- Volume 57, Issue 4, 2007
Volume 57, Issue 4, 2007
- Notification List
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Notification that new names and new combinations have appeared in volume 57, 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 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). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Nocardia ninae sp. nov., isolated from a bronchial aspirate
A Gram-positive and acid-fast filamentous bacterium (OFN 02.72T) was isolated from a bronchial aspirate from a 53-year-old patient. Chemotaxonomic data supported the affiliation of this organism to the genus Nocardia, and the phenotypic characteristics demonstrated that the strain differed from all previously described Nocardia species. Restriction enzyme analysis of the hsp65 gene (encoding the 65 kDa heat-shock protein) and sequencing of the 16S rRNA and hsp65 genes confirmed that this isolate is unique. The most closely related type strains were Nocardia alba YIM 30243T (=DSM 44684T) and Nocardia jejuensis N3-2T (=JCM 13281T) (with 16S rRNA gene sequence similarities of 98.3 and 97.2 %, respectively). On the basis of this polyphasic study, strain OFN 02.72T represents a novel species within the genus Nocardia, for which the name Nocardia ninae sp. nov. is proposed. The type strain is OFN 02.72T (=CIP 108955T=DSM 44978T).
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Leucobacter iarius sp. nov., in the family Microbacteriaceae
A novel Gram-positive bacterium, strain 40T, was isolated in the course of identifying bacteria from infective juveniles of the entomopathogenic nematode Steinernema thermophilum. Based on 16S rRNA gene analysis, strain 40T was found to be related to the type strains of recognized species of the genus Leucobacter, family Microbacteriaceae. The 16S rRNA gene sequence similarity values of strain 40T and Leucobacter albus IAM 14851T, Leucobacter luti LMG 23118T, Leucobacter alluvii LMG 23117T, Leucobacter komagatae DSM 8803T, Leucobacter chromiireducens CIP 108389T and Leucobacter aridicollis CIP 108388T, respectively, were 97.3, 97.5, 97.6, 97.6, 97.6 and 98.5 %. Chemotaxonomic analysis also supported the affiliation of strain 40T to the genus Leucobacter: the major menaquinone was MK-11, the peptidoglycan cross-linkage was of the B-type, the cell wall diamino acid was l-diaminobutyric acid and the major fatty acids were anteiso-C15 : 0 (42 %), anteiso-C17 : 0 (34 %) and iso-C16 : 0 (16 %). Based upon the biochemical and genomic analyses, strain 40T is sufficiently distinct from the type strains of recognized Leucobacter species to warrant the description of a novel species, for which the name Leucobacter iarius sp. nov. is proposed. The type strain is strain 40T (=DSM 17402T=CIP 108831T).
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Aeromicrobium panaciterrae sp. nov., isolated from soil of a ginseng field in South Korea
More LessA Gram-positive, rod-shaped, non-spore-forming and strictly aerobic bacterium (Gsoil 161T) was isolated from soil of a ginseng field in Pocheon Province, South Korea. The novel isolate was characterized using a polyphasic approach in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 161T was shown to belong to the family Nocardioidaceae and was related to Aeromicrobium marinum (98.0 % similarity to the type strain), Aeromicrobium alkaliterrae (97.6 %), Aeromicrobium fastidiosum (97.0 %) and Aeromicrobium erythreum (96.7 %); the sequence similarity with other species within the family was less than 94.4 %. It was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and C16 : 0, 10-methyl C18 : 0 (tuberculostearic acid), C16 : 0 2-OH, 10-methyl C17 : 0 and 10-methyl-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 65.5 mol%. These chemotaxonomic properties and phenotypic characteristics support the affiliation of strain Gsoil 161T to the genus Aeromicrobium. Results of physiological and biochemical tests enabled strain Gsoil 161T to be differentiated genotypically and phenotypically from currently known Aeromicrobium species. Therefore, strain Gsoil 161T represents a novel species, for which the name Aeromicrobium panaciterrae sp. nov. is proposed. The type strain is strain Gsoil 161T (=KCTC 19131T=DSM 17939T=CCUG 52476T).
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Microlunatus ginsengisoli sp. nov., isolated from soil of a ginseng field
More LessA Gram-positive, aerobic, coccus-shaped, non-endospore-forming bacterium (Gsoil 633T) was isolated from soil from a ginseng field in Pocheon province in South Korea. The novel isolate was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain Gsoil 633T was shown to belong to the family Propionibacteriaceae. The closest phylogenetic relative was Microlunatus phosphovorus DSM 19555T, with 96.1 % sequence similarity; the sequence similarity to other members of the family was less than 95.4 %. The isolate was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 69.8 mol%. The morphological and chemotaxonomic properties of the isolate were consistent with those of M. phosphovorus, but the results of physiological and biochemical tests allowed the phenotypic differentiation of strain Gsoil 633T from this species. Therefore, strain Gsoil 633T represents a novel species, for which the name Microlunatus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 633T (=KCTC 13940T=DSM 17942T).
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Actinoplanes couchii sp. nov.
More LessA Gram-positive bacterium, strain GW8-1761T, was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761T belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165T (98.9 %), A. rectilineatus IFO 13941T (98.5 %), A. palleronii JCM 7626T (97.8 %), A. utahensis IFO 13244T (97.6 %) and A. cyaneus DSM 46137T (97.6 %). Strain GW8-1761T could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C15 : 0, C16 : 0, C16 : 0 iso, C17 : 1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH)] supported the affiliation of strain GW8-1761T to the genus Actinoplanes. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761T from the most closely related species. Strain GW8-1761T therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761T (=DSM 45050T=CIP 109316T).
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Granulicoccus phenolivorans gen. nov., sp. nov., a Gram-positive, phenol-degrading coccus isolated from phenol-degrading aerobic granules
A Gram-positive bacterium, designated strain PG-02T, was isolated by serial dilution from aerobic granules obtained from a laboratory-scale sequencing batch reactor for bioremediation of phenolic wastewater. Strain PG-02T grew axenically as cocci and is an oxidase-negative and catalase-positive, non-motile facultative anaerobe. It does not reduce nitrate and grows between 15 and 37 °C, with an optimum temperature of 30 °C. The pH range for growth is between 5.0 and 8.5, with an optimum pH of 7.0. Strain PG-02T contains type A3γ peptidoglycan (ll-A2pm←Gly with alanine at position 1 of the peptide subunit). The G+C content of the DNA is 69 mol%. Menaquinone MK-9(H4) was the major isoprenoid quinone. The polar lipids included diphosphatidylglycerol and phosphatidylglycerol, while 13-methyltetradecanoic acid (i-C15 : 0) and 1,1-dimethoxy-iso-pentadecane (i-C15 : 0 DMA) were the major components in whole-cell methanolysates. PG-02T stained positively for intracellular polyphosphate granules but not poly-β-hydroxyalkanoates. It produces capsular material and possesses an autoaggregation capability. Phenotypic and 16S rRNA gene sequence analyses showed that PG-02T differed from its closest phylogenetic relatives, namely members of the suborder Propionibacterineae, which includes the genera Tessaracoccus, Microlunatus, Luteococcus, Micropruina, Propionibacterium, Propioniferax, Nocardioides, Friedmanniella and Aeromicrobium, and that it should be placed in a new genus and species as Granulicoccus phenolivorans gen. nov., sp. nov. The type strain of Granulicoccus phenolivorans is PG-02T (=ATCC BAA-1292T=DSM 17626T).
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Nocardioides marinus sp. nov.
More LessA Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14T, was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14T belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14T and the type strains of recognized species of the genus Nocardioides were low (94.1–97.1 %). Strain CL-DD14 T grew over the pH range 6–9 and temperature range 10–40 °C. The strain grew at NaCl concentrations of 0.5–8 % (w/v) with optimum growth at 1–3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the major cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14T (=KCCM 42321T=DSM 18248T).
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Ruania albidiflava gen. nov., sp. nov., a novel member of the suborder Micrococcineae
More LessA Gram-positive, coccoid, non-spore-forming bacterium, designated strain 3-6T, was isolated from farmland soil and subjected to a polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbour was the type strain of Georgenia muralis (94.2 % 16S rRNA gene sequence similarity). Chemotaxonomic characteristics of strain 3-6T were as follows: the major menaquinone was MK-8(H4); the polar lipids consisted mainly of diphosphatidylglycerol, phosphatidylglycerol and one unknown glycolipid; the predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0; mycolic acids were absent. A new murein type, l-lys–gly–l-glu–l-Glu (A4α), was found in the peptidoglycan of the cell wall. The DNA G+C content was 69.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, it is suggested that strain 3-6T represents a novel species of a new genus within the suborder Micrococcineae, for which the name Ruania albidiflava gen. nov., sp. nov. is proposed. The type strain of Ruania albidiflava is 3-6T (=CGMCC 4.3142T=DSM 18029T=JCM 13910T=PCM 2644T).
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Lechevalieria fradiae sp. nov., a novel actinomycete isolated from soil in China
More LessThe taxonomic position of a soil isolate, strain Z6T, was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genus Lechevalieria. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Lechevalieria and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genus Lechevalieria and was more closely related to the type strain of Lechevalieria aerocolonigenes than to that of Lechevalieria flava. Strain Z6T could be distinguished from both these strains using DNA–DNA relatedness data and by a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain Z6T should be assigned to the genus Lechevalieria as a representative of a novel species. The name proposed for this new taxon is Lechevalieria fradiae sp. nov. The type strain is Z6T (=CGMCC 4.3506T=JCM 14205T).
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Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier
More LessA novel psychrotolerant, Gram-positive, yellow-pigmented, aerobic bacterium, strain 0549T, was isolated from the China No. 1 glacier. The cells of the isolate were catalase-positive, motile, irregular rods. The diamino acid content of the cell-wall peptidoglycan was determined to be 2,4-diaminobutyric acid. Strain 0549T was able to grow at 4–27 °C, with optimum growth occurring at 20–22 °C. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 67 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 0549T belonged to the genus Cryobacterium and exhibited 96.5 % similarity to Cryobacterium psychrophilum JCM 1463T. On the basis of the phenotypic, chemotaxonomic and phylogenetic properties and the DNA–DNA relatedness data, strain 0549T represents a novel species of the genus Cryobacterium, for which the name Cryobacterium psychrotolerans is proposed. The type strain is 0549T (=CGMCC 1.5382T=JCM 13925T).
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- Archaea
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Haloferax larsenii sp. nov., an extremely halophilic archaeon from a solar saltern
More LessThree strains of Gram-negative, aerobic, neutrophilic, extremely halophilic archaea, designated ZJ206T, ZJ203 and ZJ204, were isolated from a solar saltern in Zhe-Jiang Province, China. Phenotypically and on the basis of 16S rRNA gene sequences, the strains were very similar. Comparative 16S rRNA gene analysis revealed 96.4–97.4 % sequence similarity to members of the genus Haloferax. The major polar lipids were C20C20 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, diglycosyl glycerol diether and sulfated diglycosyl diether. The DNA G+C content of strain ZJ206T was 62.2 mol%. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from closely related species. Therefore the isolates should be classified as members of a novel species, for which the name Haloferax larsenii sp. nov. is proposed. The type strain is ZJ206T (=CGMCC 1.5347T=JCM 13917T).
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Natronorubrum sulfidifaciens sp. nov., an extremely haloalkaliphilic archaeon isolated from Aiding salt lake in Xin-Jiang, China
More LessAn extremely haloalkaliphilic archaeon, strain AD2T, was isolated from Aiding salt lake in Xin-Jiang, China. Strain AD2T required at least 12 % NaCl for growth. MgCl2 was not required. The isolate was able to grow over a pH range of 8.0–10.0 and temperature range of 20–55 °C, with optimal growth at pH 8.7–9.2 and 44–47 °C. The major polar lipids of strain AD2T were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester; glycolipids were not detected. Analysis of its 16S rRNA gene sequence indicated that strain AD2T was phylogenetically related to members of the genus Natronorubrum, with sequence similarities to the type strains of Natronorubrum bangense, Natronorubrum tibetense and Natronorubrum aibiense of 97.1, 95.9 and 96.1 %, respectively. The G+C content of its DNA was 60.9 mol% (T m). Levels of DNA–DNA relatedness between strain AD2T and the type strains of Nrr. bangense, Nrr. tibetense and Nrr. aibiense were 49, 38 and 41 %, respectively. It was concluded that strain AD2T represents a novel species of the genus Natronorubrum, for which the name Natronorubrum sulfidifaciens sp. nov. is proposed. The type strain is AD2T (=CGMCC 1.6307T=JCM 14089T).
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Haloplanus natans gen. nov., sp. nov., an extremely halophilic, gas-vacuolate archaeon isolated from Dead Sea–Red Sea water mixtures in experimental outdoor ponds
More LessTo study biological phenomena in the Dead Sea and to simulate the effects of mixing Dead Sea water with Red Sea water, experimental mesocosms were operated at the Dead Sea Works at Sedom, Israel. Dense communities of red halophilic archaea developed in mesocosms filled with 80 % Dead Sea water and 20 % Red Sea water after enrichment with phosphate. The most common type of colonies isolated from these brines belonged to the genus Halorubrum. A few white–pinkish opaque colonies contained pleomorphic flat cells with gas vesicles. Three strains isolated from the latter colonies were characterized in depth. Their 16S rRNA gene sequences showed only 91 % similarity to the closest cultured relative (Haloferax mediterranei), indicating that the new strains represent a novel species of a new genus. The name Haloplanus natans gen. nov., sp. nov. is proposed for this novel organism. The type strain of Haloplanus natans is RE-101T (=DSM 17983T=JCM 14081T).
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Ignicoccus hospitalis sp. nov., the host of ‘Nanoarchaeum equitans’
A novel chemolithoautotrophic and hyperthermophilic member of the genus Ignicoccus was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland. The new isolate showed high similarity to the two species described to date, Ignicoccus islandicus and Ignicoccus pacificus, in its physiological properties as well as in its unique cell architecture. However, phylogenetic analysis and investigations on the protein composition of the outer membrane demonstrated that the new isolate was clearly distinct from I. islandicus and I. pacificus. Furthermore, it is the only organism known so far which is able to serve as a host for ‘Nanoarchaeum equitans’, the only cultivated member of the ‘Nanoarchaeota’. Therefore, the new isolate represents a novel species of the genus Ignicoccus, which we name Ignicoccus hospitalis sp. nov. (type strain KIN4/IT=DSM 18386T=JCM 14125T).
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- Bacteroidetes
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Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell
More LessA Gram-negative, non-motile, filamentous, rod-shaped, non-spore-forming bacterium (strain F2T) was isolated from the surface of an electricity-harvesting electrode incubated in marine sediments. Strain F2T does not contain c-type cytochromes, flexirubin or carotenoids. It is a facultative anaerobe that can ferment sugars by using a mixed acid fermentation pathway and it can grow over a wide range of temperatures (4–42 °C). The DNA G+C (44.9 mol%) content and chemotaxonomic characteristics (major fatty acids, a-15 : 0 and 15 : 0) were consistent with those of species within the phylum Bacteroidetes. Phylogenetic analysis of the 16S rRNA nucleotide and elongation factor G amino acid sequences indicated that strain F2T represents a unique phylogenetic cluster within the phylum Bacteroidetes. On the basis of 16S rRNA gene sequence phylogeny, the closest relative available in pure culture, Alkaliflexus imshenetskii, is only 87.5 % similar to strain F2T. Results from physiological, biochemical and phylogenetic analyses showed that strain F2T should be classified as a novel genus and species within the phylum Bacteroidetes, for which the name Prolixibacter bellariivorans gen. nov., sp. nov. is proposed. The type strain is F2T (=ATCC BAA-1284T=JCM 13498T).
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Echinicola vietnamensis sp. nov., a member of the phylum Bacteroidetes isolated from seawater
The taxonomic position of a novel marine, heterotrophic, gliding, halotolerant and light-pink-pigmented bacterium, designated strain KMM 6221T, was examined by using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KMM 6221T is affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, with levels of similarity of 94.7–95.0 % to strains of Echinicola pacifica. Growth of strain KMM 6221T was observed with 0–15 % NaCl and at 6–44 °C. The DNA G+C content of strain KMM 6221T was 45.9 mol%. On the basis of molecular distinctiveness supported by phenotypic and chemotaxonomic data, strain KMM 6221T is considered to represent a novel species of the genus Echinicola, for which the name Echinicola vietnamensis sp. nov. is proposed. The type strain is KMM 6221T (=DSM 17526T=LMG 23754T).
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Tamlana crocina gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae, isolated from beach sediment in Korea
More LessA Gram-negative, aerobic, saffron-coloured marine bacterium, designated HST1-43T, was isolated from beach sediment on the coast in Jeju, Korea, and its taxonomic status was established in a polyphasic study. 16S rRNA gene sequence analyses revealed that the isolate belonged to the family Flavobacteriaceae. The closest phylogenetic neighbours of strain HST1-43T were members of the genera Algibacter, Gaetbulibacter and Yeosuana, with levels of sequence similarity in the range 96.3–96.5 %. The isolate was non-motile and required sea salts or natural seawater for growth. The optimum temperature and pH ranges for growth were 25–30 °C and pH 6.1–8.1, respectively. MK-6 was the major menaquinone. The dominant cellular fatty acids were iso-C15 : 0, C18 : 0, C16 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH. The DNA G+C content was 36.2±0.4 mol%. On the basis of phylogenetic distance and phenotypic characteristics, the isolate is considered to represent a novel genus and species in the family Flavobacteriaceae, for which the name Tamlana crocina gen. nov., sp. nov. is proposed. The type strain is HST1-43T (=KCTC 12721T=JCM 14021T).
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Zeaxanthinibacter enoshimensis gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae, isolated from seawater off Enoshima Island, Japan
More LessA novel marine, Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, gliding and oxidase- and catalase-positive bacterium (strain TD-ZE3T) was isolated from a seawater sample collected off the Pacific coastline of Japan near Enoshima Island (Fujisawa, Kanagawa). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TD-ZE3T belonged to a distinct lineage in the family Flavobacteriaceae, with 90.5 % sequence similarity with the nearest species Robiginitalea biformata. Strain TD-ZE3T could be distinguished from other members of the family Flavobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. The DNA G+C content was 46.5 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c and menaquinone-6 was the only respiratory quinone. Zeaxanthin was the major carotenoid pigment produced; flexirubin-type pigments were not produced. Strain TD-ZE3T degraded gelatin, starch and Tween 80. Based on its unique phenotypic, genotypic and phylogenetic features, strain TD-ZE3T represents a novel taxon, for which the name Zeaxanthinibacter enoshimensis gen. nov., sp. nov. is proposed. The type strain is TD-ZE3T (=NBRC 101990T=CCUG 53613T).
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Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China
More LessStrain A54T was isolated from rhizospheric soil of turf grasses irrigated with reclaimed water in Taoranting Park, Beijing, China. Phenotypic, chemotaxonomic and polygenetic analyses established the affiliation of the isolate to the genus Dyadobacter. Strain A54T possessed 97.7, 94.4 and 94.7 % 16S rRNA gene sequence similarity with respect to the type strains of Dyadobacter fermentans, D. hamtensis and D. crusticola, respectively. Furthermore, DNA–DNA hybridization did not show significant relatedness (<25 % hybridization) between strain A54T and D. fermentans ATCC 700827T. Therefore, these results indicate that strain A54T belongs to a novel species of the genus Dyadobacter, for which the name Dyadobacter beijingensis sp. nov. is proposed. The type strain is strain A54T (=CGMCC 1.6375T=JCM 14200T).
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Prevotella timonensis sp. nov., isolated from a human breast abscess
More LessGram-negative anaerobic rods were isolated from a human breast abscess. Based on genotypic and phenotypic characteristics, the novel strain belonged to the genus Prevotella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that it was closely related to Prevotella buccalis (94 % 16S rRNA gene sequence similarity), Prevotella salivae (90 %) and Prevotella oris (89.1 %). The major cellular fatty acid was C14 : 0 (19.5 %). The new isolate represents a novel species in the genus Prevotella, for which the name Prevotella timonensis sp. nov. is proposed. The type strain is strain 4401737T (=CIP 108522T=CCUG 50105T).
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- Proteobacteria
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Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov.
More Less[Pasteurella] trehalosi is an important pathogen of sheep, being primarily associated with serious systemic infections in lambs but also having an association with pneumonia. The aim of the present investigation was to characterize a broad collection of strains tentatively identified as [P.] trehalosi in order to reclassify and rename this taxon to support improvements in our understanding of the pathogenesis and epidemiology of this important organism. The type strain for [P.] trehalosi, strain NCTC 10370T, was included along with 42 field isolates from sheep (21), cattle (14), goats (1), roe deer (3) and unknown sources (3). An extended phenotypic characterization was performed on all 43 strains. Amplified fragment length polymorphism (AFLP) was also performed on the isolates. Two of the field isolates were subjected to 16S rRNA gene sequencing. These sequences, along with five existing sequences for [P.] trehalosi strains and 12 sequences for other taxa in the family Pasteurellaceae, were subjected to a phylogenetic analysis. All the isolates and the reference strains were identified as [P.] trehalosi. A total of 17 out of 22 ovine isolates produced acid from all glycosides, while only four out of 14 bovine isolates produced acid from all glycosides. All 22 ovine isolates were haemolytic and CAMP-positive, while no other isolate was haemolytic and only two bovine isolates were CAMP-positive. Nineteen AFLP types were found within the [P.] trehalosi isolates. All [P.] trehalosi isolates shared at least 70 % similarity in AFLP patterns. The largest AFLP type included the type strain and 7 ovine field isolates. Phylogenetic analysis indicated that the seven strains studied (two field isolates and the five serovar reference strains) are closely related, with 98.6 % or higher 16S rRNA gene sequence similarity. As both genotypic and phenotypic testing support the separate and distinct nature of these organisms, we propose the transfer of [P.] trehalosi to a new genus, Bibersteinia, as Bibersteinia trehalosi comb. nov. The type strain is NCTC 10370T (=ATCC 29703T). Bibersteinia trehalosi can be distinguished from the existing genera of the family by the observation of only nine characteristics; catalase, porphyrin, urease, indole, phosphatase, acid from dulcitol, (+)-d-galactose, (+)-d-mannose and (+)-d-trehalose.
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Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water
More LessA total of 34 Halomonas strains were isolated from saline water in Anmyeondo, Korea. Ten of these strains, considered to belong to novel species, were subjected to a polyphasic taxonomic investigation. The strains were Gram-negative, moderately halophilic, motile and non-spore-forming rods that contained Q-9 as the predominant ubiquinone and C18 : 1 ω7c, C16 : 0 and either summed feature 4 (C16 : 1 ω7c/C15 : 0 iso 2-OH) or C19 : 0 cyclo ω8c as the major fatty acids. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the ten isolates formed four separate lineages in the genus Halomonas. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that they represent four novel species in the genus Halomonas, for which the names Halomonas gomseomensis sp. nov. (type strain M12T=KCTC 12662T=DSM 18042T), Halomonas janggokensis sp. nov. (type strain M24T=KCTC 12663T=DSM 18043T), Halomonas salaria sp. nov. (type strain M27T=KCTC 12664T=DSM 18044T) and Halomonas denitrificans sp. nov. (type strain M29T=KCTC 12665T=DSM 18045T) are proposed.
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Sulfitobacter litoralis sp. nov., a marine bacterium isolated from the East Sea, Korea
A Gram-negative, aerobic, halophilic bacterium, designated strain Iso 3T, was isolated from the East Sea in Korea. Strain Iso 3T was motile by means of polar flagella, occasionally formed rosette-like aggregates and contained 18 : 1ω7c as the dominant cellular fatty acid. Strain Iso 3T grew at NaCl concentrations of 1–10 % and temperatures of 4–30 °C. The optimal growth temperature was 20 °C. Analysis of the 16S rRNA gene sequence revealed that this strain is affiliated with a subcluster of the Alphaproteobacteria. However, strain Iso 3T generated metabolic energy by sulfide oxidation. The 16S rRNA gene sequence similarity between strain Iso 3T and the type strain of the most closely related species, Sulfitobacter pontiacus, was 97.7 %. DNA–DNA relatedness between strain Iso 3T and Sulfitobacter pontiacus DSM 10014T was 24.1 %. On the basis of phenotypic properties and phylogenetic distinctiveness, strain Iso 3T is classified within a novel Sulfitobacter species, for which the name Sulfitobacter litoralis sp. nov. is proposed, with the type strain Iso 3T (=KCTC 12521T=DSM 17584T).
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Trabulsiella odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus Shiraki
More LessBacterial strains Eant 3-9T and Eant 3-3, isolated from the gut of the termite Odontotermes formosanus, were characterized using a polyphasic taxonomic approach. Cells of these organisms were Gram-negative, non-pigmented, rod-shaped, non-endospore-forming and facultatively anaerobic. Phenotypic, physiological and genetic characteristics of the two strains were highly similar. Phylogenetic analyses using 16S rRNA gene sequences showed that strain Eant 3-9T formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Trabulsiella; its closest neighbour was Trabulsiella guamensis DSM 16940T (98.1 % similarity). Genomic DNA–DNA relatedness between strains Eant 3-9T and Eant 3-3 was 96±4 %, indicating that they belong to a single species. Eant 3-9T displayed DNA–DNA relatedness values of 48±5 and 14±3 % with T. guamensis DSM 16940T and Salmonella typhimurium ATCC 13311T, respectively, indicating that Eant 3-9T warrants novel species status in the genus Trabulsiella. Eant 3-9T and Eant 3-3 could be further distinguished from T. guamensis DSM 16940T using whole-cell protein profiles and a range of physiological and biochemical characteristics. It is evident from genotypic and phenotypic data that Eant 3-9T represents a novel species in the genus Trabulsiella, for which the name Trabulsiella odontotermitis sp. nov. is proposed. The type strain is Eant 3-9T (=BCRC 17577T=LMG 23580T); Eant 3-3 is a reference strain.
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Luteimonas composti sp. nov., a moderately thermophilic bacterium isolated from food waste
A yellow-pigmented, Gram-negative, rod-shaped bacterium (strain CC-YY255T) was isolated from compost generated from food waste collected from Kinmen County, Taiwan. 16S rRNA gene sequence analysis indicated that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Luteimonas; its closest neighbour was the type strain of Luteimonas mephitis (94.4 % sequence similarity). The isolate was distinguished from Luteimonas mephitis on the basis of several phenotypic properties. The organism utilized glucose, maltose, gentiobiose, melibiose and turanose and only a few organic acids (acetate, propionate) and amino acids (l-alanyl glycine, glycyl l-aspartic acid and glycyl l-glutamic acid) as substrates. The fatty acid profile was slightly different from that reported for Luteimonas mephitis. It is evident from the genotypic, chemotaxonomic and physiological data presented that strain CC-YY255T represents a novel species of the genus Luteimonas, for which the name Luteimonas composti sp. nov. is proposed. The type strain is CC-YY255T (=CCUG 53595T=CIP 109311T=BCRC 17598T).
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Description of Pseudochrobactrum kiredjianiae sp. nov.
A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain CCUG 49584T), isolated from a seafood processing plant sample in New Zealand, was subjected to a polyphasic taxonomic study. On the basis of 16S rRNA and recA gene sequence similarities, the isolate was allocated to the genus Pseudochrobactrum. This was confirmed by fatty acid data (major fatty acids: C18 : 1 ω7c and C19 : 0 cyclo ω8c), a polar lipid profile exhibiting major characteristics of Pseudochrobactrum (phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine), quinone system Q-10 and a polyamine pattern with the predominant compounds spermidine and putrescine. DNA–DNA hybridization with the type strains of the two established species of Pseudochrobactrum and physiological and biochemical data clearly differentiated the isolate from established Pseudochrobactrum species. As a consequence, this organism represents a novel species, for which the name Pseudochrobactrum kiredjianiae sp. nov. is proposed, with the type strain CCUG 49584T (=CIP 109227T).
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Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain
Two strains named ESC1T and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA–DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21T, O. anthropi DSM 6882T and Ochrobactrum tritici DSM 13340T. The predominant fatty acids were C18 : 1 ω7c and C18 : 1 2-OH. Strains ESC1T and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced β-galactosidase and β-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1T was 56.4 mol%. Both strains ESC1T and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1T (=LMG 22713T=CECT 7172T).
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Moraxella bovoculi sp. nov., isolated from calves with infectious bovine keratoconjunctivitis
More LessEighteen isolates of a Gram-negative coccus (strain 237T) were cultured from the eyes of dairy and beef calves affected with infectious bovine keratoconjunctivitis (IBK; ‘pinkeye’) in northern California, USA, during summer 2002. These isolates had near full-length (1397 bp) 16S rRNA gene sequences that clustered into three groups with 99.9 % sequence similarity. On the basis of 16S rRNA gene sequence, the isolates were most closely associated with Moraxella bovis and Moraxella ovis in clade I of the classical moraxellae. Biochemically, the novel isolates could be distinguished from the other members of the genus Moraxella isolated from animals on the basis of phenylalanine deaminase activity. The results of partial sequence analysis of six housekeeping genes, the 16S–23S rRNA gene interspacer region and partial 23S rRNA gene provide strong support for the inclusion of these isolates in a novel taxon, for which the name Moraxella bovoculi sp. nov. is proposed. The type strain is strain 237T (=ATCC BAA-1259T=CCUG 52049T).
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Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999
More LessThe taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9–98.2 %). Several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. Further, a comparative study based on DNA–DNA hybridization, phenotypic characterization and chemotaxonomic analysis indicated that the members of this clade, namely Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi, can be readily differentiated from each other. On the basis of the polyphasic data obtained in this study, all species of the genus Silicibacter should be transferred to the genus Ruegeria, since the latter has nomenclatural priority. It is therefore proposed that Silicibacter lacuscaerulensis and Silicibacter pomeroyi are transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov.
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Enterobacter turicensis sp. nov. and Enterobacter helveticus sp. nov., isolated from fruit powder
Four Gram-negative, facultatively anaerobic, non-spore-forming isolates of coccoid rods were obtained from fruit powder and investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis allocated the isolates to the family Enterobacteriaceae. Their phylogenetic position within the family Enterobacteriaceae was confirmed by rpoB sequence analysis and as the highest rpoB sequence similarities were obtained with Enterobacter radicincitans, Enterobacter cowanii and Enterobacter sakazakii, the isolates clearly belong to the genus Enterobacter. Biochemical data revealed that the isolates can be separated into two distinct groups that represent two novel species, as confirmed by DNA–DNA hybridizations. The two novel species can be differentiated from their nearest neighbours by the following characteristics: the utilization of sucrose, d-sorbitol, putrescine and mucate, the hydrolysis of aesculin and a negative result in the Voges–Proskauer reaction. It is therefore proposed that these novel isolates are classified as Enterobacter turicensis sp. nov. (type strain 508/05T=LMG 23730T=DSM 18397T) and Enterobacter helveticus sp. nov. (type strain 513/05T=LMG 23732T=DSM 18396T).
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Sulfurospirillum cavolei sp. nov., a facultatively anaerobic sulfur-reducing bacterium isolated from an underground crude oil storage cavity
More LessA novel facultatively anaerobic sulfur-reducing bacterium, designated strain Phe91T, was isolated from petroleum-contaminated groundwater in an underground crude oil storage cavity at Kuji in Iwate, Japan. Cells of strain Phe91T were slightly curved rods with single polar flagella. Optimum growth was observed at pH 7.0 and 30 °C. The novel strain utilized elemental sulfur, thiosulfate, sulfite, dithionite, arsenate, nitrate and DMSO as electron acceptors with lactate as an energy and carbon source, but nitrite was not utilized. Microaerophilic growth was also observed. Fumarate, pyruvate, lactate, malate, succinate, hydrogen (with acetate as a carbon source) and formate (with acetate) could serve as electron donors. Fumarate, pyruvate and malate were fermented. The DNA G+C content was 42.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Phe91T was affiliated with the genus Sulfurospirillum in the class Epsilonproteobacteria and was most closely related to Sulfurospirillum deleyianum (sequence similarity 97 %). However, the DNA–DNA hybridization value between strain Phe91T and S. deleyianum was only 14 %. Based on the physiological and phylogenetic data, Phe91T should be classified as a representative of a novel species in the genus Sulfurospirillum; the name Sulfurospirillum cavolei sp. nov. is proposed, with Phe91T (=JCM 13918T=DSM 18149T) as the type strain.
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Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba
During a study of polysaccharide-hydrolysing bacteria present in different plant sources, two strains were isolated from pulverized decaying wood of Populus alba and classified in the genus Rhizobium on basis of their almost complete 16S rRNA gene sequences. Their closest phylogenetic relatives were Rhizobium galegae USDA 4128T and Rhizobium huautlense S02T, with 98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively. recA and atpD sequence analysis showed that these species have less than 88 and 92 % similarity, respectively, to the novel strains. In contrast to their closest phylogenetic relatives, the two strains showed strong cellulase activity on plates containing CM-cellulose as a carbon source. They were also distinguishable from these species on the basis of other phenotypic characteristics. The strains were able to induce ineffective nodules on Medicago sativa and the sequence of their nodD gene was phylogenetically close to that of Ensifer meliloti 1021 (99.6 % similarity). DNA–DNA hybridization values ranged from 10 to 22 % with respect to R. galegae USDA 4128T and 14 to 25 % with respect to R. huautlense S02T, showing that the strains from this study belong to a novel species, for which the name Rhizobium cellulosilyticum sp. nov. is proposed. The type strain is ALA10B2T (=LMG 23642T=DSM 18291T=CECT 7176T).
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Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan
More LessTwo strictly anaerobic, mesophilic, sulfate-reducing bacterial strains, Pro1T and Pro16, were isolated from an estuarine sediment in the Sea of Japan of the Japanese islands and were characterized by phenotypic and phylogenetic methods. Strains Pro1T and Pro16 had almost the same physiological and chemotaxonomic characteristics. Cells of both strains were Gram-negative, motile, non-spore-forming rods. Catalase activity was not detected. The optimum NaCl concentration for growth was 3.0 % (w/v). The optimum temperature for growth was 35 °C and the optimum pH was 6.7. Both strains used formate, propionate, pyruvate, lactate, fumarate, malate, ethanol, propanol, butanol, glycerol, alanine, glucose, fructose and H2 as electron donors for sulfate reduction and did not use acetate, butyrate, succinate, methanol, glycine, serine, aspartate, glutamate, cellobiose or sucrose. Organic electron donors were incompletely oxidized mainly to acetate. Both strains also used thiosulfate as an electron acceptor. Without electron acceptors, both strains fermented pyruvate and lactate. The genomic DNA G+C contents of strains Pro1T and Pro16 were 48.6 and 46.0 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-5(H2). Major cellular fatty acids of both strains were C15 : 0, C16 : 0, C17 : 1 ω6 and C18 : 1 ω7. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the class Deltaproteobacteria. The closest recognized relative of strains Pro1T and Pro16 was Desulfobulbus mediterraneus with sequence similarities of 95.2 and 94.8 %, respectively. Based on phylogenetic, physiological and chemotaxonomic characteristics, strains Pro1T and Pro16 represent a novel species of the genus Desulfobulbus, for which the name Desulfobulbus japonicus is proposed. The type strain is Pro1T(=JCM 14043T=DSM 18378T) and strain Pro16 (=JCM 14044=DSM 18379) is a reference strain.
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Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
More LessA Gram-negative, motile and egg-shaped bacterium, strain TF-218T, was isolated from a tidal flat at Daepo Beach (Yellow Sea), Korea, and subjected to a polyphasic taxonomic analysis. Strain TF-218T grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and an aminolipid. The DNA G+C content was 64.9 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain TF-218T is phylogenetically closely related to the genera Phaeobacter, Leisingera and Marinovum of the Alphaproteobacteria. The phylogenetic and chemotaxonomic similarities suggest that strain TF-218T represents a member of the genus Phaeobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain TF-218T differs from the recognized Phaeobacter species. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain TF-218T represents a novel species of the genus Phaeobacter, for which the name Phaeobacter daeponensis sp. nov. is proposed. The type strain is TF-218T (=KCTC 12794T=JCM 13606T).
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Characterization of ‘Pseudomonas azelaica’ DSM 9128, leading to emended descriptions of Pseudomonas citronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym
More LessPolyphasic characterization of strain DSM 9128, described as ‘Pseudomonas azelaica’ by Janota-Bassalik et al. [Acta Microbiol Pol B 3, 143–153 (1971) ], and four biochemically similar isolates was performed with the aim of validly publishing the name ‘Pseudomonas azelaica’. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization, fatty acid patterns and extensive biochemical testing, it was concluded that DSM 9128, two further strains and the type strains of Pseudomonas nitroreducens and Pseudomonas multiresinivorans form a highly related cluster. However, DNA–DNA binding did not conclusively resolve whether these strains should be regarded as members of one species. Based on results gained with the above-mentioned methods, two other isolates were assigned to the species Pseudomonas citronellolis, a species very close to P. nitroreducens. Based on genetic and biochemical similarities, it is suggested that Pseudomonas multiresinivorans should be considered as a later heterotypic synonym of Pseudomonas nitroreducens. The species descriptions of P. nitroreducens and P. citronellolis are emended.
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Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus
More LessA bacterial strain, designated Dant 3-8T, isolated from the gut of the termite Odontotermes formosanus, was investigated by a polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbours being Comamonas testosteroni DSM 50244T (96.4 % sequence similarity), Comamonas koreensis KCTC 12005T (96.0 %) and Comamonas terrigena DSM 7099T (96.2 %). Strain Dant 3-8T was clearly distinguished from all of these strains by using phylogenetic analysis, DNA–DNA hybridization, whole-cell protein profiles, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that Dant 3-8T represents a novel species in the genus Comamonas, for which the name Comamonas odontotermitis sp. nov. is proposed. The type strain is Dant 3-8T (=BCRC 17576T=LMG 23579T).
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- Other Gram-Positive Bacteria
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Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue
More LessFive strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.
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Moryella indoligenes gen. nov., sp. nov., an anaerobic bacterium isolated from clinical specimens
More LessThree Gram-positive, anaerobic, non-spore-forming, rod-shaped bacteria with pointed ends were isolated from clinical specimens. The organisms were weakly saccharolytic and produced indole, acetate, butyrate and lactate as major metabolic end products. 16S rRNA gene sequence analysis indicated that the isolates had no known close relatives among recognized bacteria but that they exhibited a phylogenetic association with Clostridium rRNA cluster XIVa [as defined by Collins, M. D. et al. (1994) . Int J Syst Bacteriol 44, 812–826]. The closest recognized relatives were the type strains of Clostridium clostridioforme, Clostridium bolteae and Clostridium asparagiforme (16S rRNA gene sequence similarity values of 90.2–91.4 %). These results suggest that these three clinical isolates represent a novel species of a new genus, for which the name Moryella indoligenes gen. nov., sp. nov. is proposed. The type strain of Moryella indoligenes is AIP 220.04T (=CIP 109174T=CCUG 52648T).
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Lactobacillus secaliphilus sp. nov., isolated from type II sourdough fermentation
More LessTwo strains of Gram-positive, catalase-negative, lactic acid bacteria, strains TMW 1.1309T and TMW 1.1313, were isolated at an interval of several years from an industrial type II sourdough. They occurred at cell numbers of 8×108 c.f.u. g−1 and therefore were considered to be one of the dominant members of the microbiota in this type of fermentation. Cells of both strains grow exclusively on modified MRS containing trypsin-digested rye-bran extract. Both strains possessed identical 16S rRNA gene sequences, but could be discriminated by RAPD fingerprints. Comparative 16S rRNA and tuf gene sequence analyses positioned strain TMW 1.1309T as part of the Lactobacillus reuteri phylogenetic group within the genus Lactobacillus. The 16S rRNA gene sequence similarities to the closest related species, Lactobacillus coleohominis and Lactobacillus ingluviei were 97.1 and 95.4 %, respectively. The DNA G+C content of strain TMW 1.1309T was 48 mol%. Growth characteristics, biochemical features and DNA–DNA hybridization values below 70 % with all the nearest neighbours demonstrated that the isolates represent a novel Lactobacillus species. The name Lactobacillus secaliphilus sp. nov. is proposed for the novel isolates, with the type strain TMW 1.1309T (=DSM 17896T=CCUG 53218T).
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Vagococcus elongatus sp. nov., isolated from a swine-manure storage pit
More LessA polyphasic taxonomic study was performed on an uncharacterized Gram-positive, catalase-negative, elongated coccus-shaped bacterium isolated from a swine-manure storage pit. The bacterium, designated strain PPC9T, was facultatively anaerobic and had a DNA G+C content of 44.5 mol%. Comparative 16S rRNA gene sequencing indicated that the bacterium represented a novel subline within the genus Vagococcus, close to but distinct from Vagococcus lutrae. Strain PPC9T was readily distinguished from the five recognized species of the genus Vagococcus by using biochemical tests and molecular genetic analysis. Based on phylogenetic and phenotypic evidence strain PPC9T is considered to represent a novel species of the genus Vagococcus, for which the name Vagococcus elongatus sp. nov. is proposed. The type strain is PPC9T (=CCUG 51432T=NRRL B-41357T).
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Alkalibacillus silvisoli sp. nov., an alkaliphilic moderate halophile isolated from non-saline forest soil in Japan
More LessTwo alkaliphilic, moderately halophilic bacteria, designated BM2T and HN2, were isolated from non-saline forest soil in Japan. The cells of strain BM2T were motile, aerobic, rod-shaped and Gram-positive. The peptidoglycan was of the A1γ type, and the diamino acid was meso-diaminopimelic acid. Growth was observed at NaCl concentrations between 5.0 and 25.0 % (w/v) (the optimum being 10.0–15.0 %, w/v), at pH 7.0–10.0 (optimum, pH 9.0–9.5) and at 20–50 °C. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0 and anteiso-C17 : 0. The G+C content of total DNA of strain BM2T was 37.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain BM2T was most closely related to Alkalibacillus haloalkaliphilus DSM 5271T (98.0 % sequence similarity). DNA–DNA hybridization results indicated low levels of relatedness between strain BM2T and A. haloalkaliphilus JCM 12303T (23 and 16 % reciprocally), Alkalibacillus filiformis JCM 13893T (25 and 21 %) and Alkalibacillus salilacus JCM 13894T (27 and 19 %). On the basis of the phylogenetic and phenotypic characteristics, strain BM2T represents a novel species, for which the name Alkalibacillus silvisoli sp. nov. is proposed. The type strain is BM2T (=JCM 14193T=DSM 18495T).
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Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil
More LessA motile, Gram-positive, boron-tolerant and moderately halotolerant rod-shaped bacterium was isolated from a soil naturally high in boron minerals found in the Hisarcik area of Turkey. The novel isolate, designated T-16XT, produced spherical or ellipsoidal endospores in a non-bulging or slightly swollen sporangium in a terminal position and survived in a medium containing up to 450 mM boron. Whereas it tolerated 11 % (w/v) NaCl, it also grew without NaCl or boron. The temperature range for growth was 16–37 °C (optimum 25–28 °C) and the pH range for growth was 6.0–10.0 (optimum pH 7.5–8.5). The DNA G+C content was 35.8 mol% and the major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 at 18.2 and 45.7 % of the total fatty acids, respectively. MK-7 (90 %) was the predominant respiratory quinone system and meso-diaminopimelic acid was the predominant diamino acid of the cell-wall peptidoglycan. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the novel strain is closely related to the type strains of Gracilibacillus orientalis (96.7 % similarity), G. halotolerans (95.5 %) and G. dipsosauri (95.4 %). However, the maximum DNA hybridization value for this strain with these closely related strains was less than 26.2 %. On the basis of 16S rRNA gene sequence data and chemotaxonomic and physiological features, the organism T-16XT (=DSM 17256T=IAM 15263T=ATCC BAA-1190T) is proposed to be a member of the genus Gracilibacillus as the type strain of the novel species Gracilibacillus boraciitolerans sp. nov.
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Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue
More LessTwo strains of lactic acid bacteria, strains NRIC 0689T and NRIC 0690, were isolated from a compost of distilled shochu residue in Japan. The isolates showed quite low sequence similarity to known species of lactic acid bacteria on the basis of 16S rRNA gene sequence; the highest sequence similarities to NRIC 0689T were shown by the type strains of Lactobacillus satsumensis, L. plantarum, L. hilgardii, L. buchneri and L. parabuchneri (92.9, 92.9, 92.8, 92.6 and 92.5 %, respectively). The isolates formed a distinct subcluster in the Lactobacillus casei–Pediococcus phylogenetic cluster. Levels of DNA–DNA relatedness revealed that the isolates belonged to the same taxon. Therefore, the isolates represent a novel species, for which the name Lactobacillus composti sp. nov. is proposed. The type strain is NRIC 0689T (=JCM 14202T=DSM 18527T).
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Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans
More LessFive endospore-forming, nitrogen-fixing strains were isolated from rhizosphere soils of Zanthoxylum simulans planted in Beijing, China. Phylogenetic analysis based on full-length 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between these novel strains and Paenibacillus azotofixans ATCC 35681T (97.8–98.5 % similarity) and Paenibacillus stellifer DSM 14472T (95.4–96.3 %). Levels of 16S rRNA gene sequence similarity between the novel isolates and other species of the genus Paenibacillus were less than 95.0 %. Levels of 16S rRNA gene sequence similarity among the isolates were more than 98.0 %. DNA–DNA relatedness between the five novel isolates and P. azotofixans ATCC 35681T was 45.50–47.45 % and relatedness among the five novel strains was 95.8–99.6 %. A significant feature of the novel strains that differentiated them from P. azotofixans and other Paenibacillus species was that none of the novel strains could produce acid or gas from the following various carbohydrates: glucose, sucrose, lactose, fructose, glycerol, xylose, maltose, d-sorbitol, sodium succinate, sodium citrate, glycine or l-aspartate. Anteiso-branched C15 : 0 was the major fatty acid component (36.59 %) of novel strain JH29T. On the basis of phenotypic properties, 16S rRNA gene sequences, DNA G+C content, DNA–DNA hybridization, chemotaxonomic properties and the nifH gene sequence, the five novel strains form a very homogeneous group which is different from other related species within the genus Paenibacillus. Therefore, the five novel strains are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus zanthoxyli sp. nov. is proposed. The type strain is JH29T (=CCBAU 10243T=DSM 18202T).
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Volumes and issues
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