- Volume 138, Issue 11, 1992

We present a computerized pattern recognition model used to speciate mycobacteria based on their restriction fragment length polymorphism (RFLP) banding patterns. DNA fragment migration distances were normalized to minimize lane-to-lane variability of band location both within and among gels through the inclusion of two internal size standards in each sample. The computer model used a library of normalized RFLP patterns derived from samples of known origin to create a probability matrix which was then used to classify the RFLP patterns from samples of unknown origin. The probability matrix contained the proportion of bands that fell within defined migration distance windows for each species in the library of reference samples. These proportions were then used to compute the likelihood that the banding pattern of an unknown sample corresponded to that of each species represented in the probability matrix. As a test of this process, we developed an automated, computer-assisted model for the identification of Mycobacterium species based on their normalized RFLP banding patterns. The probability matrix contained values for the M. tuberculosis complex, M. avium, M. intracellulare, M. kansasii and M. gordonae species. Thirty-nine independent strains of known origin, not included in the probability matrix, were used to test the accuracy of the method in classifying unknowns: 37 of 39 (94.9%) were classified correctly. An additional set of 16 strains of known origin representing species not included in the model were tested to gauge the robustness of the probability matrix. Every sample was correctly identified as an outlier, i.e. a member of a species not included in the original matrix. This strategy may be readily adapted to other chromatographic and electrophoretic systems that generate peak profiles or banding patterns.

The isoprenoid quinone composition of 51 Gram-negative, aerobic, marine bacteria representing the genera Alteromonas, Marinomonas, Deleya, Pseudomonas and Shewanella was examined using high-performance liquid chromatography. Alteromonas and Marinomonas strains contained ubiquinone with eight isoprene units as their most abundant component, whilst ubiquinones with nine isoprene units predominated in Deleya and marine Pseudomonas strains. Members of the genus Shewanella contained both ubiquinones and menaquinones. The presence of two types of isoprenoid quinones in Shewanella is thought to be unique amongst Gram-negative, aerobic bacteria. In addition, methylmenaquinones were also found in Shewanella putrefaciens strains. The results demonstrate that the analysis of isoprenoid quinones offers a rapid and effective method of differentiating between some marine bacteria.

Ribosomal 5SRNA (rRNA) was isolated from 12 strains belonging to the genera Acidomonas, Acetobacter and Gluconobacter and sequenced. A dendrogram constructed from the data indicated that methylotrophic and non-methylotrophic strains of the genus Acetobacter formed two separate clusters. The non-methylotrophic members of the genus Acetobacter were phylogenetically closer to Gluconobacter than to the methylotrophic strains of Acetobacter. The methylotrophic strains of Acetobacter were recovered as a clade with the type strain of Acidomonas methanolica. These data support an earlier proposal which reclassified methylotrophic strains of Acetobacter into the genus Acidomonas.

A new Gram-negative facultatively anaerobic eubacterium isolated from a near-shore sulphidic hydrothermal area is described. It differs from known genera of Gram-negative cocci, and is thus proposed to be a representative of a new genus. This isolate, Catenococcus thiocyclus, is able to oxidize thiosulphate to tetrathionate during batch growth in the presence of organic carbon and energy sources. That energy is gained from thiosulphate oxidation is indicated by an increase in the growth yield compared with similar cultures from which the thiosulphate had been omitted. Thiosulphate—cytochrome c oxidoreductase and endogenous cytochrome c 553 were shown to be involved in thiosulphate oxidation in C. thiocyclus.

An atypical group of thermophilic catalase-negative Campylobacter strains, the ‘CH’ (Swiss) group, can be recovered from faeces of domestic cats and dogs after selection by filtration, or with the antibiotic cefoperazone. This group of strains shows no relative DNA homology with any species in rRNA superfamily VI (Vandamme et al., 1991, International Journal of Systematic Bacteriology 41, 88-103) except with four thermophilic Campylobacter species, notably C. upsaliensis. The group is homogeneous and possesses a DNA base composition, cellular morphology at the electron microscope level and phenotypic properties characteristic of Campylobacter. Nonetheless it is distinct from known species of Campylobacter in terms of conventional bacteriological tests, total cellular protein profile, rRNA gene profile, and genomic DNA homology. On the basis of an integrated study of phenotype and genotype, we conclude that these bacteria constitute a previously undescribed species for which we propose the name Campylobacter helveticus sp. nov. A species-specific recombinant DNA probe was cloned from the designated type strain (NCTC 12470) for use in identification and further analysis of the epidemiology, pathogenicity and transmission of C. helveticus.

A partial genomic library of the plant-pathogenic fungus Pseudocercosporella herpotrichoides was prepared in a bacterial plasmid vector. Plasmids from 20 random recombinant clones were radioactively labelled and used as probes in Southern blot experiments with genomic DNA isolated from seven isolates belonging to the rye-type and four isolates of the wheat-type of P. herpotrichoides. Most of the probes tested revealed polymorphisms between the two types. In addition, some of them distinguished different isolates within each type. One probe that gave strong hybridization signals may correspond with repetitive DNA sequences. It was shown by dot-blot hybridization to be specific to all the wheat-type isolates tested.