A probability matrix for the identification of species of Vibrio and related genera

A matrix for the probabilistic identification of species of Vibrio and related genera has been constructed using the data from 1091 strains collected throughout the world and classified. Thirty-eight phenons are included in the matrix, 31 of these represent previously identified species or biovars and seven represent phenons which could not be identified and may represent new species. The identification matrix incorporates 81 characters although a subset of 30 tests can be used to distinguish the 38 phenons from each other. The additional 51 tests were included to assist the identification of some strains for which the initial 30 tests were inadequate. No significant cluster overlap was found at the 5% level and the identification score for the Hypothetical Median Organism of each cluster exceeded 0.9999 in all cases.     

A probability matrix for the identification of species of Vibrio and related genera

A matrix for the probabilistic identification of species of Vibrio and related genera has been constructed using the data from 1091 strains collected throughout the world and classified. Thirty-eight phenons are included in the matrix, 31 of these represent previously identified species or biovars and seven represent phenons which could not be identified and may represent new species. The identification matrix incorporates 81 characters although a subset of 30 tests can be used to distinguish the 38 phenons from each other. The additional 51 tests were included to assist the identification of some strains for which the initial 30 tests were inadequate. No significant cluster overlap was found at the 5% level and the identification score for the Hypothetical Median Organism of each cluster exceeded 0.9999 in all cases.     

A probability matrix for the identification of vibrios

A probability matrix for computer-assisted identification of vibrios has been constructed, based on the API 20E system. Data were gathered from 173 strains representing 31 taxa of vibrios and related organisms, from a variety of sources. The matrix was tested internally by four statistical programs. Program OVERMAT tested the separation and program MOSTTYP the discretion and homogeneity of the taxa. Most of the taxa were satisfactory but a few were less so; reasons for this are discussed. Program CHARSEP and program DIACHAR tested the separation and diagnostic values, respectively, of the characters used. The overall test error was 4–5%. The matrix was assessed externally by its performance in the identification of vibrio-like strains isolated from freshwater. Of 243 wild strains, 79–4% were identified with ten taxa, with a Willcox score of ζ 0–99.     

A probability matrix for the identification of vibrios

A probability matrix for computer-assisted identification of vibrios has been constructed, based on the API 20E system. Data were gathered from 173 strains representing 31 taxa of vibrios and related organisms, from a variety of sources. The matrix was tested internally by four statistical programs. Program OVERMAT tested the separation and program MOSTTYP the discretion and homogeneity of the taxa. Most of the taxa were satisfactory but a few were less so; reasons for this are discussed. Program CHARSEP and program DIACHAR tested the separation and diagnostic values, respectively, of the characters used. The overall test error was 4.5%. The matrix was assessed externally by its performance in the identification of vibrio-like strains isolated from freshwater. Of 243 wild strains, 79.4% were identified with ten taxa, with a Willcox score of greater than or equal to 0.99.     

Biochemical tests as an aid to the identification of Monascus species

The enzymic activity of nine strains of Monascus (Fungi, Ascomycotina), representing all four accepted species as defined on cultural and microscopical features, were compared by means of API ZYM enzyme testing strips and other tests developed for use in Penicillium. Consistent results were obtained between strains of the same species, confirming their taxonomy. Eight tests showed differential activity between the species and will therefore be of value as an aid to the identification of Monascus species. Strains of M. purpureus , used in the production of red-rice, had a strong polypectase activity at pH 6 which was not evidenced in the other three species even after six weeks incubation; those of M. ruber , which often occurs on cellulosic substrates in nature, were the only ones to exhibit cellulase activity.     

A probability matrix for the identification of campylobacters, helicobacters and allied taxa

A probabilistic identification matrix for campylobacteria, comprising 67 phenotypic characters and 37 taxa, is described. The accuracy and integrity of the matrix was evaluated using established computer-assisted methods. Certain taxa (for example, Campylobacter concisus and Camp. gracilis ) demonstrated significant phenotypic diversity; previous data corroborated these findings. Differentiation between a few pairs of taxa proved difficult, although discriminatory characteristics were noted in each of these cases. The results indicate that most campylobacteria can be identified accurately and objectively with phenotypic tests when probabilistic methods of data assessment are employed.     

A comparison between biochemical tests and the 'CAMP' reaction for identification of Aeromonas spp.

Aeromonas bacteria (110 strains) from a variety of clinical, food and environmental sources, were identified using routine biochemical tests. Concurrently they were tested aerobically and anaerobically for their ability to perform synergistic haemolysis with Staphylococcus aureus (the 'CAMP' reaction). Results did not support a reported observation that the 'CAMP' reaction can he used to facilitate speciation of Aeromonas bacteria.     

An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles

Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes.     

Pulsed-field gel electrophoresis as an epidemiological tool for clonal identification of Aeromonas hydrophila

Pulsedfield gel electrophoresis (PFGE) was used to characterize Aeromonas hydrophila strains isolated from a cluster of hospital-acquired infections that occurred over approximately 1 month in a French hospital. Five isolates from patients and 10 isolates from the water supply were characterized by biotyping and antibiotic susceptibility patterns and compared with 10 epidemiologically unrelated strains isolated from patients and rivers, by PFGE of digests of chromosomal DNA. Five environmental and four clinical isolates belonged to the same biotype and antibiotic susceptibility pattern type. The endonucleases XbaI, SpeI and SwaI gave satisfactory profiles whereas DraI did not. The profiles were stable, reproducible and discriminatory. The 10 epidemiologically unrelated strains exhibited 10 different patterns after digestion with XbaI , the least expensive, suitable endonuclease. PFGE is a rapid and discriminatory technique for the typing of Aeromonas hydrophila where a common origin of infection is suspected.     

A revised probability matrix for the identification of gram-negative, aerobic, rod-shaped, fermentative bacteria

The results of the identification of 933 strains of Gram-negative, aerobic, rod-shaped, fermentative bacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae) by a probabilistic method, in a computer, are given. The identification rate on the matrix was 89.2%. Many of the strains were atypical and had caused difficulty in identification in medical diagnostic laboratories. The results are given for each taxon by genus and species.     

The interaction of complement components with Aeromonas species

The interaction of seven serum-sensitive Aeromonas strains with the complement system was investigated using a 2-h quantitative assay. Of the strains tested, four isolates activated both the alternative and classical pathways, two activated only the alternative pathway, and one strain was sensitive to the bactericidal action of complement through the classical pathway only. Two of the four Aeromonas caviae strains were such efficient activators of the complement system that when challenged with human sera deficient in normal concentrations of C3 and C4, they were still subject to complement-mediated bacterial lysis. This phenomenon, in conjunction with previous studies on complement activation by Aeromonas spp., may help account for the decreased incidence observed of systemic disease caused by Aeromonas caviae.     

New probability matrices for identification of Streptomyces

The character state data obtained for clusters defined in a previous phenetic classification were used to construct two probabilistic matrices for Streptomyces species. These superseded an original published identification matrix by exclusion of other genera and the inclusion of more Streptomyces species. Separate matrices were constructed for major and minor clusters. The minimum number of diagnostic characters for each matrix was selected by computer programs for determination of character separation indices (CHARSEP) and a selection of group diagnostic properties (DIACHAR). The resulting matrices consisted of 26 phena x 50 characters (major clusters) and 28 phena x 39 characters (minor clusters). Cluster overlap (OVERMAT program) was small in both matrices. Identification scores were used to evaluate both matrices. The theoretically best scores for the most typical example of each cluster (MOSTTYP program) were all satisfactory. Input of test data for randomly selected cluster representatives resulted in correct identification with high scores. The major cluster matrix was shown to be practically sound by its application to 35 unknown soil isolates, 77% of which were clearly identified. The minor cluster matrix provides tentative probabilistic identifications as the small number of strains in each cluster reduces its ability to withstand test variation. A diagnostic table for single-membered clusters, constructed using the CHARSEP and DIACHAR programs, was also produced.     

DNA barcoding: a tool for improved taxon identification and detection of species diversity

Recently it was decided that portions of rbcL and matK gene regions are approved and required standard barcode regions for land plants. Ideally, DNA barcoding can provide a fast and reliable way to identify species. Compiling a library of barcodes can be enhanced by the numerous specimens available in botanic gardens, museums and herbaria and in other ex situ conservation collections. Barcoding can strengthen ongoing efforts of botanic gardens and ex situ conservation collections to preserve Earth’s biodiversity. Our study aimed to detect the usability of the universal primers of the standard DNA barcode, to produce standard barcodes for species identification and to detect the discriminatory power of the standard barcode in a set of different groups of plant and fungal taxa. We studied Betula species originating from different parts of the world, and Salix taxa, bryophytes and edible and poisonous fungal species originating from Finland. In Betula and Salix, the standard DNA barcode regions, portions of matK and rbcL, were able to identify species to genus level, but did not show adequate resolution for species discrimination. Thus, supplementary barcode regions are needed for species identification. In Salix, the trnH-psbA spacer was also used, and it proved to have more resolution but, yet, not adequate levels of interspecific divergence for all studied taxa. In a set of bryophyte species, the rbcL gene region was found to possess adequate resolution for species discrimination for most genera studied. In bryophytes, matK failed to amplify properly. In fungi, the combination of ITS1 and ITS2 proved to be effective for species discrimination, although alignment difficulties were encountered. In general, closely related or recently diverged species are the greatest challenge, and the problem is most difficult in plants, both in terms of a suitable combination of barcoding regions and the universality of used primers.     

A probability matrix for the identification of gram-negative, aerobic, non-fermentative bacteria that grow on nutrient agar

Results of the identification of 621 strains of Gram-negative, aerobic, non-fermentative bacteria by a computer-based probabilistic method are given. Although many of the strains were atypical and have caused difficulty in identification in the medical diagnostic laboratory, the identification rate on this matrix was 91.5%.     

Time development of probability distributions for interacting species

A general solution to the dynamical equation for the probability distribution associated withn interacting species is obtained by employing the author's generic canonical expression for the rate functions. Interacting species models with limit-cycle dynamics and no stable equilibrium points feature probability distributions that are asymptotic for large values oft to Dirac δ-distributions concentrated on the limit-cycles, as illustrated here for an analytically solvable two-species model. For ann-species Volterra model, a stationary or temporally-averaged probability distribution should generally be much more complicated than the specialized Poisson form studied by Kerner and others.     

Medium for the presumptive identification of Aeromonas hydrophila and Enterobacteriaceae

A medium was devised for the rapid presumptive identification of Aeromonas hydrophila. It also offered good differentiation of Klebsiella, Proteus, and other enteric species. Mannitol fermentation, inositol fermentation, ornithine decarboxylation and deamination, indole production, motility, and H2S production from sodium thiosulfate and cysteine could be recorded in a single tube of the medium.     

Evaluation of 2 culture media for the isolation and enumeration of motile Aeromonas in different kinds of water

In recent years an increasing incidence of Aeromonas-related cutaneous infections and gastroenteritis has raised a serious public health problem. It appeared therefore timely to define a specific method allowing the rapid isolation and enumeration of the bacteria in their various aquatic habitats. In this line of research we have compared the growth of Aeromonas originating from different aquatic sources and raised on two media, i.e. RS-agar and PXA-agar. Whatever the aquatic system we observed that the PXA-agar medium clearly was better adapted for a quick enumeration of Aeromonas.     

Identification of motile Aeromonas strains with the MicroScan WalkAway system in conjunction with the combo negative type 1S panels

This study was performed to compare the MicroScan WalkAway automated identification system in conjunction with the new MicroScan Combo Negative type 1S panels with conventional biochemical methods for identifying 85 environmental, clinical, and reference strains of eight Aeromonas species.     

Distribution of Aeromonas species in waters with different levels of pollution

Strains of Aeromonas spp. (883) were isolated from 10 stations in the north-west of Spain. Biotyping of the strains gave: 55% Aeromonas caviae, 34% A. hydrophila, 6% A. sobria and 5% Aeromonas spp. Phenotypic characters that have been claimed to be related to virulence such as haemolysis and the Voges-Proskauer reaction were detected mostly in A. hydrophila and A. sobria. The distribution of the species was significantly related to levels of faecal pollution in waters. Aeromonas caviae predominated in sewage and waters with a high degree of faecal pollution. In less polluted waters, either fresh or marine, A. caviae and A. hydrophila were almost equally distributed. In waters with low or no faecal pollution, the proportion of A. sobria to other species increased considerably.     

Distribution of Aeromonas species in waters with different levels of pollution

Strains of Aeromonas spp. (883) were isolated from 10 stations in the north-west of Spain. Biotyping of the strains gave: 55% Aeromonas caviae , 34% A. hydrophila , 6% A. sobria and 5% Aeromonas spp. Phenotypic characters that have been claimed to be related to virulence such as haemolysis and the Voges-Proskauer reaction were detected mostly in A. hydrophila and A. sobria. The distribution of the species was significantly related to levels of faecal pollution in waters. Aeromonas caviae predominated in sewage and waters with a high degree of faecal pollution. In less polluted waters, either fresh or marine, A. caviae and A. hydrophila were almost equally distributed. In waters with low or no faecal pollution, the proportion of A. sobria to other species increased considerably.