- Volume 53, Issue 3, 2003
Volume 53, Issue 3, 2003
- All Change For Ijsem
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- Validation List No. 91
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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 previously [Int J Syst Bacteriol 27(3), iv (1977)]. Authors and other individuals wishing to have new names and/or combinations included in future lists should send (i) 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 (ii) confirmation of deposition and availability of type strains from two recognized culture collections in different countries. 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 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 1, 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 II(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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Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation
More LessEnrichments for anaerobic organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected at the Guaymas Basin (27° 01′ N, 111° 24′ W). Positive enrichments were submitted to γ-irradiation at a dose of 30 kGy. One of the resistant strains, designated strain EJ3T, formed regular motile cocci. The new strain grew between 55 and 95 °C, with an optimum growth temperature of 88 °C. The optimal pH for growth was 6·0, and the optimum NaCl concentration for growth was around 20 g l−1. Strain EJ3T was an obligately anaerobic heterotroph that utilized yeast extract, tryptone and peptone. Elemental sulfur or cystine was required for growth and reduced to hydrogen sulfide. The G+C content of the genomic DNA was 51·3 mol%. As determined by 16S rRNA gene sequence analysis, the organism was most closely related to Thermococcus celer, Thermococcus guaymasensis, Thermococcus hydrothermalis, Thermococcus profundus and Thermococcus gorgonarius. However, no significant homology was observed between them by DNA–DNA hybridization. The novel organism also possessed phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that this isolate, which constitutes the most radioresistant hyperthermophilic archaeon known to date, should be described as the type strain of a novel species, Thermococcus gammatolerans sp. nov. The type strain is EJ3T (=DSM 15229T=JCM 11827T).
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- Other Bacteria
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Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent
A novel moderately thermophilic, organotrophic, microaerophilic, facultatively chemolithotrophic bacterium, designated strain 506T, was isolated from a deep-sea hydrothermal vent site at 13°N in the East Pacific Rise. Cells were Gram-negative, non-motile rods. The organism grew in the temperature range 40–68 °C, with an optimum at 60 °C, and in the pH range 5·5–8·4, with an optimum around pH 7·5. The NaCl concentration for growth was in the range 10–50 g l−1, with an optimum at 30 g l−1. Strain 506T grew chemoorganoheterotrophically with carbohydrates, proteinaceous substrates, organic acids and alcohols using oxygen or nitrate as electron acceptor. Alternatively, strain 506T was able to grow lithoheterotrophically with molecular hydrogen as the energy source. The G+C content of the genomic DNA was 62·9 mol%. Phylogenetic analysis of the 16S rDNA sequence placed strain 506T in the family Thermaceae. On the basis of phenotypic and phylogenetic data, strain 506T (=DSM 14977T=VKM B-2274T) is proposed as the type strain of a novel species in a new genus, Oceanithermus profundus gen. nov., sp. nov.
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Chryseobacterium joostei sp. nov., isolated from the dairy environment
More LessAmong a large collection of South African dairy isolates, a novel Chryseobacterium taxon (DNA group 3) was previously delineated by a polyphasic taxonomic study ( Hugo et al., Syst Appl Microbiol 22, 586–595, 1999 ). In the present paper, this taxon is further characterized using 16S rDNA sequencing, fatty acid methyl ester analysis and a comparative phenotypic analysis, resulting in the proposal of a novel species, Chryseobacterium joostei sp. nov. (type strain Ix 5aT=LMG 18212T=CCUG 46665T).
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Spirochaeta americana sp. nov., a new haloalkaliphilic, obligately anaerobic spirochaete isolated from soda Mono Lake in California
A novel, obligately anaerobic, mesophilic, haloalkaliphilic spirochaete, strain ASpG1T, was isolated from sediments of the alkaline, hypersaline Mono Lake in California, USA. Cells of the Gram-negative strain were motile and spirochaete-shaped with sizes of 0·2–0·22×8–18 μm. Growth of the strain was observed between 10 and 44 °C (optimum 37 °C), in 2–12 % (w/v) NaCl (optimum 3 % NaCl) and between pH 8 and 10·5 (optimum pH 9·5). The novel strain was strictly alkaliphilic, required high concentrations of carbonates in the medium and was capable of utilizing d-glucose, fructose, maltose, sucrose, starch and d-mannitol. End products of glucose fermentation were H2, acetate, ethanol and formate. Strain ASpG1T was resistant to kanamycin and rifampicin, but sensitive to gentamicin, tetracycline and chloramphenicol. The G+C content of its DNA was 58·5 mol%. DNA–DNA hybridization analysis of strain ASpG1T with its most closely related species, Spirochaeta alkalica Z-7491T, revealed a hybridization value of only 48·7 %. On the basis of its physiological and molecular properties, strain ASpG1T appears to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta americana is proposed (type strain ASpG1T=ATCC BAA-392T=DSM 14872T).
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Sulfurihydrogenibium subterraneum gen. nov., sp. nov., from a subsurface hot aquifer
More LessA polyphasic taxonomic study was performed on a novel facultatively anaerobic, hydrogen- or sulfur/thiosulfate-oxidizing, thermophilic chemolithoautotroph recently isolated from subsurface hot aquifer water in a Japanese gold mine. The cells were straight to slightly curved rods, with a single polar flagellum. Growth was observed at 40–70 °C (optimum 60–65 °C; 80 min doubling time) and at pH 6·4–8·8 (optimum pH 7·5). The isolate was unable to use complex organic compounds, carbohydrates, amino acids or organic acids as sole energy and carbon sources. The G+C content of the genomic DNA was 31·3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was closely related to an uncultivated group of micro-organisms within the order Aquificales obtained from Icelandic and Japanese hot spring microbial mats, but distantly related to previously identified genera of the Aquificales such as Persephonella, Aquifex and Hydrogenobacter. The name Sulfurihydrogenibium subterraneum gen. nov., sp. nov. is proposed for this novel species; the type strain is HGMK1T (=JCM 11477T=ATCC BAA-562T=DSM 15120T).
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Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent
More LessA novel anaerobic, heterotrophic thermophile was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc, Japan. The cells were bent, flexible rods, with a single polar flagellum. Growth was observed between 40 and 70 °C (optimum temperature: 60–65 °C; doubling time, 40 min) and between pH 5·0 and 7·5 (optimum pH 6·5). The isolate was a strictly anaerobic heterotroph capable of using complex organic compounds (yeast extract, tryptone, peptone, casein and Casamino acids), ethanol and various organic acids as energy and carbon sources. Hydrogen could serve as a supplementary energy source. Elemental sulfur (S0), nitrate or arsenate was required for growth as an electron acceptor. The G+C content of the genomic DNA was 38·6 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that isolate SSM1T is closely related to Deferribacter thermophilus BMAT (98·1 %). However, the novel isolate could be clearly differentiated from D. thermophilus BMAT on the basis of its physiological and genetic properties. The name Deferribacter desulfuricans sp. nov. (type strain SSM1T=JCM 11476T=DSM 14783T) is proposed.
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Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier
Fei Zhu, Shan Wang and Peijin ZhouTwo novel psychrophilic bacterial strains (ZF-6T and ZF-8T) were isolated from the China No. 1 glacier. Polyphasic taxonomy using physiological and biochemical properties and phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates belonged to the genus Flavobacterium, and that they were distinct from each other and also from the known species of this genus. Strains ZF-6T and ZF-8T are Gram-negative and both have an optimal growth temperature of 11 °C. Strain ZF-6T is able to grow at 0–20 °C, the G+C content of its genomic DNA is 34·4 mol% and the major fatty acids of ZF-6T are C16 : 1 ω7c (17·7 %) and C15 : 1 ω6c (12·7 %). Strain ZF-8T showed a strong ability to degrade organic macromolecules such as starch, CM-cellulose, pectin and chitin. Its DNA G+C content is 35·1 mol%, and the major fatty acids are C16 : 1 ω7c (18·2 %) and C15 : 0 (9·9 %). Phylogenetic analysis based on 16S rDNA sequences indicated that ZF-6T and ZF-8T belong to the genus Flavobacterium and represent two novel species. DNA–DNA hybridization also supported the status of the two new isolates. The names Flavobacterium xinjiangense sp. nov. (type strain, ZF-6T=AS 1.2749T=JCM 11314T) and Flavobacterium omnivorum sp. nov. (type strain, ZF-8T=AS 1.2747T=JCM 11313T) are proposed for the two new isolates.
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Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney
More LessA novel thermophilic, hydrogen-oxidizing bacterium, designated 29WT, 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 cocci (0·9–1·0 μm in diameter) and straight rods (2·3–2·7 μm long) under static and agitated culture conditions, respectively. The new isolate was an obligate chemolithoautotroph growing by respiratory nitrate reduction with H2, forming N2 as a final product. A very low concentration of O2 (optimum 0·6–0·8 %, v/v) was also used as an alternative electron acceptor while reduced sulfur compounds did not serve as electron donors. Anoxic hydrogen-oxidizing growth with nitrate was observed between 50 and 72·5 °C (optimum 70 °C; 40 min doubling time), pH 5·5 and 7·6 (optimum pH 7·2), and in the presence of 1·5 and 5·0 % NaCl (optimum 2·5 %). The G+C content of the genomic DNA was 37·3 mol%. Phylogenetic analysis based on 16S rDNA sequences indicated that the isolate was a member of the recently described genus Persephonella in a potential new family within the order Aquificales. On the basis of the physiological and molecular properties of the new isolate, the name Persephonella hydrogeniphila sp. nov. is proposed. The type strain is strain 29WT (=JCM 11663T=DSM 15103T).
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- Proteobacteria
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Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium
Alteromonas-like strains KMM 241T and KMM 642, isolated from marine invertebrate specimens, were investigated to clarify their taxonomic position. The novel isolates were aerobic, Gram-negative, motile, slightly halophilic and heterotrophic and hydrolysed polysaccharides. They did not hydrolyse urea, gelatin or casein and produced acid weakly from carbohydrates. The DNA G+C content ranged between 44·6 and 44·8 mol%. DNA–DNA similarity between the two strains was 71 %. Comparison of the 16S rRNA gene sequence of strain KMM 241T revealed 94·5–94·8 % similarity to Glaciecola species. The novel strains shared several phenotypic and physiological properties with members of Glaciecola, but they differed in their lack of pigment production, their minimal and maximal growth temperatures and their ability to hydrolyse agar and carrageenan and in the utilization of organic compounds. On the basis of phenotypic and physiological characteristics as well as phylogenetic analysis, the isolates should be assigned to a novel species, Glaciecola mesophila sp. nov. The type strain is strain KMM 241T (=DSM 15026T).
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Saccharospirillum impatiens gen. nov., sp. nov., a novel γ-Proteobacterium isolated from hypersaline Ekho Lake (East Antarctica)
More LessFive Gram-negative, motile, aerobic to microaerophilic spirilla were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strains are oxidase- and catalase-positive, metabolize a variety of sugars and carboxylic acids and have an absolute requirement for sodium ions. The predominant fatty acids of the organisms are C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c, with C10 : 1 3-OH, C10 : 0 3-OH, C12 : 0 3-OH, C14 : 1 3-OH, C14 : 0 3-OH and C19 : 1 present in smaller amounts. The main polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmonomethylamine. The DNA base composition of the strains is 54–55 mol% G+C. 16S rRNA gene sequence comparisons show that the isolates are related to the genera Oceanospirillum, Pseudospirillum, Marinospirillum, Halomonas and Chromohalobacter in the γ-Proteobacteria. Morphological, physiological and genotypic differences from these previously described genera support the description of a novel genus and species, Saccharospirillum impatiens gen. nov., sp. nov. The type strain is EL-105T (=DSM 12546T=CECT 5721T).
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Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III)
More LessTo further investigate the diversity of micro-organisms capable of conserving energy to support growth from dissimilatory Fe(III) reduction, Fe(III)-reducing micro-organisms were enriched and isolated from subsurface sediments collected in Oyster Bay, VA, USA. A novel isolate, designated T118T, was recovered in a medium with lactate as the sole electron donor and Fe(III) as the sole electron acceptor. Cells of T118T were Gram-negative, motile, short rods with a single polar flagellum. Strain T118T grew between pH 6·7 and 7·1, with a temperature range of 4–30 °C. The optimal growth temperature was 25 °C. Electron donors utilized by strain T118T with Fe(III) as the sole electron acceptor included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds tested was fermented. Electron acceptors utilized with either acetate or lactate as the electron donor included Fe(III)–NTA (nitrilotriacetic acid), Mn(IV) oxide, nitrate, fumarate and oxygen. Phylogenetic analysis demonstrated that strain T118T is most closely related to the genus Rhodoferax. Unlike other species in this genus, strain T118T is not a phototroph and does not ferment fructose. However, phototrophic genes may be present but not expressed under the experimental conditions tested. No Rhodoferax species have been reported to grow via dissimilatory Fe(III) reduction. Based on these physiological and phylogenetic differences, strain T118T (=ATCC BAA-621T=DSM 15236T) is proposed as a novel species, Rhodoferax ferrireducens sp. nov.
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Jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine Roseobacter clade from the North Sea
More LessHeterotrophic bacteria were isolated from a water sample taken from the North Sea, 2 km off the coast of the island of Helgoland, by direct plating of the serially diluted sample on complex marine media. Sixteen of 80 strains from the highest sample dilution belonged to the ‘Roseobacter–Sulfitobacter–Silicibacter’ group within the α-subclass of the Proteobacteria on the basis of partial 16S rDNA sequence analysis. Phylogenetic analysis of nearly complete 16S rDNA sequences showed that the closest relative of two strains, Hel 10T and Hel 26, was Ketogulonicigenium vulgare (94·4 % similarity). These strains were Gram-negative, non-motile rods, obligate aerobes, required sodium ions and 1–7 % sea salts for growth and did not produce bacteriochlorophyll. Their optimal growth temperature was 25–30 °C. The strains had Q-10 as the dominant respiratory quinone. Chemotaxonomic analysis showed a combination of ester-linked 3-OH 10 : 0, 12 : 1 and amide-linked 3-oxo 14 : 0 (or 3-OH 14 : 1) and 3-OH 14 : 0 fatty acids, which appears to be a unique feature of strains Hel 10T and Hel 26 within this subsection of the α-subclass of the Proteobacteria. Based on 16S rDNA sequence analysis and chemotaxonomic data, the strains are assigned to a new genus and species, Jannaschia helgolandensis gen. nov., sp. nov., with the type strain Hel 10T (=DSM 14858T=NCIMB 13941T).
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Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals
More LessThe taxonomic position of the fluorescent amplified fragment length polymorphism fingerprinting groups A46 (five isolates), A51 (six isolates), A52 (five isolates) and A53 (seven isolates) obtained in a previous study were further analysed through a polyphasic approach. The 23 isolates were phylogenetically related to Vibrio splendidus, but DNA–DNA hybridization experiments proved that they belong to three novel species. Chemotaxonomic and phenotypic analyses further disclosed several features that differentiate between the 23 isolates and known Vibrio species. The names Vibrio kanaloae sp. nov. (type strain LMG 20539T=CAIM 485T; EMBL accession no. AJ316193; G+C content 44·7 mol%), Vibrio pomeroyi sp. nov. (type strain LMG 20537T=CAIM 578T; EMBL accession no. AJ491290; G+C content 44·1 mol%) and Vibrio chagasii sp. nov. (type strain LMG 21353T=CAIM 431T; EMBL accession no. AJ316199; G+C content 44·6 mol%) are respectively proposed to encompass the five isolates of A46, the six isolates of A51 and the 12 isolates of A52/A53. The three novel species can be distinguished from known Vibrio species by several phenotypic features, including utilization and fermentation of various carbon sources, β-galactosidase activity and fatty acid content (particularly of 12 : 0, 14 : 0, 14 : 0 iso and 16 : 0 iso).
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Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water
The taxonomic characteristics of two bacterial strains, RB-8T and RB-9, isolated from hydrocarbon-degrading enrichment cultures obtained from Antarctic coastal marine environments (Rod Bay, Ross Sea), were determined. These bacteria were psychrophilic, aerobic and Gram-negative with polar flagella. Growth was not observed in the absence of NaCl, occurred only at concentrations of Na+ above 20 mM and was optimal at an NaCl concentration of 3–5 % (w/v). The major cellular fatty acids were monounsaturated straight-chain fatty acids. The strains were able to synthesize the polyunsaturated fatty acid eicosapentaenoic acid (20 : 5ω3) at low temperatures. The DNA G+C contents were 41–42 mol%. The strains formed a distinct phyletic line within the γ-Proteobacteria, with less than 89·6 % sequence identity to their closest relatives within the Bacteria with validly published names. Both isolates exhibited a restricted substrate profile, with a preference for aliphatic hydrocarbons, that is typical of marine hydrocarbonoclastic micro-organisms such as Alcanivorax, Marinobacter and Oleiphilus. On the basis of ecophysiological properties, G+C content, 16S rRNA gene sequences and fatty acid composition, a novel genus and species within the γ-Proteobacteria are proposed, Oleispira antarctica gen. nov., sp. nov.; strain RB-8T (=DSM 14852T=LMG 21398T) is the type strain.
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Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov.
An anaerobic, halorespiring bacterium (strain PCE-M2T=DSM 13726T=ATCC BAA-583T) able to reduce tetrachloroethene to cis-dichloroethene was isolated from an anaerobic soil polluted with chlorinated aliphatic compounds. The isolate is assigned to the genus Sulfurospirillum as a novel species, Sulfurospirillum halorespirans sp. nov. Furthermore, on the basis of all available data, a related organism, Dehalospirillum multivorans DSM 12446T, is reclassified to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov.
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Acidovorax valerianellae sp. nov., a novel pathogen of lamb's lettuce [Valerianella locusta (L.) Laterr.]
More LessBacterial spot disease of lamb's lettuce [Valerianella locusta (L.) Laterr.] was first observed in fields in 1991. This new bacterial disease is localized in western France in high-technology field production of lamb's lettuce for the preparation of ready-to-use salad. Nineteen strains isolated in 1992 and 1993 from typical black leaf spots of naturally infected lamb's lettuce were characterized and compared with reference strains of Acidovorax and Delftia. The pathogenicity of the 19 strains was confirmed by artificial inoculation. Biochemical and physiological tests, fatty acid profiles, DNA–DNA hybridization and other nucleic acid-based tests were performed. A numerical taxonomic analysis of the 19 lamb's lettuce strains showed a single homogeneous phenon closely related to previously described phytopathogenic taxa of the genus Acidovorax. DNA–DNA hybridization studies showed that the lamb's lettuce strains were 91–100 % related to a representative strain, strain CFBP 4730T, and constituted a discrete DNA hybridization group, indicating that they belong to the same novel species. Results from DNA–rRNA hybridization, 16S rRNA sequence analysis and fatty acid analysis studies confirmed that this novel species belongs to the β-subclass of the Proteobacteria and, more specifically, to the family Comamonadaceae and the genus Acidovorax. The name Acidovorax valerianellae sp. nov. is proposed for this novel taxon of phytopathogenic bacteria. The type strain is strain CFBP 4730T (=NCPPB 4283T).
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Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children
More LessThe taxonomic position of a group of five d-sorbitol- and lactose-negative enterobacterial isolates recovered from diarrhoeal stools of children at the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), was investigated by DNA–DNA hybridization, phenotypic characterization and 16S rDNA sequencing. These strains were originally identified as ‘Hafnia alvei-like’ with the API 20E system but, in fact, show more phenotypic and genotypic resemblance to members of the genus Escherichia. By 16S rDNA sequencing, one representative strain of the ICDDR,B group was shown to be closely affiliated to the genera Escherichia and Shigella. Using the fluorimetric microplate hybridization method, the diarrhoeagenic ICDDR,B isolates were found to constitute a homogeneous taxon (⩾82 % internal DNA relatedness), with the closest affiliation to the type strains of Escherichia coli (55–64 %) and Shigella flexneri (54–60 %). The DNA–DNA hybridization levels were much lower with members of other described Escherichia species (16–45 %) and with the type strain of H. alvei (9–17 %). The G+C content of the ICDDR,B strains ranged from 50·5 to 50·7 mol%. Together with the diagnostic characteristics reported previously, including the presence of the eaeA gene of enteropathogenic E. coli and of the E. coli and Shigella-specific phoE gene, it is concluded that the ICDDR,B strains represent a novel taxon in the genus Escherichia, for which the name Escherichia albertii sp. nov. is proposed. Its type strain is Albert 19982T (=LMG 20976T=CCUG 46494T).
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Marinomonas primoryensis sp. nov., a novel psychrophile isolated from coastal sea-ice in the Sea of Japan
More LessTwo bacterial strains (KMM 3633T and KMM 3634) were isolated from marine coastal sea-ice and characterized by using phenotypic and molecular methods. The isolates were aerobic, Gram-negative, psychrophilic, halophilic and motile by means of a single polar flagellum. The DNA G+C content was 45·3–45·6 mol%. The major cellular fatty acids were C16 : 0, C16 : 1 ω9c and C18 : 1 ω7c. Comparison of almost-complete 16S rDNA sequences demonstrated that the strains were phylogenetically closely related to each other (99·5 % sequence identity), and related to Marinomonas species (94·4–96·4 % identity). DNA–DNA reassociation between KMM 3633T and KMM 3634 occurred at a level of 92 %. Based on phenotypic, chemotaxonomic and phylogenetic properties, the name Marinomonas primoryensis sp. nov. is proposed for strains KMM 3633T and KMM 3634; the type strain is KMM 3633T (=JCM 11775T=NRIC 523T).
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Description of Comamonas aquatica comb. nov. and Comamonas kerstersii sp. nov. for two subgroups of Comamonas terrigena and emended description of Comamonas terrigena
More LessThree clusters of isolates have previously been defined within the species Comamonas terrigena, on the basis of DNA–rRNA and DNA–DNA hybridization data, and of protein electrophoretic patterns and immunotyping. More detailed characterization in the current study shows that representatives of these three groups can also be differentiated phenotypically from each other. Strains of C. terrigena sensu stricto (C. terrigena DNA group 1) are pyrrolidone aminopeptidase-positive, do not grow at 40 °C, are l-alanine-positive and are always negative for 4-hydroxybenzoate. Strains of C. terrigena DNA groups 2 and 3 are pyrrolidone aminopeptidase-negative; the former is the only group that is tyrosine-negative, and only the latter can grow at 42 °C (with an optimal growth temperature of 40 °C). These findings are corroborated by differences in 16S rDNA sequence and tRNA intergenic spacer lengths. Therefore, it is proposed to rename C. terrigena DNA group 2 [containing former Aquaspirillum aquaticum and E. Falsen (EF) group 10 strains] as Comamonas aquatica sp. nov., and C. terrigena DNA group 3 (containing former EF group 10 strains) as Comamonas kerstersii sp. nov.
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Aeromonas hydrophila subsp. ranae subsp. nov., isolated from septicaemic farmed frogs in Thailand
A group of seven sucrose-negative Aeromonas strains (referred to as group Au) isolated from the internal organs of septicaemic farmed frogs (Rana rugulosa) in Thailand was subjected to a polyphasic taxonomic study including fluorescent amplified fragment length polymorphism (FAFLP) and ERIC-PCR fingerprinting, 16S rDNA sequencing, microplate DNA–DNA hybridizations and extensive phenotypic characterization. Comparison of FAFLP and ERIC-PCR fingerprints indicated that the group Au isolates belonged to the species Aeromonas hydrophila DNA hybridization group (HG) 1 in which they represent a genotypic subgroup closely affiliated to A. hydrophila subsp. hydrophila and subsp. dhakensis. One representative of the Au group exhibited ⩾99·0 % 16S rDNA sequence similarity with the type strains of the two A. hydrophila subspecies. DNA–DNA hybridization with type and reference strains of all known Aeromonas taxa revealed that the Au group represented a homogeneous taxon that exhibited the highest relatedness with members of the two A. hydrophila subspecies, ranging from 75 to 93 %. Phenotypic characterization on the basis of 152 features further revealed that the Au group isolates differed from A. hydrophila subsp. hydrophila or subsp. dhakensis in a total of 13 biochemical properties. Of these, assimilation of l-glycine and isobutyrate as sole carbon source, acid production from salicin and d-sucrose, and aesculin hydrolysis were of diagnostic value. From the results of this study, it can be concluded that the Aeromonas frog isolates of the Au group represent a new subspecies of A. hydrophila, for which the name Aeromonas hydrophila subsp. ranae subsp. nov. is proposed. Its type strain is Au-1D12T (=LMG 19707T=CCUG 46211T).
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Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov.
More LessA format for the description of single novel species is proposed, which should facilitate the reviewing process by assisting the provision of data in a standardized form. The abstract must be short and concise, highlighting phylogenetic position, morphology and chemotaxonomy for genus affiliation, the genotypic and phenotypic basis for species differentiation, and the name and deposition numbers from two public culture collections in different countries for the type strain: A Gram-negative, rod-shaped, non-spore-forming bacterium (Iso 196T) was isolated from chicken faeces. On the basis of 16S rRNA gene sequence similarity, strain Iso 196T was shown to belong to the α-2 subclass of the Proteobacteria related to Ochrobactrum tritici (95·6 %), Ochrobactrum grignonense (95·0 %) and Ochrobactrum anthropi (94·6 %), and the phylogenetic distance from any validly described species within the genus Brucella was less than 95 %. Chemotaxonomic data (major ubiquinone – Q-10; major polyamines – spermidine and putrescine; major polar lipids – phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine; major fatty acids – C18 : 1 ω7c and C19 : 0 cyclo ω8c) supported the affiliation of strain Iso 196T to the genus Ochrobactrum. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Iso 196T from the four validly published Ochrobactrum species. Iso 196T therefore represents a new species, for which the name Ochrobactrum gallinifaecis sp. nov. is proposed, with the type strain Iso 196T (=DSM 15295T =CIP 107753T).
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- Gram-Positive Bacteria
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Reappraisal of the taxonomy of the Streptococcus bovis/Streptococcus equinus complex and related species: description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. macedonicus subsp. nov. and S. gallolyticus subsp. pasteurianus subsp. nov.
More Less‘Streptococcus bovis/Streptococcus equinus’ is a large bacterial complex including different species frequently isolated from infections of humans (Streptococcus gallolyticus, Streptococcus infantarius) or animals (S. bovis, S. equinus, Streptococcus alactolyticus). The separation of S. bovis into three different biotypes has been partially correlated with genetic differentiation. In addition, recent advances in bacterial phylogeny have led to the inclusion of Streptococcus macedonicus and Streptococcus waius in this complex. The aim of this study was to improve physiological differentiation between species related to the complex and to clarify their respective phylogenetic positions. In this study, physiological, genetic and phylogenetic analyses of a set of 88 streptococcal strains were performed. The diversity of strains of S. bovis biotype II was analysed, and it was confirmed that they belong to different species, either S. equinus or S. infantarius. It was demonstrated that S. gallolyticus, S. bovis biotype II.2, S. macedonicus and S. waius form a single DNA cluster separated into three different subspecies. They are delineated by different biochemical traits, limited DNA–DNA relatedness and noticeable divergence in 16S rDNA sequences. According to the current definition of species, the names S. gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. pasteurianus subsp. nov. and S. gallolyticus subsp. macedonicus subsp. nov. are proposed for these three subspecies.
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Reclassification of Lactobacillus maltaromicus (Miller et al. 1974) DSM 20342T and DSM 20344 and Carnobacterium piscicola (Collins et al. 1987) DSM 20730T and DSM 20722 as Carnobacterium maltaromaticum comb. nov.
More LessPhenotypic and genotypic characterizations of Lactobacillus maltaromicus strains DSM 20342T and DSM 20344 provided evidence for the reclassification of this species in the genus Carnobacterium. Moreover, phenotypic and genotypic comparisons made between L. maltaromicus and Carnobacterium piscicola highlighted that these two species should be considered synonyms. For these reasons, the species Carnobacterium maltaromaticum comb. nov. (type strain DSM 20342T=ATCC 27865T=CCUG 30142T=CIP 103135T=JCM 1154T=LMG 6903T=NRRL B-14852T) is proposed to accommodate L. maltaromicus and C. piscicola.
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Actinobaculum urinale sp. nov., from human urine
A hitherto undescribed Actinomyces-like bacterium was isolated from human urine. Based on its biochemical characteristics, the unidentified bacterium did not correspond to any currently described Actinomyces species or related taxa. Comparative 16S rRNA gene sequencing showed that the unknown bacterium exhibits a specific phylogenetic association with the genus Actinobaculum, but a sequence divergence of >5 % from the two currently recognized members of this genus, Actinobaculum schaalii and Actinobaculum suis, demonstrates that it represents a distinct species. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown bacterium from urine should be classified as a novel species, Actinobaculum urinale sp. nov. The type strain of Actinobaculum urinale is CCUG 46093T (=CIP 107424T).
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Enterococcus phoeniculicola sp. nov., a novel member of the enterococci isolated from the uropygial gland of the Red-billed Woodhoopoe, Phoeniculus purpureus
More LessA facultatively anaerobic, Gram-positive, coccoid, non-spore-forming, non-motile, catalase-negative bacterium was isolated from the uropygial (preen) gland of wild Red-billed Woodhoopoes (Phoeniculus purpureus) and designated strain JLB-1T. Physiological and biochemical testing suggested that this homofermentative, lactic-acid-producing bacterium could belong to the genus Enterococcus or the genus Streptococcus. Comparison of the 16S rRNA gene sequence of strain JLB-1T with other 16S rDNA sequences in the GenBank database by blast analysis showed that its closest relatives are Enterococcus faecium, Enterococcus avium and Enterococcus asini. Strain JLB-1T may be differentiated from these species by the fact that it does not produce acid from lactose, d-mannitol, d(+)-melezitose or d-sorbitol. Furthermore, it does not hydrolyse arginine or hippurate and cannot grow in the presence of 6·5 % NaCl or 40 % bile. It differs from the streptococci in that it does not lyse erythrocytes. Strain JLB-1T is a novel member of the enterococci, for which the name Enterococcus phoeniculicola sp. nov. is proposed. The type strain is JLB-1T (=ATCC BAA-412T=DSM 14726T).
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Halobacillus salinus sp. nov., isolated from a salt lake on the coast of the East Sea in Korea
More LessA Gram-positive, rod-shaped, endospore-forming, halophilic bacterium (strain HSL-3T) was isolated from a salt lake near Hwajinpo beach on the East Sea in Korea and was subjected to a polyphasic taxonomic study. Strain HSL-3T grew optimally in the presence of 2–10 % (w/v) NaCl. Strain HSL-3T showed poor growth in the absence of NaCl and grew in the presence of less than 23 % NaCl. The cell wall peptidoglycan type of strain HSL-3T was A4β based on l-orn–d-Asp. The predominant menaquinone found in strain HSL-3T was menaquinone-7 (MK-7). Strain HSL-3T had a cellular fatty acid profile containing large amounts of branched fatty acids; the major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strain HSL-3T was 45 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain HSL-3T falls within the radiation of the cluster comprising Halobacillus species. Strain HSL-3T exhibited levels of 16S rDNA similarity of 97·4–98·4 % to the type strains of Halobacillus species. Levels of DNA–DNA relatedness between strain HSL-3T and the type strains of all validly named Halobacillus species were in the range 7·3–9·2 %. On the basis of phenotypic and phylogenetic data and the genomic distinctiveness, strain HSL-3T (=KCCM 41590T=JCM 11546T) should be placed in the genus Halobacillus as the type strain of a novel species, for which the name Halobacillus salinus sp. nov. is proposed.
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Corynebacterium glaucum sp. nov.
More LessA bacterial strain, strain IMMIB R-5091T, isolated from a cosmetic dye was characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short-chain mycolic acids consistent with the genus Corynebacterium. Comparative 16S rRNA gene sequencing showed that the isolate constitutes a distinct subline within the genus Corynebacterium, displaying >2·6 % sequence divergence from established species. The isolate could be distinguished from other members of the genus Corynebacterium by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that strain IMMIB R-5091T (=DSM 44530T=NRRL B-24142T) be classified as the type strain of a novel species, Corynebacterium glaucum sp. nov.
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Marinilactibacillus psychrotolerans gen. nov., sp. nov., a halophilic and alkaliphilic marine lactic acid bacterium isolated from marine organisms in temperate and subtropical areas of Japan
More LessA novel marine lactic acid rod bacterium has been described for eight strains isolated from living and decomposing marine organisms collected from temperate and subtropical areas of Japan. The isolates were Gram-positive, catalase-negative, non-sporulating and motile with peritrichous flagella. They were slightly halophilic, highly halotolerant and alkaliphilic; the optimum NaCl concentration for growth was 2·0–3·75 % (w/v) with a range from 0 to 17·0–20·5 % (depending on the strain); the optimum pH was between 8·0 and 9·5 with a range from 6·0 to 10·0. They were psychrotolerant, growing well at −1·8 °C with a maximum at 40–45 °C and the optimum at 37–40 °C. Lactate yields were 87–100 % per consumed glucose; the residual products were formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. The product composition was markedly affected by the pH of fermentation medium; at higher pH, the yield of lactate decreased (60–65 % at pH 9·0) and that of other products increased conversely. The cell-wall peptidoglycan type was type A4β, Orn-d-Glu, whereas that of the genus Alkalibacterium, the phylogenetically closest lactic acid bacterium, was type A4β, Orn-d-Asp. The major cellular fatty acids were C16 : 0, C16 : 1Δ9, C18 : 0 and C18 : 1Δ9 (oleic acid). The G+C content of the DNA was 34·6–36·2 mol%. The eight isolates were phenotypically homogeneous and formed a single genomic species. The 16S rRNA gene sequence analysis indicated that the isolates constituted an independent phylogenetic lineage within the radiation of lactic acid bacteria with 96·2 % similarity to the genus Alkalibacterium. The secondary structure and the nucleotide sequence of the V6 region of the 16S rRNA were characteristic of the organism among other related lactic acid genera. On the bases of phenotypic and phylogenetic distinctness, the organism was proposed to belong to a new genus and species, Marinilactibacillus psychrotolerans gen. nov., sp. nov. The type strain, M13-2T (G+C=36·2 mol%), has been deposited in the IAM, NBRC, NCIMB and NRIC culture collections as IAM 14980T, NBRC 100002T, NCIMB 13873T and NRIC 0510T, respectively.
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Actinomadura namibiensis sp. nov.
More LessStrain HAG 010767T was isolated from desert soil from Namibia during a screening programme. On the basis of analysis of 16S rDNA, the principal amino acid of the peptidoglycan, cell-wall sugars, fatty acids and polar lipids, it was possible to identify this strain as a member of the genus Actinomadura. Although DNA–DNA reassociation experiments revealed 72 % DNA similarity between strain HAG 010767T and Actinomadura kijaniata DSM 43764T, significant differences in the colour of the mycelium and physiological properties indicate that strain HAG 010767T represents a novel species of this genus, for which the name Actinomadura namibiensis sp. nov. is proposed. The type strain is strain HAG 010767T (=DSM 44197T=NRRL B-24153T).
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Bacillus barbaricus sp. nov., isolated from an experimental wall painting
More LessIn a project concerning bacterial colonization of experimental wall paintings, a large number of isolates have been acquired with high similarities in their whole-cell protein patterns obtained after SDS-PAGE. Of this group, four strains, designated V2-BIII-A2T, V2-BI-A9, V2-BI-04 and V2-BII-A8, were chosen for further characterization. Banding patterns obtained after ERIC-PCR were barely distinguishable among these four strains, indicating their affiliation within a single species. The isolates also displayed nearly identical biochemical and physiological features. The chemotaxonomic characteristics, including polar lipids, quinone systems, cell-wall diamino acid composition and fatty acid profiles, were in good agreement with those of numerous previously described Bacillus species. 16S rDNA analysis of strain V2-BIII-A2T showed that this bacterium belongs to the genus Bacillus, with highest sequence similarities to Bacillus megaterium (94·6 %), Bacillus flexus (94·4 %) and the alkaliphilic Bacillus cohnii (94·2 %). Based on almost identical biochemical, physiological and chemotaxonomic traits, ERIC-PCR-generated genomic fingerprints and comparative 16S rDNA sequence analysis, it is demonstrated that the four isolates represent a novel species of the genus Bacillus, for which the name Bacillus barbaricus sp. nov. is proposed. The type strain is V2-BIII-A2T (=CCM 4982T=DSM 14730T).
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Streptomyces speibonae sp. nov., a novel streptomycete with blue substrate mycelium isolated from South African soil
More LessAn actinomycete with blue substrate mycelium was isolated from a soil sample in Cape Town, South Africa, and designated strain PK-BlueT. The colour of the substrate mycelium was not sensitive to changes in pH. The organism produced hairy spores in Spirales-type spore chains. Chemical taxonomy indicated that it belonged to the genus Streptomyces. Strain PK-BlueT produced no diffusible pigments other than melanin, grew at 45 °C, did not degrade adenine and exhibited no antibacterial activity against Enterococcus faecium, Escherichia coli or Pseudomonas aeruginosa. Analysis of its 16S rRNA gene sequence and the results of physiological tests showed that strain PK-BlueT (=DSM 41797T=ATCC BAA-411T) represents the type strain of a novel species of Streptomyces, for which the name Streptomyces speibonae sp. nov. is proposed.
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Allofustis seminis gen. nov., sp. nov., a novel Gram-positive, catalase-negative, rod-shaped bacterium from pig semen
An unknown Gram-positive, catalase-negative, facultatively anaerobic, non-spore-forming, rod-shaped bacterium originating from semen of a pig was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a directly cross-linked cell wall murein based on l-lysine and a DNA G+C content of 39 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified rod-shaped organism formed a hitherto unknown subline related, albeit loosely, to Alkalibacterium olivapovliticus, Alloiococcus otitis, Dolosigranulum pigrum and related organisms, in the low-G+C-content Gram-positive bacteria. However, sequence divergence values of >11 % from these recognized taxa clearly indicated that the novel bacterium represents a separate genus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig semen be classified as a new genus and species, Allofustis seminis gen. nov., sp. nov. The type strain is strain 01-570-1T (=CCUG 45438T=CIP 107425T).
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‘Candidatus Phytoplasma phoenicium’ sp. nov., a novel phytoplasma associated with an emerging lethal disease of almond trees in Lebanon and Iran
Almonds (Prunus amygdalus) represent an important crop in most Mediterranean countries. A new and devastating disease of almond trees in Lebanon was recently reported, characterized by the development of severe witches’-brooms on which no flowers or fruits developed, and leading to tree death within a few years. A phytoplasma was detected in diseased trees by PCR amplification of rRNA operon sequences, and RFLP patterns of amplified DNA indicated that the phytoplasma belonged to the pigeon pea witches’-broom (PPWB) group. In the present work, the presence of a phytoplasma in symptomatic plants was confirmed by electron microscopy; this phytoplasma was graft-transmissible to almond, plum and peach seedlings. The phytoplasma was characterized by sequence analysis of rRNA genes and was shown to be different from the phytoplasmas previously described in the PPWB group. A 16S rDNA phylogenetic tree identified the almond tree phytoplasma as a member of a distinct subclade of the class Mollicutes. Oligonucleotides have been defined for specific detection of the new phytoplasma. The almond phytoplasma from Lebanon was shown to be identical to a phytoplasma that induces a disease called ‘almond brooming’ in Iran, but different from another PPWB-group phytoplasma that infects herbaceous annual plants in Lebanon. Based on its unique properties, the name ‘Candidatus Phytoplasma phoenicium’ is proposed for the phytoplasma associated with almond witches’-broom in Lebanon and Iran.
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Amycolatopsis keratiniphila sp. nov., a novel keratinolytic soil actinomycete from Kuwait
A keratinolytic, nocardioform actinomycete, strain D2T, was isolated from Kuwait marsh soil by the bait technique using animal wool. Strain D2T was an aerobic, Gram-positive organism that produced light-grey aerial mycelium but no specific spore chains. 16S rDNA sequence analyses and chemotaxonomic markers were consistent with the classification of strain D2T in the genus Amycolatopsis, i.e. it had meso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as its diagnostic sugars, the polar lipids phosphatidylinositol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and diphosphatidylglycerol, menaquinone MK-9(H4) and an iso-/anteiso-branched fatty acid pattern combined with 10-methyl-branched and 2-hydroxy-branched fatty acids. Amycolatopsis japonica was the closest phylogenetic neighbour of strain D2T, showing 99·4 % 16S rDNA sequence similarity with the novel strain. A. japonica and strain D2T could be clearly separated from each other on the basis of their low DNA–DNA reassociation value (55·9 %). These data, together with its distinct physiological traits, led to the conclusion that strain D2T represented a novel species within the genus Amycolatopsis, for which the name Amycolatopsis keratiniphila (type strain D2T=DSM 44409T=NRRL B24117T) is proposed.
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- Unicellular Eukaryotes
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Rhodotorula benthica sp. nov. and Rhodotorula calyptogenae sp. nov., novel yeast species from animals collected from the deep-sea floor, and Rhodotorula lysiniphila sp. nov., which is related phylogenetically
More LessThree novel species of the genus Rhodotorula are described. Rhodotorula benthica sp. nov. (type strain JCM 10901T =SY-91T) and Rhodotorula calyptogenae sp. nov. (type strain JCM 10899T =SY-86T) were respectively isolated from the tubeworm Lamellibrachia sp. and the giant white clam Calyptogena sp., collected from the deep-sea floor of the Pacific Ocean off Japan. Rhodotorula lysiniphila sp. nov. (type strain JCM 5951T) is proposed for strains isolated previously in Japan and Pakistan. The three species were placed phylogenetically into a species complex comprising Rhodotorula laryngis, Rhodotorula minuta, Rhodotorula pallida and Rhodotorula slooffiae. R. minuta and R. slooffiae are closely related in both the D1/D2 region of the 26S rDNA and the internal transcribed spacer and 5·8S rDNA regions. R. benthica and R. laryngis were closer to R. pallida based on the D1/D2 region. Other relationships were not clear.
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Cryptococcus nemorosus sp. nov. and Cryptococcus perniciosus sp. nov., related to Papiliotrema Sampaio et al. (Tremellales)
More LessThree mycocinogenic strains representing the genus Cryptococcus were isolated on glucuronate agar from plants and turf collected in the Prioksko-terrasny biosphere reserve (Russia). These isolates fit the standard description of Cryptococcus laurentii, but differ from its type strain in both their mycocin-sensitivity profiles and the killing patterns of their mycocins. Sequence analyses of the D1/D2 domain of the 26S rDNA and of the internal transcribed spacer region confirmed that these isolates represent two novel species, for which the names Cryptococcus nemorosus sp. nov. (type strain VKM Y-2906T) and Cryptococcus perniciosus sp. nov. (type strain VKM Y-2905T) are proposed. Morphological, physiological and biochemical characteristics, as well as mycocinotyping and molecular analysis, show a close affinity between these two novel anamorphic species and the teleomorphic species Papiliotrema bandonii (Tremellales).
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- Evolution, Phylogeny And Biodiversity
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Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal β-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing
Whilst searching for a molecular method to identify the different species of Raoultella and Klebsiella oxytoca, it was observed that the OXY-1 and OXY-2 β-lactamase-producing K. oxytoca isolates displayed two distinguishable enterobacterial repetitive intergenic consensus (ERIC)-1R profiles. It was hypothesized that the two groups of chromosomal β-lactamases might correspond to two groups of strains in the K. oxytoca taxon. To confirm this hypothesis, clinical isolates and reference strains of K. oxytoca were studied by determination of the sequence of their bla OXY genes, and of a partial fragment of their 16S rRNA (387 bp) and rpoB (512 bp) genes. The sequence data were phylogenetically analysed by using the parsimony method. Four clinical isolates possessed a bla OXY-1 gene and nine possessed a bla OXY-2 gene. The mean percentage of rpoB and 16S rRNA gene identity was >99 % within each group of strains, whereas it was 96·56±0·24 % for rpoB genes and 97·80±0·22 % for 16S rRNA genes between the group of strains harbouring the bla OXY-1 gene and the group harbouring the bla OXY-2 gene. The phylogenetic tree resulting from combined analysis of the 16S rRNA and rpoB datasets showed that the K. oxytoca isolates were monophyletic and separated into two clades; these clades included strains with either the bla OXY-1 gene or the bla OXY-2 gene. This result was supported with high bootstrap values of 97 and 99 %, respectively. Moreover, the two groups of strains displayed distinct ERIC-1R profiles, with bands characteristic of each profile. Thus, the chromosomal bla OXY gene sequence is able to delineate not only two groups of β-lactamases in K. oxytoca, but also two clades in the K. oxytoca taxon, in a manner similar to the sequence of housekeeping genes. These results suggest that K. oxytoca should be divided into two genetic groups, group OXY-1 represented by K. oxytoca strain SL781 (=CIP 104963) and group OXY-2 by K. oxytoca strain SL911 (=CIP 106098).
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Phylogenetic relationships between Bacillus species and related genera inferred from comparison of 3′ end 16S rDNA and 5′ end 16S–23S ITS nucleotide sequences
More LessThe nucleotide sequences of the 3′ end of the 16S rDNA and the 16S–23S internal transcribed spacer (ITS) of 40 Bacillaceae species were determined. These included 21 Bacillus, 9 Paenibacillus, 6 Brevibacillus, 2 Geobacillus, 1 Marinibacillus and 1 Virgibacillus species. Comparative sequence analysis of a 220 bp region covering a highly conserved 150 bp sequence located at the 3′ end of the 16S rRNA coding region and a conserved 70 bp sequence located at the 5′ end of the 16S–23S ITS of the 40 species and six sequences available in GenBank were used to infer the phylogenetic relationships between all 46 taxa. When a maximal distance (D max, where D refers to the number of nucleotide substitutions per site) of 0·31 was introduced as a threshold to determine groupings, 10 phylogenetically distinct clusters were revealed. Twenty-six Bacillus species were separated in seven groups (I, II, III, IV, V, VI and X), but Bacillus circulans remained ungrouped. All six Brevibacillus species under study were in Group VII. The nine Paenibacillus species fell into two distinct groups (VIII and IX). Species with D max values within 0·05 were considered to be very closely related. These were Bacillus psychrophilus and Bacillus psychrosaccharolyticus in Group II; ‘Bacillus maroccanus’ and Bacillus simplex in Group II; Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus mojavensis and Bacillus subtilis in Group VI; Bacillus fusiformis and Bacillus sphaericus in Group VI; Brevibacillus brevis and Brevibacillus formosus in Group VII; Paenibacillus gordonae and Paenibacillus validus in Group VIII; and Bacillus anthracis, Bacillus cereus, Bacillus mycoides and Bacillus thuringiensis in Group X. The phylogenetic classification presented here is, in general, in agreement with current classifications based on phenotypic and molecular data. Our findings suggest, however, that in some cases, further divisions or, conversely, further groupings might be warranted. Should current classifications be re-examined in the light of our results, D max values of 0·31 and 0·05, as exemplified here, may prove useful threshold values for the grouping of Bacillaceae into taxa akin to genera and species, respectively. These D max thresholds may also reveal, in a different way, bacterial species for which further characterization might be warranted for proper classification and/or reassignment.
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DNA–DNA hybridization study of Burkholderia species using genomic DNA macro-array analysis coupled to reverse genome probing
The present study was aimed at simplifying procedures to delineate species and identify isolates based on DNA–DNA reassociation. DNA macro-arrays harbouring genomic DNA of reference strains of several Burkholderia species were produced. Labelled genomic DNA, hybridized to such an array, allowed multiple relative pairwise comparisons. Based on the relative DNA–DNA relatedness values, a complete data matrix was constructed and the ability of the method to discriminate strains belonging to different species was assessed. This simple approach led successfully to the discrimination of Burkholderia mallei from Burkholderia pseudomallei, but also discriminated Burkholderia cepacia genomovars I and III, Burkholderia multivorans, Burkholderia pyrrocinia, Burkholderia stabilis and Burkholderia vietnamiensis. Present data showed a sufficient degree of congruence with previous DNA–DNA reassociation techniques. As part of a polyphasic taxonomic scheme, this straightforward approach is proposed to improve species definition, especially for application in the rapid screening necessary for large numbers of clinical or environmental isolates.
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Missing links in the divergence of Chlamydophila abortus from Chlamydophila psittaci
Pathological and serological evidence and DNA–DNA reassociation data indicate that Chlamydophila psittaci and Chlamydophila abortus are separate species. C. psittaci causes avian systemic disease and C. abortus causes abortion. Both previously belonged to Chlamydia psittaci are associated with zoonotic and enzootic outbreaks. Genetic studies suggest that they are closely related and because of the recent availability of diverse C. psittaci strains and comparative data for several genes, it was possible to explore this relationship. The parrot C. psittaci strain 84/2334 was found to have DNA sequences that were identical to an extrachromosomal plasmid in duck C. psittaci strain N352, to rnpB in strain R54 from a brown skua and to the rrn intergenic spacer in parakeet strain Prk/Daruma (from Germany, Antarctica and Japan, respectively). Analysis of ompA and the rrn spacer revealed progressive diversification of the strains, with 84/2334 resembling what might have been a recent ancestor of C. abortus. Another C. psittaci strain (VS225) showed evidence of having undergone convergent evolution towards the C. abortus-like genotype, whereas strain R54 diverged independently. For the first time, these studies link C. abortus in an evolutionary context to the C. psittaci lineage. It has been concluded that C. abortus diverged from C. psittaci, and so strain R54 was designated a C. psittaci strain. It is recommended that characterization of C. psittaci and C. abortus strains should utilize more than a single method and more than a single gene.
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Phylogenetic analysis of members of the genus Aeromonas based on gyrB gene sequences
More LessThe phylogenetic relationships of all known species of the genus Aeromonas were investigated by using the sequence of gyrB, a gene that encodes the B-subunit of DNA gyrase. Nucleotide sequences of gyrB were determined from 53 Aeromonas strains, including some new isolates, which were also characterized by analysis of the 16S rDNA variable regions. The results support the recognition of the family Aeromonadaceae, as distinct from Plesiomonas shigelloides and other enteric bacteria. This phylogenetic marker revealed strain groupings that are consistent with the taxonomic organization of all Aeromonas species described to date. In particular, gyrB results agreed with 16S rDNA analysis; moreover, the former showed a higher capacity to differentiate between species. The present analysis was useful for the elucidation of reported discrepancies between different DNA–DNA hybridization sets. Additionally, due to the sequence diversity found at the intraspecies level, gyrB is proposed as a useful target for simultaneous identification of species and strains. In conclusion, the gyrB gene has proved to be an excellent molecular chronometer for phylogenetic studies of the genus Aeromonas.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Opinions
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Valid publication of the genus name Thermodesulfobacterium and the species names Thermodesulfobacterium commune (Zeikus et al. 1983) and Thermodesulfobacterium thermophilum (ex Desulfovibrio thermophilus Rozanova and Khudyakova 1974). Opinion 71
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that the date of valid publication of the genus name Thermodesulfobacterium and of the species names Thermodesulfobacterium commune and Thermodesulfobacterium thermophilum is 1995. Thermodesulfobacterium mobile Rozanova and Pivovarova 1988 is an illegitimate, later synonym of Thermodesulfobacterium thermophilum.
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Strain DSM 6035 is the type strain of Lactobacillus panis (Wiese et al. 1996). Opinion 72
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that strain DSM 6035 is the type strain of Lactobacillus panis with the consequence that the name Lactobacillus panis has been validly published.
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Paenibacillus durus (Collins et al. 1994, formerly Clostridium durum Smith and Cato 1974) has priority over Paenibacillus azotofixans (Seldin et al. 1984). Opinion 73
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that the name Paenibacillus durus has priority over Paenibacillus azotofixans, and that the latter is a later synonym of the former. The type strain is therefore strain ATCC 27763 (=DSM 1735).
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Strain NCIMB 13488 may serve as the type strain of Halorubrum trapanicum. Opinion 74
More LessThe Judicial Commission of the International Committee on Systematics of Prokaryotes decided that strain NCIMB 13488 may serve as the type strain of Halorubrum trapanicum.
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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 69 (2019)
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Volume 2 (1952)
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Volume 1 (1951)