- Volume 44, Issue 4, 1994
Volume 44, Issue 4, 1994
- Original Papers Relating To Systematic Bacteriology
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Descriptions of Prevotella tannerae sp. nov. and Prevotella enoeca sp. nov. from the Human Gingival Crevice and Emendation of the Description of Prevotella zoogleoformans
More LessAbstractPrevotella tannerae sp. nov. and Prevotella enoeca sp. nov. from the human gingival crevice are described. These organisms are obligately anaerobic, non-spore-forming, nonmotile, gram-negative, rod-shaped bacteria that ferment carbohydrates and produce succinic and acetic acids. Bile inhibits growth. Some strains (38%) of P. tannerae produce colonies with a tan to black pigment when they are grown on rabbit blood agar. The type strains are P. tannerae ATCC 51259 and P. enoeca ATCC 51261. In addition, the description of Prevotella zoogleoformans is emended to exclude strains now recognized as members of Prevotella heparinolytica.
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Isolation and Characterization of Methanolobus bombayensis sp. nov., a Methylotrophic Methanogen That Requires High Concentrations of Divalent Cations
More LessAbstractMethanolobus bombayensis B-1T (= OCM 438T) (T = type strain) was isolated from Arabian Sea sediments obtained near Bombay, India. This strain grew on methylamines, methanol, and dimethyl sulfide, but it did not catabolize H2-CO2, acetate, or formate. The cells were nonmotile, irregular coccoids (diameter, 1.0 to 1.5 µm) and occurred singly. Electron micrographs revealed that a cell membrane and a protein cell wall were present. The cells grew fastest at mesophilic temperatures, at a neutral pH, and at salinity levels near the salinity level of the ocean, and they required about 30 mM divalent cations (Mg2+ and Ca2+). The cells grew in mineral medium, but growth was greatly stimulated by yeast extract and peptones. The guanine-plus-cytosine content of the DNA was 39.2 ± 0.1 mol%. A comparison of 16S rRNA sequences showed that strain B-1T was phylogenetically related to Methanolobus vulcani, but the sequences of these organisms differed by 2%.
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Transfer of Nocardioides fastidiosa Collins and Stackebrandt 1989 to the Genus Aeromicrobium as Aeromicrobium fastidiosum comb. nov.
More LessAbstractThe 16S rRNA sequences of aerobic LL-diaminopimelic acid-containing coryneform bacteria were compared, and the sequence of Nocardioides fastidiosa exhibited a high level of similarity to the sequence of Aeromicrobium erythreum but not to the sequences of the other species of the genus Nocardioides. Furthermore, analyses of menaquinone systems and cellular fatty acids revealed that N. fastidiosa was similar to A. erythreum but differed from the other Nocardioides species. On the basis of chemotaxonomic data and DNA-DNA hybridization and comparative 16S rRNA results, we propose that N. fastidiosa should be transferred to the genus Aeromicrobium as Aeromicrobium fastidiosum comb. nov. (type strain, IFO 14897).
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Isolation and Characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an Anaerobic Bacterium Which Reductively Dechlorinates Chlorophenolic Compounds
More LessAbstractAn organism that is able to reductively ortho-dechlorinate 2,4-dichlorophenol and 3-chloro-4-hydroxyphenylacetate (3-C1-4-OHPA) was isolated from a methanogenic lake sediment. This organism, an anaerobic, motile, Gram-type-positive, rod-shaped bacterium, grew in the presence of 0.1% yeast extract when pyruvate, lactate, formate, or hydrogen was used as the electron donor for reductive dehalogenation of 3-C1-4-OHPA. Sulfite, thiosulfate, and sulfur were reduced to sulfide, nitrate was reduced to nitrite, and fumarate was reduced to succinate. Dissimilatory reduction of sulfate could not be demonstrated, and no adenylylsulfate reductase was detected with an immunoassay. The organism fermented two pyruvate molecules to one lactate molecule, one acetate molecule, and one carbon dioxide molecule. The pH and temperature optima for both growth and dechlorination of 3-C1-4-OHPA were 7.5 and 38°C, respectively. The doubling time under these conditions was approximately 3.5 h. On the basis of the results of a 16S rRNA analysis and the inability of the organism to use sulfate as an electron acceptor, strain JW/IU-DC1 is described as the type strain of the new taxon Desulfitobacterium dehalogenans gen. nov., sp. nov.
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Phylogenetic Position of the Genus Hydrogenobacter
AbstractThe genus Hydrogenobacter consists of extremely thermophilic, obligately chemolithotrophic organisms that exhibit anaerobic anabolism but aerobic catabolism. Preliminary studies of the phylogenetic position of these organisms based on limited 16S ribosomal DNA sequence data suggested that they belong to one of the earliest branching orders of the Bacteria. In this study, the complete 16S ribosomal DNA sequences of two type strains, Hydrogenobacter thermophilus TK-6 and Calderobacterium hydrogenophilum Z-829, and another isolate, Hydrogenobacter sp. strain T3, were determined, and the phylogenetic positions of these organisms were examined. Our results revealed that the two type strains are members of a single genus, the genus Hydrogenobacter. Our results also verified the previous conclusion that the Aquifex-Hydrogenobacter complex belongs to a very early branching order, the “ “Aquificales.” “ Within this order, the relationships among the various organisms are such that only a single family, the “ “Aquificaceae,” can be recognized at this time. Given the early branching point of the “ “Aquificales,” “the characteristics of these organisms support the view that the last common ancestor of existing life was thermophilic and suggest that this ancestor may have fixed carbon chemoautotrophically.
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Rhodococcus luteus Is a Later Subjective Synonym of Rhodococcus fascians
More LessAbstractThe results of DNA-DNA hybridization studies and 16S ribosomal DNA sequence comparisons and chemotaxonomic data clearly indicated that Rhodococcus luteus Nesterenko et al. 1982 (O. A. Nesterenko, T. M. Nogina, S. A. Kasumova, E. I. Kvasnikow, and S. G. Batrakov, Int. J. Syst. Bacteriol. 32:1–14, 1982) and Rhodococcus fascians (Tilford) Goodfellow 1984 (M. Goodfellow, Syst. Appl. Microbiol. 5:225–229, 1984) represent a single species. On the basis of priority R. luteus must be considered a later subjective synonym of R. fascians.
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Photobacterium histaminum sp. nov., a Histamine-Producing Marine Bacterium
More LessAbstractA total of 23 strains of halophilic histamine-producing bacteria previously isolated from marine fish and seawater were studied phenotypically, genotypically, and phylogenetically. These organisms are facultatively anaerobic, gram-negative, short rods that are motile by means of one to three unsheathed polar flagella. They are mesophilic and nonluminescent, produce oxidase, utilize D-glucose but not D-mannitol as a carbon and energy source, and accumulate poly-β-hydroxybutyrate. The guanine-plus-cytosine contents of the DNAs are ca. 41 mol%. Genomic DNA hybridization experiments revealed that some of the isolates exhibited low levels of reassociation (less than 40%) with previously described Photobacterium species. 16S rRNA gene sequence information confirmed the phylogenetic position of one of the isolates, strain C-8T (T = type strain), as a member of the genus Photobacterium. Therefore, we concluded that these organisms are members of a new species of the genus Photobacterium and propose the name Photobacterium histaminum sp. nov. for them. The type strain is strain C-8 (= JCM 8968).
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Porphyromonas gingivicanis sp. nov. and Porphyromonas crevioricanis sp. nov., Isolated from Beagles
More LessAbstractTwo new species, Porphyromonas gingivicanis and Porphyromonas crevioricanis, are proposed for black-pigmented, asaccharolytic, anaerobic, nonmotile, non-spore-forming, gram-negative, rod-shaped organisms. These organisms were isolated from the gingival crevicular fluids of beagles. P. gingivicanis and P. crevioricanis do not grow in the presence of 20% bile. They exhibit less than 5% DNA-DNA homology with the type strains of Porphyromonas gingivalis (strain ATCC 33277), Porphyromonas endodontalis (strain ATCC 35406), and Porphyromonas asaccharolytica (strain ATCC 25260), which were isolated from humans, or with the type strains of Porphyromonas salivosa (strain NCTC 11632) and Porphyromonas circumdentaria (strain NCTC 12469), which were isolated from cats. The major cellular fatty acid of P. gingivicanis and P. crevioricanis is 13-methyltetradecanoic acid (iso-C15:0 acid). Glutamate and malate dehydrogenases are present in both species, and 6-phosphogluconate and glucose-6-phosphate dehydrogenases are absent; neither organism exhibits trypsin activity. P. gingivicanis and P. crevioricanis produce large amounts of acetic and isovaleric acids and minor amounts of isobutyric and succinic acids as end products of metabolism in GAM medium. P. gingivicanis also produces large amounts of butyric acid and small amounts of propionic acid, while P. crevioricanis produces large amounts of propionic acid and minor amounts of butyric and phenylacetic acids. The G+C contents of the DNA of P. gingivicanis is 41 to 42 mol%; the G+C content of the DNA of P. crevioricanis is 44 to 45 mol%. Catalase is produced by P. gingivicanis but not by P. crevioricanis; strains of P. crevioricanis agglutinate sheep erythrocytes, but strains of P. gingivicanis do not. The type strain of P. gingivicanis is NUM 301 (= ATCC 55562), and the type strain of P. crevioricanis is NUM 402 (= ATCC 55563).
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Streptococcus phocae sp. nov., a New Species Isolated from Clinical Specimens from Seals
More LessAbstractA new beta-hemolytic streptococcal species, Streptococcus phocae, was isolated from organ specimens obtained from seals. This taxon is described on the basis of the results of a study of 22 strains. S. phocae was serologically somewhat heterogeneous (group antigen -/F/C). Strains belonging to this species exhibited high levels of DNA-DNA homology to each other, as determined by DNA-DNA hybridization, but low levels of DNA-DNA homology to the type strains of other streptococcal species. A simple scheme for the differentiation of S. phocae from other beta-hemolytic streptococci is presented. Strain 8399 H1 (= NCTC 12719) is the type strain of S. phocae.
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Cellular Fatty Acid Composition as a Chemotaxonomic Marker for the Differentiation of Phenospecies and Hybridization Groups in the Genus Aeromonas
AbstractNinety genotypically characterized Aeromonas strains, including members of all 14 currently established genospecies, were studied by performing gas-liquid chromatographic analysis of their cellular fatty acid methyl esters (FAMEs). A total of 44 fatty acids and two alcohols were found in members of the genus Aeromonas. All 90 strains contained 12:0, 13:0 iso, 14:0, 15:0 iso 30H, 16:0, 16:1 ω7c, 17:0 iso, iso 17:1 ω9c, summed feature 3 (16:1 iso I and/or 14:0 30H), and summed feature 7 (18:1 ω7c, 18:1 ω9t, and/or 18:1 ω12t), whereas all but one strain (99%) also contained 15:0 iso. Although the FAME profiles were very similar, minor quantitative variations could be used to differentiate phenospecies and/or hybridization groups. A cluster analysis of the mean data revealed five FAME clusters, which were compared with phenotypic and genotypic groups identified in the genus Aeromonas. Hybridization groups that constituted the Aeromonas hydrophila complex, the Aeromonas caviae complex, and the Aeromonas sobria complex were basically grouped into distinct FAME clusters. The taxonomic positions of hybridization groups 7 and 11 in these clusters, however, remained unclear. All of our results were highly reproducible. A new database of Aeromonas FAME fingerprints was generated, and this database can be used for rapid identification of unknown aeromonads. Using a large set of well-characterized aeromonads, we demonstrated for the first time that gas-liquid chromatographic FAME analysis can be used to differentiate the majority of the phenospecies and/or hybridization groups in the genus Aeromonas.
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Description of Bacillus laevolacticus (ex Nakayama and Yanoshi 1967) sp. nov., nom. rev.
More LessAbstractThe name “Bacillus laevolacticus” Nakayama and Yanoshi 1967 was not included on the Approved Lists of Bacterial Names and therefore has no standing in bacteriological nomenclature. In this study 22 catalase-positive, acid-tolerant, facultatively anaerobic, lactic acid-producing Bacillus strains were examined taxonomically and compared with a number of strains belonging to phenetically similar Bacillus species (Bacillus coagulans, Bacillus smithii, ““Bacillus vesiculiferous”) and with Sporolactobacillus. The G+C contents (43 to 45 mol%), DNA-DNA homology values (72 to 98%), and results of phenetic similarity analyses revealed that the members of the “B. laevolacticus” group were very homogeneous in their phenotypic and genotypic characteristics and clearly distinguishable from other Bacillus and Sporolactobacillus species. On the basis of these findings, revival of the name Bacillus laevolacticus is proposed.
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Rhodoplanes gen. nov., a New Genus of Phototrophic Bacteria Including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov.
More LessAbstractTwo new strains (AS130 and AS140) of phototrophic purple nonsulfur bacteria isolated from activated sludge were characterized and compared with Rhodopseudomonas rosea and some other species of the genus Rhodopseudomonas. The new isolates produced pink photosynthetic cultures, had rod-shaped cells that divided by budding, and formed intracytoplasmic membranes of the lamellar type together with bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series. They were also characterized by their capacity for complete denitrification and their production of both ubiquinone-10 and rhodoquinone-10 as major quinones. The isolates were phenotypically most similar to R. rosea but exhibited low levels of genomic DNA hybridization to this species and to all other Rhodopseudomonas species compared. Phylogenetic analyses on the basis of PCR-amplified 16S rRNA gene sequences showed that our isolates and R. rosea formed a cluster distinct from other members of the genus Rhodopseudomonas. The phenotypic, genotypic, and phylogenetic data show that the new isolates and R. rosea should be placed in a new single genus rather than included in the genus Rhodopseudomonas. Thus, we propose to transfer R. rosea to a new genus, Rhodoplanes, as Rhodoplanes roseus gen. nov., comb. nov. (type species) and to designate strains AS130 and AS140 a new species, Rhodoplanes elegans sp. nov.
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Phylogenetic Analysis of Members of the Genus Porphyromonas and Description of Porphyromonas cangingivalis sp. nov. and Porphyromonas cansulci sp. nov.
AbstractThe partial 16S rRNA gene sequences of representative strains of two groups of anaerobic, gram-negative, pigmented, asaccharolytic, rod-shaped bacteria isolated from subgingival plaque of dogs with naturally occurring periodontal disease were determined. A comparative analysis of the rRNA sequence data revealed that the two groups of organisms represent previously unknown lines of descent within the genus Porphyromonas. On the basis of our phylogenetic findings and the phenotypic distinctiveness of the organisms, two new species, Porphyromonas cangingivalis and Porphyromonas cansulci, are proposed.
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Acholeplasma brassicae sp. nov. and Acholeplasma palmae sp. nov., Two Non-Sterol-Requiring Mollicutes from Plant Surfaces
Two mollicutes (strains 0502T [T = type strain] and J233T), which were isolated from the surfaces of broccoli (Brassica oleracea var. italica) plants or the crown tissues of the coconut palm (Cocos nucifera), were capable of sustained growth in serum-free (or cholesterol-free) mycoplasma broth media. Examination by electron and dark-field microscopic techniques revealed that the cells of each strain were small, nonhelical, nonmotile, pleomorphic, and coccoid and that each cell was surrounded by a single cytoplasmic membrane. No evidence of a cell wall was found. The organisms were filterable and grew rapidly in most conventional mycoplasma culture medium formulations containing horse or fetal bovine sera under either aerobic or anaerobic conditions. The optimum temperature for growth of both organisms was 30°C, but multiplication occurred over a temperature range from 18 to 37°C. Both strains catabolized glucose, but did not hydrolyze arbutin, arginine, or urea. The genome size of strain 0502T was 1,215 kbp, and the DNA base composition (guanine-plus-cytosine content) was 35.5 mol%. The genome size of strain J233T was 1,610 kbp, and the DNA base composition was 30.0 mol%. The two isolates were not serologically related to each other or to the type strains of 11 previously described Acholeplasma species. Strain 0502 (= ATCC 49388) is the type strain of Acholeplasma brassicae sp. nov., and strain J233 (= ATCC 49389) is the type strain of Acholeplasma palmae sp. nov.
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Taxonomic Descriptions of Eight New Non-Sterol-Requiring Mollicutes Assigned to the Genus Mesoplasma
AbstractTwenty mollicute strains isolated primarily from insect hosts were characterized and arranged into eight new species in the genus Mesoplasma. Morphological examination of the organisms by electron and dark-field microscopic techniques revealed that the cells of each strain were small, nonhelical, nonmotile, pleomorphic, and coccoid and that each cell was surrounded by a single cytoplasmic membrane with no evidence of a cell wall. Although the new mollicutes grew well in media containing horse or fetal bovine serum, growth in serum-free or cholesterol-free medium occurred only when the medium contained 0.04% polyoxyethylene sorbitan (Tween 80). The optimum temperature for growth was usually 30°C, but multiplication generally occurred over a temperature range of 10 to 32°C. All strains catabolized glucose. Most strains did not hydrolyze arginine or urea, although three related strains isolated from fireflies (the strain PUPA-2T [T = type strain] group) did hydrolyze arginine. The genome sizes ranged from 825 to 930 kbp, and the DNA base compositions (guanine-plus-cytosine contents) ranged from 26.5 to 31.6 mol%. The proposed type strains of the eight new species were not serologically related to the type strains of four other Mesoplasma species, five Entomoplasma species, 11 Acholeplasma species, and 100 Mycoplasma species and subspecies. Strain PS-1 (= ATCC 49582) is the type strain of Mesoplasma pleciae sp. nov., strain PUPA-2 (= ATCC 49581) is the type strain of Mesoplasma photuris sp. nov., strain YJS (= ATCC 43706) is the type strain of Mesoplasma syrphidae sp. nov., strain CHPA-2 (= ATCC 49578) is the type strain of Mesoplasma chauliocola sp. nov., strain ELCA-2 (= ATCC 49579) is the type strain of Mesoplasma corruscae sp. nov., strain GRUA-1 (= ATCC 49580) is the type strain of Mesoplasma grammopterae sp. nov., strain BARC 779 (= ATCC 49583) is the type strain of Mesoplasma coleopterae sp. nov., and strain BARC 857 (= ATCC 49584) is the type strain of Mesoplasma tabanidae sp. nov.
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Chemical And Molecular Classification of Saccharomonospora Strains
More LessAbstractThe results of our experiments showed that the 5’-terminal sequences of 23S rRNAs can be used to distinguish different genera of actinomycetes, including the genera Streptomyces, Micromonospora, Amycolatopsis, and Saccharomonospora. There are small differences (<1%) among the sequences of some strains belonging to the genera Streptomyces (two strains) and Saccharomonospora (seven strains). On the basis of the results of morphological and biochemical analyses, strain 9022 belongs in the genus Saccharomonospora; however, there are distinct differences in the cell wall compositions and the 5’ termini of the 23S rRNA sequences of this strain and members of the genus Saccharomonospora. Hence, strain 9022 cannot be classified in the genus Saccharomonospora.
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Polyphasic Taxonomy of Rhizobia: Emendation of the Genus Sinorhizobium and Description of Sinorhizobium meliloti comb, nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov.
AbstractA total of 80 bacterial strains isolated from different Sesbania and Acacia species growing in various sites in Senegal (West Africa) were compared with 35 reference strains of Rhizobium, Bradyrhizobium, Azorhizobium, and Agrobacterium species and with 33 representative strains of the different groups of Brazilian isolates described on the basis of the results of a numerical analysis of the whole-cell protein patterns obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Fifty-two strains could be placed in three protein electrophoretic clusters, two of which were different from the clusters containing various reference or representative strains, while 30 other strains could not be placed in any group. The strains belonging to the three clusters were studied by determining their nodulation host ranges and their morphological, physiological, and auxanographic characteristics. Representative strains of the three clusters were also genotypically characterized by determining their DNA base compositions, by performing DNA-DNA and DNA-rRNA hybridization experiments, and by determining their 16S rRNA gene sequences. Our results showed that two of the clusters identified on the basis of SDS-PAGE data are genotypically and phenotypically distinct groups that belong on the Rhizobium meliloti-Rhizobium fredii rRNA branch. The third cluster is localized on the Rhizobium loti rRNA branch in the vicinity of Rhizobium huakuii and contains strains isolated in Africa, in Brazil, and in New Zealand from different leguminous species. On the basis of the results of the present study, we propose to emend the genus Sinorhizobium and to reclassify R. meliloti as Sinorhizobium meliloti comb. nov. In addition, two new species, Sinorhizobium saheli and Sinorhizobium teranga, are proposed for isolates from Senegal.
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Numerical Taxonomy of Rhizobium Strains from Legumes of the Temperate Zone
More LessAbstractPhenotypic properties (growth characteristics, utilization of carbon and nitrogen sources, and intrinsic antibiotic resistance) of 53 Rhizobium strains isolated from root nodules of the temperate-zone legumes Astragalus spp. (29 strains), Oxytropis campanulata (7 strains), Hedysarum alpinum (7 strains), Ononis arvensis (3 strains), Glycyrrhiza spp. (4 strains), and Coronilla varia (3 strains) were compared with those of other Rhizobium, Brady rhizobium, and Agrobacterium strains. The final matrix, containing 83 strains and 56 nonsymbiotic features, was used for computer cluster analysis. The dendrogram showed that the new strains of temperate-zone rhizobia formed a cluster separate from both Rhizobium and Bradyrhizobium spp. Two large groups of temperate-zone rhizobia were revealed. Group 1 included rhizobial strains originating from different geographical regions with a temperate climate, while group 2 included strains from the same geographical origin, South Siberia. The strains of recognized Rhizobium species were clustered, in general, with each other as expected from phylogenetic relatedness.
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Diversity of Borrelia burgdorfeii Sensu Lato Evidenced by Restriction Fragment Length Polymorphism of rrf (5S)-rrl (23S) Intergenic Spacer Amplicons
More LessThe organization of the ribosomal genes is unique in Borrelia burgdorferi in that the rrl (23S) and rrf (5S) genes are tandemly duplicated. We took advantage of this uniqueness to assess the restriction polymorphism of PCR products obtained with primers at the 3′ end of the first rrf gene and at the 5′ end of the second rrl gene. An amplicon that was 226 to 266 bp long was generated from 99 of 100 B. burgdorferi sensu lato strains. The nuclease MseI restriction polymorphism of the amplicons provided a useful tool for identifying B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii (formerly group VS461), and Borrelia japonica (formerly group F63B). Furthermore, it allowed us to recognize four new genomic groups, which were confirmed by DNA-DNA hybridization data. Two of these genomic groups comprised European strains, and the other two groups contained American strains. The American genomic groups involved vectors with enzootic cycles quite different from those of B. burgdorferi sensu stricto, which previously was the only Lyme disease Borrelia species known to occur in the United States. Our method could be used for rapid screening of strain collections and for epidemiological and medical purposes.
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Phylogenetic Analysis of Five Strains of Gram-Negative, Obligately Anaerobic, Sulfur-Reducing Bacteria and Description of Desulfuromusa gen. nov., Including Desulfuromusa kysingii sp. nov., Desulfuromusa bakii sp. nov., and Desulfuromusa succinoxidans sp. nov.
More LessGram-negative, mesophilic, obligately anaerobic strains Kysw2T (T = type strain), Kyval, and Kyprop isolated from an anoxic mud sample obtained from the Kysing Fjord south of Århus (Denmark) and strains GypropT and GylacT isolated from the Guayamas Basin (Gulf of California) all exhibit complete oxidation of a wide range of electron donors (e. g., dicarboxylic acids and amino acids) linked to stoichiometric reduction of elemental sulfur to hydrogen sulfide. A comparative 16S ribosomal DNA sequence analysis revealed that these five strains, together with a previously described isolate (strain Gö11), constitute a coherent cluster of descent. This cluster belongs phylogenetically to a branch of the delta subclass of the Proteobacteria and is characterized by members of the genera Pelobacter and Desulfuromonas. Within the cluster strains Kysw2T and Kyval, strains Gyprop1 and Kyprop, and strains GylacT and Gö11 have identical 16S ribosomal DNA sequences. The levels of DNA-DNA relatedness were 89% between strains Kysw2T and Kyval, 98% between strains GypropT and Kyprop, and 73% between strains GylacT and Gö11. The levels of DNA-DNA relatedness between members of the three DNA relatedness groups were less than 30%. On the basis of genomic data and phenotypic characteristics, a new genus, Desulfuromusa, is described; this new genus includes three new species, for which the names Desulfuromusa kysingii, Desulfuromusa bakii, and Desulfuromusa succinoxidans are proposed. The type species of the genus Desulfuromusa is D. kysingii. Strains Kysw2 (= DSM 7343), Gyprop (= DSM 7345), and Gylac (= DSM 8270) are the type strains of D. kysingii, D. bakii, and D. succinoxidans, respectively.
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Actinopolyspora iraqiensis sp. nov., a New Halophilic Actinomycete Isolated from Soil
More LessHalophilic actinomycete strains, IQ-H1T (T = type strain) and IQ-H2, were isolated from extremely saline soil samples in Iraq. Besides morphological properties, strains IQ-H1T and IQ-H2 have a type IV cell wall, type PIII phospholipid, and menaquinone MK-9 (H4, H6), which are characteristic of Actinopolyspora spp. In addition, both strains required high concentrations of sodium chloride (10 to 15% [wt/vol] and 15 to 25% [wt/vol] NaCl, respectively), for optimal growth. However, strains IQ-H1T and IQ-H2 differed from other previously described species of the genus Actinopolyspora in cultural, morphological, and physiological characteristics. In addition, the size of the internal transcribed spacer in the rDNA (gene encoding rRNA) of IQ-H1T was different from those of known published species, while the size of the internal transcribed spacer of IQ-H2 was similar to that of Actinopolyspora halophila JCM 3278T. Thus, we propose strain IQ-H1T as a new species and name it Actinopolyspora iraqiensis sp. nov. Strain IQ-H1T has been deposited in the culture collection of the Institute of Microbiology, Academia Sinica, Beijing, the People's Republic of China (strain A.S. 4.1193).
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Rhodococcus chubuensis Tsukamura 1982 Is a Later Subjective Synonym of Gordona sputi (Tsukamura 1978) Stackebrandt 1989 comb. nov.
More LessThe genus Gordona was proposed by Tsukamura in 1971 (M. Tsukamura, J. Gen. Microbiol. 68:15-24,1971) and was revived in 1988 by Stackebrandt et al. (E. Stackebrandt, J. Smida, and M. D. Collins, J. Gen. Appl. Microbiol. 34:341-348, 1988) to accommodate Rhodococcus species containing mycolic acids with 48 to 66 carbon atoms and MK-9(H2) as the predominant menaquinone type. On the basis of mycolic acid composition as determined by high-performance liquid chromatography, DNA-DNA similarity data (S1 nuclease procedure), and the rRNA gene restriction patterns of the type strains, we propose that Rhodococcus chubuensis Tsukamura 1982 is a subjective synonym of Gordona sputi (Tsukamura 1978) Stackebrandt 1989 comb. nov. We found that R. chubuensis type strain ATCC 33609, and G. sputi type strain ATCC 29627 exhibit identical mycolic acid profiles, 97% DNA relatedness (difference in thermal denaturation midpoints, 1.0°C), and similar ribotypes after PvuII endonuclease digestion. Thus, as defined by the type strains and considering the priority of the name G. sputi, these two species should be regarded as a single species named Gordona sputi; an emended description of this taxon is given.
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Transfer of Rhodococcus aichiensis Tsukamura 1982 and Nocardia amarae Lechevalier and Lechevalier 1974 to the Genus Gordona as Gordona aichiensis comb. nov. and Gordona amarae comb. nov.
More LessAbstractWe investigated the taxonomic status of Rhodococcus aichiensis DSM 43978T (T = type strain) and Nocardia amarae DSM 43392T by using both chemotaxonomic and genetic methods. The occurrence of MK-9(H2) as the predominant menaquinone, the presence of relatively long-chain mycolic acids (48 to 62 carbon atoms), and the phylogenetic position as determined by a 16S ribosomal DNA sequence analysis provide strong evidence that both R. aichiensis and N. amarae should be transferred to the genus Gordona as Gordona aichiensis and Gordona amarae, respectively.
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Halococcus salifodinae sp. nov., an Archaeal Isolate from an Austrian Salt Mine
AbstractA novel extremely halophilic archaeon (archaebacterium) was isolated from rock salt obtained from an Austrian salt mine. The deposition of the salt is thought to have occurred during the Permian period (225 × 106 to 280 × 106 years ago). This organism grew over a pH range of 6.8 to 9.5. Electron microscopy revealed cocci in tetrads or larger clusters. The partial 16S rRNA sequences, polar lipid composition, and menaquinone content suggested that this organism was related to members of the genus Halococcus, while the whole-cell protein patterns, the presence of several unknown lipids, and the presence of pink pigmentation indicated that it was different from previously described coccoid halophiles. We propose that this isolate should be recognized as a new species and should be named Halococcus salifodinae. The type strain is Blp (= ATCC 51437 = DSM 8989). A chemotaxonomically similar microorganism was isolated from a British salt mine.
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Genetic Relationships among Eubacterium Species
More LessAbstractThe genetic relationships among Eubacterium species were assessed by using DNAs from American Type Culture Collection type strains of 10 species and two subspecies of the genus Eubacterium, i.e., Eubacterium aerofaciens, E. alactolyticum, E. brachy, E. lentum, E. limosum, E. nodatum, E. rectale, E. saburreum, E. timidum, E. yurii subsp. yurii, and E. yurii subsp. margaretiae. The DNA base compositions (determined by high-performance liquid chromatography) of these species varied widely, from 38 to 62 mol% G+C. Seven Eubacterium species showed significant differences (nearly 10%) in G+C content compared with E. limosum, the type species of the genus. DNA-DNA hybridization (by the membrane filter method) showed that two subspecies, E. yurii subsp. yurii and E. yurii subsp. margaretiae, and two strains of E. timidum exhibited high levels of DNA relatedness. However, the DNA reassociations among the 10 Eubacterium species studied were 1 to 16%. None of the species examined shared a high level of DNA reassociation with the type species of the genus Eubacterium. The protein profile patterns (determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of whole bacterial cells from these Eubacterium species were distinct, and no major peptide bands were shared among the 10 Eubacterium species. Therefore, the Eubacterium species we tested must be considered genetically distinct from each other.
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Ancestral Divergence of Rickettsia bellii from the Spotted Fever and Typhus Groups of Rickettsia and Antiquity of the Genus Rickettsia
More LessAbstractThe eubacterial genus Rickettsia belongs to the α subgroup of the phylum Proteobacteria. This genus is usually divided into three biotypes on the basis of vector host and antigenic cross-reactivity characteristics. However, the species Rickettsia bellii does not fit into this classification scheme; this organism has characteristics common to both the spotted fever group and the typhus group biotypes and also exhibits some unique features. Sequences of the 16S rRNA and 23S rRNA genes from Rickettsia rickettsii (spotted fever group), Rickettsia prowazekii (typhus group), and R. bellii were studied to determine the position of R. bellii in the rickettsial classification scheme. The 23S rRNA gene sequences described in this paper are the first 23S rRNA sequences reported for any member of the Rickettsiaceae. The 23S rRNA gene contains substantially more phylogenetic information than is contained in the 16S rRNA sequences, and the 23S rRNA gene sequence has diverged about 1.9 times faster in the three Rickettsia species which we studied. Taken together, the molecular data obtained from the two genes indicate that R. bellii is not a member of either the spotted fever group or the typhus group; rather, this organism appears to be the product of a divergence which predates the separation of the genus into the spotted fever group and the typhus group. Consequently, different combinations of the ancestral characteristics retained by R. bellii have been retained in the more derived lineages of the genus. A comparison of the 16S rRNA and 23S rRNA gene sequences of Rickettsia strains with other proteobacterial sequences confirmed that the genus Rickettsia is a unique deeply branching member of the α subgroup of the Proteobacteria and that the Rickettsia species form a monophyletic cluster. While divergence of the contemporary members of the genus Rickettsia occurred recently, the unique evolutionary line represented by this genus appears to be very old.
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Haloincola saccharolytica subsp. senegalensis subsp. nov., Isolated from the Sediments of a Hypersaline Lake, and Emended Description of Haloincola saccharolytica
AbstractA new halophilic chemoorganotrophic bacterium (strain H150T [T = type strain]) related to Haloincola saccharolytica was isolated from the hypersaline sediments of Retba Lake in Senegal. This organism was a rod-shaped, motile, non-spore-forming, gram-negative obligate anaerobe that grew optimally in the presence of 10% NaCl and at 40°C. The DNA base composition was 31.7 ± 0.3 mol% guanine plus cytosine. The fermentation products from glucose were acetate, H2, and CO2. The fermentable substrates included cellobiose, fructose, glucose, maltose, lactose, glycerol, mannitol, mannose, ribose, raffinose, and sucrose. Penicillin G, cephalosporin C, novobiocin, vancomycin, and chloramphenicol inhibited growth. As determined by DNA-DNA hybridization, strain H150T was 71% related to H. saccharolytica, with ΔTm value of 6.0°C. However, strain H150T exhibited marked phenotypic differences, particularly in the range of substrates used, when it was compared with the type species of the genus Haloincola. For this isolate we propose the name Haloincola saccharolytica subsp. senegalensis subsp. nov.; strain H150 (= DSM 7379) is the type strain of this taxon.
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The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations
The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G+C-content gram-positive genera, thereby providing an almost complete picture of the genealogical interrelationships of the clostridia. The results of our phylogenetic analysis corroborate and extend previous findings in showing that the genus Clostridium is extremely heterogeneous, with many species phylogenetically intermixed with other sporeforming and non-sporeforming genera. The genus Clostridium is clearly in need of major revision, and the rRNA structures defined in this and previous studies may provide a sound basis for future taxonomic restructuring. The problems and different possibilities for restructuring are discussed in light of the phenotypic and phylogenetic data, and a possible hierarchical structure for the clostridia and their close relatives is presented. On the basis of phenotypic criteria and the results of phylogenetic analyses the following five new genera and 11 new combinations are proposed: Caloramator gen. nov., with Caloramator fervidus comb. nov.; Filifactor gen. nov., with Filifactor villosus comb. nov.; Moorella gen. nov., with Moorella thermoacetica comb. nov. and Moorella thermoautotrophica comb. nov.; Oxobacter gen. nov., with Oxobacter pfennigii comb. nov.; Oxalophagus gen. nov., with Oxalophagus oxalicus comb. nov.; Eubacterium barkeri comb. nov.; Paenibacillus durum comb. nov.; Thermoanaerobacter kivui comb. nov.; Thermoanaerobacter thermocopriae comb. nov.; and Thermoanerobacterium thermosaccharolyticum comb. nov.
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NOTES: New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev.
More LessOur present knowledge concerning the genotypic, chemotaxonomic, and phenotypic characteristics of members of the genus Flavobacterium and some related genera, including the genus Weeksella, was used to revise the classification of these organisms. The generically misclassified organisms Flavobacterium balustinum, Flavobacterium gleum, Flavobacterium indologenes, Flavobacterium indoltheticum, Flavobacterium meningosepticum, and Flavobacterium scophthalmum are included in a new genus, Chryseobacterium, with Chryseobacterium gleum as the type species. The generically misclassified organism Flavobacterium breve is included in the revived genus Empedobacter as Empedobacter brevis, whereas the generically misclassified organism Weeksella zoohelcum is included in the new genus Bergeyella as Bergeyella zoohelcum.
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Comparative Analysis of the 16S rRNA Gene Sequence of the Putative Agent of Proliferative Ileitis of Hamsters
More LessAbstractProliferative ileitis of hamsters is consistently associated with the presence of intracellular bacteria in affected ileal epithelial cells. The 16S rRNA gene sequence of the putative etiologic agent of proliferative ileitis was determined by using cell culture-maintained organisms. The highest level of relatedness (98.4%) was observed with a newly described obligately intracellular bacterium obtained from porcine intestines, and the level of homology with Desulfovibrio desulfuricans was 87.5%.
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Comparison of 16S rRNA Genes within the T960 and Parvo Biovars of Ureaplasmas Isolated from Humans
More LessTwo-by-two sequence alignment revealed that the levels of homology between 16S rRNA gene sequences of strains belonging to the two biovars of Ureaplasma urealyticum (class Mollicutes) ranged from 98.5 to 98.9%. Within the biovars, three serovars of the T960 biovar exhibited levels of homology of ≥99.7%, and the four serovars of the parvo biovar exhibited levels of homology of ≥99.7%. A dendrogram of the Mycoplasma pneumoniae-Ureaplasma clade of the Mollicutes reflected the distinctiveness of the biovars.
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Proposal of Minimal Standards for Describing New Species of the Family Campylobacteraceae †
More LessThe International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria has agreed in principle on minimum requirements for the description of new species of the family Campylobacteraceae. These requirements, as well as methods for determining specific characteristics, are proposed as minimal standards for the description of new species. In addition to specified phenotypic characteristics, molecular data are required. The placement of a new species should be consistent with the current view on classification usually based on methods such as nucleic acid sequencing, hybridization, or protein fingerprinting.
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- Original Papers Relating To The Systematics Of Yeasts
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Candida caseinolytica sp. nov., a New Species of Yeast Occurring in Necrotic Tissue of Opuntia and Stenocereus Species in the Southwestern United States and Baja California, Mexico
More LessAbstractWe describe Candida caseinolytica, a new yeast species which occurs in rotting tissues of opuntias and other cacti in the North American Sonoran Desert and a few other localities. This small-celled, slowly growing yeast does not ferment any sugar and assimilates a limited number of carbon compounds, including 2- and 5-ketogluconic acids. It exhibits strong extracellular proteolytic activity on casein at pH 6.5, but gelatin is not hydrolyzed or is only weakly hydrolyzed by a few strains. The type strain of C. caseinolytica is strain UCD-FST 83-438.3 (= ATCC 90546 = CBS 7781).
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Molecular Characterization and Application of Random Amplified Polymorphic DNA Analysis of Mrakia and Sterigmatomyces Species
AbstractThe qualitative and quantitative monosaccharide spectra of purified yeast cell walls revealed that there are three phylogenetically distinct lineages of sterigma-forming basidiomycetous yeasts: (i) Kurtzmanomyces and Sterigmatomyces species, which contain high levels of mannose; (ii) Tilletiopsis species, which contain glucose, galactose, and small amounts of mannose; and (iii) Fellomyces, Kockovaella, Sterigmatosporidium, and Tsuchiyaea species, which appear to be closely related on the basis of their high levels of glucose and the presence of xylose. The yeast cell wall neutral sugars of Sporobolomyces antarcticus and Sterigmatomyces aphidis were similar to those of members of the genus Tilletiopsis. However, the possibility that these taxa are conspecific was eliminated by the results of a random amplified polymorphic DNA (RAPD) analysis. The conspecificity of Mrakia frigida and Mrakia nivalis, the conspecificity of Mrakia gelida and Mrakia stokesii, and the conspecificity of Sterigmatomyces halophilus and Sterigmatomyces indicus were confirmed by RAPD analysis results. RAPD analysis was found to be a simple and highly sensitive method which can be used to differentiate species at the DNA level; it can replace nuclear DNA-nuclear DNA hybridization experiments for species identification, characterization, and delimitation.
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Rapid Characterization of Four Species of the Saccharomyces Sensu Stricto Complex According to Mitochondrial DNA Patterns
More LessAbstractSeveral strains of the four sibling species of the genus Saccharomyces (S. bayanus, S. cerevisiae, S. paradoxus, and S. pastorianus) were characterized by using a rapid and simple method of restriction analysis of mitochondrial DNA. Patterns obtained with four-cutter endonucleases (such as AluI, DdeI, HinfI, and RsaI) made it possible to differentiate each species. 5. cerevisiae and S. paradoxus presented a greater number of large fragments than S. pastorianus and S. bayanus with all the assay enzymes. With AluI and DdeI, species-specific bands clearly permitted differentiation between S. pastorianus and S. bayanus. To test the resolution of this method, wild Saccharomyces strains were analyzed. The correct assignment of these strains to a known taxon by this rapid method was confirmed by means of electrophoretic karyotyping.
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Phylogeny of the Yeast Genera Hanseniaspora (Anamorph Kloeckera), Dekkera (Anamorph Brettanomyces), and Eeniella as Inferred from Partial 26S Ribosomal DNA Nucleotide Sequences
More LessAbstractPartial 26S ribosomal DNA sequences of species assigned to the genera Hanseniaspora, Kloeckera, Dekkera, Brettanomyces, and Eeniella were determined. A phylogenetic analysis of the sequences showed that the genus Eeniella is derived within the genus Brettanomyces and that the genus Hanseniaspora (anamorph Kloeckera) is not closely related to the genus Dekkera (anamorph Brettanomyces). As a consequence, the name Eeniella is reduced to synonymy with the name Brettanomyces. In addition, our data do not support reassignment of certain Hanseniaspora species to the recently revived genus Kloeckeraspora.
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Electrophoretic Karyotypes of Authentic Strains of the Sensu Stricto Group of the Genus Saccharomyces †
More LessAbstractA comparative electrophoretic karyotyping study was performed with several certified authentic strains of the four species that could be distinguished by nuclear DNA (nDNA)-nDNA reassociation data within the sensu stricto group of the genus Saccharomyces. A multivariate analysis of the polymorphisms observed in pulsed-fleld gel electrophoretic profiles (numbers and molecular weights of separated units) revealed that the strains could be separated into four clusters that corresponded to the taxa that were distinguished on the basis of nDNA comparisons. Discrepancies between nDNA reassociation data and membership in the corresponding clusters were observed only with two strains of Saccharomyces paradoxus. Blind tests carried out with additional industrial strains confirmed the general validity of the statistical model created for comparison of karyotypes within the species included in Saccharomyces sensu stricto.
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Synonymy of Candida methylica with Candida boidinii and of Candida methanolophaga with Candida succiphila
More LessSome Candida species which can use methanol as a sole carbon source were studied by performing chemotaxonomic tests; we determined the ubiquinone systems of these organisms, their DNA base compositions, their electrophoretic karyotypes, and their DNA relatedness values. The type strains of Candida methanolophaga and Candida succiphila had similar DNA base compositions and exhibited 90% DNA relatedness. All Candida boidinii and Candida methylica strains had DNA G+C contents of 30.8 to 31.0 mol%, and these organisms exhibited 87 to 101% DNA relatedness to the type strain of C. boidinii. We propose that C. methanolophaga and C. methylica should be synonyms of C. succiphila and C. boidinii, respectively.
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- Matters Relating To The International Committee On Systematic Bacteriology
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Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
More LessBecause a natural entity “species” cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.
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- Errata
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