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Volume 35,
Issue 3,
1985
Volume 35, Issue 3, 1985
- Book Reviews
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- Original Papers Relating To Systematic Bacteriology
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Pyrimidine Deoxyribonucleotide Metabolism in Members of the Class Mollicutes
More LessCell extracts from six Acholeplasma species, six Mycoplasma species, and Spiroplasma floricola 23-6T (T = type strain) were examined for enzyme activities of pyrimidine deoxyribonucleotide metabolism. All of these organisms had thymidine kinase and thymidine phosphorylase activities, and all lacked deoxycytidine triphosphatase activity. The 13 members of the Mollicutes were separated into three groups by the presence or absence of the following four enzyme activities: (i) the adenosine triphosphate-insensitive deoxyuridine triphosphate-specific hydrolyzing deoxyuridine triphosphatase, (ii) a deoxyuridine monophosphate phosphatase, (iii) deoxycytidine deaminase, and (iv) deoxycytidine monophosphate deaminase. Five of the six Acholeplasma species (all Acholeplasma species except Acholeplasma florum L1T) had all four enzymatic activities. The six Mycoplasma species only had the deoxycytidine and deoxycytidine monophosphate deaminase activities. The only two plant isolates studied, A. florum L1T and S. floricola 23-6T, lacked all four enzymatic activities.
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Cloned Ribosomal Ribonucleic Acid Genes from Pseudomonas aeruginosa as Probes for Conserved Deoxyribonucleic Acid Sequences
More LessRibosomal ribonucleic acid (rRNA) genes were isolated from a PstI digest of Pseudomonas aeruginosa chromosomal deoxyribonucleic acid (DNA), cloned in Escherichia coli, and used as probes for conserved gene sequences. Recombinant plasmid pHF1 contained an 8,800-base pair insertion containing 5S, 16S, and 23S rRNA genes. We constructed subclones of pHF1 containing parts of the 16S and 23S rRNA genes (pHF1.1) and parts of the 23S and 5S rRNA genes (pHF1.2). DNA-DNA hybridization experiments in which we used filter-bound chromosomal DNA from various bacteria and 35S-labeled plasmid rRNA genes (rDNA) indicated that the homology values reflected the actual phylogenetic distances to P. aeruginosa. Compared with oligonucleotide sequence analysis of 16S rRNA, a good correlation was found between DNA-rDNA homology values and SAB (similarity coefficient of 16S rRNAs) values above 0.4. The use of rDNA instead of rRNA in hybridization experiments offers several advantages; e.g., rDNA can easily be labeled in vitro, and the degree of relatedness can be expressed in terms of percent homolgy and does not have to be determined by laborious measurement of thermal stability, as in the case of rRNA.
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Hyphomonas oceanitis sp.nov., Hyphomonas hirschiana sp. nov., and Hyphomonas jannaschiana sp. nov.
More LessVarious characteristics of seven recently isolated bacterial strains were determined and compared with the characteristics of the three extant strains of the genus Hyphomonas (ex. Pongratz 1957) Moore et al. 1984. On the basis of these results, three new species, Hyphomonas oceanitis sp. no., Hyphomonas jannaschiana sp. no v., and Hyphomonas hirschiana sp. no v., are proposed for inclusion within this genus.
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Restriction Site Polymorphism of Ribosomal Ribonucleic Acid Gene Sets in Members of the Genus Bacillus
More LessHybridization of cloned ribosomal sequences to EcoRI-restricted genomic deoxyribonucleic acids of eight species and strains of the genus Bacillus produced multiband patterns consistent with the presence of 9 to 11 operons per genome. The basic structure of the repeating ribosomal gene set is highly conserved with the exception of one internalEcoRI site located near the abutment region between the 16S and 23S ribosomal ribonucleic acid determinants. In each of the Bacillus species studied, there are two abutment regions that differ in size by 0.2 kilobase; the larger region contains genes for isoleucine and alanine transfer ribonucleic acids at one-third the proportion of the smaller region. The occurrence of the EcoRI site in strains of Bacillus subtilis and Bacillus licheniformis gave rise upon cleavage to 1.2- and 1.4-kilobase abutment families. The absence of the EcoRI site in Bacillus globigii, Bacillus pumilus, and Bacillus amyloliquefaciens resulted in the emergence of 1.9- and 2.1-kilobase abutment families. Mixtures of the two types of families were not found in the Bacillus genomes studied.
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Dictyoglomus thermophilum gen. nov., sp. nov., a Chemoorganotrophic, Anaerobic, Thermophilic Bacterium
More LessWe describe a new caldoactive bacterium, Dictyoglomus thermophilum, which was isolated from a slightly alkaline hot spring. This organism is a nonsporeforming, nonmotile, obligately anaerobic rod-shaped bacterium that stains gram negative and occurs singly, in pairs, in filaments, in bundles, and as spherical bodies. The cell surface structure is of the complex gram-negative type. Large spherical bodies are formed by associations of separate rods in numbers ranging from a few to perhaps as many as 100; these spherical bodies are surrounded by common outer wall membrane. The temperature range for growth is between 50 and 80°C, with optimum growth at 78°C the pH range for growth is between 5.9 and 8.3. The doubling time at 73° and pH 7.2 is about 2.5 h. Growth is inhibited by streptomycin, tetracycline, neomycin, chloramphenicol, vancomycin, tunicamycin, and sodium dodecyl sulfate. The deoxyribonucleic acid base composition is 29 mol% guanosine plus cytosine. The type strain is strain ATCC 35947.
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Deoxyribonucleic Acid Base Compositions and Nucleotide Distributions of 65 Strains of Budding Bacteria
More LessA total of 65 strains of appendaged or prosthecate, budding bacteria from our culture collection were selected for a study of deoxyribonucleic acid (DNA) base composition and nucleotide distribution. These strains represented 11 genera, including 4 genera of hyphal, budding bacteria which have not been formally described yet. The DNA species were thermally denatured, and absorbance-temperature profiles were recorded. The midpoints, widths, and asymmetries of the melting transitions were determined. When the DNA base compositions and nucleotide distributions were plotted on a dissimilarity map, it became evident that the strains of each genus occupied a distinct area. The distribution of strains within such an area indicated the degree of heterogeneity of a genus. When 16 Hyphomicrobium strains were analyzed, they formed five clusters within their generic area. These clusters correlated well with groups which had been previously established by DNA base composition analyses, by DNA-DNA homology studies, and by numerical taxonomy. Nine of the strains investigated were distinguished by melting profiles which were skewed uniquely to the left.
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Genome Size Determinations for 33 Strains of Budding Bacteria
More LessThe genome sizes of 33 strains of budding bacteria were determined by deoxyribonucleic acid renaturation kinetics. The M r values ranged from 1.67 × 109 to 4.43 × 109 for strains representing the following genera: Hyphomicrobium (seven strains; M r, 2.08 × 109 to 2.73 × 109), Hyphomonas (six strains; M r, 1.67 × 109 to 2.13 × 109), Pedomicrobium (five strains; M r, 2.81 × 109 to 3.43 × 109), genus T (two strains; M r, 2.32 × 109 to 2.46 × 109), genus D (one strain; M r, 1.73 × 109), genus F (one strain; M r, 2.03 × 109), Pirella (seven strains; M r, 2.73 × 109 to 4.43 × 109), and Planctomyces (four strains; M r, 2.67 × 109 to 3.65 × 109). The taxa designated genus T, genus D, and genus F represented new budding bacteria which will be formally described elsewhere. The genome size ranges of Hyphomicrobium spp., Hyphomonas spp., and Pedomicrobium spp. were relatively small compared with those of Planctomyces spp. and Pirella spp. The plotting of genome sizes against deoxyribonucleic acid base compositions demonstrated distinct cluster areas, some of which allowed clear separation of the genera studied.
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Deoxyribonucleic Acid Hybridizations Among Strains of Streptococcus salivarius and Streptococcus bovis
More LessThe genetic relationships among 33 streptococci that were identified as Streptococcus salivarius or Streptococcus bovis and were isolated from humans were determined by deoxyribonucleic acid-deoxyribonucleic acid hybridization on membrane filters. The phenotypic characteristics of these bacteria were determined by their action on 20 substrates in a commercially prepared system, as well as by colony morphology and conventional tests. The S. salivarius strains were biochemically heterogeneous but genetically homogeneous. Although there were some phenotypic similarities between S. bovis and S. salivarius, these two species were genetically distinct. Within S. bovis there was genetic heterogeneity. Typical S. bovis strains (S. bovis biotype I) were genetically homologous with some, but not all, of the S. bovis variant strains (S. bovis biotype II). Other S. bovis biotype II strains formed a separate genetic group, the members of which were biochemically somewhat different from other S. bovis biotype II strains.
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Microbispora viridis, a New Species of Actinomycetales
More LessA new species of Actinomycetales is described, for which we propose the name Microbispora viridis. This organism produces a new peptide antibiotic, SF-2240. M. viridis is characterized by its green aerial mass color and longitudinally paired spores, which have rugose surfaces with vertical ridges. The type strain of M. viridis is strain SF-2240 (= IFO 14382).
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Mycoplasma pirum sp. nov., a Terminal Structured Mollicute from Cell Cultures
More LessMore than 200 mycoplasma isolates recovered from a variety of contaminated cell cultures from 1968 to the present were found to belong to a distinct serological group (serogroup 38). An analysis of representative strains of this collection showed that they possessed all of the characteristics of organisms belonging to the genus Mycoplasma. These organisms were capable of fermenting glucose and of hydrolyzing arginine, and they required cholesterol or serum for growth. These organisms were unusual in that they possessed an organized terminal structure or tip, a morphological structure which has been found in at least six other species in the genus Mycoplasma. These organisms were also serologically distinct from all previously established species in the genus Mycoplasma and the genus Acholeplasma. On the basis of these findings and other morphological, biological, and serological characteristics of the strains recovered, we propose that mycoplasmas with these properties belong to a new species, Mycoplasma pirum sp. nov. Strain HRC 70-159 (= ATCC 25960) is the type strain of this species.
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Brucella, a Monospecific Genus as Shown by Deoxyribonucleic Acid Hybridization
More LessA total of 51 strains (including type, reference, vaccine, and field strains) representing all species and biovars of Brucella formed a single deoxyribonucleic acid-deoxyribonucleic acid hybridization group (S1 nuclease method). Accordingly, we propose that only one species, Brucella melitensis, be recognized in the genus. We recommend that other specific epithets formerly associated with the generic name Brucella be used in a vernacular form for biovar designation (e.g., Brucella melitensis biovar Abortus 1).
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Spiroplasma melliferum, a New Species from the Honeybee (Apis mellifera)
Twenty-eight strains of spiroplasma subgroup I-2 isolated from insects and flower surfaces were similar in their serological properties. Strain BC-3T (T = type strain), which was isolated from the honeybee, was chosen as a representative of this cluster and was characterized according to accepted standards. This strain and other strains of the cluster entered the hemocoel of their insect hosts after per os acquisition, caused pathology in various tissues, and reduced adult longevity. Growth in SM-1 or M1D medium occurred at 20 to 37°C, with optimum growth at about 32 to 35°C. Cholesterol was required for growth. Glucose, fructose, and other carbohydrates were fermented, and arginine was catabolized. Seventeen strains, including strain BC-3T, reacted with considerable homogeneity in deformation tests and were completely separable from strains of subgroup I-1 (Spiroplasma citri) and subgroup I-3 (corn stunt spiroplasma). A group of five subgroup I-2 strains showed homogeneity upon one-dimensional polyacrylamide gel electrophoresis of cell proteins. Strain BC-3T was also serologically distinct from subgroups I-4 through I-8; from Spiroplasma floricola, Spiroplasma apis, and Spiroplasma mirum; and from representative strains of spiroplasma groups II and VI through XI. Previously published studies on strain BC-3T and related strains demonstrated that (i) these organisms comprise a unique subgroup of the S. citri complex (group I); (ii) deoxyribonucleic acid-deoxyribonucleic acid homologies between strain BC-3T and strains of other group I subgroups do not exceed 70%; (iii) the patterns of protein sharing among group I strains revealed by two-dimensional polyacrylamide gel electrophoresis support molecular genetic indications of partial relatedness; (iv) the EcoRI restriction endonuclease patterns of deoxyribonucleic acids from strain BC-3T and serologically related strains show close relatedness; (v) sequencing of 5S ribosomal ribonucleic acid suggests some degree of relatedness with all organisms now classified in the Mollicutes; (vi) strain BC-3T is capable of viscotactic and chemotactic responses; (vii) strain BC-3T possesses fibrils that may mediate various types of motility; and (viii) a lytic virus (SpV4) isolated from Spiroplasma sp. strain B63 (a representative of subgroup I-2) is morphologically and genomically distinct from other spiroplasma viruses and forms plaques only on lawns of subgroup I-2 spiroplasmas. Previous work on strain AS 576, another member of subgroup I-2, demonstrated (i) a viscotactic response, (ii) moderate sensitivity to osmotic environments, (iii) susceptibility to tetracycline and aminoglycoside antibiotics, (iv) growth in a relatively simple, chemically defined medium, (v) nutritional utilization patterns in defined medium, and (vi) a genome molecular weight of 109. On the basis of our new findings and the previously described properties of strain BC-3T and related subgroup I-2 strains, we propose that spiroplasma strains with the characteristics described here be classified as a new species, Spiroplasma melliferum. Strain BC-3, the type strain, has been deposited in the American Type Culture Collection as strain ATCC 33219.
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Reclassification of the Genus Pasteurella Trevisan 1887 on the Basis of Deoxyribonucleic Acid Homology, with Proposals for the New Species Pasteurella dagmatis, Pasteurella canis, Pasteurella stomatis, Pasteurella anatis, and Pasteurella langaa
More LessDeoxyribonucleic acid (DNA)-DNA hybridization was used to determine the genetic relationships among a variety of previously established or proposed species of Pasteurella and their positions within the family Pasteurellaceae Pohl 1981. Our results indicated that the genus Pasteurella sensu stricto, which can be separated from the Actinobacillus group, consists of at least the following 11 species: Pasteurella multocida, with three subspecies (P. multocida subsp. multocida, P. multocida subsp. septica, and P. multocida subsp. gallicida); Pasteurella dagmatis sp. nov., containing organisms previously labeled Pasteurella “gas,” Pasteurella new species 1, or Pasteurella pneumotropica type Henriksen; Pasteurella gallinarum; Pasteurella canis sp. nov., previously labeled P. multocida biotype 6 or “dog type” strains; Pasteurella stomatis sp. nov., which contains Pasteurella strains isolated from dogs and cats; Pasteurella avium (Hinz and Kunjara) Mutters et al. 1985; Pasteurella volantium Mutters et al. 1985, a new species consisting of V-factor-requiring strains that occur in humans and birds; Pasteurella anatis sp. nov.; Pasteurella langaa sp. nov., containing strains previously designated taxa 1 and 4 of Bisgaard; and two new species, which were provisionally designated Pasteurella species A and Pasteurella species B. The previously recognized taxa Pasteurella ureae, Pasteurella haemolytica biotypes A and T, Pasteurella testudinis, and P. pneumotropica biotypes Jawetz and Heyl do not belong to the genus Pasteurella but are more closely related to the Actinobacillus group. The exact taxonomic positions of Pasteurella aerogenes, P. multocida biotype 1, group HB-5, “Pasteurella piscicida,” the SP group, and the bovine lymphangitis group are still unknown, but these organisms do not belong to the genus Pasteurella.
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Eubacterium uniforme sp. nov. and Eubacterium xylanophilum sp. nov., Fiber-Digesting Bacteria from the Rumina of Sheep Fed Corn Stover
More LessA study was made of gram-positive nonsporeforming strains isolated from the rumina of sheep fed corn stover with or without different amounts of corn grain. Two groups of xylanolytic, non-cellulolytic strains were found. A total of 13 strains fermented a variety of carbon sources and produced formic, acetic, and lactic acids and ethanol from xylan. The name proposed for this group of strains is Eubacterium uniforme. The type strain of this species is strain X3C39 (= ATCC 35992). Three strains utilized only cellobiose and xylan of the carbohydrate energy sources tested and produced formic, acetic, and butyric acids from xylan. The name proposed for this group of strains is Eubacterium xylanophilum; the type strain is strain X6C58 (= ATCC 35991).
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Antigens and Enzymes of Bacteroides of the Bacteroides fragilis Group Compared by Crossed Immunoelectrophoresis
More LessIn this work we were primarily concerned with antigens of Bacteroides strains belonging to the B. fragilis group. The following two antisera were produced: anti-Bacteroides fragilis E1T (T = type strain) and anti-Bacteroides distasonis. Reference patterns for both of these species were established by crossed immunoelectrophoresis, and these patterns yielded 62 and 70 precipitates, respectively. The crossed reactions of B. fragilis E1T and B. distasonis with Bacteroides fragilis E2, Bacteroides thetaiotaomicron, Bacteroides ovatus, and Bacteroides vulgatus were studied to test both for total antigens and for certain enzymes (esterase, phosphatase, malate dehydrogenase, and glucose-6-phosphate dehydrogenase). Our results showed that B. thetaiotaomicron is the species which is closest to B. fragilis, demonstrating more than 70% common antigens, whereas none of the species examined was very closely related to B. distasonis. Species-specific antigens, such as the phosphatase of B. fragilis, as well as antigens common to the group, such as malate dehydrogenase, were also demonstrated in crossed immunoelectrophoresis. This may allow immunological identification of each species.
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Actinomadura yumaensis sp. nov.
More LessA new species of Actinomadura, for which we propose the name Actinomadura yumaensis, was isolated from a soil sample from Yuma County, Ariz. Whole-cell hydrolysates contain the meso isomer of diaminopimelic acid and the sugar madurose; thus, the cell wall composition type is type III. No nitrogenous phospholipids are present (type PI). Spores are formed in short spiral chains on branched, almost verticillate sporophores. The spores are ovoid and have smooth surfaces. This microorganism produces the polyether ionophore antibiotic X-14868A and is characterized by grayish yellow to dark yellowish brown substrate mycelium, white aerial hyphae (when produced) with light gray spores, and yellowish to greenish soluble pigments. Glucose, maltose, sucrose, and trehalose are the only sugars that support good growth on ISP medium 9. The type strain of A. yumaensis is strain LL-C23024 (= NRRL 12515).
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Reassignment of Actinobacillus actinomycetemcomitans to the Genus Haemophilus as Haemophilus actinomycetemcomitans comb. nov.
More LessSerological techniques were used to assess the relationships among the following species: Actinobacillus equuli, Actinobacillus lignieresii, Actinobacillus pleuropneumoniae, “Actinobacillus seminis” Actinobacillus suis, Actinobacillus actinomycetemcomitans Haemophilus aphrophilus, Haemophilus paraphrophilus, Haemophilus segnis, Haemophilus parainfluenzae, Haemophilus influenzae, Haemophilus parahaemolyticus, Haemophilus aegyptius, and Gardnerella vaginalis. Deoxyribonucleic acid-deoxyribonucleic acid hybridization analyses of A. actinomycetemcomitans, H. segnis, H. aphrophilus, and H. paraphrophilus showed that these four species have measurable deoxyribonucleic acid relatedness of 28% or greater, consistent with their placement in a single genus. These bacterial species also demonstrated common antigens by immunodiffusion. In view of these genetic and serological relationships and previous inclusion of X- and V-factor-independent bacterial species in the genus Haemophilus, reassignment of A. actinomycetemcomitans to the genus as Haemophilus actinomycetemcomitans comb. nov. is proposed.
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Taxonomic Position of Campylobacter cryaerophila sp. nov.
More LessA total of 90 aerotolerant Campylobacter strains, which were isolated mainly from animal abortions, were examined by using a wide range of biochemical and physiological tests. The resulting data, together with data for reference Campylobacter strains that were similarly examined, were compared by using several numerical taxonomic analysis methods. Our analyses demonstrated that there is a strong similarity between the aerotolerant strains and strains of Campylobacter fetus, Campylobacter jejuni, Campylobacter coli, and Campylobacter sputorum. For practical purposes this study revealed four possible taxa; one taxon consisted of C. fetus strains, one taxon consisted of the C. sputorum strains, and a third taxon consisted of the thermophilic strains, having C. coli and C. jejuni strains as separate entities. The fourth group consisted of all of the aerotolerant strains and was considered a new species of Campylobacter. All of the aerotolerant strains exhibited a tolerance to lower temperatures and higher oxygen concentrations than previously observed with strains of Campylobacter; the name Campylobacter cryaerophila sp. nov. is suggested for these strains. In this paper we present identification characteristics of C. cryaerophila strains and a description of the new species.
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Physiological Characteristics and Deoxyribonucleic Acid Relatedness of Human Isolates of Streptococcus bovis and Streptococcus bovis (var.)
More LessThe current classification of Streptococcus bovis is problematic. Many bovine strains, including the type strain, are not typical of S. bovis strains derived from humans, especially in physiologic characteristics. Further, a number of strains physiologically resembling some S. intermedius (MG) strains carry the group D antigen and have been classified as S. bovis (var.) strains. In this work, we compared the physiologic characteristics and deoxyribonucleic acid relatedness of human strains of S. bovis and S. bovis (var.), the bovine type strain, and selected bile-tolerant, esculin-hydrolyzing strains of viridans streptococci. Our results indicate a lack of relationship between strains derived from humans and the bovine S. bovis type strain. Although, like the classic S. bovis strains of human origin, the bovine type strain was able to hydrolyze starch, it differed from human S. bovis strains in that it failed to form acid from mannitol and melibiose. The S. bovis (var.) strains did not hydrolyze starch or form acid from mannitol. They were distinguished from the bile-tolerant, esculin-hydrolyzing S. intermedius (MG) strains by their inability to decarboxylate arginine, their ability to form acid from melibiose, and their production of the Lancefield group D antigen. All S. bovis strains of human origin, including the S. bovis (var.) strains, formed a single deoxyribonucleic acid homology group distinct from the bovine type strain. Further, none of the S. bovis strains were homologous to the S. intermedius (MG) or S. salivarius strains studied. Our findings suggest that S. bovis (var.) forms a subspecies of strains of human origin and that S. bovis strains derived from humans should be removed from the S. bovis taxon.
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