoenzyme patterns, but suggested that the ‘phenetic’ distances between strains were larger than indicated by the isoenzyme patterns.

Behavioral Analysis and Identification of Gifted Children

Summary Two samples, one gifted, the other “normal,” of 30 children each (11 to 13 years of age) were matched on age, sex, race, and father's occupation. A parent of each child completed the Children's Behavioral Classification Project instrument, and a profile of 30 scaled scores was obtained for each protocol. A discriminant analysis on the basis of the profiles classified 50 of the 60 Ss correctly into their respective sample category, either gifted or normal. Though the results of a multivariate analysis of variance showed no significant differences between the groups when the 30 profile factors were viewed as a whole, univariate analyses on the separate factors yielded significant group differences on several related factors. These were interpreted with caution. Additional factors displayed significant sex differences and one demonstrated a group-by-sex interaction effect. Coefficients of pattern similarity (the rp ) were computed among all pairs of the 60 Ss. An unweighted average linkage cluster an...

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.