Deoxyribonucleic Acid Homology Research Articles

Use of restriction fragment length polymorphism, immunoblotting, and polymerase chain reaction in the differentiation of avian poxviruses.

Restriction deoxyribonucleic acid (DNA) fragment profile analysis coupled with immunogenic protein profile analysis has provided useful information in determining the differences between vaccine strains and field isolates of fowlpox virus (FPV). The DNA of strains examined in this study clearly fell into 3 minor groups of restriction patterns similar but distinct from one another: restriction patterns exhibited by the vaccine strains except 1 vaccine strain, Vac-82; restriction profiles indicated by Vac-82 and field isolates FI-38 and FI-42; and restriction patterns indicated by field isolates FI-43, FI-51, FI-54, and FI-56. Furthermore, when the strains were analyzed and compared by immunoblotting analysis, they showed group differences similar to the differences in restriction profiles. Both techniques provided high sensitivity in verifying differences between vaccine strains and field isolates of FPV. The disparity found in restriction fragments or immunogenic protein profile between vaccine strains and field isolates does not exclude the appreciable high degree of DNA sequence conservation and homology. However, the minor disparity observed in these strains suggests a molecular basis for why vaccinated commercial flocks could have continually been infected by variant strains of FPV. A rapid and sensitive polymerase chain reaction method, which amplified a product from the 4b core protein gene of the FPV genome, was developed for identification and differentiation of members of the genus Avipoxvirus. Whereas total DNA from either vaccine strains or field isolates was used as template for amplifying a predicted product of 578 or 1409 bp, only cleavage of the amplified product (1409 bp) represented an additional detection technique for species differentiation. An attempt to distinguish between strains on the basis of amplification product was partially successful.

Capnocytophaga sputigena bacteremia associated with acute leukemia.

During a three-year period, Capnocytophaga sputigena bacteremia occurred in three patients with acute leukemia receiving induction therapy on a hematology ward. Oral pathology such as periodontitis or severe mucositis was considered to be the most likely source of bacteremia. All three blood culture isolates were identified as that species by deoxyribonucleic acid (DNA) homology studies. Because of the phenotypical similarity of Capnocytophaga species, it is difficult to differentiate them by conventional bacteriological methods. All three isolates were susceptible to antibiotics active against most anaerobes. However, production of beta-lactamase was found in two isolates, one of which proved resistant to both piperacillin and ceftazidime. Therefore, the empiric use of imipenem or clindamycin may be justified in febrile granulocytopenic patients with cancer who develop significant oral lesions.

Heterogeneity of S-layer proteins of Lactobacillus acidophilus strains.

An S-layer (surface regular array) was found in the cell wall from six out of ten strains of Lactobacillus acidophilus examined by electron microscopic observations. All of the six strains which were shown to carry the S-layers belonged to the deoxyribonucleic acid (DNA) homology group A, but not to B, which had been classified by Johnson et al (Int. J. Syst. Bacteriol. 30: 53-68, 1980). On the other hand, the other four strains which possessed no S-layers were in the homology group B. The apparent molecular weights of the S-layer proteins ranged from 41 to 49 kDa as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Of the S-layer proteins from the six strains, three were susceptible to chemical cleavage with N-chlorosuccinimide, giving different peptide maps. All of the six S-layer proteins were fragmented by limited proteolysis with Staphylococcus aureus V8 protease, and gave markedly different peptide patterns by the subsequent peptide mapping analysis, except that the peptide maps of the S-layer proteins from the two strains which were in the same subgroup were identical.

Dekkera, Brettanomyces and Eeniella: Electrophoretic comparison of enzymes and DNA–DNA homology

The taxonomic status of various species of Dekkera, Brettanomyces and Eeniella was examined by electrophoretic comparison of enzymes, by deoxyribonucleic acid homology and by physiological characterization. These studies demonstrated that two teleomorphic Dekkera species, D. anomala and D. bruxellensis (synonym D. intermedia), and four anamorphic Brettanomyces species, B. anomalus (synonym B. claussenii), B. bruxellensis (synonym B. abstinens, B. custersii, B. intermedius, B. lambicus), B. custersianus and B. naardenensis, can be recognized. The anamorphic genus Eeniella remained as a separate, monotypic taxon.

A Group of Indole-negative Bovine Strains with High Deoxyribonucleic Acid Homology to Pasteurella multocida

A group of nine bovine Pasteurella strains not producing indole were investigated for their taxonomic relationships with Pasteurella multocida, Pasteurella haemolytica and Pasteurella canis. For all strains, DNA-DNA hybridization has revealed a high genetic relatedness at the species level to P. multocida and significantly lower homologies of only 18-41% towards P. haemolytica and 11-15% towards P. canis. Guanine plus cytosine values of 38.0 to 42.1 mol% and several phenotypic characters have been found to be different from the established pattern for P. multocida subspecies. It is suggested that the strains represent a new taxon, possibly another P. multocida subspecies.

Genotypic and Phenotypic Differentiation of Flavobacterium indologenes Yabuuchi et al 1983 from Flavobacterium gleum Holmes et al 1984

The type and eight strains of Flavobacterium indologenes were clearly differentiated from the type and two reference strains of Flavobacterium gleum by deoxyribonucleic acid-deoxyribonucleic acid homology data and phenotypic characteristics. Phenotypic characteristics useful to differentiate the two species are presented.

The Deoxyribonucleic Acid Homology Relationships between the Antibiotic-resistant Bifidobacteria and Each Original Strain

The Deoxyribonucleic Acid Homology Relationships between the Antibiotic-resistant Bifidobacteria and Each Original Strain

Pseudoamycolata halophobica gen. nov., sp. nov.

A new genus and species, Pseudoamycolata halophobica, is proposed for two closely related strains formerly assigned to Amycolata (Nocardia) autotrophica. The following characteristics are important for defining the genus Pseudoamycolata•. a type IV cell wall composition (presence of miso-diaminopimelic acid, arabinose, and galactose); lack of mycolates; phospholipid type PII (presence of phosphatidylethanolamine); menaquinone MK-8(H4) as the major menaquinone; iso- and anteiso-branched fatty acids; and a guanine-plus-cytosine content of 72 mol%. P. halophobica is readily differentiated from morphologically similar members of the genera Amycolata and Amycolatopsis by phospholipid composition and menaquinone composition, respectively. In addition, it can be distinguished from Amycolata and Amycolatopsis species by low levels of deoxyribonucleic acid-deoxyribonucleic acid homology (12 to 15 and 7 to 10%, respectively) and a number of physiological characteristics. The type strain of P. halophobica is strain VKM Ac-1069 (= DSM 43089).

Staphylococcus felis, a New Species from Clinical Specimens from Cats

A new species, Staphylococcus felis, was isolated from clinical specimens from cats and is described on the basis of a study of 39 strains. The newly described species is phenotypically similar to strains of Staphylococcus simulans, but has low levels of deoxyribonucleic acid-deoxyribonucleic acid homology (<10%) with S. simulans JCM 2424T and related staphylococci. S. felis strains were coagulase negative and susceptible to novobiocin and bacitracin. A simple scheme for the differentiation of S. felis from related staphylococci is presented. The type strain is strain GD521 (= ATCC 49168 = JCM 7469).

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.

Clostridium intestinalis sp. nov., an Aerotolerant Species Isolated from the Feces of Cattle and Pigs

Clostridium intestinalis sp. nov. is described on the basis of five strains isolated from the feces of cattle and pigs. The isolates are aerotolerant, gram-positive, sporeforming, motile rods. They differ from all the validly described aerotolerant species of the genus Clostridium by carbohydrate fermentation pattern, guanine-plus-cytosine content of the deoxyribonucleic acid, and deoxyribonucleic acid homologies. The fermentation products from peptone-yeast extract-Fildes solution-1 % (wt/vol) glucose broth are major amounts of acetic and butyric acids. The guanine-plus-cytosine content of the deoxyribonucleic acid is 26 to 28 mol%. The type strain of Clostridium intestinalis is Catt39 (= ATCC 49213 and JCM 7506).

Rhizobium galegae, a New Species of Legume Root Nodule Bacteria

Studies of root nodule bacteria isolated from Galega orientalis and Galega officinalis are reviewed, and as a result a new species, Rhizobium galegae, is proposed. The type strain of the species is R. galegae HAMBI 540 (= ATCC 43677), which forms nitrogen-fixing root nodules on G. orientalis. Deoxyribonucleic acid homology distinguishes R. galegae from other rhizobia, whereas nodulation of Galega sp. and sensitivity to phage gal 1/R phenotypically separate the strains currently included in the species from other members of the genus Rhizobium. Other criteria supporting the formation of a new species include ribosomal ribonucleic acid-deoxyribonucleic acid homology data, protein and lipopolysaccharide patterns, serological properties, and numerical taxonomy data.

Actinomadura malachitica and Microtetraspora viridis Are Synonyms and Should Be Transferred as Actinomadura viridis comb. nov.

We compared strain SF2461, Microtetraspora viridis JCM 3112T (T = type strain), Microtetraspora viridis subsp. intermedia JCM 3113T, and Actinomadura malachitica JCM 3297T by using morphological, cultural, physiological, and chemotaxonomic characteristics, as well as deoxyribonucleic acid homology. All of our results indicated that these four strains belong to the same species and that they are far from the other type strains of Microtetraspora species. Therefore, we propose that Actinomadura malachitica is a synonym of Microtetraspora viridis and that Microtetraspora viridis should be transferred to the genus Actinomadura as Actinomadura viridis comb, nov., with strain JCM 3112 (= ATCC 27103) as the type strain.

DNA-DNA homology studies among strains ofHaloferax and other halobacteria

Deoxyribonucleic acid (DNA)-DNA hybridization was used to determine the relationships of the type strains of the three species of the genusHaloferax to 21 halobacterial strains representing isolates from hypersaline habitats and collection strains. Two genotypic groups with high DNA homology were obtained, belonging to the speciesHaloferax gibbonsii andHaloferax mediterranei. The highest DNA relatedness (≥74%) was obtained in theHalobacterium salinarium group.Halobacterium denitrificans showed very low DNA homology with the other halobacteria investigated. The G+C content of the eight strains ofHaloferax tested ranged between 59.1 and 65.5 mol%.

Clostridium tetanomorphum sp. nov., nom. rev.

A total of 46 glutamate-degrading strains of the genus Clostridium, including 36 new isolates, were examined for deoxyribonucleic acid (DNA)-DNA homology, protein patterns produced by polyacrylamide gel electrophoresis, and physiological characteristics in order to determine the differences between cochlearium and Clostridium tetanomorphum. Thirty-four newly isolated strains could be assigned to the group; two strains were classified as nontoxigenic tetani strains. The levels of DNA-DNA homology between C. cochlearium and were only 10 to 19%, and the protein patterns showed that there were great differences between both groups and other glutamate-degrading species. Biochemical tests supported these results. In contrast to C. cochlearium, all strains fermented carbohydrates (at least glucose and maltose); they also produced lipase and degraded ethanolamine. Moreover, C. cochlearium, like other glutamate-degrading species, needed a higher concentration of yeast extract than when it was grown on glutamate. On the basis of our results we propose C. tetanomorphum sp. nov., nom. rev. The type strain is strain NCTC 543 (= DSM 4474).

Phenotypic Characteristics Correlated with Deoxyribonucleic Acid Sequence Similarities for Three Species of Gluconobacter: G. oxydans (Henneberg 1897) De Ley 1961, G. frateurii sp. nov., and G. asaii sp. nov.

In Bergey’s Manual of Systematic Bacteriology, vol. 1, only one species is listed in the genus Gluconobacter. One other species, Gluconobacter ceririus, was proposed by Yamada and Akita in 1984. However, recent deoxyribonucleic acid-deoxyribonucleic acid homology studies have produced evidence of at least three distinct homology groups that are believed to represent three species within this genus. In this paper we report results obtained by using 35 strains and 58 phenotypic characteristics. Three tests were useful in differentiating the three Gluconobacter species. Homology group I strains grew to an optical density (OD) of only 0.5 U or less on medium containing ribitol or arabitol as the primary carbon source, and they grew to an OD of only 0.5 U or less after three passages (24 h of incubation each) in nicotinate-deficient media. We propose that the name Gluconobacter oxydans (Henneberg 1897) De Ley 1961 be retained for these strains. Homology group II strains grew to an OD of more than 1.0 U on medium containing ribitol or arabitol as the primary carbon source, and they grew to an OD of more than 1.0 U after three passages (24 h of incubation each) in nicotinate-deficient media. We propose that the group II gluconobacters be named Gluconobacter frateurii sp. nov. All of the typical strains of homology group ΙΠ grew to an OD of 0.5 U or less on medium containing ribitol or arabitol as the primary carbon source, but they grew to an OD of 1.0 U or more after three passages (24 h of incubation each) in nicotinate-deficient media. We propose that the group III gluconobacters be named Gluconobacter asaii sp. nov.

Ribosomal Ribonucleic Acid Cistron Similarities and Deoxyribonucleic Acid Homologies of Neisseria, Kingella, Eikenella, Simonsiella, Alysiella, and Centers for Disease Control Groups EF-4 and M-5 in the Emended Family Neisseriaceae

We detected distinct taxonomic relationships among the true Neisseria species, Kingella kingae, Kingella denitrificans, Eikenella corrodens, all Simonsiella species, the type strain of Alysiella filiformis, and members of Centers for Disease Control groups EF-4 and M-5. All these taxa constitute one large separate cluster having high levels of ribosomal ribonucleic acid cistron similarity (thermal denaturation temperature range, 74 to 81°C) in ribosomal ribonucleic acid superfamily III. There are at least four subbranches. We found high deoxyribonucleic acid (DNA)-DNA homology values between Neisseria gonorrhoeae and some other true Neisseria species and within the following species: Simonsiella muelleri, Simonsiella crassa, Simonsiella steedae, Kingella denitrificans, and Eikenella corrodens. All of the members of this large cluster have genome base compositions in the range from 42.8 to 57.7 mol% guanine plus cytosine. The molecular complexities of the genomic DNAs are 2.2 x 109 to 2.7 x 109 for Simonsiella and Alysiella species and 1.4 x 109 to 1.8 x 109 for the other members of this large cluster. We formally propose that this large cluster represents the emended family Neisseriaceae containing the following genera and groups: Neisseria, Kingella (not the generically misnamed Kingella indologenes), Eikenella, Simonsiella, Alysiella (not some misnamed strains), and Centers for Disease Control groups EF-4 and M-5. The genera and subgenera Acinetobacter, Moraxella, Branhamella, Psychrobacter, the false neisseriae, and Kingella indologenes should be removed from the Neisseriaceae, as they belong to superfamilies I and II.

Bacillus glucanolyticus, a New Species That Degrades a Variety of -Glucans

A new species, Bacillus glucanolyticus, is proposed for a group of facultatively anaerobic endospore-forming bacteria isolated from soil that hydrolyze various β-glucans, including carboxymethyl cellulose and pustulan. Of the 14 strains examined, 11 were phenotypically homogeneous, and five of these strains showed high levels of deoxyribonucleic acid (DNA) relatedness (>68%) to a reference strain. Two pustulan-hydrolyzing strains were atypical, with low levels of DNA relatedness (52 to 57%), and a third strain was not classified as B. glucanolyticus. B. glucanolyticus strains produce motile microcolonies similar to those of Bacillus alvei but can be distinguished from this taxon by several phenotypic characteristics and a higher DNA base composition (48 mol%). B. glucanolyticus is similar to Bacillus circulans and related species; indeed, four strains were received as B. circulans, but distinctive phenotypic characteristics and low levels of DNA homology with B. circulans, Bacillus amylolyticus, Bacillus lautus, Bacillus pabuli, and Bacillus validus strains support its introduction as a new species. The type strain of B. glucanolyticus is strain S93 (= DSM 5162T).

A New Species of Actinomycete, Amycolata alni

A new species of the genus Amycolata, Amycolata alni, is proposed for strains which were mostly isolated from root nodules and rhizospheres of alder trees and were formerly assigned to the species Amycolata autotrophica. Strains of this new species could be differentiated from representatives of A. autotrophica by deoxyribonucleic acid homology data (17 to 29% relatedness), as well as by their ability to grow on salicin and D-gluconate, their failure to produce acid from cellobiose and meso-inositol, their resistance to penicillin and carbenicillin (10 µg/ml), and other characteristics. Phenotypic features and low levels of deoxyribonucleic acid homology distinguish A. alni from two other species of the genus Amycolata, Amycolata saturnea and Amycolata hydrocarbonoxydans. The type strain of A. alni is strain 3LS (= VKM Ac-901).

Acidomonas gen. nov., Incorporating Acetobacter methanolicus as Acidomonas methanolica comb. nov.

A new genus of acidophilic, facultatively methylotrophic bacteria is described. These organisms are gram-negative, nonsporeforming, nonmotile, and rod shaped and grow at pH 2.0 to 5.5. These characteristics are unique among the methanol-utilizing bacteria. The deoxyribonucleic acid base composition is 63 to 65 mol% guanine plus cytosine. Acetobacter methanolicus TK 0705T (T = type strain) is a typical strain in this group. These bacteria are distinguished from type and representative strains of Acetobacter, Gluconobacter, Acidiphilium, and Thiobacillus on the basis of deoxyribonucleic acid-deoxyribonucleic acid homology. A new genus, Acidomonas, is proposed to include this group.of methylotrophic bacteria. The type species of the genus Acidomonas is Acidomonas methanolica comb, nov., with type strain TK 0705 (= IMET 10945).