- Volume 54, Issue 2, 2004
Volume 54, Issue 2, 2004
- Validation List No. 96
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 53, part 6, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Archaea
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Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney
More LessA novel hyperthermophilic archaeon, designated strain SY1T, was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. The cells were irregular cocci (1·2 to 2·1 μm in diameter), occurring singly or in pairs, and stained Gram-negative. Growth was observed between 70 and 97 °C (optimum, 85 °C; 220 min doubling time), pH 6·5 and 8·8 (optimum, pH 8·0), and salinity of 2·2 and 5·3 % (optimum, 3·5 %). It was a strictly aerobic heterotroph capable of growing on complex proteinaceous substrates such as yeast extract and tryptone. The G+C content of the genomic DNA was 54·4 mol%. Phylogenetic analysis based on the 16S rDNA sequence of the isolate indicated that the isolate was closely related to Aeropyrum pernix strain K1T. However, no significant genetic relatedness was observed between them by DNA–DNA hybridization. On the basis of the molecular and physiological traits of the new isolate, the name Aeropyrum camini sp. nov. is proposed, with the type strain SY1T (=JCM 12091T=ATCC BAA-758T).
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Taxonomic study of Halorubrum distributum and proposal of Halorubrum terrestre sp. nov.
More LessHalorubrum distributum (basonym, Halobacterium distributum) is an extremely halophilic, aerobic archaeon isolated from saline soils, which was described on the basis of phenotypic features of several strains. The designated type strain of the species (1mT=VKM B-1733T=JCM 9100T) was shown recently to differ from the other strains. In this study, Halorubrum distributum isolates have been characterized with regard to phenotypic features, polar lipid content, comparison of 16S rRNA gene sequences and DNA–DNA hybridization. On the basis of these data, a novel species that includes the other isolates is proposed, with the name Halorubrum terrestre sp. nov. The type strain of this novel species is 4pT (=VKM B-1739T=JCM 10247T). The DNA G+C content of this novel species is 64·2–64·9 mol% (64·4 mol% for the type strain).
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- Other Bacteria
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Classification of phytoplasma strains in the elm yellows group (16SrV) and proposal of ‘Candidatus Phytoplasma ulmi’ for the phytoplasma associated with elm yellows
More LessElm yellows group (16SrV) phytoplasmas, which are associated with devastating diseases in elm, grapevine, blackberry, cherry, peach and several other plant species in America, Europe and Asia, represent one of the most diverse phytoplasma clusters. On the basis of phylogenetic analysis of 16S rDNA sequences, elm yellows group phytoplasmas form a discrete subclade within the phytoplasma clade. Three phylogenetic parameters, namely 16S rRNA, ribosomal protein and secY genes, have been evaluated for their usefulness in differentiating elm yellows group phytoplasmas. RFLP analysis of 16S rRNA sequences differentiated the elm yellows group phytoplasmas into five subgroups. Twelve RFLP subgroups were differentiated on the basis of ribosomal protein and 13 were differentiated using secY gene sequences. Phylogenetic analysis of the ribosomal protein genes and secY gene alone or in combination indicated that the subgroups constitute 12 genetically distinct lineages, each of which appears to have evolved under different ecological constraints such as specific vector or plant hosts. On the basis of unique DNA and biological properties, it is proposed that the elm yellows phytoplasma EY1T represents a novel taxon, ‘Candidatus Phytoplasma ulmi’.
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Mycoplasma ovis comb. nov. (formerly Eperythrozoon ovis), an epierythrocytic agent of haemolytic anaemia in sheep and goats
More LessEperythrozoon ovis, an erythrocytic agent that causes haemolytic anaemia in sheep and goats, occurs worldwide and is currently thought to be a rickettsia. To determine the relationship between this agent and other haemotrophic bacterial parasites, the 16S rRNA gene of this organism was sequenced. Phylogenetic analysis revealed that this wall-less bacterium is not a rickettsia, but a mycoplasma. This mycoplasma is related closely to several other uncultivated, epierythrocytic mycoplasmas that comprise a recently identified group, the haemotrophic mycoplasmas (haemoplasmas). The haemoplasma group is composed of former Eperythrozoon and Haemobartonella species, as well as newly identified epierythrocytic mycoplasmas. Haemoplasmas parasitize the surface of erythrocytes of a wide variety of vertebrate animal hosts and are transmitted mainly by blood-feeding arthropod vectors. Recognition that E. ovis is a mycoplasma provides a new approach to dealing with this bacterium. It is proposed that E. ovis should be reclassified as Mycoplasma ovis comb. nov.
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Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica
More LessA taxonomic study was performed on three strains isolated from microbial mats in Lake Fryxell, McMurdo Dry Valleys, Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the family Flavobacteriaceae, in which they form a distinct lineage. The isolates are Gram-negative, chemoheterotrophic, aerobic, rod-shaped cells. They are psychrophilic and yellow-pigmented, with DNA G+C contents in the range 37·8–38·9 mol%. Whole-cell fatty acid profiles revealed mainly branched fatty acids and 17 : 0 2-OH. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, it is proposed that the isolates represent a novel species in a new genus, Gillisia limnaea gen. nov., sp. nov. The type strain is LMG 21470T (=DSM 15749T).
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Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark
More LessA number of bacteria were isolated from sea water in Skagerrak, Denmark, at 30 m depth. Two of the isolates, strains D28 and D30T, belonged to the Flavobacteriaceae within the Cytophaga–Flavobacterium–Bacteroides group. Sequencing of 16S rRNA genes of the two strains indicated strongly that they belonged to the genus Tenacibaculum and that they showed greatest similarity to the species Tenacibaculum amylolyticum and Tenacibaculum mesophilum. DNA–DNA hybridization values, DNA base composition and phenotypic characteristics separated the Skagerrak strains from the other species within Tenacibaculum. Thus, it is concluded that the strains belong to a novel species within the genus Tenacibaculum, for which the name Tenacibaculum skagerrakense sp. nov. is proposed, with strain D30T (=ATCC BAA-458T=DSM 14836T) as the type strain.
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‘Candidatus Rhabdochlamydia porcellionis’, an intracellular bacterium from the hepatopancreas of the terrestrial isopod Porcellio scaber (Crustacea: Isopoda)
More LessIntracellular bacteria were observed in the hepatopancreas of the terrestrial isopod Porcellio scaber. Comparative 16S rRNA gene sequence analysis and electron microscopic observations were used to determine the taxonomic position of these intracellular bacteria. Phylogenetic analysis and a complex developmental cycle affiliate these bacteria to the order Chlamydiales, within which they form a distinctive lineage, close to the family Simkaniaceae. They share <92 % 16S rRNA gene sequence similarity with their closest relative and <88 % similarity with other members of the order Chlamydiales. A specific signature oligonucleotide sequence was identified and used as a probe, enabling the identification of intracellular bacteria in infected hepatopancreatic tissue. According to the distinctive morphology of their elementary bodies, which are rod-shaped rather than spherical and contain translucent oblong structures, their genomic properties and their crustacean host, the name ‘Candidatus Rhabdochlamydia porcellionis' is proposed for intracellular bacteria in the hepatopancreas of P. scaber.
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Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov.
Sixty strains of Gram-negative, anaerobic, rod-shaped bacteria from human sources initially assigned to Leptotrichia buccalis (n=58) and ‘Leptotrichia pseudobuccalis’ (n=2) have been subjected to polyphasic taxonomy. Full-length 16S rDNA sequencing, DNA–DNA hybridization, RAPD, SDS-PAGE of whole-cell proteins, cellular fatty acid analysis and enzymic/biochemical tests supported the establishment of four novel Leptotrichia species from this collection, Leptotrichia goodfellowii sp. nov. (type strain LB 57T=CCUG 32286T=CIP 107915T), Leptotrichia hofstadii sp. nov. (type strain LB 23T=CCUG 47504T=CIP 107917T), Leptotrichia shahii sp. nov. (type strain LB 37T=CCUG 47503T=CIP 107916T) and Leptotrichia wadei sp. nov. (type strain LB 16T=CCUG 47505T=CIP 107918T). Light and electron microscopy showed that the four novel species were Gram-negative, non-spore-forming and non-motile rods. L. goodfellowii produced arginine dihydrolase, β-galactosidase, N-acetyl-β-glucosaminidase, arginine arylamidase, leucine arylamidase and histidine arylamidase. L. shahii produced α-arabinosidase. L. buccalis and L. goodfellowii fermented mannose and were β-galactosidase-6-phosphate positive. L. goodfellowii, L. hofstadii and L. wadei were β-haemolytic. L. buccalis fermented raffinose. With L. buccalis, L. goodfellowii showed 3·8–5·5 % DNA–DNA relatedness, L. shahii showed 24·5–34·1 % relatedness, L. hofstadii showed 27·3–36·3 % relatedness and L. wadei showed 24·1–35·9 % relatedness. 16S rDNA sequencing demonstrated that L. hofstadii, L. shahii, L. wadei and L. goodfellowii each formed individual clusters with 97, 96, 94 and 92 % similarity, respectively, to L. buccalis.
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Cellulophaga pacifica sp. nov.
Three marine, heterotrophic, aerobic, agarolytic, pigmented and gliding bacteria were isolated in June 2000 from a sea water sample that was collected in the Gulf of Peter the Great, Sea of Japan, and analysed in a polyphasic taxonomic study. 16S rDNA sequence analysis indicated that strains KMM 3664T, KMM 3669 and KMM 3915 were members of the family Flavobacteriaceae. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic data, the isolates were classified in the genus Cellulophaga as members of a novel species, Cellulophaga pacifica sp. nov. The type strain is KMM 3664T (=JCM 11735T=LMG 21938T).
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- Proteobacteria
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Asaia krungthepensis sp. nov., an acetic acid bacterium in the α-Proteobacteria
Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60·2–60·5 mol% G+C, with a range of 0·3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA–DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q10. On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08T (=BCC 12978T=TISTR 1524T=NBRC 100057T=NRIC 0535T), which had a DNA G+C content of 60·3 mol% and was isolated from a heliconia flower (‘paksaasawan’ in Thai; Heliconia sp.) collected in Bangkok, Thailand.
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Wautersia gen. nov., a novel genus accommodating the phylogenetic lineage including Ralstonia eutropha and related species, and proposal of Ralstonia [Pseudomonas] syzygii (Roberts et al. 1990) comb. nov.
More LessComparative 16S rDNA sequence analysis indicates that two distinct sublineages, with a sequence dissimilarity of >4 % (bootstrap value, 100 %), exist within the genus Ralstonia: the Ralstonia eutropha lineage, which comprises Ralstonia basilensis, Ralstonia campinensis, R. eutropha, Ralstonia gilardii, Ralstonia metallidurans, Ralstonia oxalatica, Ralstonia paucula, Ralstonia respiraculi and Ralstonia taiwanensis; and the Ralstonia pickettii lineage, which comprises Ralstonia insidiosa, Ralstonia mannitolilytica, R. pickettii, Ralstonia solanacearum and Ralstonia syzygii comb. nov. (previously Pseudomonas syzygii). This phylogenetic discrimination is supported by phenotypic differences. Members of the R. eutropha lineage have peritrichous flagella, do not produce acids from glucose and are susceptible to colistin, in contrast to members of the R. pickettii lineage, which have one or more polar flagella, produce acid from several carbohydrates and are colistin-resistant. Members of the R. pickettii lineage are viable for up to 6 days on tryptic soy agar at 25 °C, whereas members of the R. eutropha lineage are viable for longer than 9 days. It is proposed that species of the R. eutropha lineage should be classified in a novel genus, Wautersia gen. nov. Finally, based on the literature and new DNA–DNA hybridization data, it is proposed that Pseudomonas syzygii should be renamed Ralstonia syzygii comb. nov.
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Thalassomonas ganghwensis sp. nov., isolated from tidal flat sediment
More LessA Gram-negative, aerobic, halophilic bacterium, designated strain JC2041T, was isolated from a sediment sample of getbol, the Korean tidal flat. Results of 16S rDNA sequence analyses indicated a moderate relationship to Thalassomonas viridans within the γ-Proteobacteria (94·9 % similarity). Depending on the tree-making algorithm used, the isolate either formed a monophyletic clade with T. viridans or was recovered as a sister group of a class containing the genera Thalassomonas and Colwellia. Phenotypic features of the getbol isolate were similar to those of T. viridans, but several physiological and chemotaxonomic properties, including nitrate reduction, amylase, lecithinase, Tweenase and utilization of 13 carbon sources, distinguished strain JC2041T from T. viridans. The polyphasic data presented in this study indicate that the isolate should be classified as a novel species in the genus Thalassomonas. The name Thalassomonas ganghwensis sp. nov. is therefore proposed for the getbol isolate; the type strain is JC2041T (=IMSNU 14005T=KCTC 12041T=DSM 15355T).
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Ancylobacter rudongensis sp. nov., isolated from roots of Spartina anglica
More LessA curved, ring-like bacterium, strain AS 1.1761T, isolated from the roots of Spartina anglica, was studied by a polyphasic approach. According to phylogenetic analysis, strain AS 1.1761T belongs to the genus Ancylobacter, with 99·21 % 16S rDNA sequence similarity to Ancylobacter aquaticus, the only species described so far in this genus. However, strain AS 1.1761T had no significant DNA–DNA binding with the type strain of A. aquaticus. In addition, strain AS 1.1761T differed from A. aquaticus in many phenotypic features. Based on molecular and phenotypic data, a novel species, Ancylobacter rudongensis sp. nov., is proposed. The type strain is AS 1.1761T (=JCM 11671T).
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Characterization of the marine propionate-degrading, sulfate-reducing bacterium Desulfofaba fastidiosa sp. nov. and reclassification of Desulfomusa hansenii as Desulfofaba hansenii comb. nov.
More LessA rod-shaped, slightly curved sulfate reducer, designated strain P2T, was isolated from the sulfate–methane transition zone of a marine sediment. Cells were motile by means of a single polar flagellum. The strain reduced sulfate, thiosulfate and sulfite to sulfide and used propionate, lactate and 1-propanol as electron donors. Strain P2T also grew by fermentation of lactate. Propionate was oxidized incompletely to acetate and CO2. The DNA G+C content was 48·8mol%. Sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P2T was related to the genera Desulfonema, Desulfococcus, Desulfosarcina, ‘Desulfobotulus’, Desulfofaba, Desulfomusa and Desulfofrigus. These genera include incomplete as well as complete oxidizers of substrates. Strain P2T shared important morphological and physiological traits with Desulfofaba gelida and Desulfomusa hansenii, including the ability to oxidize propionate incompletely to acetate. The 16S rRNA gene similarities of P2T to Desulfofaba gelida and Desulfomusa hansenii were respectively 92·9 and 91·5%. Combining phenotypic and genotypic traits, we propose strain P2T to be a member of the genus Desulfofaba. The name Desulfofaba fastidiosa sp. nov. (type strain P2T=DSM 15249T=ATCC BAA-815T) is proposed, reflecting the limited number of substrates consumed by the strain. In addition, the reclassification of Desulfomusa hansenii as a member of the genus Desulfofaba, Desulfofaba hansenii comb. nov., is proposed. A common line of descent and a number of shared phenotypic traits support this reclassification.
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Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina)
On the basis of data from phenotypic and genotypic characterization and analysis of 16S rRNA gene sequences, two novel species belonging to the genus Sulfitobacter are described. Strains KMM 3584T, a pale-yellowish, non-motile strain isolated from a starfish (Stellaster equestris), and KMM 3554T, which is motile by means of a single subpolar flagellum and was isolated from sea grass (Zostera marina), are marine, Gram-negative, aerobic, rod-shaped organisms. Both strains have the ability to degrade gelatin, but not casein, chitin, agar, DNA, Tween 80 or starch. Strain KMM 3584T decomposed alginate and grew at NaCl concentrations of 1–8 % and temperatures of 12–37°C, whereas strain KMM 3554T grew in 1–12% NaCl and at temperatures of 10–30°C. The predominant fatty acid was 18:1ω7, amounting to up to 80% of the total fatty acids. The other characteristic feature was the presence of 18:2 isomers. The DNA G+C contents of KMM 3584T and KMM 3554T were respectively 60·0 and 63·7 mol%. The level of DNA similarity between the two strains was 33%. DNA from KMM 3584T and KMM 3554T had hybridization values of 5–24% and 10–41%, respectively, with DNA from the type strains of Sulfitobacter pontiacus, Sulfitobacter brevis, Sulfitobacter mediterraneus and Staleya guttiformis. It is proposed that strains KMM 3584T (=LMG 20554T=ATCC BAA-321T) and KMM 3554T (=LMG 20555T=ATCC BAA-320T) represent two novel species, Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively.
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Aeromonas simiae sp. nov., isolated from monkey faeces
Two Aeromonas strains, IBS S6874T and IBS S6652, were isolated from the faeces of two healthy monkeys (Macaca fascicularis) from Mauritius that were kept in quarantine in the Centre for Primatology, Strasbourg, France. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates formed an unknown genetic lineage within the genus Aeromonas. The two isolates had nearly identical sequences (0·1 % nucleotide substitution) that were related closely to those of recognized Aeromonas species (1·7–3·5 % nucleotide substitution). DNA–DNA hybridization showed that strains IBS S6874T and IBS S6652 had high DNA–DNA similarity (89 %) to each other and a low level of DNA–DNA similarity to closely related taxa (18 % relatedness to Aeromonas trota and 16 % relatedness to Aeromonas schubertii). Phenotypically, the two monkey isolates differed from most previously described mesophilic Aeromonas species by their lack of haemolysis on sheep-blood agar and inability to produce indole, gas from glucose or acid from mannitol. They differed from the most closely related species, A. schubertii, by their ability to produce acid from d-cellobiose and d-sucrose and by their pyrazinamidase activity. The name Aeromonas simiae sp. nov. is proposed for these isolates; strain IBS S6874T (=CIP 107798T=CCUG 47378T) is the type strain.
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Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea
More LessA Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.
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Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments
More LessTo assess the physiological and phylogenetic diversity of culturable halophilic bacteria in deep-sea hydrothermal-vent environments, six isolates obtained from low-temperature hydrothermal fluids, sulfide rock and hydrothermal plumes in North and South Pacific Ocean vent fields located at 1530–2580 m depth were fully characterized. Three strains were isolated on media that contained oligotrophic concentrations of organic carbon (0·002 % yeast extract). Sequencing of the 16S rRNA gene indicated that all strains belonged to the genus Halomonas in the γ-subclass of the Proteobacteria. Consistent with previously described species, the novel strains were slightly to moderately halophilic and grew in media containing up to 22–27 % total salts. The isolates grew at temperatures as low as −1 to 2 °C and had temperature optima of 30 or 20–35 °C. Both the minimum and optimum temperatures for growth were similar to those of Antarctic and sea-ice Halomonas species and lower than typically observed for the genus as a whole. Phenotypic tests revealed that the isolates were physiologically versatile and tended to have more traits in common with each other than with closely related Halomonas species, presumably a reflection of their common deep-sea, hydrothermal-vent habitat of origin. The G+C content of the DNA for all strains was 56·0–57·6 mol%, and DNA–DNA hybridization experiments revealed that four strains (Eplume1T, Esulfide1T, Althf1T and Slthf2T) represented novel species and that two strains (Eplume2 and Slthf1) were related to Halomonas meridiana. The proposed new species names are Halomonas neptunia (type strain Eplume1T=ATCC BAA-805T=CECT 5815T=DSM 15720T), Halomonas sulfidaeris (type strain Esulfide1T=ATCC BAA-803T=CECT 5817T=DSM 15722T), Halomonas axialensis (type strain Althf1T=ATCC BAA-802T=CECT 5812T=DSM 15723T) and Halomonas hydrothermalis (type strain Slthf2T=ATCC BAA-800T=CECT 5814T=DSM 15725T).
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Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodii
More LessTwo strictly aerobic, halophilic strains of the γ-Proteobacteria, designated JC2042T and JC2043T, were obtained from a sediment sample of getbol, the Korean tidal flat. Comparative 16S rDNA sequence studies revealed that the test strains were related most closely to the type strains of the genera Alteromonas (93·5–95·5 %) and Glaciecola (91·1–93·3 %). Phylogenetic analyses demonstrated that strains JC2042T and JC2043T formed a distinct monophyletic clade within the family Alteromonadaceae and clustered distantly with the genera Alteromonas and Glaciecola. Physiological, biochemical and chemotaxonomic data also indicated that the two getbol isolates were significantly different from members of these two genera and others with validly published names. Cells were rod-shaped and motile with a polar flagellum. The major isoprenoid quinone was Q8. The predominant cellular fatty acids were C16 : 0, C18 : 1 ω7c and a mixture of C16 : 1 ω7c and iso-C15 : 0 2-OH. DNA G+C contents were 48–54 mol%. On the basis of this polyphasic study, Aestuariibacter gen. nov. is proposed with two novel species, Aestuariibacter salexigens sp. nov. (type strain, JC2042T=IMSNU 14006T=KCTC 12042T=DSM 15300T) and Aestuariibacter halophilus sp. nov. (type strain, JC2043T=IMSNU 14007T=KCTC 12043T=DSM 15266T). Aestuariibacter salexigens is the type species of the genus. In addition, an emended description of Alteromonas macleodii is proposed.
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- Gram-Positive Bacteria
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Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source
More LessThe taxonomic position of an actinomycete, strain 1BDZT, isolated from a clinical human source was determined using a polyphasic approach. Phylogenetic analysis based on almost complete 16S rDNA sequences showed that this organism consistently formed a distinct line with the Amycolatopsis methanolica subclade within the genus Amycolatopsis, and shared moderately low 16S rDNA similarity (<96·5 %) with other species. The organism was also found to have chemical and morphological properties typical of members of the genus Amycolatopsis. A range of phenotypic characteristics readily distinguished this strain from representatives of all species of Amycolatopsis with validly published names. On the basis of these data, a novel species, Amycolatopsis palatopharyngis sp. nov., is proposed to accommodate strain 1BDZT (=AS 4.1729T=PCM 2600T).
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Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago
A sample of mossy soil taken from the eastern lava flow of northern Candlemas Island, South Sandwich archipelago, yielded six isolates of aerobic, endospore-forming bacteria. Miniaturized routine phenotypic tests and other observations, amplified rDNA restriction analysis and SDS-PAGE analysis suggested that the strains represent a novel taxon. 16S rDNA sequence comparisons support the proposal of a novel species, Bacillus shackletonii sp. nov., the type strain of which is LMG 18435T (=CIP 107762T).
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Nocardia tenerifensis sp. nov.
More LessA Gram-positive, non-spore-forming bacterium (GW39-1573T) was isolated from soil of the Spanish island of Tenerife. 16S rRNA gene sequence similarity studies showed that strain GW39-1573T belonged to the genus Nocardia and was most closely related to Nocardia brasiliensis (98·0 %), Nocardia beijingensis (97·3 %), Nocardia transvalensis (97·5 %), Nocardia asteroides (97·2 %) and Nocardia farcinica (97·0 %). Strain GW39-1573T could be distinguished from all other validly described Nocardia species by sequence similarity values of less than 97 %. Chemotaxonomic data [major menaquinone: MK-8(H4, ω-cycl); major polar lipids: diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and an unknown glycolipid and an unknown phospholipid; major fatty acids: C16 : 0, C18 : 1 ω9c and 10 methyl C16 : 0] and the presence of mycolic acids supported the affiliation of strain GW39-1573T to the genus Nocardia. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW39-1573T from those related species that showed 16S rRNA gene sequence similarity values of greater than 97 %. Strain GW39-1573T merits species status, and the name Nocardia tenerifensis is proposed with the type strain GW39-1573T (=DSM 44704T=CIP 107929T).
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Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum
More LessIn a previous study that was based primarily on 16S rDNA sequencing, two groups of bifidobacteria that had been recovered from a pig caecum were proposed to belong to two novel species, termed ‘Bifidobacterium pyschroaerophilum’ and ‘Bifidobacterium aerophilum’. In this study, based on DNA G+C content and partial heat-shock protein 60 (HSP60) gene sequences, the assignment of ‘B. pyschroaerophilum’, corrected to Bifidobacterium pyschraerophilum, to the genus Bifidobacterium was confirmed. The DNA G+C content of ‘B. aerophilum’ was relatively low, which was consistent with its segregation into subcluster II of the 16S rDNA phylogenetic tree. Based on partial 16S rDNA and HSP60 gene sequences, the species was transferred to a novel genus and reclassified as Aeriscardovia aeriphila gen. nov., sp. nov. Biochemical profiles and growth parameters were established for both novel species. Interestingly, each had a high tolerance to oxygen and grew on agar media under aerobic conditions, a trait that may relate to their caecal habitat. Under aerobic growth conditions, the short-rod morphology of A. aeriphila lengthened considerably. This appeared to arise from incomplete cell division. In addition, B. pyschraerophilum was unusual in that it grew at temperatures as low as 4 °C. On the basis of genetic, phylogenetic and phenotypic data, the identities of Bifidobacterium pyschraerophilum sp. nov. (type strain, T16T=LMG 21775T=NCIMB 13940T) and Aeriscardovia aeriphila gen. nov., sp. nov. (type strain, T6T=LMG 21773T=NCIMB 13939T) are confirmed.
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Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol-contaminated soil
The taxonomic relationships of two actinomycetes provisionally assigned to the genus Rhodococcus were determined using a polyphasic taxonomic approach. The generic assignment was confirmed by 16S rRNA gene similarity data, as the organisms, strains MTCC 1534 and W 4937T, were shown to belong to the Rhodococcus rhodochrous subclade. These organisms had phenotypic properties typical of rhodococci; they were aerobic, Gram-positive, weakly acid-fast actinomycetes that showed an elementary branching-rod–coccus growth cycle and contained meso-diaminopimelic acid, arabinose and galactose in whole-organism hydrolysates, N-glycolated muramic acid residues, dehydrogenated menaquinones with eight isoprene units as the predominant isoprenologue and mycolic acids that co-migrated with those extracted from the type strain of R. rhodochrous. The strains had identical phenotypic profiles and belong to the same genomic species, albeit one distinguished from Rhodococcus pyridinivorans, with which they formed a distinct phyletic line. They were also distinguished from representatives of all of the species classified in the R. rhodochrous 16S rRNA gene tree using a set of phenotypic features. The genotypic and phenotypic data show that the strains merit recognition as a novel species of Rhodococcus. The name proposed is Rhodococcus gordoniae sp. nov., with the type strain W 4937T (=DSM 44689T=NCTC 13296T).
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Anaerotruncus colihominis gen. nov., sp. nov., from human faeces
Phenotypic and phylogenetic studies were performed on two isolates of an unidentified Gram-positive, anaerobic, non-spore-forming, rod-shaped bacterium that was isolated from human faeces. The organisms were catalase-negative, produced acetic and butyric acids as end products of metabolism and possessed a DNA G+C content of approximately 54 mol%. Comparative 16S rRNA gene sequencing demonstrated that the two isolates were related closely to each other and formed a hitherto unknown sublineage within the Clostridium leptum rRNA cluster of organisms. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium should be classified in a novel genus as Anaerotruncus colihominis gen. nov., sp. nov. The type strain of Anaerotruncus colihominis is WAL 14565T=CCUG 45055T=CIP 107754T.
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Reclassification of Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov.
More LessComparison of the hypervariable region (269–279 bases in length) at the 5′ end of the 16S rDNA sequences of 29 bacterial strains that were identified previously as Brevibacillus brevis showed that 13 strains clustered with Aneurinibacillus species, eight strains clustered with Bacillus species and eight strains clustered with Brevibacillus species. Based on DNA–DNA hybridization results, 27 strains, not including [Brevibacillus brevis] NCIMB 13288 and [Brevibacillus brevis] DSM 6472, were reidentified as Aneurinibacillus migulanus, Aneurinibacillus thermoaerophilus, Bacillus methanolicus, Bacillus oleronius, Brevibacillus agri, Brevibacillus brevis and Brevibacillus parabrevis. [Brevibacillus brevis] NCIMB 13288, which was located in the Aneurinibacillus cluster, showed low DNA–DNA relatedness (<14 %) and low 16S rDNA sequence similarity (96·8–97·9 %) to other Aneurinibacillus species. [Brevibacillus brevis] DSM 6472, which was located in the Brevibacillus cluster, also showed low DNA–DNA relatedness (<12 %) and low 16S rDNA sequence similarity (95·4–98·8 %) to other Brevibacillus species. These genotypic and phylogenetic data, plus phenotypic and chemotaxonomic characteristics, suggest that [Brevibacillus brevis] NCIMB 13288 (=IAM 15048) and [Brevibacillus brevis] DSM 6472 (=NRRL NRS-887) represent novel species of the genera Aneurinibacillus and Brevibacillus, respectively, for which the names Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. are proposed.
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Tepidibacter formicigenes sp. nov., a novel spore-forming bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent
More LessA novel anaerobic, Gram-positive, sporulating and strictly chemoorganoheterotrophic bacterium, designated strain DV1184T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were short, straight rods (4 μm long and 0·8 μm wide) and were motile with peritrichous flagella. They grew between 35 and 55 °C (optimum, 45 °C), between pH 5·0 and 8·0 (optimum, 6·0) and at 20–60 g sea salts l−1 (optimum sea salts concentration, 30 g l−1). Strain DV1184T was able to ferment yeast extract, tryptone, peptone, glucose, sucrose, maltose and pyruvate. The main fermentation products from glucose were (in decreasing order) formate, acetate and ethanol. The genomic DNA G+C content was 29 mol%. Phylogenetic analysis of the 16S rRNA gene located the strain within cluster XI of the lineage that encompasses the genus Clostridium and related genera in the bacterial domain. On the basis of 16S rDNA sequence comparison and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel species, Tepidibacter formicigenes sp. nov. The type strain is DV1184T (=CIP 107893T=DSM 15518T).
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Streptococcus minor sp. nov., from faecal samples and tonsils of domestic animals
Nine isolates, which were obtained from tonsils, anal swabs and faeces of dogs and from tonsils of a cat and a calf, constituted a homogeneous but unidentified taxon after screening with tRNA intergenic length polymorphism analysis and whole-cell protein fingerprinting. 16S rDNA sequence analysis classified representative strains in the genus Streptococcus. Highest sequence similarity (95·9 %) was obtained with Streptococcus ovis. Growth characteristics, biochemical features, DNA–DNA hybridization and DNA G+C contents of selected strains demonstrated that they represent a single, novel streptococcal species. The name Streptococcus minor sp. nov. is proposed for the novel species; the type strain (ON59T=LMG 21734T=CCUG 47487T) was isolated from a dog tonsil.
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Nocardiopsis aegyptia sp. nov., isolated from marine sediment
An actinomycete, strain SNG49T, was isolated from marine sediment of Abu Qir Bay, on the western seashore of Alexandria, Egypt. The bacterium was aerobic and Gram-positive. It produced beige to light-yellow aerial mycelium, brown substrate mycelium and straight to flexuous hyphae, but no specific spore chains. 16S rDNA sequence analysis and chemotaxonomic markers were consistent with classification of strain SNG49T in the genus Nocardiopsis, i.e. meso-diaminopimelic acid; no diagnostic sugars; phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol as polar lipids; menaquinones of the MK-10 series from MK-10(H0) to MK-10(H8); and iso/anteiso-branched and 10-methyl-branched fatty acids, the principal fatty acids being anteiso-17 : 0 and tuberculostearic acid. Nocardiopsis lucentensis and Nocardiopsis alba are the phylogenetic neighbours of strain SNG49T, respectively showing 98·8 and 98·7 % 16S rRNA gene sequence similarity; however, moderate DNA–DNA reassociation values between these two species and strain SNG49T (44 and 60 %, respectively) showed that strain SNG49T could be clearly separated from them. These data, together with distinct physiological traits, led to the conclusion that this isolate represents a novel species within the genus Nocardiopsis, for which the name Nocardiopsis aegyptia is proposed. The type strain is SNG49T (=DSM 44442T=NRRL B-24244T).
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Deinococcus indicus sp. nov., an arsenic-resistant bacterium from an aquifer in West Bengal, India
More LessAn arsenic- and radiation-resistant bacterium, strain Wt/1aT, was isolated from water from an arsenic-contaminated aquifer located in the Chakdah district of West Bengal, India. The bacterium stains Gram-negative and is rod-shaped, non-motile, non-sporulating and red-pigmented. Cell-wall peptidoglycan contains ornithine as the diamino acid, MK-8 is the major menaquinone, C15 : 1 and C16 : 1 are the major fatty acids and the DNA G+C content of the organism is 65·8 mol%. Based on these phenotypic and chemotaxonomic characteristics, strain Wt/1aT was identified as a member of the genus Deinococcus. Strain Wt/1aT exhibited maximum 16S rRNA gene sequence similarity (95 %) with Deinococcus grandis; however, strain Wt/1aT exhibited only 14 % similarity to D. grandis IAM 13005T at the DNA–DNA level. Furthermore, strain Wt/1aT (compared to D. grandis IAM 13005T) is more resistant to arsenate and arsenite, is positive for arginine dihydrolase, utilizes a number of carbon sources and exhibits quantitative differences in fatty acid composition and qualitative differences in lipid composition. Strain Wt/1aT is identified as a novel species of the genus Deinococcus, for which the name Deinococcus indicus sp. nov. is proposed. The type strain of Deinococcus indicus is Wt/1aT (=MTCC 4913T=DSM 15307T).
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Genetic evidence that Weissella kimchii Choi et al. 2002 is a later heterotypic synonym of Weissella cibaria Björkroth et al. 2002
More LessThe taxonomic positions of Weissella kimchii and Weissella cibaria were examined using phenotypic tests, 16S rRNA gene sequencing and DNA–DNA hybridization. The two species displayed very similar sugar-fermentation patterns and produced the d-form of lactic acid. Phylogenetic analysis showed that W. cibaria is the closest neighbour of W. kimchii, sharing about 99·7 % similarity in the 16S rRNA gene sequence. DNA–DNA hybridization experiments further reinforced these results, demonstrating a 98·2 % reassociation level between W. cibaria LMG 17699T and W. kimchii DSM 14295T. On the other hand, strain RO5, an isolate from paddy rice silage, exhibited 99·4 % 16S rRNA gene sequence similarity and a DNA reassociation level of more than 97 % with both type strains. Therefore, it is proposed that the species W. kimchii should be reclassified as W. cibaria.
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Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies
Novel thermophilic, anaerobic, Gram-positive, rod-shaped bacteria, strains SL9 and OCA1, were isolated from oilfields in France and Australia, respectively. Both strains, together with Thermoanaerobacter yonseiensis KB-1T (=DSM 13777T), Thermoanaerobacter tengcongensis MB4T (=DSM 15242T) and Carboxydibrachium pacificum JMT (=DSM 12653T), possessed genomic (DNA–DNA hybridization studies) and phylogenetic similarities with Thermoanaerobacter subterraneus SEBR 7858T (=DSM 13054T), which was isolated recently from an oilfield reservoir in south-west France. Marked phenotypic differences exist between the three oilfield isolates (T. subterraneus, strain OCA1 and strain SL9): they include temperature range for growth and substrates used. Differences were also observed in the DNA G+C contents of all organisms. Similarly to T. subterraneus, strains SL9 and OCA1, and also T. yonseiensis, T. tengcongensis and Carboxydibrachium pacificum, produced acetate and l-alanine as major end products of glucose metabolism [0·8–1·0 mol l-alanine produced (mol glucose consumed)−1] and reduced thiosulfate, but not sulfate, to sulfide. Because of these significant metabolic and phylogenetic differences between the oilfield isolates (T. subterraneus, strain OCA1 and strain SL9), T. yonseiensis, T. tengcongensis and Carboxydibrachium pacificum and other Thermoanaerobacter species, it is proposed to reassign them as a novel genus and species, Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov., with the creation of four novel subspecies, Caldanaerobacter subterraneus subsp. subterraneus subsp. nov., comb. nov., Caldanaerobacter subterraneus subsp. yonseiensis subsp. nov., comb. nov., Caldanaerobacter subterraneus subsp. tengcongensis subsp. nov., comb. nov. and Caldanaerobacter subterraneus subsp. pacificus subsp. nov., comb. nov.
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Microbacterium ulmi sp. nov., a xylanolytic, phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra
A xylanolytic and phosphate-solubilizing bacterium isolated from sawdust of Ulmus nigra in Salamanca was characterized by a polyphasic approach. The novel strain, designated XIL02T, was Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped and non-motile. Phylogenetically and chemotaxonomically, it was related to members of the genus Microbacterium. According to 16S rRNA gene sequence analysis, it is closely related to Microbacterium arborescens and Microbacterium imperiale; however, DNA–DNA hybridization showed reassociation values less than 70 % with the type strains of these species. In chemotaxonomic analyses, the major menaquinones detected were MK-12, MK-13 and MK-11 and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; the peptidoglycan was of the type B2β. The G+C content determined was 69 mol%. Based on the present data, it is proposed that strain XIL02T (=LMG 20991T=CECT 5976T) be classified as the type strain of a novel Microbacterium species, for which the name Microbacterium ulmi sp. nov. is proposed.
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Yania halotolerans gen. nov., sp. nov., a novel member of the suborder Micrococcineae from saline soil in China
A novel coccoid, halotolerant actinobacterium, designated strain YIM 70085T, was isolated from a soil sample that was collected in Xinjiang Province, China, and characterized by using a polyphasic approach. Optimum growth temperature was 28 °C and growth occurred optimally in culture media that contained 10 % KCl. The peptidoglycan type was A4α, l-lys–gly–l-Glu. Whole-cell sugars consisted of xylose, mannose and galactose. Phospholipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phospholipid, one unknown glycolipid and traces of phosphatidylinositol. Menaquinones were MK-8 (83 %), MK-7 (12 %) and MK-9 (15 %). Predominant fatty acids were i-C15 : 0 (44·29 %), ai-C15 : 0 (35·60 %) and ai-C17 : 0 (9·74 %). The DNA G+C content was 53·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 70085T occupies a branch that is distinct from, although very close to, the family Micrococcaceae in the suborder Micrococcineae. Based on its phenotypic characteristics, phylogenetic position (as determined by 16S rRNA gene sequence analysis) and 16S rDNA signature nucleotide data, it is concluded that the isolate represents a novel member of the suborder Micrococcineae, for which the name Yania halotolerans gen. nov., sp. nov. is proposed. The type strain is YIM 70085T (=CCTCC AA001023T=DSM 15476T).
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Cellulomonas xylanilytica sp. nov., a cellulolytic and xylanolytic bacterium isolated from a decayed elm tree
More LessA Gram-positive, aerobic, non-motile bacterium was isolated from a decayed elm tree. Phylogenetic analysis based on 16S rDNA sequences revealed 99·0 % similarity to Cellulomonas humilata. Chemotaxonomic data that were determined for this isolate included cell-wall composition, fatty acid profiles and polar lipids; the results supported the placement of strain XIL11T in the genus Cellulomonas. The DNA G+C content was 73 mol%. The results of DNA–DNA hybridization with C. humilata ATCC 25174T, in combination with chemotaxonomic and physiological data, demonstrated that isolate XIL11T should be classified as a novel Cellulomonas species. The name Cellulomonas xylanilytica sp. nov. is proposed, with strain XIL11T (=LMG 21723T=CECT 5729T) as the type strain.
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Reclassification of Lactobacillus kefirgranum Takizawa et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended description of L. kefiranofaciens Fujisawa et al. 1988
Fourteen homofermentative lactic acid bacteria that were isolated from kefir grains and kefir fermented milks were assigned to either Lactobacillus kefiranofaciens or Lactobacillus kefirgranum, based on their characteristic morphotypes, phenotypic features and SDS-PAGE profiles of whole-cell proteins. Further genotypic analyses on representative strains from both taxa demonstrated that L. kefiranofaciens and L. kefirgranum share 100 % 16S rDNA sequence similarity and belong phylogenetically to the Lactobacillus acidophilus species group. DNA–DNA binding values of >79 % and analogous DNA G+C contents of 37–38 mol% showed that the strains studied belonged to one species: L. kefirgranum is a later synonym of L. kefiranofaciens. An emended description is proposed for L. kefiranofaciens. Due to the specific morphological and biochemical characteristics of these taxa in kefir grain formation, it is proposed that L. kefirgranum should be reclassified as L. kefiranofaciens subsp. kefirgranum subsp. nov.
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Xylanibacterium ulmi gen. nov., sp. nov., a novel xylanolytic member of the family Promicromonosporaceae
A bacterial strain designated XIL08T was isolated from an elm tree affected by Dutch elm disease. Strain XIL08T is Gram-positive, aerobic, rod-shaped and non-motile. The complete 16S rDNA sequence of this micro-organism was obtained and phylogenetic analysis based on the neighbour-joining method indicated that the closest related organism belongs to the genus Xylanimonas of the family Promicromonosporaceae, suborder Micrococcineae. Cell-wall analyses revealed the presence of type A4α, l-lys–l-ala–d-Glu peptidoglycan. The cell-wall sugars found were rhamnose in large amounts, fucose, mannose and galactose and traces of arabinose and glucose. HPLC analysis of menaquinones revealed two peaks, the main peak corresponding to MK-9(H4) and the smaller one to MK-8(H4). The major fatty acid found was anteiso-C15 : 0. Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The G+C content of the DNA was 72 mol%. Isolate XIL08T hydrolysed xylan but not cellulose. Growth was observed with many carbohydrates including acetate and xylan as the only carbon source. Catalase activity was not detected. The data from this polyphasic study suggest that this bacterium belongs to a novel genus of the family Promicromonosporaceae. It is proposed that isolate XIL08T (=LMG 21721T=CECT 5731T) be classified in a new genus, Xylanibacterium gen. nov., as the type strain of Xylanibacterium ulmi sp. nov.
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Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens
More LessComparative 16S rDNA studies on six strains of actinomycete isolated from clinical specimens revealed that they belong to the genus Nocardia and are closely related to Nocardia seriolae, Nocardia otitidiscaviarum, Nocardia uniformis, Nocardia pseudobrasiliensis and Nocardia crassostreae. However, the novel organisms consistently formed a clade distinct from that of the five latter species. Determination of DNA–DNA relatedness indicated that these strains could be classified under three novel species. Based on their phenotypic and phylogenetic characters, three novel species of the genus Nocardia are established: Nocardia inohanensis sp. nov. for IFM 0092T (=NBRC 100128T=JCM 11891T=DSM 44667T), Nocardia yamanashiensis sp. nov. for IFM 0265T (=NBRC 100130T=JCM 11893T=DSM 44669T) and Nocardia niigatensis sp. nov. for IFM 0330T (=NBRC 100131T=JCM 11894T=DSM 44670T), IFM 0260, IFM 0636 and IFM 0833.
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Streptomyces scabrisporus sp. nov.
More LessThe taxonomic position was determined for a soil actinomycete, isolate KM-4927T, that produced the antibiotic hitachimycin. The strain was assigned to the genus Streptomyces on the basis of 16S rDNA analysis, where it formed a separate clade. The strain is characterized by grey aerial cell mass, spiral spore chains and a rugose spore surface, menaquinones of the MK-9(H4, H2, H6) types and cell-wall chemotype I. DNA–DNA reassociation with 21 phylogenetically neighbouring Streptomyces type strains showing similar morphological characteristics to strain KM-4927T indicated that this isolate is only moderately related to other Streptomyces species. On the basis of genomic and physiological properties, the novel species Streptomyces scabrisporus sp. nov. is proposed; the type strain is strain KM-4927T (=JCM 11712T=NRRL B-24202T).
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Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil
More LessThe taxonomic position of an actinomycete isolated from a hypermagnesian ultramafic soil was examined using a polyphasic approach. The strain, designated SBHR OA6T, was shown to have chemical and morphological properties typical of members of the genus Nocardia. The organism was most closely associated with Nocardia asteroides using 16S rRNA gene sequence data. It showed a distinctive set of phenotypic properties that distinguished it from representatives of all species with validly published names classified in the genus Nocardia. The combined genotypic and phenotypic data show that strain SBHR OA6T (=DSM 44717T=NCIMB 13955T) merits description as the type strain of a novel Nocardia species, Nocardia neocaledoniensis sp. nov.
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Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment
An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).
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Reclassification of Brevibacterium liquefaciens Okabayashi and Masuo 1960 as Arthrobacter nicotianae Giovannozzi-Sermanni 1959
More LessBrevibacterium liquefaciens ATCC 14929T was reclassified as Corynebacterium liquefaciens by Lanéelle et al. (1980) . A further study by Stackebrandt et al. (1983) described the same strain, indicating high genomic and chemotaxonomic relatedness to Arthrobacter nicotianae; however, reclassification was not formally proposed. Because of the discrepancies between their previous work and the data of Collins & Kroppenstedt (1983) , Lanéelle and colleagues re-examined B. liquefaciens and withdrew their recommendation for the assignment of B. liquefaciens to the genus Corynebacterium ( Lanéelle et al., 1984 ). Formal reclassification of B. liquefaciens as A. nicotianae is now proposed.
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Bacillus galactosidilyticus sp. nov., an alkali-tolerant β-galactosidase producer
A novel Bacillus isolate from raw milk and four strains from diverse origins that were identified previously as Bacillus lentus, Bacillus firmus and Bacillus circulans showed a high degree of similarity in amplified rDNA restriction analysis, SDS-PAGE and routine phenotypic tests, whilst 16S rDNA sequence comparisons and DNA relatedness data showed that this taxon was different from related Bacillus species. On the basis of these data, Bacillus galactosidilyticus sp. nov. is proposed, with the type strain LMG 17892T (=DSM 15595T=Logan B2188T=MB 800T).
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- Unicellular Eukaryotes
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Malassezia nana sp. nov., a novel lipid-dependent yeast species isolated from animals
Five isolates of a novel species of the yeast genus Malassezia were isolated from animals in Japan and Brazil. Phylogenetic trees based on the D1/D2 domains of the large-subunit (26S) rDNA sequences and nucleotide sequences of the internal transcribed spacer 1 region showed that the isolates were conspecific and belonged to the genus Malassezia. They were related closely to Malassezia dermatis and Malassezia sympodialis, but were clearly distinct from these two species and the other six species of Malassezia that have been reported, indicating that they should be classified as a novel species, Malassezia nana sp. nov. Morphologically and physiologically, M. nana resembles M. dermatis and M. sympodialis, but can be distinguished from these species by its inability to use Cremophor EL (Sigma) as the sole lipid source and to hydrolyse aesculin. The type strain of M. nana is NUSV 1003T (=CBS 9557T=JCM 12085T).
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- Evolution, Phylogeny And Biodiversity
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Polyphyly of true branching cyanobacteria (Stigonematales)
More LessCyanobacteria with true branching are classified in Subsection V (formerly order Stigonematales) in the phylum Cyanobacteria. They exhibit a high degree of morphological complexity and are known from particular biotopes. Only a few stigonematalean morphotypes have been cultured, and therefore the high variability of morphotypes found in nature is under-represented in culture. Axenic cultures of Chlorogloeopsis and Fischerella sensu Rippka et al. were, to date, the only representatives of this Subsection in phylogenetic studies. The 16S rDNA sequence analysis data in this report confirm that heterocyst-forming cyanobacteria are a monophyletic group. However, unlike previous studies have suggested, these 16S rDNA data on new Stigonematales strains show that the true branching cyanobacteria are polyphyletic and can be separated into at least two major groups defined by their branching type, the first group being characterized by T-branching and the second group by Y-branching. Cyanobacteria with intercalary heterocysts and either no branching or false-branching also formed separate clusters. In consequence, our phylogenetic data do not correlate with the bacteriological and traditional classifications, which distinguish filamentous heterocystous cyanobacteria with or without true branching (Nostocales/Stigonematales).
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The leucine-responsive regulatory protein (lrp) gene for characterization of the relationship among Xanthomonas species
More LessCharacterization of strains of Xanthomonas axonopodis pv. citri by using DNA fingerprints that were generated from primers for enterobacterial repetitive intergenic consensus (ERIC) elements led to the discovery of differential sequences for a leucine-responsive regulatory protein (lrp) gene in two subgroups of strains with different host ranges on Citrus spp. DNA hybridization and PCR-based assays that used different sets of primers were designed to detect the core sequence, as well as to obtain the entire sequence of the lrp gene for several Xanthomonas species and pathovars. Higher variability was observed at the nucleotide level than at the amino acid level among the different species and pathovars, revealing selection pressure on the lrp gene, which is presumably due to an essential role of the gene in bacterial metabolism. Moderate variability in the 3′ and 5′ domains was used to study relationships among different species within the genus Xanthomonas. Species of this genus that were isolated from citrus, as well as other pathovars of X. axonopodis, showed highly similar lrp gene sequences, whereas other Xanthomonas species, especially Xanthomonas campestris, had sequences that were more dissimilar to that of X. axonopodis. Thus, the lrp gene sequence is useful to distinguish X. axonopodis pv. citri groups and promising for polyphasic taxonomic analysis of the genus Xanthomonas. Data from analysis of lrp gene sequences support the current concepts for classification of xanthomonads, which are based on other approaches.
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Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD
More LessThe heterocystous cyanobacteria are currently placed in subsections IV and V, which are distinguished by cellular division in one plane (false branching) and in more than one plane (true branching), respectively. Published phylogenies of 16S rRNA gene sequence data support the monophyly of the heterocystous cyanobacteria, with members of subsection V embedded within subsection IV. It has been postulated that members of subsection V arose from within subsection IV. Therefore, phylogenetic analysis of nucleotide sequences of the nitrogen-fixation gene nifD from representatives of subsections IV and V was performed by using maximum-likelihood criteria. The heterocystous cyanobacteria are supported as being monophyletic, with the non-heterocystous cyanobacteria as their closest relative. However, neither subsection IV nor subsection V is monophyletic, with representatives of both subsections intermixed in two sister clades. Analysis of nifD does not support recognition of two distinct subsections.
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Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison
More LessThe taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)