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Volume 43,
Issue 2,
1993
Volume 43, Issue 2, 1993
- Original Papers Relating To Systematic Bacteriology
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Antigenic Relationships among Bacteroides Species Studied by Rocket-Line Immunoelectrophoresis
More LessAbstractAntigenic relationships among the 10 Bacteroides species, Porphyromonas gingivalis, Prevotella bivia, and Prevotella intermedia were investigated by rocket-line Immunoelectrophoresis, using antigenic extracts prepared from type strains and antisera to Bacteroides fragilis, Bacteroides distasonis, Bacteroides thetaiotaomicron, Porphyromonas gingivalis, and Prevotella intermedia. Among the members of the genus Bacteroides, B. fragilis, Bacteroides caccae, Bacteroides stercoris, Bacteroides vulgatus, B. thetaiotaomicron, and Bacteroides ovatus were found to be closely related, and B. distasonis and Bacteroides merdae were the species that were most distantly related to B. fragilis; Bacteroides eggerthii and Bacteroides uniformis were in an intermediate position. Porphyromonas gingivalis, Prevotella bivia, and Prevotella intermedia shared very low percentages of common antigens with the Bacteroides species. Detection of enzymic activities in immunoprecipitates allowed us to identify some antigens to enzymes and to study the immunological similarities of the enzymes. The malate dehydrogenases of the Bacteroides species were genus specific, and the gIucose-6-phosphate dehydrogenases of most species exhibited antigenic similarities. The esterases of B. distasonis and B. thetaiotaomicron appeared to be species specific, whereas the esterases and phosphatases of B. fragilis cross-reacted with the esterases and phosphatases of B. stercoris and B. vulgatus, as did the phosphatases of B. distasonis and B. merdae. The phosphatases of B. eggerthii, B. uniformis, Porphyromonas gingivalis, and Prevotella intermedia were antigenically similar.
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Treponema denticola (ex Brumpt 1925) sp. nov., nom. rev., and Identification of New Spirochete Isolates from Periodontal Pockets
More LessAbstractStandard growth and isolation methods were used to obtain five new treponema strains in pure culture from deep periodontal pockets. The strains were identified to the species level by various methods, including agglutination, immunofluorescence, a dot blot immunoassay, electron microscopy, gas-liquid chromatography of metabolic volatile fatty acids, and DNA hybridization. Two isolates were strains of Treponema socranskii; the other three were strains of “Treponema denticola” a species described in 1925 by Brumpt. Because no type strain was designated for this species previously, the name was not included on the Approved Lists of Bacterial Names and has no current nomenclatural standing. We propose that Treponema denticola (ex Brumpt) sp. nov., nom. rev. is a valid and distinct species of the genus Treponema and designate strain ATCC 35405 as the type strain and strains ATCC 33520 and ATCC 35404 as reference strains. T. denticola appears to be the species that is most frequently isolated from periodontal pockets. Unless new isolation and cultivation techniques are introduced, it appears that present technology can yield only isolates belonging to the currently described oral anaerobic spirochete species and that there is little chance of isolating the larger treponemes.
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Mycobacterium intermedium sp. nov.
More LessAbstractStrains of a new type of slowly growing mycobacterium were repeatedly isolated from sputum from a patient with pulmonary disease. This photochromogenic organism grew at 22, 31, 37, and 41°C, possessed catalase, acid phosphatase, esterase, β-galactosidase, and arylsulfatase activities, and hydrolyzed Tween. It did not produce nicotinic acid or have nitrate reductase, acetamidase, benzamidase, isonicotinamidase, nicotinamidase, pyrazinamidase, succinidamidase, and acid phosphatase activities. Urease activity was variable. The organism is susceptible to ethambutol and resistant to isoniazid and streptomycin. A mycolic acid analysis revealed the presence of α-mycolates, α′-mycolates, and keto-mycolates. The results of comparative 16S rRNA sequencing placed this organism at an intermediate position between the rapidly and slowly growing mycobacteria. On the basis of the pattern of enzymatic activities and metabolic properties, the results of fatty acid analyses, and the unique 16S rRNA sequence, we propose that this organism represents a new species, for which we propose the name Mycobacterium intermedium. The type strain is strain 1669/91; a culture of this strain has been deposited in the Deutsche Sammlung von Mikroorganismen und Zellkulturen as strain DSM 44049.
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Relatedness of Three Species of “False Neisseriae,” Neisseria caviae, Neisseria cuniculi, and Neisseria ovis, by DNA-DNA Hybridizations and Fatty Acid Analysis
More LessAbstractDNA-DNA hybridization was used to determine the levels of genomic relatedness of the three species of “false neisseriae,” Neisseria caviae, Neisseria cuniculi, and Neisseria ovis. The reference strains of these species exhibited high levels of intraspecies relatedness (93 to 100% for N. caviae, 79 to 100% for N. cuniculi, and 68 to 100% for N. ovis) but low levels of interspecific relatedness (less than 34%) to each other and to various species belonging to the β subclass of the Proteobacteria (Kingella kingae, Neisseria gonorrhoeae, Neisseria meningitidis, and Oligella urethralis) or to the y subclass (Branhamella catarrhalis, Kingella indologenes, Moraxella atlantae, Moraxella bovis, Moraxella lacunata subsp. lacunata, Moraxella lacunata subsp. liquefaciens, Moraxella nonliquefaciens, Moraxella osloensis, and Moraxella phenylpyruvica). However, the levels of DNA-DNA hybridization for the three species of “false neisseriae” were significantly higher with the species belonging to the γ subclass (average, 13.7%) than with the species belonging to the β subclass (average, 4.5%). These data suggest that N. caviae, N. cuniculi, and N. ovis are three separate genomic species in the γ subclass. An ascendant hierarchical classification based only on fatty acid profiles distinguished four main classes containing (i) most of the “classical moraxellae,” the “false neisseriae,” and B. catarrhalis, (ii) only Acinetobacter spp., (iii) M. nonliquefaciens and “misnamed moraxellae” (M. atlantae, M. osloensis, and M. phenylpyruvica), and (iv) the “true neisseriae,” the three Kingella species, and O. urethralis. Fatty acids that distinguish these four classes were identified. The fatty acid profiles of the two strains of Psychrobacter immobilis which we studied are not very similar to the profiles of the other taxa. Our results support the hypothesis that the three species of “false neisseriae,” B. catarrhalis, the “classical moraxellae,” and Acinetobacter spp. should be included in the same family.
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Characterization of Bacillus brevis with Descriptions of Bacillus migulanus sp. nov., Bacillus choshinensis sp. nov., Bacillus parabrevis sp. nov., and Bacillus galactophilus sp. nov.
More LessAbstractThirty-five Bacillus brevis strains obtained from culture collections, including protein-producing isolates, were taxonomically studied by using numerical analysis, DNA base composition, and DNA-DNA hybridization. Six DNA relatedness groups were represented, and these groups correlated well with clusters based on the numerical analysis. The B. brevis strains were separated into B. brevis sensu stricto, four new species, and an unidentified species of the genus Bacillus. Bacillus migulanus sp. nov., Bacillus choshinensis sp. nov., Bacillus parabrevis sp. nov., and Bacillus galactophilus sp. nov. are proposed.
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Clostridium ljungdahlii sp. nov., an Acetogenic Species in Clostridial rRNA Homology Group I
More LessAbstractClostridium ljungdahlii sp. nov. strain ATCC 49587T (T = type strain) was isolated from chicken yard waste for its ability to produce ethanol from synthesis gas. This gram-positive, motile, sporeforming rod’s metabolism was primarily acetogenic. C. ljungdahlii grew with carbon monoxide, hydrogen and carbon dioxide, ethanol, pyruvate, arabinose, xylose, fructose, or glucose. Methanol, ferulic acid, lactate, galactose, and mannose did not support growth. The G+C content was 22 to 23 moI%. C. ljungdahlii is the first acetogen in clostridial 23S rRNA homology group I.
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Staphylococcus pasteuri sp. nov., Isolated from Human, Animal, and Food Specimens
More LessAbstractA new novobiocin-susceptible species of the genus Staphylococcus, Staphylococcus pasteuri, is described on the basis of the results of a study of seven strains isolated from human, animal, and food specimens. DNA relatedness experiments (S1 nuclease method) showed that these strains form a homogeneous genomic species related at DNA homology levels of 2 to 13% to 27 type strains representing known Staphylococcus species. The use of a method based on rRNA gene restriction site polymorphism provides clear-cut distinction between this new species and Staphylococcus wameri, which is the most similar species phenotypically. The type strain of the new species is strain BM9357 (= ATCC 51129).
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Comparative Study of “Micrococcus sp.” Strains CCM 168 and CCM 1405 and Members of the Genus Salinicoccus
More LessAbstractTwo culture collection strains, CCM 168 and CCM 1405, previously assigned to the genus Micrococcus were shown by molecular chemical characterization to belong to the genus Salinicoccus. A more detailed comparison of the physiological and biochemical properties of these strains and comparison with the type strain of Salinicoccus roseus indicated high degrees of relatedness among the three strains. DNA-DNA hybridization studies confirmed the high degrees of relatedness. All of the data demonstrate quite clearly that strains CCM 168 and CCM 1405 are members of the species S. roseus.
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DNA Relatedness between Xenorhabdus spp. (Enterobacteriaceae), Symbiotic Bacteria of Entomopathogenic Nematodes, and a Proposal To Transfer Xenorhabdus luminescens to a New Genus, Photorhabdus gen. nov.
More LessAbstractThe levels of DNA relatedness for a broad sample of Xenorhabdus strains isolated from different species of entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) and from different geographical sources were estimated by the hydroxyapatite method. The level of DNA-DNA relatedness for the two phases of each isolate tested was not significantly different from 100%, demonstrating unequivocally that the phase variation demonstrated by all Xenorhabdus spp. is not due to contamination. The isolates of the described Xenorhabdus species coalesced into different DNA relatedness groups, confirming that Xenorhabdus nematophilus, Xenorhabdus bovienii, Xenorhabdus poinarii, and Xenorhabdus beddingii, defined on the basis of phenotypic differences, are valid species. The symbiont of Steinemema intermedia also coalesced with the X. bovienii isolates. This was the only symbiont of seven recently described and unamed Steinemema spp. (including Steinemema ritteri, Steinemema rara, and Steinemema anomali) that formed a group with any of the previously described Xenorhabdus species; new species descriptions are required to accommodate the other taxa, but too few isolates were available to allow satisfactory descriptions of them. The DNA relatedness data also showed that the bacteria currently classified as Xenorhabdus luminescens are significantly different from all other Xenorhabdus strains. These data strongly support indications from previous studies of phenotypic characteristics, cellular fatty acids, and DNA relatedness that X. luminescens should be classified as a separate genus. A new genus, Photorhabdus, with an amended description of the type species, Photorhabdus luminescens, is proposed.
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Spiroplasma monobiae sp. nov. from the Vespid Wasp Monobia quadridens (Hymenoptera: Vespidae)
AbstractSpiroplasma strain MQ-1T (T = type strain) from the hemolymph of the vespid wasp Monobia quadridens differed serologically from other spiroplasma species, groups, and subgroups. Cells of strain MQ-1T were helical and motile and possessed a single cytoplasmic membrane, with no evidence of a cell wall. The organism grew in conventional mycoplasma medium, in serum fraction, SM-1, MID, and SP-4 liquid media, and on SP-4 solid medium in either aerobic or anaerobic environments. The optimum temperature for growth was 32°C, but multiplication occurred over a wide temperature range (10 to 37°C). The doubling time at 32°C in MID medium was 1.9 h. Strain MQ-1T catabolized glucose but hydrolyzed neither arginine nor urea. Previous work showed that strain MQ-1T has a unique methylase, previously known only in eucaryotes. Also, strain MQ-1T induces production of tumor necrosis factor in bone marrow macrophages. The guanine-plus-cytosine content of the DNA was 28 ± 1 moI%. The genome size of strain MQ-1T was 940 kb (627 MDa); a similar strain, MQ-8, had a genome size of 985 kb (657 MDa). Strain MQ-1T and its allies have the smallest genomes known in the genus Spiroplasma. Strain MQ-1 (= ATCC 33825) is designated the type strain of a new species, Spiroplasma monobiae.
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Spiroplasma clarkii sp. nov. from the Green June Beetle (Coleoptera: Scarabaeidae)
AbstractSpiroplasma strain CN-51 (T = type strain), isolated from the gut of the cetoniine scarabaeid beetle Cotinus nitida, was serologically distinct from other spiroplasma species, groups, and subgroups. Cells of strain CN-5T were shown by light microscopy to be helical, motile filaments. Cells in early passages exhibited strong translational motility that tended to be lost in later passages. Electron microscopy showed that the cells were bounded by a single cytoplasmic membrane with no evidence of a cell wall. The organism was not susceptible to penicillin. Strain CN-5T grew well in SM-1, MID, and SP-4 liquid media and on solid SP-4 medium under aerobic or anaerobic conditions. The doubling time at 30°C, the optimum temperature, was 4.3 h. The strain also grew in 1% serum fraction medium. Strain CN-5T produced acid from glucose and catabolized arginine, but did not hydrolyze urea. The guanine-plus-cytosine content of the DNA was 29 ± 1 mol%. The genome size was 1,770 kb (1,186 MDa). Other uncloned isolates obtained from C. nitida or the cetoniine hermit flower beetle Osmoderma eremicola exhibited similar or identical serological patterns. Since no other hosts were discovered in extensive studies, strain CN-5T (previously designated group IX) appears to represent a cluster of relatively host-specific cetoniine beetle-associated strains. Strain CN-5 (= ATCC 33827) is designated the type strain of a new species, Spiroplasma clarkii.
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A New Actinomycete Species, Nocardiopsis lucentensis sp. nov.
More LessAbstractA new species of the genus Nocardiopsis, for which we propose the name Nocardiopsis lucentensis sp. nov. (type strain, strain DSM 44048), was isolated from a salt marsh soil sample near Alicante, Spain. Whole-cell hydrolysates contain the meso isomer of diaminopimelic acid and no characteristic sugar; thus, the cell wall composition is type III. Menaquinone MK-10(H8) is the major menaquinone, and the phospholipid type is type PHI (phosphatidylcholine present). Spore chains are rectiflexibilis, and in the early stages of sporulation zig-zag-shaped aerial hyphae are observed. This microorganism produces compatible solutes of the ectoine type and is characterized by a yellowish to yellowish brown substrate mycelium and a white aerial mycelium. This organism exhibits only 40 to 50% DNA relatedness to other Nocardiopsis spp.
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Spiroplasma insolitum sp. nov., a New Species of Group I Spiroplasma with an Unusual DNA Base Composition
Spiroplasma strain M55, isolated from a fall flower in Maryland, showed patterns of partial serological cross-reactivity with the other seven group I spiroplasma subgroups but was not serologically related to other spiroplasma groups. Strain M55 had less than 70% DNA-DNA homology with group I subgroups previously assigned binomial names and was unique among the group I subgroups in possessing a higher guanine-plus-cytosine content in its DNA (28 ± 1 mol%, versus 26 ± 1 mol% for other group I subgroups). The genome size was 1,850 kb (1,233 MDa). Extensive data on the metabolism of strain M55 and the community ecology of this and similar strains have been reported. These circumstances fulfill criteria proposed by the Subcommittee on the Taxonomy of Mollicutes for elevation of mollicute subgroups to species status. Accordingly, strain M55 was characterized according to proposed minimal standards for species descriptions. Cells of strain M55 were shown by light microscopy to be helical, motile filaments. Electron microscopy showed that the cells possessed no cell wall and were bounded by a single membrane; they were insensitive to penicillin (1,000 U/ml). Strain M55 was culturable in M1D and SP-4 liquid media under aerobic (with or without enhanced carbon dioxide) or anaerobic environments. Optimal growth occurred at 30°C, with a doubling time of 7.2h. Growth occurred from 15 to 37°C but not at 10 or 42°C. Strain M55 did not utilize urea or hydrolyze arginine but did produce acid from glucose. As a consequence of these studies, strain M55 is designated the type strain (M55T; ATCC 33502T) of a new species, Spiroplasma insolitum.
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Assignment of Fatty Acid-ß-Oxidizing Syntrophic Bacteria to Syntrophomonadaceae fam. nov. on the Basis of 16S rRNA Sequence Analyses
More LessAfter enrichment from Chinese rural anaerobic digestor sludge, anaerobic, sporing and nonsporing, saturated fatty acid-ß-oxidizing syntrophic bacteria were isolated as cocultures with H2- and formate-utilizing Methanospirillum hungatei or Desulfovibrio sp. strain G-11. The syntrophs degraded C4 to C8 saturated fatty acids, including isobutyrate and 2-methylbutyrate. They were adapted to grow on crotonate and were isolated as pure cultures. The crotonate-grown pure cultures alone did not grow on butyrate in either the presence or the absence of some common electron acceptors. However, when they were reconstituted with M. hungatei, growth on butyrate again occurred. In contrast, crotonate-grown Clostridium kluyveri and Clostridium sticklandii, as well as Clostridium sporogenes, failed to grow on butyrate when these organisms were cocultured with M. hungatei. The crotonate-grown pure subcultures of the syntrophs described above were subjected to 16S rRNA sequence analysis. Several previously documented fatty acid-ß-oxidizing syntrophs grown in pure cultures with crotonate were also subjected to comparative sequence analyses. The sequence analyses revealed that the new sporing and nonsporing isolates and other syntrophs that we sequenced, which had either gram-negative or gram-positive cell wall ultrastructure, all belonged to the phylogenetically gram-positive phylum. They were not closely related to any of the previously known subdivisions in the gram-positive phylum with which they were compared, but were closely related to each other, forming a new subdivision in the phylum. We recommend that this group be designated Syntrophomonadaceae fam. nov.; a description is given.
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Taxonomic Study of Corynebacterium Group ANF-1 Strains: Proposal of Corynebacterium afermentans sp. nov. Containing the Subspecies C. afermentans subsp. afermentans subsp. nov. and C. afermentans subsp. lipophilum subsp. nov.
More LessWe have determined the cell wall composition, guanine-plus-cytosine (G+C) contents of the DNA, rRNA gene restriction patterns, and the levels of DNA-DNA relatedness of 11 strains identified biochemically as Centers for Disease Control (CDC) Corynebacterium group absolute nonfermenter 1 (Corynebacterium group ANF-1). For seven of these strains, growth is abundant on 5% sheep blood agar, which differentiates them from the four other strains, whose growth requires a lipid supplement such as Tween 80. Two of the lipid-requiring strains produced mucoid colonies on 1% Tween 80-supplemented sheep blood agar. All strains possess cell wall component type IV, short-chain mycolic acids, and G+C contents of DNA of 66 to 68 mol% as determined by reverse-phase high-performance liquid chromatography. DNA-relatedness experiments by an S1 nuclease procedure showed that nine of these strains, including two of the lipid-requiring strains, constitute a new genomic species less than 40% related to Corynebacterium species and other coryneform groups. The lipid-requiring strain T18502 exhibited 98% DNA relatedness with another lipid-requiring strain, T88593 (difference in thermal denaturation midpoint [?Tm ] = 2°C) and 71 to 77% similarity with the nonlipophilic strains (?Tm range of from 2 to 5°C). Conversely, the DNA relatedness between strain LCDC 88199 and the six other nonlipophilic strains ranged from 86 to 100% (?Tm range of from 1 to 3°C) and was only 73 and 76% with the lipophilic strains T18502 and T88593, respectively (?Tm , 3 and 4°C). These results indicated that these two cultural types of bacteria constitute two subspecies within the new genomic species. These subspecies can be identified within the genus Corynebacterium by their phenotypic characteristics and rRNA gene restriction patterns by PvuII and EcoRI endonuclease digestion. The two mucoid strains were not related to other Corynebacterium group ANF-1 strains or Corynebacterium species reference strains. Further studies should allow the determination of the taxonomic status of these mucoid strains. Therefore, we propose a new species, Corynebacterium afermentans sp. nov., which contains two subspecies: C. afermentans subsp. afermentans subsp. nov. (type strain, LCDC 88199 = CIP 103499) for nonlipophilic Corynebacterium group ANF-1 strains and C. afermentans subsp. lipophilum subsp. nov. (type strain, T18502 = CIP 103500) for two lipid-requiring Corynebacterium group ANF-1 strains.
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Proposal of Quinella ovalis gen. nov., sp. nov., Based on Phylogenetic Analysis
More LessQuin's oval is a relatively large bacterium often seen in the rumens of sheep fed diets containing some readily fermented carbohydrates. It has not been obtained in axenic cultures, but a number of its features have been determined by various methods, such as studying cell suspensions purified from rumen fluid by differential centrifugation. We obtained similarly purified suspensions from a sheep fed a diet containing a large amount of molasses. Nearly complete 16S rRNA sequence analysis of these cells as well as cells of Selenomonas ruminantium subsp. ruminantium GA192 (ATCC 12561; type strain) and S. ruminantium subsp. lactilytica HD4 (ATCC 27209) was done. These sequences were compared with those of other bacteria. Evolutionary distance estimates indicated that Quin's oval was most closely related to the Selenomonas-Megasphaera-Sporomusa group in the gram-positive phylum but that it belongs in a new genus. We propose the name Quinella ovalis gen. nov., sp. nov., with its description based on previously known features.
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Kibdelosporangium albatum sp. nov., Producer of the Antiviral Antibiotics Cycloviracins
More LessA new species of the genus Kibdelosporangium is described. This soil organism forms long straight spore chains and numerous sporangiumlike structures on the aerial mycelium. The new species has type IV cell walls and pattern A whole-cell sugars (meso-diaminopimelic acid, arabinose, and galactose are present), type PII phospholipids, MK-9(H4) as the major menaquinone, and no mycolic acids. On the basis of morphology and chemotaxonomy, the single isolate is assigned to the genus Kibdelosporangium. The isolate differs from two previously described species of the genus in fatty acid composition, the absence of melanin formation, and many physiological and biochemical characteristics and is identified as a new species. Accordingly, the name Kibdelosporangium albatum sp. nov. is proposed for this isolate. The type strain is R761-7 (= ATCC 55061).
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Eubacterium saphenus sp. nov., Isolated from Human Periodontal Pockets
More LessA new species, Eubacterium saphenus sp. nov., established on the basis of the results of DNA-DNA hybridization, was proposed for strains isolated from human periodontal pockets. Differential characteristics are given.
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Phylogenetic Analysis of Rhizobia and Agrobacteria Based on 16S rRNA Gene Sequences
More LessAbstractThe phylogenetic relationships of members of the genera Rhizobium, Agrobacterium, Bradyrhizobium, and Azorhizobium were studied by direct sequencing of their amplified 16S rRNA genes. Comparative analysis of the sequence data confirmed that the genera Bradyrhizobium and Azorhizobium belong to distinct phylogenetic lineages. The genera Rhizobium and Agrobacterium were found to be phylogenetically heterogeneous, and several subgroupings in which Rhizobium and Agrobacterium species were intermixed were evident. The present findings show that the genus and species definitions of these organisms are in need of revision. Different possibilities for this are discussed in the light of sequencing data.
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Assignment of the Agent of Tyzzer's Disease to Clostridium piliforme comb. nov. on the Basis of 16S rRNA Sequence Analysis
More LessThe small-subunit rRNA (16S rRNA) sequence of Tyzzer's bacillus (also known as “Bacillus piliformis”) was elucidated by using the polymerase chain reaction followed by reverse transcriptase sequencing. By using maximum-likelihood analysis, a phylogenetic tree was constructed from this and other 16S rRNA sequences available from the first release of the Ribosomal Database Project (G. J. Olsen, R. Overbeek, N. Larsen, T. L. Marsh, M. J. McCaughey, M. A. Maciukenas, W.-M. Kuan, T. J. Macke, Y. Xing, and C. R. Woese, Nucleic Acids Res. 20:2199-2200, 1992). Tyzzer's bacillus grouped with a specific set of anaerobic bacteria, most of which are Clostridium spp. The closest identified relatives are Clostridium coccoides, Clostridium oroticum, Clostridium clostridiiforme, Clostridium symbiosum, and Streptococcus hansenii. Clostridium amino-valericum and “Acetitomaculum ruminis” are also solidly allied with this ensemble. We propose that Tyzzer's bacillus be reclassified as Clostridium piliforme on the basis of its 16S rRNA sequence.
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