- Volume 53, Issue 4, 2003
Volume 53, Issue 4, 2003
- Validation List No. 92
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the 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 2, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- New Taxa
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- Archaea
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Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines
More LessFour novel, thermoacidophilic, crenarchaeotic cocci that grew anaerobically and heterotrophically were isolated from an acidic hot spring in the Philippines; two representative strains were characterized in detail. Most cells were regular cocci, 0·8–1·1 μm in width, which occurred singly or in pairs. They were non-motile and grew at 45–80 °C (optimum 70–75 °C) and pH 2·3–5·4 (optimum 3·5–4·0). They utilized starch, glycogen, gelatin, beef extract, yeast extract and peptone as carbon and energy sources. Growth was stimulated by the presence of sulfur as an electron acceptor. The lipid fraction contained cyclic and acyclic tetraether core lipids. The DNA G+C content was 31 mol%; phylogenetic analysis based on 16S rDNA sequences showed that the novel cocci represent an independent lineage in the phylum Crenarchaeota, distantly related to Acidilobus aceticus and an allied strain, NC12. Caldisphaera lagunensis gen. nov., sp. nov. is proposed to accommodate the four strains. The type strain is IC-154T(=JCM 11604T =MCC-UPLB 1331T =ANMR 0165T).
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- Other Bacteria
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Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna–Matthews–Olson protein) gene sequences
More LessA new taxonomy of the green sulfur bacteria is proposed, based on phylogenetic relationships determined using the sequences of the independent 16S rRNA and fmo (Fenna–Matthews–Olson protein) genes, and supported by the DNA G+C content and sequence signatures. Comparison of the traditional classification system for these bacteria with their phylogenetic relationship yielded a confusing picture, because properties used for classification (such as cell morphology, photosynthetic pigments and substrate utilization) do not concur with their phylogeny. Using the genetic information available, strains and species assigned to the genera Chlorobium, Pelodictyon and Prosthecochloris are considered, and the following changes are proposed. Pelodictyon luteolum is transferred to the genus Chlorobium as Chlorobium luteolum comb. nov. Pelodictyon clathratiforme and Pelodictyon phaeoclathratiforme are transferred to the genus Chlorobium and combined into one species, Chlorobium clathratiforme comb. nov. The name Pelodictyon will become a synonym of Chlorobium. Strains known as Chlorobium limicola subsp. thiosulfatophilum that have a low DNA G+C content (52–52·5 mol%) are treated as strains of Chlorobium limicola; those with a high DNA G+C content (58·1 mol%) are transferred to Chlorobaculum gen. nov., as Chlorobaculum thiosulfatiphilum sp. nov. Chlorobium tepidum is transferred to Chlorobaculum tepidum comb. nov., and defined as the type species of the genus Chlorobaculum. Strains assigned to Chlorobium phaeobacteroides, but phylogenetically distant from the type strain of this species, are assigned to Chlorobium limicola and to Chlorobaculum limnaeum sp. nov. Strains known as Chlorobium vibrioforme subsp. thiosulfatophilum are transferred to Chlorobaculum parvum sp. nov. Chlorobium chlorovibrioides is transferred to ‘Chlorobaculum chlorovibrioides’ comb. nov. The type strain of Chlorobium vibrioforme is phylogenetically related to Prosthecochloris, and is therefore transferred to this genus as Prosthecochloris vibrioformis comb. nov. Consequently, the name Chlorobium vibrioforme will become a synonym of Prosthecochloris vibrioformis, and other strains that were assigned to this species are now considered to belong to Chlorobium luteolum, Chlorobium phaeovibrioides and ‘Chlorobaculum chlorovibrioides’, according to their phylogenetic relatedness.
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‘Candidatus Phytoplasma ziziphi’, a novel phytoplasma taxon associated with jujube witches'-broom disease
Phylogenetic relationships of five jujube witches'-broom (JWB) phytoplasma isolates from four different districts, and other phytoplasmas, were investigated by 16S rDNA PCR amplification and sequence analysis. The 16S rDNA sequences of any pair of the five isolates of JWB phytoplasmas were >99·5 % similar. The JWB phytoplasma 16S rDNA sequences were most closely related to that of the elm yellows (EY) phytoplasma in 16S-group VIII. Phylogenetic analysis of the 16S rDNA sequences from the JWB phytoplasma isolates, together with sequences from most of the phytoplasmas archived in GenBank, produced a tree in which the JWB isolates clustered as a discrete subgroup. The uniqueness of the JWB phytoplasma appears to be correlated with a specific insect vector (Hishimonus sellatus) and the host plant (Zizyphus jujuba), or with a specific geographical distribution. The unique properties of the JWB phytoplasma sequences clearly indicate that it represents a novel taxon, ‘Candidatus Phytoplasma ziziphi’.
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Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent
A novel thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium designated strain TRT was isolated from a sample of a deep-sea hydrothermal chimney collected at the Rainbow vent field on the Mid-Atlantic Ridge (36°14′N). Gram-negative, non-spore-forming, non-motile rods occurred singly or in pairs. The organism grew in the temperature range 37–80 °C with an optimum at 70 °C and at pH 5·5–8·4 with an optimum around 6·7. The NaCl range for growth was 10–50 g l−1 with an optimum of 30 g l−1. Strain TRT grew chemoorganoheterotrophically with carbohydrates, proteinaceous substrates, organic acids and alcohols using oxygen or nitrate as electron acceptors. The isolate was able to grow at oxygen concentrations from 0·5 to 21 %. Oxygen concentrations that promoted fastest growth ranged from 4 to 8 % under agitation. The novel isolate was able to grow lithoheterotrophically with molecular hydrogen as the energy source. The G+C content of the genomic DNA was 68·4 mol%. Phylogenetic analysis of the 16S rDNA sequence placed strain TRT within the phylum Deinococcus–Thermus of the Bacteria. On the basis of phenotypic and phylogenetic data, it is proposed that this isolate should be described as a member of a novel species of a new genus as Vulcanithermus mediatlanticus gen. nov., sp. nov. The type strain is TRT (=DSM 14978T =VKM B-2292T =JCM 11956T).
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Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.
A phylogenetically novel aerobic bacterium was isolated from an anaerobic–aerobic sequential batch reactor operated under enhanced biological phosphorus removal conditions for wastewater treatment. The isolation strategy used targeted slowly growing polyphosphate-accumulating bacteria by combining low-speed centrifugations and prolonged incubation on a low-nutrient medium. The isolate, designated strain T-27T, was a Gram-negative, rod-shaped aerobe. Cells often appeared to divide by budding replication. Strain T-27T grew at 25–35 °C with an optimum growth temperature of 30 °C, whilst no growth was observed below 20 °C or above 37 °C within 20 days incubation. The pH range for growth was 6·5–9·5, with an optimum at pH 7·0. Strain T-27T was able to utilize a limited range of substrates, such as yeast extract, polypepton, succinate, acetate, gelatin and benzoate. Neisser staining was positive and 4,6-diamidino-2-phenylindole-stained cells displayed a yellow fluorescence, indicative of polyphosphate inclusions. Menaquinone 9 was the major respiratory quinone. The cellular fatty acids of the strain were mainly composed of iso-C15 : 0, C16 : 1 and C14 : 0. The G+C content of the genomic DNA was 66 mol%. Comparative analyses of 16S rRNA gene sequences indicated that strain T-27T belongs to candidate division BD (also called KS-B), a phylum-level lineage in the bacterial domain, to date comprised exclusively of environmental 16S rDNA clone sequences. Here, a new genus and species are proposed, Gemmatimonas aurantiaca (type strain T-27T=JCM 11422T=DSM 14586T) gen. nov., sp. nov., the first cultivated representative of the Gemmatimonadetes phyl. nov. Environmental sequence data indicate that this phylum is widespread in nature and has a phylogenetic breadth (19 % 16S rDNA sequence divergence) that is greater than well-known phyla such as the Actinobacteria (18 % divergence).
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- Proteobacteria
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Seven novel species of Acinetobacter isolated from activated sludge
More LessThirteen isolates of Acinetobacter were obtained from activated sludge plants in Victoria, Australia. Earlier 16S–23S rDNA genomic fingerprinting and partial 16S rDNA sequence data had suggested that these isolates might contain previously undescribed species. This view was confirmed here. A polyphasic taxonomic approach involving phenotypic characterization, near-complete 16S rDNA sequence data and DNA–DNA hybridization analyses support the view that seven novel genomic species can be differentiated in this group of isolates. However, when fluorescence in situ hybridization (FISH) studies were performed with a 16S-rRNA-targeted probe specific for the genus Acinetobacter, used to identify Acinetobacter in activated sludge plants, all these strains responded positively. This suggests that these isolates would not have been missed in earlier FISH studies where their role as polyphosphate-accumulating bacteria has been questioned. This report describes these isolates and proposes that they be named Acinetobacter baylyi (type strain B2T=DSM 14961T =CIP 107474T), Acinetobacter bouvetii (type strain 4B02T=DSM 14964T =CIP 107468T), Acinetobacter grimontii (type strain 17A04T=DSM 14968T =CIP 107470T), Acinetobacter tjernbergiae (type strain 7N16T=DSM 14971T =CIP 107465T), Acinetobacter towneri (type strain AB1110T=DSM 14962T =CIP 107472T), Acinetobacter tandoii (type strain 4N13T=DSM 14670T =CIP 107469T) and Acinetobacter gerneri (type strain 9A01T=DSM 14967T =CIP 107464T).
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Zooshikella ganghwensis gen. nov., sp. nov., isolated from tidal flat sediments
More LessTwo red pigment-producing bacterial strains with a metallic green sheen were isolated from a sediment sample of getbol, the Korean tidal flat. Phylogenetic analysis based on 16S rDNA sequences showed that these isolates represent a phyletic lineage within the γ-Proteobacteria that is distantly related to the genus Hahella. No bacterial species with validly published names showed ⩾92 % 16S rRNA similarity with the getbol isolates. The strains were Gram-negative, chemo-organotrophic, aerobic and required NaCl (1–7 %) for growth. They produced pigments with maximum absorption at 540 nm, which indicated the presence of prodigiosin, a well-known red pigment previously detected in Serratia marcescens. The major isoprenoid quinone was ubiquinone-9. The predominant cellular fatty acids were saturated and monounsaturated straight-chain fatty acids. The DNA G+C contents ranged from 40 to 42 mol%. The combination of physiological, biochemical and chemotaxonomic data clearly separated the test strains from other phylogenetically related genera in the γ-Proteobacteria. On the basis of polyphasic evidence from this study, it is proposed that the two getbol isolates should be classified in a novel genus, Zooshikella gen. nov., as Zooshikella ganghwensis sp. nov.
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Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria
More LessTwo bacterial strains, HTCC2503T and HTCC2517, were isolated from the Bermuda Atlantic Time Series Station in the western Sargasso Sea, Atlantic Ocean, by new high-throughput culture methods that rely on dilution to extinction in very-low-nutrient media. Characterization of the two strains by polyphasic approaches revealed that they belonged to the same species. These isolates are Gram-negative, strictly aerobic, chemoheterotrophic, slightly motile short rods with a single flagellum. The temperature, pH and NaCl concentration ranges for growth were 10–37 °C, 6·0–9·0 and 0·75–20 % (w/v), respectively. Colonies on marine agar were very small (0·3–0·8 mm in diameter), yellowish-brown and very hard. Carotenoid pigments were synthesized but bacteriochlorophyll a was not. Several kinds of pentose, hexose, sugar alcohol, oligosaccharide and amino acid were utilized as sole carbon sources. Oxidase was produced, but catalase was not. All cellular fatty acids were even-numbered monounsaturated or saturated fatty acids and the major fatty acid was cis-7-octadecenoic acid (73·3 %). The DNA G+C content of strain HTCC2503T was 60·8 mol%. Phylogenetic analyses of 16S rRNA gene sequences clearly indicated that the strains formed a distinct lineage, allied with activated sludge environmental clone H9, in the α-Proteobacteria. The clade containing strains HTCC2503T and HTCC2517 and clone H9 could not be phylogenetically associated with any of the six known orders of the α-Proteobacteria. From this polyphasic evidence, it is proposed that the novel strains should be classified as Parvularcula bermudensis gen. nov., sp. nov. The type strain is HTCC2503T (=ATCC BAA-594T =KCTC 12087T) and the reference strain is HTCC2517.
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Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov.
More LessThirteen Ralstonia pickettii-like isolates from the environment (water, soil and activated sludge) and human clinical samples (including respiratory secretions of cystic fibrosis patients) were investigated in a polyphasic taxonomic study that employed 16S rDNA sequence analysis, DNA–DNA hybridization, determination of DNA base composition, whole-cell protein analysis, biochemical characterization and PCR-based assays. All isolates were classified as a novel Ralstonia species, for which the name Ralstonia insidiosa sp. nov. is proposed. The type strain, LMG 21421T (=CCUG 46789T), was isolated from the sputum of a patient with acute lymphoblastic leukaemia. R. insidiosa can be differentiated from other species of the genus Ralstonia and phenotypically similar species (including the Burkholderia cepacia complex and Achromobacter xylosoxidans) by a variety of biochemical tests, whole-cell protein analysis and several PCR-based assays. Some outstanding issues in the taxonomy of the genus Ralstonia are also discussed.
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Sterolibacterium denitrificans gen. nov., sp. nov., a novel cholesterol-oxidizing, denitrifying member of the β-Proteobacteria
More LessA bacterial strain (Chol-1ST) that is able to oxidize cholesterol to CO2 and reduce nitrate to dinitrogen was enriched and isolated from an upflow sludge bed (USB) anoxic reactor that treats sanitary landfill leachate from the city of Montevideo, Uruguay. Cells of strain Chol-1ST were Gram-negative, rod-shaped to slightly curved, measured 0·5–0·6×1·0-1·3 μm and were motile by a single polar flagellum. Strain Chol-1ST grew optimally at 30–32 °C and pH 7·0, with a doubling time of 44–46 h when cholesterol was used as the sole carbon and energy source. The metabolism of strain Chol-1ST was strictly respiratory, with oxygen or nitrate as the terminal electron acceptor. The presence of ubiquinone Q-8 as the sole respiratory lipoquinone indicated that strain Chol-1ST belonged to the β-subclass of the Proteobacteria. Phosphatidylethanolamine was the predominant polar lipid and the G+C content of the DNA was 65·3 mol%. The fatty acid profile of strain Chol-1ST, cultivated under denitrifying conditions by using a defined mineral medium supplemented with cholesterol, was characterized by the following major components: summed feature 4 (C16 : 1 ω7c and/or iso C15 : 0 2-OH), C16 : 0, C18 : 1 ω7c and hydroxy acid C10 : 0 3-OH. Minor components included C10 : 0, C11 : 0, C12 : 0, C14 : 0, C15 : 0, C19 : 0, C19 : 0 10-methyl and hydroxylated acids C8 : 0 3-OH and C16 : 0 3-OH. Analysis of the 16S rDNA sequence showed that strain Chol-1ST represents a separate lineage within the Thauera, Azoarcus, Zoogloea and Rhodocyclus assemblage of the β-Proteobacteria. Strain Chol-1ST had highest sequence similarity (96·5 %) with strain 72Chol, a denitrifying β-Proteobacterium. On the basis of polyphasic evidence, strain Chol-1ST (=DSM 13999T =ATCC BAA-354T) is proposed as the type strain of Sterolibacterium denitrificans gen. nov., sp. nov.
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Characterization of several Psychrobacter strains isolated from Antarctic environments and description of Psychrobacter luti sp. nov. and Psychrobacter fozii sp. nov.
More LessEleven psychrophilic bacteria isolated from Antarctic coastal marine environments were subjected to a polyphasic taxonomic study. The isolates were oxidase-positive, halotolerant, Gram-negative, non-motile coccobacilli with a strictly oxidative metabolism. The DNA G+C content ranged from 44 to 47 mol%. DNA–DNA hybridization experiments showed six homology groups, two of them related at the species level to the type strain of Psychrobacter immobilis, LMG 7203T (70–83 %). The highest DNA relatedness of two other groups to known Psychrobacter species was found to the type strain of Psychrobacter glacincola, LMG 21282T (51–57 %), and no significant similarity was found between Psychrobacter type strains and the last two groups. The predominant cellular fatty acids detected were typical of the genus Psychrobacter and included 18 : 1ω9c, 16 : 1ω7c and 17 : 1ω8c. 16S rRNA gene sequence analysis confirmed that the strains isolated belonged to the genus Psychrobacter. The results of the study assigned five isolates to P. immobilis, three isolates to P. glacincola and three isolates to novel Psychrobacter species. The names Psychrobacter luti sp. nov. (type strain NF11T=LMG 21276T= CECT 5885T) and Psychrobacter fozii sp. nov. (type strain NF23T=LMG 21280T =CECT 5889T) are proposed for these organisms.
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Assignment of ‘Alteromonas marinoglutinosa’ NCIMB 1770 to Pseudoalteromonas mariniglutinosa sp. nov., nom. rev., comb. nov.
The taxonomic position of the marine bacterium ‘Alteromonas marinoglutinosa’ NCIMB 1770 was investigated in a polyphasic study. Analysis of 16S rDNA sequence and DNA–DNA reassociation values confirmed the phylogenetic position of strain NCIMB 1770 within the genus Pseudoalteromonas as a separate species, distinct from all Pseudoalteromonas species with validly described names. On the basis of physiological and molecular properties, it is proposed that strain NCIMB 1770 is classified as Pseudoalteromonas mariniglutinosa sp. nov., nom. rev., comb. nov., with the type strain NCIMB 1770T (=KMM 3635T).
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Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater treatment plant
More LessA novel bacterial species, Rhodocista pekingensis sp. nov., was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. Cells of R. pekingensis were Gram-negative, motile by a single polar flagellum, vibrioid to spiral, 0·6–0·8 μm in width and 0·8–1·5 μm in length. R-bodies were not observed. Phototrophically grown cells contained lamellar photosynthetic membranes and bacteriochlorophyll a. Cell growth was anaerobically phototrophic or aerobically chemoheterotrophic. Anaerobically grown cultures were pink-reddish. Thiamin and vitamin B12, but not biotin, were required for growth and 0·05 % yeast extract stimulated growth. Acetate, lactate, pyruvate and succinate supported growth. Cysts were formed when butyrate was used as the sole carbon source. Molecular hydrogen (H2), but not sulfide or thiosulfate, was used as an electron donor. The major cellular quinone was Q-9. The DNA G+C content of cells was 68·8 mol%. The type strain of Rhodocista pekingensis is 3-pT (=AS 1.2194T =JCM 11669T).
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Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals
A bacterium previously isolated from a diseased colony of the scleractinian coral Dichocoenia stokesi (common name elliptical star coral) was subjected to a detailed polyphasic taxonomic characterization. The isolate, designated WP1T, was halophilic and strictly aerobic and formed golden-orange-pigmented colonies after prolonged incubation. Cells of WP1T were Gram-negative, rod-shaped and showed a characteristic branching rod morphology. Chemotaxonomically, WP1T was characterized by having Q-10 as the major respiratory lipoquinone and sym-homospermidine as the main component of the cellular polyamine content. The predominant constituent in the cellular fatty acid profile was C18 : 1 ω7c, along with C19 : 0 cyclo ω8c and C16 : 0. Other fatty acids present in smaller amounts were C17 : 0, C18 : 0, C16 : 1 ω7c, C20 : 1 ω7c and C18 : 1 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Minor amounts of diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were present. The G+C content of the genomic DNA was 66·3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that WP1T represents a separate subline of descent within the order ‘Rhizobiales’ of the ‘Alphaproteobacteria’. The new line of descent falls within the group of families that includes the Rhizobiaceae, Bartonellaceae, Brucellaceae and ‘Phyllobacteriaceae’, with no particular relative within this group. The 16S rRNA gene sequence similarity to all established taxa within this group was not higher than 92·0 % (to Mesorhizobium mediterraneum). To accommodate this emerging coral pathogen, the creation of a new genus and species is proposed, Aurantimonas coralicida gen. nov., sp. nov. (type strain WP1T=CIP 107386T =DSM 14790T).
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Reclassification of Desulfobacterium macestii as Desulfomicrobium macestii comb. nov.
More LessPhylogenetic, chemotaxonomic and metabolic data obtained for Desulfobacterium macestii indicate that this species is not a member of the genus Desulfobacterium, but of the genus Desulfomicrobium. Phylogenetically, it is closely related to Desulfomicrobium baculatum and Desulfomicrobium norvegicum, but it can be differentiated from these species by its metabolic properties. It is therefore proposed to reclassify Desulfobacterium macestii as Desulfomicrobium macestii comb. nov.
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Dechlorosoma suillum Achenbach et al. 2001 is a later subjective synonym of Azospira oryzae Reinhold-Hurek and Hurek 2000
More LessIn order to clarify the taxonomic position of Dechlorosoma suillum, which shares 99·9 % 16S rDNA sequence identity (1433 of 1435 bp) with Azospira oryzae, we compared the two species in a polyphasic taxonomic approach. Results of 122 physiological and biochemical tests for D. suillum DSM 13638T and Azospira oryzae 6a3T were identical, except for the lack of growth of Azospira oryzae 6a3T with perchlorate as the terminal electron acceptor. Presence of a nifH gene and nitrogenase activity, a key feature of Azospira, were also detected in D. suillum by Southern hybridization and by the acetylene reduction assay, respectively. Whole-cell SDS-PAGE profiles of SDS-soluble proteins of strains DSM 13638T and 6a3T were almost identical. DNA–DNA hybridization studies showed more than 90 % binding between D. suillum and two strains of Azospira oryzae. These data provide evidence that the two bacteria belong to the same species and that D. suillum is a later subjective synonym of Azospira oryzae.
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Schlegelella thermodepolymerans gen. nov., sp. nov., a novel thermophilic bacterium that degrades poly(3-hydroxybutyrate-co-3-mercaptopropionate)
A novel thermophilic bacterium, strain K14T, capable of degrading poly(3-hydroxybutyrate) as well as copolymers containing 3-hydroxybutyrate and 3-mercaptopropionate linked by thioester bonds, was isolated. 16S rDNA sequence analysis showed that strain DhA-71, a dehydroabietic acid-degrading bacterium, was the nearest phylogenetic neighbour and that both strains should be placed as members of a newly created genus, Schlegelella gen. nov., in the Rubrivivax subgroup of the β-Proteobacteria. Strain K14T (=LMG 21644T=DSM 15344T) is proposed as the type strain of Schlegelella thermodepolymerans gen. nov., sp. nov. Its phylogenetic, morphological, biochemical and chemotaxonomic characteristics are described in detail.
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Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea
More LessTwo Gram-negative, motile, non-spore-forming, yellow-pigmented and slightly halophilic strains (SW-46T and SW-52) were isolated from sea water of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strains SW-46T and SW-52 were characterized chemotaxonomically by having ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and C18 : 1 ω7c as the major fatty acid. Their DNA G+C content was 64·0–64·1 mol%. Strains SW-46T and SW-52 showed 1 bp difference in their 16S rDNA sequences and a mean DNA–DNA relatedness level of 94·4 %. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-46T and SW-52 fall within the α-subclass of the Proteobacteria and form a coherent cluster with Erythrobacter longus, Erythrobacter litoralis and Erythrobacter citreus. Levels of 16S rDNA similarity between strains SW-46T and SW-52 and the type strains of these three Erythrobacter species were 96·5–97·9 %. Levels of DNA–DNA relatedness between strains SW-46T and SW-52 and the type strains of E. longus, E. litoralis and E. citreus were 3·6–14·7 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic data, strains SW-46T and SW-52 should be placed in the genus Erythrobacter as a novel species, for which the name Erythrobacter flavus sp. nov. is proposed. The type strain is SW-46T (=KCCM 41642T =JCM 11808T).
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- Gram-Positive Bacteria
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Eubacterium pyruvativorans sp. nov., a novel non-saccharolytic anaerobe from the rumen that ferments pyruvate and amino acids, forms caproate and utilizes acetate and propionate
Two similar Gram-positive rods were isolated from 10−6 dilutions of ruminal fluid from a sheep receiving a mixed grass hay/concentrate diet, using a medium containing pancreatic casein hydrolysate as sole source of carbon and energy. The isolates did not ferment sugars, but grew on pyruvate or trypticase, forming caproate as the main fermentation product and valerate to a lesser extent. Acetate and propionate were utilized. One of these strains, I-6T, was selected for further study. Strain I-6T was a non-motile coccal rod, 1·2×0·4 μm, with a Gram-positive cell wall ultrastructure and a G+C content of 56·8 mol%. No spores were visible, and strain I-6T did not survive heating at 80 °C for 10 min. Its rate of NH3 production was 375 nmol (mg protein)−1 min−1, placing it in the ‘ammonia-hyperproducing’ (or HAP) group of ruminal bacteria. 16S rDNA sequence analysis (1296 bases) indicated that it represents a novel species within the ‘low-G+C’ Gram-positive group, for which the name Eubacterium pyruvativorans sp. nov. is proposed. Among cultivated bacteria, strain I-6T was most closely related (89 % identity) to other asaccharolytic Eubacterium isolates from the mouth and the rumen. It was 98 % identical to uncultured bacterial sequences amplified by others from ruminal digesta.
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Alkaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dismutating bacterium isolated from a methanogenic environment
More LessTwo bacterial strains were isolated from methanogenic butyrate-oxidizing mixed cultures. The cells were straight to slightly curved, Gram-positive rods that were motile by means of multiple flagella and formed endospores. Growth was observed in the temperature range 15–45 °C (optimum 37 °C) and pH range 5·5–9·0 (optimum pH 7·5). The novel isolates were strictly anaerobic chemo-organotrophs capable of utilizing yeast extract, peptone, tryptone and a variety of sugars and organic acids, but not glucose. None of the accessory electron acceptors tested (elemental sulfur, thiosulfate or fumarate) improved growth, except crotonate, which was dismutated to butyrate and acetate. The G+C content of the DNA of one of the isolates, strain B11-2T, was 30·6 mol%. Phylogenetic analysis based on 16S rDNA sequence similarity between strain B11-2T and some other strictly anaerobic, spore-forming bacteria indicated that the novel isolates represented a species in cluster XI within the low-GC Gram-positive bacteria, being most closely related to Alkaliphilus transvaalensis JCM 10712T. DNA–DNA relatedness between strain B11-2T and A. transvaalensis JCM 10712T was 21 %. On the basis of physiological and molecular properties, and cellular fatty acid and cell wall compositions, the novel isolates are proposed to represent a novel species of the genus Alkaliphilus, for which the name Alkaliphilus crotonatoxidans is proposed (type strain B11-2T=AS 1.2897T=JCM 11672T).
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Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica
More LessTwo unique psychrophilic strains (CMS 76rT and CMS 81yT) were isolated from a cyanobacterial mat sample from a pond in Wright Valley, McMurdo, Antarctica. Both isolates were assigned to the genus Leifsonia, since they were Gram-positive, curved rods, non-motile, catalase-positive, contained dl-2,4-diaminobutyric acid, menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol, had a high content of anteiso- and iso-branched fatty acids and had a DNA G+C content of 64–66 mol%. In addition, both isolates were related to the five reported species of Leifsonia at a level of about 95–96 % 16S rDNA sequence similarity and differed from one another by 2·5 %. Strains CMS 76rT and CMS 81yT also differed from one another in many other phenotypic characteristics and exhibited only 30 % relatedness at the DNA–DNA level, thus indicating that they represent two different species. Furthermore, these two isolates also showed many distinct differences with respect to the reported species of Leifsonia in terms of their phenotypic characteristics, biochemical properties, chemotaxonomic features, sensitivity to various antibiotics and 16S rDNA similarity, clearly indicating that strains CMS 76rT (=MTCC 4210T =DSM 15304T =CIP 107783T) and CMS 81yT (=MTCC 4657T =DSM 15303T =CIP 107785T) represent the type strains of two novel species of Leifsonia, for which the names Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov. are proposed.
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Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake
More LessA novel, psychrophilic, Gram-positive bacterium (designated strain LV3T) from a lake near the McMurdo Ice Shelf, Antarctica, has been isolated and characterized. This organism formed red-pigmented colonies, had an optimal growth temperature of 18 °C and grew on a variety of media between −2 and 21 °C. Scanning electron micrographs of strain LV3T that showed small rods with unusual bulbous protuberances during all phases of growth were of particular interest. The G+C content of the genomic DNA was approximately 62 mol%. The cell walls contained ornithine as the diamino acid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Cells grown at −2 °C contained significant amounts of anteiso-C15 : 1. The major menaquinones found in strain LV3T were MK-11 and MK-12. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain LV3T was a member of the family Microbacteriaceae and related to, but distinct from, organisms belonging to the genera Agreia, Leifsonia and Subtercola. In addition, alignments of 16S rRNA sequences showed that the sequence of strain LV3T contained a 13 bp insertion that was found in only a few related sequences. Based on the low growth temperature, unusual cell shape, distinct 16S rRNA gene sequence and structure and cell-wall amino acid and menaquinone compositions, Rhodoglobus vestalii gen. nov., sp. nov. is proposed, with the type strain LV3T (=ATCC BAA-534T =CIP 107482T).
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Nocardia caishijiensis sp. nov., a novel soil actinomycete
More LessA soil isolate, strain F829T, which had provisionally been assigned to the genus Nocardia, was subjected to a polyphasic taxonomic study. An almost complete 16S rDNA sequence was determined for this strain; the sequence was aligned with available sequences for nocardiae and phylogenetic trees were inferred using three tree-making algorithms. The organism showed a combination of phenotypic properties typical of nocardiae and formed a distinct phyletic line within the evolutionary radiation of species of the genus Nocardia, being most closely related to Nocardia asteroides ATCC 19247T. Strain F829T was readily distinguished from representatives of species of Nocardia with validly published names on the basis of phenotypic data, notably from the type strain of N. asteroides. It is proposed that the organism be recognized as a novel species of Nocardia, Nocardia caishijiensis sp. nov. The type strain is F829T (=AS 4.1728T =JCM 11508T).
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Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov.
More LessThe taxonomic status of Hongia koreensis was investigated by molecular systematic methods. On the basis of 16S rDNA phylogeny, H. koreensis was closely associated with Kribbella flavida and Kribbella sandramycini and formed a monophyletic clade with these species. These three taxa shared over 98 % 16S rDNA sequence similarity and many chemotaxonomic properties, which strongly indicates that they belong to the same genus. DNA–DNA pairing was employed to elucidate the genomic relatedness among these taxa. H. koreensis represented a distinct genomic species that can be differentiated from members of the genus Kribbella. Physiological characteristics and phospholipid and cellular fatty acid compositions can be also used to separate H. koreensis from species of the genus Kribbella. On the basis of data presented in this and earlier studies, it is proposed that H. koreensis Lee et al. 2000 should be transferred to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov.
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Corynebacterium sphenisci sp. nov., isolated from wild penguins
Six unidentified Gram-positive, rod-shaped organisms recovered from the cloacae of apparently healthy wild penguins were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of a cell wall based on meso-diaminopimelic acid and long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types, consistent with the genus Corynebacterium. Corynomycolic acids, which are characteristic of the genus, were also detected, albeit in small amounts. Comparative 16S rRNA gene sequencing studies showed that the unidentified organisms were phylogenetically related to corynebacteria and represent a novel subline associated with a small subcluster of species that includes Corynebacterium xerosis, Corynebacterium amycolatum and Corynebacterium freneyi. The unknown isolates were readily distinguished from their closest phylogenetic relatives and all other Corynebacterium species with validly published names by using a combination of biochemical and chemotaxonomic criteria. Based on both phenotypic and 16S rRNA gene sequence considerations, it is proposed that the unknown isolates recovered from penguins be classified as a novel species in the genus Corynebacterium, Corynebacterium sphenisci sp. nov. The type strain is CECT 5990T (=CCUG 46398T).
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Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov.
Taxonomic studies were performed on four strains (D-1/D-an/IIT, C/C-an/B1T, A-1/C-an/C1T and A-1/C-an/IT) of anaerobic, Gram-positive, spore-forming bacteria originally isolated from a mat sample retrieved from a shallow, moated area around Lake Fryxell, an Antarctic freshwater lake. Phylogenetic analyses based on 16S rRNA gene sequence data indicated that these strains are affiliated with cluster I clostridia and form a coherent group with Clostridium estertheticum and Clostridium laramiense. Similarity values among 16S rRNA gene sequences within this assemblage ranged between 96·7 and 99·8 %. Despite the close phylogenetic relationship, several distinguishing phenotypic traits were found among the novel strains using a polyphasic approach. All strains were psychrophilic, but the temperature optimum for growth differed markedly, ranging from 4 to 16 °C. In addition, substrate utilization patterns, fermentation end products, cellular fatty acid profiles and morphological traits enabled a clear differentiation between the strains. DNA–DNA hybridization experiments revealed that each of the four novel strains represents a distinct species, with DNA–DNA similarity values to related strains in the range 16–62 %. In contrast, the type strains of C. estertheticum and C. laramiense shared 79 % DNA–DNA similarity, indicating a close relationship at the species level. On the basis of genetic and phenotypic properties, it is proposed to designate four novel species of the genus Clostridium to harbour the newly isolated strains: Clostridium frigoris sp. nov. (type strain D-1/D-an/IIT=DSM 14204T =ATCC BAA-579T), Clostridium lacusfryxellense sp. nov. (type strain C/C-an/B1T=DSM 14205T =ATCC BAA-580T), Clostridium bowmanii sp. nov. (type strain A-1/C-an/C1T=DSM 14206T =ATCC BAA-581T) and Clostridium psychrophilum sp. nov. (type strain A-1/C-an/IT=DSM 14207T =ATCC BAA-582T). It is also proposed to unite C. laramiense and C. estertheticum under C. estertheticum. The subspecies C. estertheticum subsp. laramiense subsp. nov. is established, represented by strain ATCC 51254T (=DSM 14864T). The type strain of C. estertheticum subsp. estertheticum remains NCIMB 12511T (=DSM 8809T).
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Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney
A strictly anaerobic, slightly halophilic and moderately thermophilic, sporulating rod designated strain DVird3T was isolated from deep-sea hydrothermal vent samples collected at a depth of approximately 800 m on the Atlantic Ocean Ridge. Strain DVird3T possessed a few laterally inserted flagella, had a DNA G+C content of 33·1 mol% and grew optimally at pH 6·6 and at 45 °C. Growth was observed at temperatures between 20 and 58 °C and at pH values between 5·8 and 8·2. The optimum NaCl concentration for growth was 3 % sea salt (30 g l−1); no growth was observed in the presence of 15 or 60 g sea salt l−1. Strain DVird3T is heterotrophic and utilizes some sugars and various single amino acids. Acetate was the main fatty acid detected from carbohydrate fermentation, together with H2 and CO2. Gelatin was used as an energy source. It performed the Stickland reaction. Phylogenetically, strain DVird3T branched with members of cluster XI of the order Clostridiales, with Clostridium halophilum as its closest relative (similarity of 94·6 %). On the basis of its phenotypic, genotypic and phylogenetic characteristics, strain DVird3T (=DSM 15212T =CIP 107654T) is proposed as the type strain of a novel species of the genus Clostridium, Clostridium caminithermale sp. nov.
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Paenibacillus agarexedens sp. nov., nom. rev., and Paenibacillus agaridevorans sp. nov.
Twenty-two agarolytic, aerobic, spore-forming strains were characterized taxonomically by DNA–DNA reassociation experiments, riboprint analyses, 16S rDNA sequencing and phenetic similarity analyses. Based on riboprint analyses, the strains formed eight ribogroups, six of which contained 2–6 strains and two encompassed single strains. Within the multi-strain ribogroups, similarities ranged from 91–99 %. Phylogenetic analyses of representatives of the eight groups by 16S rDNA sequence analysis showed that the strains were affiliated to the genus Paenibacillus, but relatedness to described Paenibacillus species was only moderate (<97·8 % sequence similarity). Published DNA–DNA similarity values for most of the agarolytic strains, supplemented with new data, supported the distinctiveness of the eight ribogroups. Intragroup DNA–DNA similarity values ranged from 80 to 104 %, while intergroup DNA–DNA similarities were <35 %. Based on genomic distinctiveness and supported by the presence of distinguishing phenotypic properties, multi-strain groups 1 and 2 are proposed as novel species, Paenibacillus agarexedens sp. nov., nom. rev. (type strain, DSM 1327T=CIP 107437T) and Paenibacillus agaridevorans sp. nov. (type strain, DSM 1355T=CIP 107436T).
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Halobacillus karajensis sp. nov., a novel moderate halophile
More LessA moderately halophilic, Gram-positive, spore-forming bacterium was isolated from surface saline soil of the Karaj region, Iran. The strain, designated MA-2T, was strictly aerobic with rod-shaped cells that occurred singly, in pairs or short chains. It contained l-orn–d-Asp-type peptidoglycan and the major respiratory lipoquinone was MK-7. It was non-motile and had an ellipsoidal endospore located centrally or subterminally. Growth occurred at 10–49 °C and in the pH range 6·0–9·6. Strain MA-2T grew at salinities of 1–24 % (w/v) NaCl, showing optimal growth at 10 % (w/v). The DNA G+C content was 41·3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MA-2T was associated with Bacillus rRNA group 1. The micro-organisms showing the closest phylogenetic relationship to strain MA-2T were Halobacillus litoralis and Halobacillus trueperi. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA–DNA similarity data, it is proposed that strain MA-2T (=DSM 14948T =LMG 21515T) should be placed in the genus Halobacillus as the type strain of a novel species, Halobacillus karajensis sp. nov.
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Corynebacterium atypicum sp. nov., from a human clinical source, does not contain corynomycolic acids
More LessAn unusual Gram-positive, facultatively anaerobic, catalase-positive, diphtheroid-shaped organism originating from an unknown human clinical source was characterized by biochemical, molecular chemical and molecular phylogenetic methods. Based on its morphological and biochemical characteristics and the presence of a murein based on meso-diaminopimelic acid, the unidentified organism was tentatively assigned to the genus Corynebacterium. However, the unknown organism was found to lack the distinctive, short-chain corynomycolic acids that are considered to be characteristic of this genus. Despite the absence of these characteristic lipids, comparative 16S rRNA gene sequencing showed that the unknown bacterium was phylogenetically a member of the genus Corynebacterium and was distinct from all currently known species. Based on both phenotypic and 16S rRNA sequence considerations, it is proposed that the unknown organism be classified as a novel species, Corynebacterium atypicum sp. nov. The type strain of C. atypicum is strain R2070T (=CCUG 45804T =CIP 107431T).
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Description of Enterococcus canis sp. nov. from dogs and reclassification of Enterococcus porcinus Teixeira et al. 2001 as a junior synonym of Enterococcus villorum Vancanneyt et al. 2001
Strains from anal swabs and chronic otitis externa in dogs were shown to be phylogenetically related to the Enterococcus faecium species group. They shared a number of phenotypic characteristics with these species, but they could be easily differentiated by biochemical reactions. In addition, the canine strains were unusual in their nearly complete failure to grow on sodium azide-containing enterococci-selective media and in their Voges–Proskauer reactions (usually negative). By using 16S rRNA sequencing and DNA–DNA hybridization of representative strains, as well as tDNA interspacer gene PCR and SDS-PAGE of whole-cell proteins, the group of canine strains was shown to constitute a novel enterococcal species. The name Enterococcus canis sp. nov. is proposed for this species, with LMG 12316T (=CCUG 46666T) as the type strain. Concurrently, the taxonomic situation and nomenclatural position of Enterococcus porcinus were investigated. As no phenotypic or genotypic differences were found between this species and Enterococcus villorum, the name E. porcinus is considered to be a junior synonym of E. villorum.
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Alicyclobacillus sendaiensis sp. nov., a novel acidophilic, slightly thermophilic species isolated from soil in Sendai, Japan
More LessAn acidophilic, slightly thermophilic bacterium, designated strain NTAP-1T, that produces a thermostable extracellular acid collagenase activity with potential industrial applications was isolated from soil of Aoba-yama Park, Sendai, Japan. The temperature range for growth was 40–65 °C, with an optimum at 55 °C, and the pH range for growth was 2·5–6·5, with an optimum at pH 5·5. Analysis of the 16S rDNA sequence of strain NTAP-1T showed that it is most closely related to strains of the genus Alicyclobacillus. Consistently, the major constituents of the cell-membrane lipid of strain NTAP-1T were ω-alicyclic fatty acids. However, DNA–DNA reassociation studies showed only low similarities (less than 33 %) to any type strain of Alicyclobacillus. On the basis of the phenotypic and genotypic properties, a novel species is proposed, Alicyclobacillus sendaiensis sp. nov., represented by strain NTAP-1T (=JCM 11817T =ATCC BAA-609T).
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Streptococcus oligofermentans sp. nov., a novel oral isolate from caries-free humans
More LessFive streptococcal strains were isolated from dental plaque and saliva of caries-free humans. The cells were Gram-positive, non-spore-forming, non-motile cocci that were arranged in short chains. The strains were catalase-negative, facultatively anaerobic and produced lactic acid exclusively from glucose fermentation. Biochemical analysis that used both conventional methods and the commercial API 20 Strep system showed that the five strains fermented only a few kinds of sugar. The mean DNA G+C content of the five novel strains was 39·5±0·8 mol%. Phylogenetic analysis based on 16S rDNA sequence homology indicated that the new isolates represented a novel member of the mitis group of the genus Streptococcus, related most closely to the recently described species Streptococcus sinensis. DNA–DNA relatedness between novel strain LMG 21535T and type strains of phylogenetically related species of oral streptococci was 7·1–16·4 %. Therefore a novel Streptococcus species, Streptococcus oligofermentans sp. nov., is proposed. The type strain is LMG 21535T=AS 1.3089T.
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Leuconostoc inhae sp. nov., a lactic acid bacterium isolated from kimchi
More LessSix strains of a hitherto unknown bacterium isolated from kimchi, a fermented vegetable food produced in Korea, were characterized by using phenotypic methods, phylogenetic analysis and DNA–DNA hybridization. The novel strains were Gram-positive, non-spore-forming, heterofermentative and spherical or lenticular lactic acid bacteria. Comparative 16S rRNA gene sequencing and DNA relatedness demonstrated that the unknown strains represented a novel clade within the genus Leuconostoc and were close to, but distinct from, Leuconostoc gelidum. The unknown strains were clearly distinguished from all described members of the genus Leuconostoc by using RFLP patterns of genus-specific 16S rRNA gene PCR products with a single endonuclease, BsmAI. Based on the polyphasic evidence, the unknown isolates are classified as Leuconostoc inhae sp. nov. The type strain is strain IH003T (=KCTC 3774T =DSM 15101T).
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Tepidibacter thalassicus gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, fermentative bacterium from a deep-sea hydrothermal vent
A moderately thermophilic, anaerobic, endospore-forming bacterium (strain SC 562T) was isolated from a hydrothermal vent chimney located at 13° N on the East-Pacific Rise at a depth of 2650 m. Cells of strain SC 562T were straight to slightly curved rods, which were 0·7–0·9 μm in diameter and 3·5–6·0 μm in length with peritrichous flagella. Strain SC 562T formed round, refractile endospores in terminally swollen sporangia. The temperature range for growth was 33–60 °C, with an optimum at 50 °C. The pH range for growth was 4·8–8·5, with an optimum at pH 6·5–6·8. Growth of strain SC 562T was observed at NaCl concentrations ranging from 1·5 to 6 % (w/v). The substrates utilized by strain SC 562T included casein, peptone, albumin, yeast extract, beef extract, alanine plus proline and starch. Glucose, maltose, pyruvate, valine and arginine each slightly stimulated growth in the presence of yeast extract. The products of glucose fermentation were ethanol, acetate, H2 and CO2. Strain SC 562T reduced elemental sulfur to hydrogen sulfide. The G+C content of the DNA of strain SC 562T was 24 mol%. 16S rDNA sequence analysis revealed that the isolated organism belonged to cluster XI of the Clostridium subphylum. On the basis of its physiological properties and phylogenetic analyses, it is proposed that strain SC 562T represents the sole species of a novel genus, Tepidibacter; the name Tepidibacter thalassicus is proposed for strain SC 562T (=DSM 15285T =UNIQEM 215T).
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Isolation of Corynebacterium falsenii and description of Corynebacterium aquilae sp. nov., from eagles
Biochemical, molecular chemical and molecular genetic studies were performed on seven unidentified Gram-positive, rod-shaped organisms recovered from eagles. The strains were provisionally identified as Corynebacterium jeikeium with the commercial API Coryne system, but they were able to grow under anaerobic conditions and were non-lipophilic. Comparative 16S rRNA gene sequencing studies demonstrated that the isolates belonged phylogenetically to the genus Corynebacterium. Three strains were identified genotypically as Corynebacterium falsenii; the remaining four strains corresponded to a hitherto unknown lineage within the genus Corynebacterium, associated with a small subcluster of species that included Corynebacterium diphtheriae and its close relatives. The unknown bacterial strains were readily distinguished from these and other species of the genus by biochemical tests. Based on both phenotypic and phylogenetic evidence, it is proposed that the unknown bacterial strains from eagles should be classified as Corynebacterium aquilae sp. nov. (type strain is S-613T=CECT 5993T =CCUG 46511T).
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- Unicellular Eukaryotes
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Three new combinations from the Cryptococcus laurentii complex: Cryptococcus aureus, Cryptococcus carnescens and Cryptococcus peneaus
More LessFifteen strains of the Cryptococcus laurentii complex were reclassified based on sequence analyses of 18S rDNA, the D1/D2 region of the 26S rDNA and the internal transcribed spacer regions, as well as physiological and biochemical properties. The strains were divided into phylogenetic groups I and II. The type strain of C. laurentii (CBS 139T=ATCC 18803T =JCM 9066T =MUCL 30398T =NRRL Y-2536T) was in phylogenetic group I. Phylogenetic group II, which was phylogenetically distant from phylogenetic group I, clustered with Cryptococcus dimennae and Bullera globispora. In phylogenetic group I, the type strain of Torula aurea (CBS 318T=ATCC 32063T =IFO 0372T =NRRL Y-1582T) appeared to be a separate species from C. laurentii, and the designation Cryptococcus aureus comb. nov. is proposed for Torula aurea. Cryptococcus flavescens (formerly Torula flavescens, type strain CBS 942T=ATCC 10668T =DBVPG 6007T =MUCL 30414T) was treated as a synonym of C. laurentii; however, this is a distinct species. The type strains of Torulopsis carnescens (CBS 973T=ATCC 32064T =MUCL 30641T =NRRL Y-1503T), Rhodotorula peneaus (CBS 2409T=ATCC 13546T =MUCL 30643T =NRRL Y-2005T) and Cryptococcus victoriae belonged to phylogenetic group II. Two new combinations, Cryptococcus carnescens comb. nov. (type strain CBS 973T=ATCC 32064T =MUCL 30641T =NRRL Y-1503T) and Cryptococcus peneaus comb. nov. (type strain CBS 2409T=ATCC 13546T =MUCL 30643T =NRRL Y-2005T), are proposed from this group.
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Phylogenetic analysis identifies the ‘megabacterium’ of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov.
An organism commonly referred to as ‘megabacterium’ colonizes the gastric isthmus of many species of birds. It is weakly Gram-positive and periodic acid–Schiff-positive and stains with silver stains. Previous studies have shown that it has a nucleus and a cell wall similar to those seen in fungi. Calcofluor white M2R staining suggests that the cell wall contains chitin, a eukaryote-specific substance, and rRNA in situ hybridization demonstrates that it is a eukaryote. To characterize this organism phylogenetically, DNA was extracted from purified cells. rDNA was readily amplified by PCR with pan-fungal DNA primer sets and primer sets derived from the newly determined sequence, but not with bacteria-specific primer sets. Specific primer sets amplified rDNA from isthmus scrapings from an infected bird, but not from a non-infected bird or other control DNA. The sequence was confirmed to derive from the purified organism by in situ rRNA hybridization using a specific probe. Phylogenetic analysis of sequences of the 18S rDNA and domain D1/D2 of 26S rDNA showed the organism to be a previously undescribed anamorphic ascomycetous yeast representing a new genus. The name Macrorhabdus ornithogaster gen. nov., sp. nov. is proposed for this organism. The type material is CBS 9251T (=NRRL Y-27487T).
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- Evolution, Phylogeny And Biodiversity
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Reclassification of ATCC 9341 from Micrococcus luteus to Kocuria rhizophila
More LessStrain ATCC 9341, currently known as Micrococcus luteus, has been designated as a quality-control strain in a number of applications. It is also cited as the standard culture in several official methods and manuals, as well as the Code of Federal Regulations. Over the years, it has become apparent that ATCC 9341 does not resemble other M. luteus strains; however, its phenotypic characteristics alone were ambiguous. Recently, a polyphasic study was performed in which molecular data were combined with cytochemical properties and physiological characteristics. The results clearly indicate that ATCC 9341 is a member of the genus Kocuria. Thus, it is proposed to reclassify ATCC 9341 as Kocuria rhizophila and to alert users worldwide of this name change.
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Phylogeny of the photosynthetic euglenophytes inferred from the nuclear SSU and partial LSU rDNA
More LessPrevious studies using the nuclear SSU rDNA have indicated that the photosynthetic euglenoids are a monophyletic group; however, some of the genera within the photosynthetic lineage are not monophyletic. To test these results further, evolutionary relationships among the photosynthetic genera were investigated by obtaining partial LSU nuclear rDNA sequences. Taxa from each of the external clades of the SSU rDNA-based phylogeny were chosen to create a combined dataset and to compare the individual LSU and SSU rDNA datasets. Conserved areas of the aligned sequences for both the LSU and SSU rDNA were used to generate parsimony, log-det, maximum-likelihood and Bayesian trees. The SSU and LSU rDNA consistently generated the same seven terminal clades; however, the relationship among those clades varied depending on the type of analysis and the dataset used. The combined dataset generated a more robust phylogeny, but the relationships among clades still varied. The addition of the LSU rDNA dataset to the euglenophyte phylogeny supports the view that the genera Euglena, Lepocinclis and Phacus are not monophyletic and substantiates the existence of several well-supported clades. A secondary structural model for the D2 region of the LSU rDNA was proposed on the basis of compensatory base changes found in the alignment.
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Emended phenotypic characterization of Prototheca zopfii: a proposal for three biotypes and standards for their identification
More LessA representative selection of Prototheca zopfii strains isolated from different environmental habitats or clinical cases was characterized in a polyphasic approach in order to assess their intraspecies taxonomic position. Recently, the recognition of distinct phenotypic clusters has been reported as the assignment of ‘variants’. In the present study, 11 strains were compared by a number of phenotypic and genetic criteria, including growth characteristics, biochemical reactions and serotyping results. Based on emended standards for biotype identification, P. zopfii strains showed auxanographic differences and distinct assimilation patterns with respect to utilization of amino acids and glycerol. Serotyping by means of immunoblotting revealed that all isolates of variant II obtained from clinical cases, i.e. isolates from bovine mastitis or from human enteropathia, showed specific antigen patterns. They were found to be different from strains assigned to the other two variants with respect to their immunogenic antigens. Furthermore, comparison of partial 18S rDNA sequences confirmed distinct differences between the former variants. Based on these results, it is proposed that P. zopfii merits classification as a species comprising three biotypes.
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- International Committee On Systematics Of Prokaryotes
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- Request For An Opinion
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Description of new Ensifer strains from nodules and proposal to transfer Ensifer adhaerens Casida 1982 to Sinorhizobium as Sinorhizobium adhaerens comb. nov. Request for an Opinion
A group of four diverse rhizobial isolates and two soil isolates that are highly related to Ensifer adhaerens were characterized by a polyphasic approach. On the basis of DNA–DNA hybridizations and phenotypic features, these strains cannot be distinguished clearly form Ensifer adhaerens, a soil bacterium that was described in 1982, mainly on the basis of phenotypic characteristics. Phylogenetically, Ensifer and Sinorhizobium form a single group in the 16S rDNA dendrogram of the α-Proteobacteria, as well as in an analysis of partial recA gene sequences. They may therefore be regarded as a single genus. Because Sinorhizobium was proposed in 1988, according to the Bacteriological Code (1990 Revision) the older name, Ensifer, has priority. However, there are several reasons why a change from Sinorhizobium to Ensifer may not be the best solution and making an exception to Rule 38 may be more appropriate. We therefore propose the species Sinorhizobium adhaerens comb. nov. and put forward a Request for an Opinion to the Judicial Commission regarding the conservation of Sinorhizobium adhaerens over Ensifer adhaerens.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 46 (1996)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)