Deoxyribonucleic Acid-deoxyribonucleic Acid Hybridization Research Articles

Characterization of Buttiauxella and Kluyvera Species by Analysis of Whole Cell Fatty Acid Patterns

The cellular fatty acid methyl ester (FAME) composition of Buttiauxella spp. (66 strains, including all 7 recognized genomospecies), and Kluyvera spp. (17 strains, including all 4 recognized genomospecies) was determined by gas-liquid chromatographic analysis. All 83 strains contained 14:0, 16:0, 17:0 cyclo, summed feature 3 (16:1 iso I and/or 14:0 3OH), summed feature 3 (16:1 ω7c and/or 15:0 iso 2OH), and summed feature 7 (18:1 ω7c, 18:1 ω9t, and/or 18:1 ω12t). The homogeneity of both genera as revealed by biochemical reactions and by deoxyribonucleic acid-deoxyribonucleic acid hybridization was also reflected in the fatty acid composition. Only small interspecies differences were detected. Although the FAME profiles were very similar, quantitative variations in summed feature 7 and 15:0 could be helpful to differentiate the genera. In some cases, a species differentiation also was possible.

Occurrence of V-factor (NAD) independent strains of Haemophilus paragallinarum

Strains of Bisgaard taxon 31, isolated from chickens in South Africa suffering from a respiratory disease with clinical symptoms and gross lesions similar to infectious coryza, showed great phenotypical similarities with Haemophilus paragallinarum infection except for NAD requirement, ß-galactosidase activity and maltose fermentation. Deoxyribonucleic acid-deoxyribonucleic acid hybridization confirmed a high level of genetic relatedness (DNA binding value, 89%) with Haemophilus paragallinarum. Guanine+cytosine content and genome size data also support the classification of taxon 31 strains within the species Haemophilus paragallinarum.

Glutamate Dehydrogenase and 2-Oxoglutarate Reductase Electrophoretic Patterns and Deoxyribonucleic Acid-Deoxyribonucleic Acid Hybridization among Human Oral Isolates of Fusobacterium nucleatum

The electrophoretic mobilities of glutamate dehydrogenase and 2-oxoglutarate reductase were compared for three reference strains and 30 human, oral isolates of Fusobacterium nucleatum. Both enzymes allowed the same strains to be grouped into three electrophoretic clusters, designated groups Fn-1, Fn-2, and Fn-3. Group Fn-1 contained the type strain of F. nucleatum, strain ATCC 25586, and nine clinical isolates. Group Fn-2 comprised 20 strains and appeared to contain the strains of F. nucleatum that are isolated most commonly from oral cavities. Strain NCTC 10953 (formerly “Fusobacterium polymorphum”) was a member of this cluster. Strains of group Fn-3 were rarely isolated; this group contained three isolates and reference strain NCTC 11362, which was listed previously as “Fusobacterium fusiforme.” The deoxyribonucleic acid (DNA) base compositions of all strains were between 25 and 27 mol% guanine plus cytosine. Under optimal conditions of DNA-DNA hybridization, all of the strains exhibited high levels of DNA homology (73 to 99%) to the three reference DNA probes belonging to groups Fn-1, Fn-2, and Fn-3. However, under stringent DNA hybridization conditions there was evidence of more genetic homogeneity within each group.

Fluorometric Deoxyribonucleic Acid-Deoxyribonucleic Acid Hybridization in Microdilution Wells as an Alternative to Membrane Filter Hybridization in which Radioisotopes Are Used To Determine Genetic Relatedness among Bacterial Strains

Fluorometric hybridization in microdilution wells was developed to determine genetic relatedness among microorganisms. Total chromosomal deoxyribonucleic acid (DNA) for hybridization reactions was labeled with photoreactive biotin (photobiotin). The biotinylated DNA was hybridized with single-stranded unlabeled DNAs which had been immobilized on the surfaces of microdilution wells. After hybridization, biotinylated DNA was quantitatively detected with beta-D-galactosidase and a fluorogenic substrate, 4-methylumbelliferyl-beta-D-galactopyranoside. Homology values obtained with this fluorometric direct binding method were compared with values obtained with two membrane filter methods, one in which photobiotin labeling was used and one in which radioisotope labeling was used. The results showed that the fluorometric direct binding method in which microdilution wells are used could be an alternative to radioisotope and membrane filter hybridization methods.

Enterococcus raffinosus sp. nov., Enterococcus solitarius sp. nov. and Enterococcus pseudoavium sp. nov.

Deoxyribonucleic acid base composition, deoxyribonucleic acid-deoxyribonucleic acid hybridization, and biochemical studies were performed on some enterococci from clinical sources of uncertain taxonomic position. Our results indicate that 6 human strains, a single clinical isolate and a strain from bovine mastitis are genetically distinct from each other and all other previously described Enterococcus species and constitute three new species, for which the names Enterococcus raffinosus, Enterococcus solitarius and Enterococcus pseudoavium are proposed.

Staphylococcus delphini sp. nov., a Coagulase-Positive Species Isolated from Dolphins

A new coagulase-positive species of the genus Staphylococcus, Staphylococcus delphini, is described on the basis of a study of two strains isolated from purulent skin lesions of dolphins. The new species is established and differentiated from the other coagulase-positive Staphylococcus species primarily on the basis of its deoxyribonucleic acid-deoxyribonucleic acid hybridization relationships, its cell wall composition, its bacteriolytic activity pattern, its penicillin-binding protein profile, its biochemical reactions, and the relatively high guanine-plus-cytosine content of its deoxyribonucleic acid. The type strain is strain Heidy (= DSM 20771).

Nocardia seriolae sp. nov. Causing Nocardiosis of Cultured Fish

Five strains of bacteria causing nocardiosis in cultured fishes (yellowtails [Seriola quinqueradiata] and Japanese flounder [Paralichthys olivaceus]) were studied to establish their taxonomic status. Well-developed fragmenting vegetative mycelium was observed. The chemotype was type IVA containing meso-diaminopimelic acid, arabinose, and galactose. The predominant isoprenoid quinone was MK-8(H4), and mycolic acids were present. These morphological and chemical properties are characteristic of the genus Nocardia. The physiological and biochemical characteristics were most similar to those of Nocardia asteroides; however, these organisms were different in their decomposition of urea, growth temperature, utilization of nitrogen sources, survival at 50°C for 8 h, mycolic and fatty acid profiles, and deoxyribonucleic acid-deoxyribonucleic acid hybridization characteristics. Therefore, we propose a new species for these strains, Nocardia seriolae. The type strain is strain JCM 3360.

The genus Campylobacter: a decade of progress.

In 1977, microbiologists and clinicians were awakened to the importance of the genus Campylobacter when it was learned that one species, Campylobacter jejuni, was a major cause of human enteritis. In the following decade substantial advances were made in diagnosis, isolation technology, identification, classification, serotyping, and epidemiology. The genus has undergone rapid expansion as advantage was taken of the deoxyribonucleic acid-deoxyribonucleic acid hybridization technique in defining new species. The 14 species now included in the genus, however, constitute a widely diverse group, and one species, C. pylori, which is associated with human gastroduodenitis, is under consideration for reassignment to another genus. The nomenclature of the subspecies of C. fetus has been resolved and the role of C. fetus subsp. fetus as an agent of human infections has been more clearly defined. The thermophilic campylobacteria that are etiological agents of human enteritis now include three species, C. jejuni, C. coli, and C. laridis. Recently defined species that have also been implicated as enteritis-causing agents include C. hyointestinalis, "C. upsaliensis," "C. cinaedi," and "C. fennelliae." The aerotolerant campylobacteria are now included in the species C. cryaerophila, and the campylobacteria isolated from salt marshes are included in C. nitrofigilis. The taxonomy and nomenclature of C. sputorum have been revised. C. sputorum now consists of three biovars (biotypes). Two of these, biovar sputorum and biovar bubulus, were previously considered to be separate subspecies and the third, biovar fecalis, was previously regarded as a separate species and known as "C. fecalis." The former subspecies C. sputorum subsp. mucosalis has been elevated to the rank of species. C. mucosalis is metabolically closely related to C. consisus. Human pathogens have not been identified among C. sputorum, C. mucosalis, or C. concisus. The goal of this article is to review developments during the last 10 years with emphasis on changes in taxonomy that are important from the perspective of the clinical microbiologist.

Spiroplasma phoeniceum sp. nov., a New Plant-Pathogenic Species from Syria

Sixteen spiroplasma isolates, recovered over a 2-year period from symptomatic periwinkle plants (Catharanthus roseus) collected in eight different locations in Syria, were compared with other established Spiroplasma species or serogroups. Serological analysis of selected representatives of the new isolates revealed sharing of some antigenic components with several spiroplasmas currently classified within subgroups of group I of the genus. Strain P40Twas selected as the type strain and examined, meeting the criteria proposed by the International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Mollicutes. The organism was shown to belong to the class Mollicutes by its morphology, ultrastructure of its limiting membrane, colony characteristics, and filtration patterns. The helicity and motility of the cells indicated its placement within the family Spiroplasmataceae. Although some serological cross-reactions could be observed with representatives of group I subgroups, strain P40Tcould be readily distinguished from other plant or insect pathogenic spiroplasmas in subgroup I-1 (Spiroplasma citri), subgroup I-2 (S. melliferum), or subgroup I-3 (S. kunkelii) and from spiroplasmas assigned to subgroups I-4 through I-7 and groups II through XI. Cholesterol was required for growth. Glucose was fermented, and arginine was hydrolyzed. The base composition (guanine plus cytosine) of the deoxyribonucleic acid of strain P40Twas found to be 26 mol%. Deoxyribonucleic acid-deoxyribonucleic acid hybridization comparisons between strain P40Tand other subgroup I representatives revealed approximately 60% relatedness to S. citri and S. kunkelii and 50% relatedness to S. melliferum. Experimental transmission of two of the new isolates (P40Tand P354) occurred through inoculation of spiroplasma broth cultures into leafhoppers (Macrosteles fascifrons), multiplication of the organism in the insects, and subsequent transmission of the organism by insect feeding on aster or periwinkle plants. The organism was also successfully recovered from broth cultures of symptomatic tissues of experimentally infected periwinkle plants, thus fulfilling Koch’s postulates. We propose that such strains be named Spiroplasma phoeniceum. Strain P40Thas been deposited in the American Type Culture Collection (= ATCC 43115T)

Chemotaxonomic and Molecular-Genetic Studies of the Genus Thermus: Evidence for a Phylogenetic Relationship of Thermus aquaticus and Thermus ruber to the Genus Deinococcus

For a detailed pheno- and genotypic characterization of the genus Thermus, the following seven representative strains were analyzed: Three extremely thermophilic strains (optimal temperature for growth, 65 to 75°C), Thermus aquaticus DSM 625, “Thermus flavus” DSM 674, and “Thermus thermophilus” DSM 579; and four moderately thermophilic strains (optimal temperature for growth 55 to 60°C), Thermus ruber DSM 1279 and three new isolates (strains H1, H2, and H3) from sewage. All of these strains exhibited isobranched pentadecanoic and heptadecanoic acids as principal components of their fatty acids, possessed unsaturated menaquinones with eight isoprene units, and had deoxyribonucleic acid guanine-plus-cytosine contents of 59 to 65.5 mol%, and their cell walls contained a murein structure of the A3β variation (interpeptide bridge, Gly2). The clustering of the organisms into extremely and moderately thermophilic strains correlated well with molecular properties, such as the absorption spectra of their pigments and the ratio of pentadecanoic acid to heptadecanoic acid. This grouping was confirmed by the results of 16S ribosomal ribonucleic acid cataloging and deoxyribonucleic acid-deoxyribonucleic acid hybridization. Our data confirm current proposals for classification of the genus Thermus into the following two distinct species: T. aquaticus for the extremely thermophilic strains and T. ruber for the moderately thermophilic strains. Phylogenetically, representatives of the genus Thermus show a remote but significant relationship to Deinococcus species (similarity coefficients, 0.22 to 0.29); members of these two genera share a common peptidoglycan type.

Streptococcus canis sp. nov.: A Species of Group G Streptococci from Animals

β-Hemolytic group G streptococci from cows with mastitis and from dogs with different pathological conditions were characterized and named Streptococcus canis sp. nov. These animal group G strains were differentiated from Streptococcus dysgalactiae (group G strains of human origin, as well as group L strains and certain animal and human group C strains) by simple physiological and biochemical tests. Deoxyribonucleic acid-deoxyribonucleic acid hybridization showed that the S. canis strains differed from S. dysgalactiae, Streptococcus pyogenes, Streptococcus equi, and Streptococcus salivarius. These organisms contain a rare cell wall peptidoglycan type, namely, Lys-Thr-Gly. The specific epithet of S. canis, which has been in use for many years in veterinary textbooks to designate group G strains isolated from dogs, was chosen for this proposed new species because it comprises animal but not human group G streptococci. The type strain is strain STR-T1 (= DSM 20715).

Genetic Relatedness between the Type Strain of Streptococcus anginosus and Minute-Colony-Forming Beta-Hemolytic Streptococci Carrying Different Lancefield Grouping Antigens

The taxonomic relationships among Streptococcus anginosus type strain NCTC 10713, beta-hemolytic streptococci belonging to serological groups A, C, G, and F, and related organisms were determined by using deoxyribonucleic acid-deoxyribonucleic acid hybridization (S1 nuclease method), deoxyribonucleic acid base composition, and conventional biochemical tests. Minute-colony-forming beta-hemolytic streptococci which carry various Lancefield grouping antigens (antigens A, C, F, and G) or none of the known group antigens were closely related genetically and biochemically to the type strain of the S. anginosus, which carries group G antigen.

Transfer of Pasteurella ureae Jones 1962 to the Genus Actinobacillus Brumpt 1910: Actinobacillus ureae comb. nov.

Because deoxyribonucleic acid-deoxyribonucleic acid hybridization has shown that the species Pasteurella ureae belongs to the genus Actinobacillus Brumpt 1910, we propose the transfer of P. ureae to the genus Actinobacillus under the new combination Actinobacillus ureae. The type strain of A. ureae is strain S. D. Henriksen 3520/59 (= ATCC 25976 = NCTC 10219).

Proposal of Vibrio mediterranei sp. nov.: A New Marine Member of the Genus Vibrio

Vibrio strains isolated from plankton, sediments, and seawater in two coastal areas south of Valencia, Spain, were genotypically and phenotypically different from other Vibrio species. The guanine-plus-cytosyine content of the strains was 43 mol%. Deoxyribonucleic acid-deoxyribonucleic acid hybridization studies revealed that the strains were genetically homogeneous and exhibited very low levels of genetic relatedness to Vibrio parahaemolyticus ATCC 17802T(T = type strain) (0%), Vibrio harveyi NCMB 1280T(11%), Vibrio vulnificus NCMB 2046T(7%), Vibrio nereis NCMB 1897T(0%), Vibrio natriengens NCMB (9%), and Vibrio splendidus NCMB 1T(0%). Strain CECT 621 of the Colección Española de Cultivos Tipo was designated the type strain of the proposed new species Vibrio mediterranei.

Deoxyribonucleic Acid Relatedness of Enterococcus hirae and "Streptococcus durans" Homology Group II

Enterococcus hirae and “Streptococcus durans” homology group II were found to be highly related by using deoxyribonucleic acid-deoxyribonucleic acid hybridization and well-characterized strains. The “S. durans” homology group II strains used in this study were from cattle feces and human sputum. Therefore, we conclude the “S. durans” (homology group II) belongs to the same taxon as E. hirae and that the habitat of this species includes human and cattle sources.

Enterococcus mundtii sp. nov.

Deoxyribonucleic acid base composition, deoxyribonucleic acid-deoxyribonucleic acid hybridization, and biochemical studies were performed on some problematic enterococci of unknown taxonomic position. Our results indicate that some motile, nonpigmented strains are members of Enterococcus gallinarum, whereas motile, yellow-pigmented strains belong to Enterococcus casseliflavus. Four nonmotile, yellow-pigmented strains were biochemically and genetically distinct from all previously described Enterococcus species and constitute a new species, for which the name Enterococcus mundtii is proposed. The type strain of Enterococcus mundtii is strain NCDO 2375.

Deoxyribonucleic Acid Relatedness of Enterococcus hirae and "Streptococcus durans" Homology Group II

Enterococcus hirae and “Streptococcus durans” homology group II were found to be highly related by using deoxyribonucleic acid-deoxyribonucleic acid hybridization and well-characterized strains. The “S. durans” homology group II strains used in this study were from cattle feces and human sputum. Therefore, we conclude the “S. durans” (homology group II) belongs to the same taxon as E. hirae and that the habitat of this species includes human and cattle sources.

Deoxyribonucleic Acid Homology and Other Comparisons among Obligately Thermophilic Hydrocarbonoclastic Bacteria, with a Proposal for Thermoleophilum minutum sp. nov.

Bacterial strains in our culture collection similar to the recently proposed species Thermoleophilum album were examined for generic relatedness. We compared these obligately thermophilic hydrocarbonoclastic bacteria by determing the electrophoretic patterns of enzymes and soluble proteins and by using deoxyribonucleic acid-deoxyribonucleic acid hybridization techniques. Included in the hybridization study together with these strains were members of the genera Thermus, Thermomicrobium, and Bacillus. Our results confirmed that Thermoleophilum is a valid genus since no measurable reassociation was observed with the members of the other genera examined. There are two homology groups within the genus Thermoleophilum; T. album strain HS-5T (= ATCC 35263T) (T = type strain) represents the type species of the genus, and Thermoleophilum minutum sp. nov. is a second species proposed here. The type strain of T. minutum is strain YS-4 (= ATCC 35265).

Guanine-Plus-Cytosine Compositions of and Deoxyribonucleic Acid Hybridization Comparisons between Mycoplasma hyopneumoniae and Mycoplasma flocculare

Among the mycoplasmal species commonly isolated from porcine lungs are Mycoplasma hyopneumoniae and Mycoplasma flocculare. The former organism is a proven agent of enzootic porcine pneumonia, whereas the latter organism is of little or no pathogenicity. These mycoplasmas show considerable antigenic cross-reactivity. The deoxyribonucleic acids of M. hyopneumoniae strain 11 and M. flocculare strain Ms42T (T = type strain) each had a guanine-plus-cytosine content of 33 mol%. We also determined the extent of deoxyribonucleic acid sequence homology as reflected in deoxyribonucleic acid-deoxyribonucleic acid hybridization values. Approximately 10% heterologous hybridization was observed. Thus, our data support the previous classification of these organisms as separate species within the genus Mycoplasma.

Comamonas Davis and Park 1962 gen. nov., nom. rev. emend., and Comamonas terrigena Hugh 1962 sp. nov., nom. rev.

The historical and present taxonomic and nomenclatural status of the following taxa were examined: “Vibrio terrigenus” Gunther 1894, “Vibrio percolans” Mudd and Warren 1923, “Vibrio alcaligenes” Lehmann and Neumann 1927, “Lophomonas alcaligenes” Galarneault and Leifson 1956, “Comamonas percolans” Davis and Park 1962, “Comamonas terrigena” Hugh 1962, “Pseudomonas terrigena” Hugh 1965, “Vibrio cyclosites” Gray and Thornton 1928, “Vibrio neocistes” Gray and Thornton 1928, “Vibrio cuneatus” Gray and Thornton 1928, and “Comamonas compransoris” Nozhevnikova and Zavarzin 1974. Most of these organisms have been misnamed. Deoxyribonucleic acid-ribosomal ribonucleic acid hybridization experiments localized “C. terrigena” (“V. percolans”) NCIB 8193, “V. neocistes” NCIB 2582, and “V. cyclosites” NCIB 2581 on the Pseudomonas acidovorans ribosomal ribonucleic acid branch in the direct vicinity of Pseudomonas testosteroni. Deoxyribonucleic acid-deoxyribonucleic acid hybridization experiments, serological studies, gel electropherograms of soluble proteins, and a numerical analysis of phenotypic features supported placement of these strains and clinical isolate CCUG 12940 in a single taxon, for which we propose revival of the name Comamonas terrigena Hugh 1962. The type strain is strain NCIB 8193 (= ATCC 8461 = LMG 1253 = CCUG 15327). C. terrigena is the type species of the genus Comamonas Davis and Park 1962 nom. rev. An extensive phenotypic description of C. terrigena is given, and this species can be differentiated from P. acidovorans and P. testosteroni. “Achromobacter cystinovorum” NCIB 4854 is misnamed and was found to be very closely related to P. acidovorans. “V. alcaligenes” NCTC 9239 was found to be misnamed and is closely related to Pseudomonas diminuta, which is itself inappropriately retained in the genus Pseudomonas. The classification of “V. cuneatus” NCIB 8194 as Pseudomonas fluorescehs is confirmed. “C. compransoris” DSM 1231 and “V. cyclosites” ATCC 14635 (the so-called synonymous strain of “V. cyclosites” NCIB 2581) are definitely not members of C. terrigena. These two strains differ considerably from each other, as well as from all of the other strains investigated; their exact taxonomic position is unknown.