- Volume 55, Issue 2, 2005
Volume 55, Issue 2, 2005
- Validation List No. 102
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 54, part 6, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). 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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- Archaea
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Methanofollis formosanus sp. nov., isolated from a fish pond
More LessA mesophilic, hydrogenotrophic methanogen, strain ML15T, was isolated from an aquaculture fish pond near Wang-gong, Taiwan. The cells were irregular cocci, non-motile, 1·5–2·0 μm in diameter and Gram-negative. Cells of strain ML15T lysed easily in the presence of SDS (0·1 g l−1) and the S-layer protein had an M r of 138 800. The catabolic substrates utilized by this strain included formate and H2/CO2, but not acetate, methanol, trimethylamine or secondary alcohols. Growth did not occur in minimal medium, but was observed when yeast extract and tryptone were added. Strain ML15T grew fastest at 37 °C, pH 6·6–7·0 and with 3 % NaCl. Acetate was not required for cell growth. Trace amounts of tungstate promoted cell growth. The G+C contents of DNA of Methanofollis aquaemaris N2F9704T and strain ML15T were 59·1 and 58·4 mol%, respectively. Sequence analysis of the 16S rRNA genes of strain ML15T and selected Methanofollis species revealed similarities of 95–97 %. Based on the data presented here, it is proposed that strain ML15T (=OCM 789T=DSM 15483T) represents a novel species, Methanofollis formosanus sp. nov.
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- Other Bacteria
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Flavobacterium antarcticum sp. nov., a novel psychrotolerant bacterium isolated from the Antarctic
More LessA yellow-pigmented, Gram-negative and aerobic bacterial strain, designated AT1026T, was isolated from a terrestrial sample from the Antarctic. Results of 16S rRNA gene sequence analysis indicated that the Antarctic isolate belonged to the genus Flavobacterium, with the highest sequence similarity to Flavobacterium tegetincola (96·4 %). Cells were non-motile, non-gliding and psychrotolerant, with optimum and maximum temperatures of about 20 and 25 °C. Flexirubins were absent. The major isoprenoid quinone (MK-6), predominant cellular fatty acids (iso-C15 : 1 G, iso-C15 : 0 and a mixture of C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38 mol%) of the Antarctic isolate were consistent with those of the genus Flavobacterium. In contrast, several phenotypic characters can be used to differentiate this isolate from other flavobacteria. The polyphasic data presented in this study indicated that this isolate should be classified as a novel species in the genus Flavobacterium. The name Flavobacterium antarcticum sp. nov. is therefore proposed for the Antarctic isolate; the type strain is AT1026T (=IMSNU 14042T=KCTC 12222T=JCM 12383T).
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‘Candidatus Borrelia texasensis’, from the American dog tick Dermacentor variabilis
More LessTXW-1, a Borrelia strain isolated in March 1998 from an adult male Dermacentor variabilis tick feeding on a coyote from Webb county, Texas, USA, was characterized by using randomly amplified polymorphic DNA (RAPD) analysis, RFLP and sequence analysis of flaB and rrs (16S rRNA gene), DNA–DNA hybridization analysis, SDS-PAGE and Western blotting with mAbs. It shows different banding patterns in RFLP analysis of flaB and forms distinct branches in phylogenetic analysis derived from flaB and rrs genes. It differs from other borreliae based on the banding patterns obtained by RAPD analysis. This strain contains a small, 38-kDa endoflagellar protein. DNA–DNA hybridization experiments revealed that the levels of DNA reassociation between TXW-1 and previously described relapsing fever borreliae were 38·64 % (Borrelia turicatae), 38·40 % (Borrelia parkeri), 7·39 % (Borrelia hermsii) and 18·30 % (Borrelia coriaceae). However, the level of DNA relatedness between B. parkeri and B. turicatae was 78·78 %. Sequence analyses of flaB and rrs genes indicate that the similarities of nucleotide sequences among TXW-1 and B. turicatae or B. parkeri are less than that between B. turicatae and B. parkeri, and that the genetic distances among TXW-1 and B. turicatae or B. parkeri are greater than that between B. turicatae and B. parkeri. TXW-1 lacks an ospC gene. Electron microscope observations showed that this spirochaete had different morphological structures compared to previously described relapsing fever borreliae. All the results obtained from the above-mentioned analyses indicate that TXW-1 is different from other described Borrelia species and that it represents a novel species of Borrelia. We have been unable to revive frozen cultures and so can not meet the requirements of the Bacteriological Code to deposit viable type material at two different culture collections. Therefore we use the Candidatus designation; based on these results, the species ‘Candidatus Borrelia texasensis' is proposed.
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Flavobacterium granuli sp. nov., isolated from granules used in a wastewater treatment plant
More LessA Gram-negative, rod-shaped, non-spore-forming bacterium (designated strain Kw05T) was isolated from granules used in the wastewater treatment plant of a beer-brewing factory in Kwang-Ju, Republic of Korea. On the basis of 16S rRNA gene sequence similarity, strain Kw05T was shown to belong to the family Flavobacteriaceae, and was most closely related to Flavobacterium limicola (96·6 %), Flavobacterium hibernum (96·3 %), Flavobacterium hydatis (96·1 %) and Flavobacterium xinjiangense (96·1 %). The G+C content of the genomic DNA of strain Kw05T was 36·2 mol%, within the range of 32–37 mol% for the genus Flavobacterium. Chemotaxonomic data (major menaquinone MK-6; major fatty acids iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and iso-C17 : 1 ω9c) supported the classification of strain Kw05T within the genus Flavobacterium. Kw05T therefore represents a novel species, for which the name Flavobacterium granuli sp. nov. is proposed. The type strain is Kw05T (=KCTC 12201T=IAM 15099T).
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Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes
More LessTaxonomic studies were performed on seven strains isolated from microbial mats in Antarctic lakes of the McMurdo Dry Valleys. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains are related to the genus Flavobacterium; sequence similarity values with their nearest phylogenetic neighbours ranged from 97·0 to 98·7 %. Results of DNA–DNA hybridization and comparison of repetitive extragenic palindromic DNA-PCR fingerprinting patterns revealed that these strains are members of two distinct species. Genotypic results, together with phenotypic characteristics, allowed these species to be differentiated from related recognized Flavobacterium species. The isolates are psychrophilic, Gram-negative, chemoheterotrophic, rod-shaped cells. Their whole-cell fatty acid profiles are similar and include C15 : 0, C15 : 0 anteiso, C15 : 0 iso, C15 : 1 ω6c, C16 : 0 iso, C16 : 0 iso 3-OH, C16 : 1 iso and summed feature 3 (which comprises C15 : 0 iso 2-OH and/or C16 : 1 ω7c) as the major fatty acid components. On the basis of these results, two novel species are proposed: Flavobacterium fryxellicola sp. nov., consisting of three strains with LMG 22022T (=CIP 108325T) as the type strain; and Flavobacterium psychrolimnae sp. nov., consisting of four strains with LMG 22018T (=CIP 108326T) as the type strain. DNA G+C contents of F. fryxellicola and F. psychrolimnae are 35·2–35·9 and 33·8–34·5 mol%, respectively.
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Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea
More LessFour Gram-negative, rod-shaped bacterial strains, TF-26T, TF-28, TF-42 and TF-53, were isolated from a tidal flat in the Yellow Sea, Korea, and their taxonomic positions were determined by a polyphasic characterization. The strains grew optimally in the presence of 2–3 % (w/v) NaCl and at 30–37 °C. The predominant menaquinone detected in the four strains was MK-6. These strains contained large amounts of fatty acids C16 : 1 ω7c and/or iso-C15 : 0 2-OH, iso-C15 : 0, iso-C16 : 0 3-OH, C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C contents of the four strains were 32·3–32·8 mol%. Strains TF-26T, TF-28, TF-42 and TF-53 showed 16S rRNA gene sequence similarity levels of 99·8–100 % and DNA–DNA relatedness levels of 82–87 %. The four strains exhibited 16S rRNA gene sequence similarity levels of 95·0–98·0 % to the type strains of the five current Tenacibaculum species, and DNA–DNA relatedness levels between the four strains and two phylogenetic relatives, Tenacibaculum mesophilum DSM 13764T and Tenacibaculum skagerrakense DSM 14836T, were less than 21 %. On the basis of phenotypic, phylogenetic and genetic data, strains TF-26T, TF-28, TF-42 and TF-53 were classified in the genus Tenacibaculum as members of a novel species, for which the name Tenacibaculum lutimaris sp. nov. (type strain, TF-26T=KCTC 12302T=DSM 16505T) is proposed.
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Prevotella multiformis sp. nov., isolated from human subgingival plaque
More LessFour bacterial strains isolated from the human oral cavity, PPPA19, PPPA21T, PPPA28 and PPPA30, were characterized by determining phenotypic and biochemical features, cellular fatty acid profiles and the phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that each of the isolates was a member of the genus Prevotella. These strains were related to Prevotella denticola with about 95 % similarity. The strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. However, the cells of these strains were often cocci (coccobacilli), depending on the cultivation time. Colonies of different sizes were detected on Eggerth Gagnon agar plates for these strains. The cells forming large colonies were cocci, whereas those forming small colonies were cocci and rods. However, 16S rRNA gene sequence comparison of colonies of different sizes revealed that only a single organism was present. Although these strains had phenotypic characteristics that were similar to those of P. denticola JCM 8528, they could be differentiated from P. denticola JCM 8528 by aesculin hydrolysis and d-cellobiose fermentation in API 20A tests. DNA–DNA hybridization experiments revealed the genomic distinction of these four strains with respect to P. denticola JCM 8528. On the basis of these data, a novel Prevotella species, Prevotella multiformis sp. nov., is proposed, with PPPA21T (=JCM 12541T=DSM 16608T) as the type strain.
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Adhaeribacter aquaticus gen. nov., sp. nov., a Gram-negative isolate from a potable water biofilm
More LessA Gram-negative bacterium was isolated from a freshwater biofilm developed on a stainless steel surface under a fluid velocity of 0·26 m s−1. The strain, MBRG1.5T, was cultivated on R2A agar and formed pink colonies. Light microscopy and negative staining in a transmission electron microscope showed that the cells were rod-shaped, approximately 2·8–4·1 μm long by 0·9–1·7 μm wide in size and produced large quantities of extracellular fibrillar material. Additionally, following growth in batch culture, transmission electron microscopy showed that many cells plasmolysed. Stationary-phase cells were more variable in size and shape. The DNA G+C content was 40·0 mol%. The most abundant fatty acids were 15 : 0 iso (22·5 %), followed by 16 : 1ω5c (16·9 %) and 15 : 0 iso 2-OH (16·5 %). Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the family ‘Flexibacteraceae’ of the Cytophaga–Flavobacterium–Bacteroides group. Phenotypic and genotypic analyses indicated that the strain could not be assigned to any recognized genus; therefore a novel genus and species, Adhaeribacter aquaticus gen. nov., sp. nov., is proposed, with MBRG1.5T (=DSM 16391T=NCIMB 14008T) as the type strain.
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Marinicola seohaensis gen. nov., sp. nov., isolated from sea water of the Yellow Sea, Korea
More LessA Gram-negative, non-flagellated, non-spore-forming and rod-shaped bacterial strain, SW-152T, was isolated from sea water of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strain SW-152T grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Polar lipids detected in strain SW-152T were phosphatidylethanolamine, diphosphatidylglycerol and unidentified lipids. The DNA G+C content was 40·3 mol%. Phylogenetic trees based on 16S rRNA gene sequences exhibited that strain SW-152T forms a distinct evolutionary lineage within the Cytophaga–Flavobacterium–Bacteroides (CFB) group. Strain SW-152T exhibited low 16S rRNA similarity levels of less than 89·4 % to members belonging to the CFB group. Phenotypic properties of strain SW-152T differentiate it from phylogenetically related taxa. On the basis of phenotypic and phylogenetic data, strain SW-152T (=KCTC 12312T=JCM 12600T) was classified in a novel genus and species, Marinicola seohaensis gen. nov., sp. nov.
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Algoriphagus yeomjeoni sp. nov., isolated from a marine solar saltern in the Yellow Sea, Korea
More LessTwo Gram-negative, rod-shaped bacterial strains, MSS-160T and MSS-161, were isolated from a marine solar saltern in the Yellow Sea, Korea, and subjected to a polyphasic taxonomic study. The two strains grew optimally in the presence of 2 % (w/v) NaCl and at 25–30 °C. Strains MSS-160T and MSS-161 contained MK-7 as the predominant menaquinone and large amounts of fatty acids C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C15 : 0. The DNA G+C content of the two strains was 41 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains were phylogenetically affiliated to the genus Algoriphagus. Strains MSS-160T and MSS-161 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 91 %; they exhibited 16S rRNA similarity levels of 96·6–99·3 % to the type strains of Algoriphagus species with validly published names. DNA–DNA relatedness levels between the two strains and the type strains of five Algoriphagus species were lower than 46 %. On the basis of phenotypic, phylogenetic and genetic data, strains MSS-160T and MSS-161 were classified in the genus Algoriphagus as members of a novel species, for which the name Algoriphagus yeomjeoni sp. nov. (type strain, MSS-160T=KCTC 12309T=JCM 12598T) is proposed.
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- Proteobacteria
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Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta
Highly diverse Bradyrhizobium strains nodulate genistoid legumes (brooms) in the Canary Islands, Morocco, Spain and the Americas. Phylogenetic analyses of ITS, atpD, glnII and recA sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely Bradyrhizobium japonicum and three unnamed genospecies. DNA–DNA hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name Bradyrhizobium canariense is proposed. B. canariense populations experience homologous recombination at housekeeping loci, but are sexually isolated from sympatric B. japonicum bv. genistearum strains in soils of the Canary Islands. B. canariense strains are highly acid-tolerant, nodulate diverse legumes in the tribes Genisteae and Loteae, but not Glycine species, whereas acid-sensitive B. japonicum soybean isolates such as USDA 6T and USDA 110 do not nodulate genistoid legumes. Based on host-range experiments and phylogenetic analyses of symbiotic nifH and nodC sequences, the biovarieties genistearum and glycinearum for the genistoid legume and soybean isolates, respectively, were proposed. B. canariense bv. genistearum strains display an overlapped host range with B. japonicum bv. genistearum isolates, both sharing monophyletic nifH and nodC alleles, possibly due to the lateral transfer of a conjugative chromosomal symbiotic island across species. B. canariense is the sister species of B. japonicum, as inferred from a maximum-likelihood Bradyrhizobium species phylogeny estimated from congruent glnII+recA sequence partitions, which resolves eight species clades. In addition to the currently described species, this phylogeny uncovered the novel Bradyrhizobium genospecies alpha and beta and the photosynthetic strains as independent evolutionary lineages. The type strain for B. canariense is BTA-1T (=ATCC BAA-1002T=LMG 22265T=CFNE 1008T).
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Psychrobacter cibarius sp. nov., isolated from jeotgal, a traditional Korean fermented seafood
More LessTwo novel Psychrobacter-like bacterial strains, JG-219T and JG-220, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of strains JG-219T and JG-220 were Gram-negative, non-motile coccobacilli. Growth of the two strains was observed at 4–32 °C. They grew optimally in the presence of 2–5 % (w/v) NaCl. Strains JG-219T and JG-220 contained C18 : 1 ω9c and C17 : 1 ω8c as the major fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains JG-219T and JG-220 were 43·5 and 43·0 mol%, respectively. The two strains showed no difference in their 16S rRNA gene sequences but exhibited minor differences in their phenotypic properties. Strains JG-219T and JG-220 exhibited levels of 16S rRNA gene sequence similarity of 95·2–98·7 % to the type strains of recognized Psychrobacter species. The mean level of DNA–DNA relatedness between strains JG-219T and JG-220 was 84·4 %. The two strains exhibited levels of DNA–DNA relatedness of 1·5–32·9 % to the type strains of eight phylogenetically related Psychrobacter species. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, the two strains were classified as representing a novel species within the genus Psychrobacter, Psychrobacter cibarius sp. nov. The type strain is JG-219T (=KCTC 12256T=DSM 16327T).
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Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process
More LessA polychlorophenol-degrading strain, designated MT1T, and three MT1-like strains, MT101, MT103 and MT104, were isolated from a cold (4–8 °C) fluidized-bed process treating chlorophenol-contaminated groundwater in southern Finland. The organisms were Gram-negative, rod-shaped, catalase-positive, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strains belonged to the α-4 subclass of the Proteobacteria and were members of the genus Novosphingobium. The highest 16S rRNA gene sequence similarity observed for these strains was 96·5 % with the type strains of Novosphingobium hassiacum, Novosphingobium aromaticivorans and Novosphingobium subterraneum. Chemotaxonomic data (major ubiquinone: Q-10; major polyamine: spermidine; major polar lipids: phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid; major fatty acids: 18 : 1ω7c, 16 : 1ω7c and 2-OH 14 : 0) as well as the ability to reduce nitrate supported the affiliation of the strains to the genus Novosphingobium. Based on the phylogenetic analysis, whole-cell fatty acid composition as well as biochemical and physiological characteristics, the MT1-like strains were highly similar and could be separated from all recognized Novosphingobium species. The novel species Novosphingobium lentum sp. nov. is proposed to accommodate strains MT1T (=DSM 13663T=CCUG 45847T), MT101 (=CCUG 45849), MT103 (=CCUG 45850) and MT104 (=CCUG 45851).
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Thioreductor micantisoli gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the ε-Proteobacteria isolated from hydrothermal sediments in the Mid-Okinawa Trough
More LessA novel mesophilic, hydrogen-oxidizing, sulfur-reducing bacterium, designated strain BKB25Ts-YT, was isolated from hydrothermal sediments at Iheya North in the Mid-Okinawa Trough, Japan. Cells were Gram-negative, motile rods (1·8–2·1 μm long and 0·5–0·7 μm wide). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. Elemental sulfur and nitrate served as electron acceptors, respectively yielding hydrogen sulfide and ammonium. Growth was observed at 20–42 °C (optimum 32 °C; 3 h doubling time), pH 5·0–6·5 (optimum 6·0) and in the presence of 2·0–4·0 % NaCl (optimum 2·5 %) via respiratory S0 reduction with H2. The G+C content of the genomic DNA was 37·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate represented the first strain for which taxonomic properties have been characterized within the previously uncultivated ε-Proteobacteria Group G. On the basis of the physiological and molecular properties of the novel isolate, the genus name Thioreductor gen. nov. is proposed, with Thioreductor micantisoli sp. nov. as the type species. The type strain is BKB25Ts-YT (=JCM 12457T=DSM 16661T).
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Malikia granosa gen. nov., sp. nov., a novel polyhydroxyalkanoate- and polyphosphate-accumulating bacterium isolated from activated sludge, and reclassification of Pseudomonas spinosa as Malikia spinosa comb. nov.
More LessA Gram-negative, motile, rod-shaped bacterium, designated strain P1T, was isolated from activated sludge of a municipal wastewater treatment plant. Phylogenetic analysis of its 16S rRNA gene sequence placed the novel isolate among representatives of the family Comamonadaceae. The closest relatives in reconstructed phylogenetic trees were Pseudomonas spinosa, Macromonas bipunctata and Hydrogenophaga species. Strain P1T was not able to grow anaerobically or autotrophically, reduced nitrate to nitrite and required vitamins for growth. Ubiquinone 8 (Q8) and 3-hydroxy-substituted fatty acids were present, but 2-hydroxy fatty acids were absent. The G+C content of the DNA was 67 mol%. Phenotypic characteristics allowed a clear differentiation of strain P1T from representatives of the genera Hydrogenophaga and Macromonas, whereas DNA–DNA hybridization experiments revealed that strain P1T did not belong to the species P. spinosa. As a peculiarity, cells of strain P1T and P. spinosa ATCC 14606T were able to accumulate large amounts of polyhydroxyalkanoates and polyphosphate in the form of large intracellular granules. Apparently in both strains nitrogen limitation stimulates the production of polyhydroxyalkanoates, whereas carbon starvation induces the formation of polyphosphates. Based upon phylogenetic and phenotypic evidence, it is proposed to establish the novel taxon Malikia granosa gen. nov., sp. nov., represented by the type strain P1T (=DSM 15619T=JCM 12706T=CIP 108194T). The most closely related species of strain P1T was P. spinosa. This species has been misclassified, and it is proposed to transfer it to the new genus Malikia as Malikia spinosa gen. nov., comb. nov. The type strain is ATCC 14606T (=DSM 15801T).
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Nereida ignava gen. nov., sp. nov., a novel aerobic marine α-proteobacterium that is closely related to uncultured Prionitis (alga) gall symbionts
More LessA Gram-negative, slightly halophilic, non-pigmented, strictly aerobic, chemo-organotrophic bacterium was isolated from Mediterranean sea water off the Spanish coast near Valencia. This strain was poorly reactive, being unable to grow in most carbon sources analysed in minimal medium. However, good growth was observed when more complex media and longer incubation times were used. Phylogenetic analysis based on an almost complete 16S rRNA gene sequence placed strain 2SM4T within the Roseobacter group, in the vicinity of uncultured bacteria described as gall symbionts of several species of the red alga Prionitis. Sequence similarity values between strain 2SM4T and the closest neighbouring species were below 95·0 %. The cellular fatty acid composition of the Mediterranean strain confirmed its position within the ‘Alphaproteobacteria’, sharing 18 : 1ω7c as the major cellular fatty acid. The phylogenetic distance from any taxon with a validly published name and also a number of distinguishing features support the designation of strain 2SM4T as representing a novel genus and species, for which the name Nereida ignava gen. nov., sp. nov. is proposed. The type strain is 2SM4T (=CECT 5292T=DSM 16309T=CIP 108404T=CCUG 49433T).
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Uruburuella suis gen. nov., sp. nov., isolated from clinical specimens of pigs
More LessFive strains of an unusual Gram-negative, catalase-positive, oxidase-positive, coccobacillus-shaped bacterium isolated from the lungs and heart of pigs with pneumonia and pericarditis were characterized by phenotypic and molecular genetic methods. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the family Neisseriaceae, although they did not appear to correspond to any recognized genus or species. Comparative 16S rRNA gene sequencing showed that the five unidentified strains were phylogenetically highly related to each other and represent a hitherto unknown subline within the family Neisseriaceae. On the basis of both phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from pigs be classified as a novel genus and species within the family Neisseriaceae, for which the name Uruburuella suis gen. nov., sp. nov. is proposed. The type strain of U. suis is 1258/02T (=CCUG 47806T=CECT 5685T).
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Jannaschia rubra sp. nov., a red-pigmented bacterium isolated from sea water
More LessA Gram-negative, slightly halophilic, strictly aerobic, chemo-organotrophic bacterium was isolated from Mediterranean sea water near Valencia (Spain). Comparison of the almost complete 16S rRNA gene sequence showed that strain 4SM3T belonged to the Roseobacter group, with Jannaschia helgolandensis as its closest relative, with a similarity of 98·7 %. DNA–DNA hybridization analysis showed that the Mediterranean isolate had a level of relatedness of less than 42 % with J. helgolandensis and therefore that it represented a novel species of the genus Jannaschia. Phenotypic characteristics gave further evidence that the two organisms are not related at the species level. Isolate 4SM3T grows on solid media as irregular pink–red colonies that penetrate into the agar. Cells are rods, motile by a tuft of polar flagella. The DNA base composition is 64·6 mol% G+C. Morphological, physiological and genotypic differences from related species support the description of a novel species, Jannaschia rubra sp. nov., with strain 4SM3T (=CECT 5088T=DSM 16279T) as the type strain.
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Marichromatium indicum sp. nov., a novel purple sulfur gammaproteobacterium from mangrove soil of Goa, India
More LessA reddish-brown bacterium was isolated from photoheterotrophic enrichments of mangrove soil from the western coast of India, in a medium that contained 10 % (w/v) NaCl. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA100T clusters with species of the genus Marichromatium of the class ‘Gammaproteobacteria’. Cells of strain JA100T are Gram-negative, motile rods with monopolar single flagella; they require NaCl, the optimum concentration being 1–4 %, and tolerate concentrations up to 13 %. The strain has vesicular internal membrane structures, bacteriochlorophyll a and, most probably, carotenoids of the spirilloxanthin series. No growth factors are required. A reduced sulfur source is required for growth, and, during growth on reduced sulfur sources as electron donors, sulfur is intermediately deposited as a single large granule within the cell. Strain JA100T could not grow at the expense of other tricarboxylic acid cycle intermediates, except malate. On the basis of 16S rRNA gene sequence analysis and its morphological and physiological characteristics, strain JA100T is sufficiently different from other Marichromatium species to justify its designation as a novel species, for which the name Marichromatium indicum sp. nov. is proposed. The type strain is JA100T (=DSM 15907T=ATCC BAA-741T=JCM 12653T).
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Hahella ganghwensis sp. nov., isolated from tidal flat sediment
More LessA marine bacterial strain, designated FR1050T, was isolated from a sediment sample of getbol (Korean tidal flat). Phylogenetic investigations based on 16S rRNA gene sequence analysis showed that the isolate formed a robust monophyletic clade with Hahella chejuensis within the γ-Proteobacteria. Sequence similarity between strain FR1050T and the type strain of Hahella chejuensis was 94·7 %. Cells were Gram-negative, aerobic, rod-shaped, motile and halophilic; optimum growth occurred at sea salt concentrations of 4–6 %. The major fatty acids were C18 : 1 ω9c (39·0 %) and C16 : 0 (18·1 %). The DNA G+C content was 44 mol%. The polyphasic data obtained showed that strain FR1050T is affiliated to the genus Hahella but represents a novel species for which the name Hahella ganghwensis sp. nov. is proposed. The type strain is FR1050T (=KCTC 12277T=JCM 12486T).
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Arcobacter cibarius sp. nov., isolated from broiler carcasses
More LessTwenty Gram-negative, rod-shaped, slightly curved, non-spore-forming bacteria that gave a negative result in Arcobacter species-specific PCR tests but that yielded an amplicon in an Arcobacter genus-specific PCR test were isolated from 13 unrelated broiler carcasses. Numerical analysis of the profiles obtained by SDS-PAGE of whole-cell proteins clustered all isolates in a single group distinct from the other Arcobacter species. DNA–DNA hybridization among four representative strains exhibited DNA binding values above 91 %. DNA–DNA hybridization with reference strains of the current four Arcobacter species revealed binding levels below 47 %. The G+C contents ranged between 26·8 and 27·3 mol%. Pairwise comparison of 16S rRNA gene sequences revealed the mean values for similarity to the type strain of Arcobacter cryaerophilus (97·5 %), Arcobacter butzleri (96·5 %), Arcobacter skirrowii (96·0 %) and Arcobacter nitrofigilis (95·0 %). The levels of similarity to Campylobacter and Helicobacter species were below 88 and 87 %, respectively. The isolates could be distinguished from other Arcobacter species by the following biochemical tests: catalase, oxidase and urease activities; reduction of nitrate; growth at 25 and 37 °C under aerobic conditions; growth on 2–4 % (w/v) NaCl media; and susceptibility to cephalothin. These data demonstrate that the 20 isolates represent a single novel Arcobacter species, for which the name Arcobacter cibarius sp. nov. is proposed, with LMG 21996T (=CCUG 48482T) as the type strain.
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Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil
More LessThree strains isolated from the soil of a garden in Tokyo, Japan, were characterized physiologically, biochemically and in terms of fatty acid profile, DNA–DNA relatedness and 16S rRNA gene sequence. The isolates were Gram-negative, aerobic, rod-shaped cells with polar flagellation. According to DNA–DNA similarity, the strains belonged to the same species. The bacteria grew at temperatures from 10 to 37 °C, with an optimum around 25–30 °C. Growth was observed at pH values from 5·6 to 8·0. The DNA G+C content ranged from 63·4 to 64·0 mol%. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation with members of the family ‘Xanthomonadaceae’. The closest relationship was seen with Fulvimonas soli and Frateuria aurantia, but, in terms of physiology and fatty acid profile, the bacteria described were rather distant from Fulvimonas and Frateuria. On the basis of phenotypic and phylogenetic distinctness, it is proposed that the isolates represent a novel species in a novel genus, namely Dyella japonica gen. nov., sp. nov. The type strain is XD53T (=IAM 15069T=DSM 16301T=ATCC BAA-939T).
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Psychrobacter vallis sp. nov. and Psychrobacter aquaticus sp. nov., from Antarctica
Twelve strains of psychrophilic bacteria were isolated from cyanobacterial mat samples collected from various water bodies in the McMurdo Dry Valley region of Antarctica. All the isolates were Gram-negative, non-motile, coccoid, psychrophilic, halotolerant bacteria and had C16 : 1 ω7c, C17 : 1 ω8c and C18 : 1 ω9c as the major fatty acids, ubiquinone-8 as the respiratory quinone and DNA G+C content of 41–46 mol%. Based on these characteristics, the isolates were assigned to the genus Psychrobacter. Based on their SDS-PAGE profiles, the 12 isolates could be categorized into three groups. Six isolates of Group I were identified as representing strains of Psychrobacter okhotskensis. However, using detailed phenotypic and chemotaxonomic characteristics and phylogenetic analysis based on their 16S rRNA gene sequences, strain CMS 39T, the only strain from Group II, and strain CMS 56T, a representative strain of Group III, were different from each other and from all recognized species of Psychrobacter. Therefore, it is proposed to classify CMS 39T (=DSM 15337T=MTCC 4208T) and CMS 56T (=DSM 15339T=MTCC 4386T) as representing the type strains of novel species of Psychrobacter, for which the names Psychrobacter vallis sp. nov. and Psychrobacter aquaticus sp. nov., respectively, are proposed.
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Caminibacter mediatlanticus sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge
More LessA thermophilic, anaerobic, chemolithoautotrophic bacterium, designated strain TB-2T, was isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge at 36° 14′ N 33° 54′ W. The cells were Gram-negative rods approximately 1·5 μm in length and 0·75 μm in width. Strain TB-2T grew between 45 and 70 °C (optimum 55 °C), 10 and 40 g NaCl l−1 (optimum 30 g l−1) and pH 4·5 and 7·5 (optimum pH 5·5). Generation time under optimal conditions was 50 min. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Nitrate or sulfur was used as the electron acceptor, with resulting production of ammonium and hydrogen sulfide, respectively. Oxygen, thiosulfate, sulfite, selenate and arsenate were not used as electron acceptors. Growth was inhibited by the presence of acetate, lactate, formate and peptone. The G+C content of the genomic DNA was 25·6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Caminibacter hydrogeniphilus and Caminibacter profundus (95·9 and 96·3 % similarity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Caminibacter, Caminibacter mediatlanticus sp. nov. The type strain is TB-2T (=DSM 16658T=JCM 12641T).
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Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments
More LessTwo psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria were isolated from marine Arctic sediments sampled off the coast of Svalbard with thiosulfate as the electron donor and CO2 as carbon source. Comparative analysis of 16S rRNA gene sequences suggested that the novel strains, designated SVAL-DT and SVAL-ET, represent members of the genus Thiomicrospira. Further genotypic (DNA–DNA relatedness, DNA G+C content) and phenotypic characterization revealed that the strains represent members of two novel species. Both organisms are obligately autotrophic and strictly aerobic. Nitrate was not used as an electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate and sulfur. The temperature limits for growth of both strains were between −2 °C and 20·8 °C, with optima of 11·5–13·2 °C (SVAL-ET) and 14·6–15·4 °C (SVAL-DT), which is about 13–15 °C lower than the optima of all other recognized Thiomicrospira species. The maximum growth rate on thiosulfate at 14 °C was 0·14 h−1 for strain SVAL-ET and 0·2 h−1 for strain SVAL-DT. Major fatty acids of SVAL-DT are C16 : 1, C18 : 0 and C16 : 0, and those of SVAL-ET are C16 : 1, C18 : 1, C16 : 0 and C14 : 1. Cells of SVAL-DT and SVAL-ET are rods, like those of their closest relatives. To our knowledge the novel strains are the first psychrophilic, chemolithoautotrophic, sulfur-oxidizing bacteria so far described. The names Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov. are proposed for SVAL-ET (=ATCC 700955T=DSM 13458T) and SVAL-DT (=ATCC 700954T=DSM 13453T), respectively.
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Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov.
More LessGram-negative, non-spore-forming, rod-shaped bacteria, T7-09T and TR6-08T, were isolated from soil from a ginseng field in South Korea and characterized to determine their taxonomic position. 16S rRNA gene sequence analysis showed that the two isolates shared 99·5 % sequence similarity. Strains T7-09T and TR6-08T were shown to belong to the Proteobacteria and showed the highest levels of sequence similarity to Pseudoxanthomonas broegbernensis DSM 12573T (98·1 %), Pseudoxanthomonas mexicana AMX 26BT (97·4–97·5 %), Pseudoxanthomonas japonensis 12-3T (96·5–96·6 %), Pseudoxanthomonas taiwanensis ATCC BAA-404T (95·7 %) and Xanthomonas campestris ATCC 33913T (96·3–96·5 %). The sequence similarity values with respect to any species with validly published names in related genera were less than 96·5 %. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with C15 : 0 iso as the predominant acid supported the assignment of the novel isolates to the order ‘Xanthomonadales’. The two isolates could be distinguished from the established species of the genus Pseudoxanthomonas by the presence of quantitative unsaturated fatty acid C17 : 1 iso ω9c and by their unique biochemical profiles. The results of DNA–DNA hybridization clearly demonstrated that T7-09T and TR6-08T represent separate species. On the basis of these data, it is proposed that T7-09T (=KCTC 12208T=IAM 15116T) and TR6-08T (=KCTC 12207T=IAM 15115T) be classified as the type strains of two novel Pseudoxanthomonas species, for which the names Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov., respectively, are proposed.
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Yersinia aleksiciae sp. nov.
More LessYersinia kristensenii consists of phenotypically heterogeneous strains. This is reflected by the existence of strains with various multilocus enzyme electrophoresis and 16S rRNA gene sequence types. Strains originally phenotyped as members of Y. kristensenii were studied using 16S rRNA gene sequencing, DNA–DNA hybridization, determination of the DNA base composition and various phenotypic tests. The results were compared to those of Yersinia type strains. Based on levels of DNA–DNA relatedness, a specific 16S rRNA gene sequence type and the presence of lysine decarboxylase activity, a novel species, Yersinia aleksiciae sp. nov., is proposed. The type strain is Y159T (=WA758T=DSM 14987T=LMG 22254T).
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Phylogenetic position and emended description of the genus Methylovorus
More LessThe genus Methylovorus, currently represented by the restricted facultative methylotroph Methylovorus glucosotrophus Govorukhina and Trotsenko 1991 and the obligate methylotroph Methylovorus mays Doronina et al. 2001 , is here established by direct sequencing of amplified 16S rRNA genes and DNA–DNA hybridization to be clearly separated from the extant ribulose monophosphate (RuMP) pathway methylobacteria and to form a distinct branch within the β-Proteobacteria.
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Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching
Six new Vibrio-like isolates originating from different species of bleached and healthy corals around Magnetic Island (Australia) were investigated using a polyphasic approach. Phylogenetic analyses based on 16S rRNA, recA and rpoA gene sequences split the isolates in two new groups. Strains LMG 22223T, LMG 22224, LMG 22225, LMG 22226 and LMG 22227 were phylogenetic neighbours of Photobacterium leiognathi LMG 4228T (95·6 % 16S rRNA gene sequence similarity), whereas strain LMG 22228T was related to Enterovibrio norvegicus LMG 19839T (95·5 % 16S rRNA gene sequence similarity). The two new groups can be distinguished from closely related species on the basis of several phenotypic features, including fermentation of d-mannitol, melibiose and sucrose, and utilization of different compounds as carbon sources, arginine dihydrolase activity, nitrate reduction, resistance to the vibriostatic agent O/129 and the presence of fatty acids 15 : 0 iso and 17 : 0 iso. The names Photobacterium rosenbergii sp. nov. (type strain LMG 22223T=CBMAI 622T=CC1T) and Enterovibrio coralii sp. nov. (type strain LMG 22228T=CBMAI 623T=CC17T) are proposed to accommodate these new isolates. The G+C contents of the DNA of the two type strains are respectively 47·6 and 48·2 mol%.
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Pseudomonas pachastrellae sp. nov., isolated from a marine sponge
Two Gram-negative, non-fermentative, non-denitrifying, non-pigmented, rod-shaped bacteria that were motile by means of polar flagella, designated strains KMM 330T and KMM 331, were isolated from a deep-sea sponge specimen and subjected to a polyphasic taxonomic study. The new isolates exhibited 16S rRNA gene sequence similarity of 99·9 %, and their mean level of DNA–DNA relatedness was 82 %. Phylogenetic analysis based on their 16S rRNA gene sequences placed the strains within the genus Pseudomonas as an independent deep clade. Strain KMM 330T shared highest sequence similarity (96·3 %) with each of Pseudomonas fulva NRIC 0180T, Pseudomonas parafulva AJ 2129T and Pseudomonas luteola IAM 13000T; sequence similarity to other recognized species of the genus Pseudomonas was below 95·7 %. The marine sponge isolates KMM 330T and KMM 331 could be distinguished from the other recognized Pseudomonas species based on a unique combination of their phenotypic characteristics, including growth in 8 or 10 % NaCl, the absence of pigments, the inability to denitrify and lack of carbohydrate utilization. On the basis of phylogenetic analysis, physiological and biochemical characterization, strains KMM 330T and KMM 331 should be classified as a novel species of the genus Pseudomonas, for which the name Pseudomonas pachastrellae sp. nov. is proposed. The type strain is KMM 330T (=JCM 12285T=NRIC 0583T=CCUG 46540T).
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Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the ε-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough
More LessTwo novel denitrifying bacteria, designated strains MI55-1T and E9I37-1T, were isolated from deep-sea hydrothermal vent chimney structures at the Iheya North hydrothermal field in the Mid-Okinawa Trough, Japan. Both isolates were strict chemolithoautotrophs growing by respiratory nitrate reduction with H2, forming N2 as a metabolic product. Oxygen (at low concentrations) could serve as an alternative electron acceptor for growth of the isolates. Growth of strain MI55-1T was observed at temperatures between 40 and 57 °C (optimum, 55 °C; doubling time, 2 h), at pH values between 5·4 and 6·9 (optimum, pH 6·4) and in the presence of between 1·5 and 4·0 % (w/v) NaCl (optimum, 2·5 %). Growth of strain E9I37-1T was observed at temperatures between 28 and 40 °C (optimum, 37 °C; doubling time, 2·5 h), at pH values between 5·6 and 7·6 (optimum, pH 7·0) and in the presence of between 1·5 and 3·5 % (w/v) NaCl (optimum, 3·0 %). The G+C contents of the genomic DNA of strains MI55-1T and E9I37-1T were 29·6 and 35·5 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MI55-1T and E9I37-1T belonged to groups A and F of the ε-Proteobacteria, but that they had distant phylogenetic relationships with any species, within the phylogenetic groups, that had validly published names (sequence similarities were less than 91 %). On the basis of the physiological and molecular characteristics of the novel isolates, it is proposed that they should each be classified in a novel genus: Nitratiruptor tergarcus gen. nov., sp. nov., with MI55-1T (=JCM 12459T=DSM 16512T) as the type strain, and Nitratifractor salsuginis gen. nov., sp. nov., with E9I37-1T (=JCM 12458T=DSM 16511T) as the type strain.
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Martelella mediterranea gen. nov., sp. nov., a novel α-proteobacterium isolated from a subterranean saline lake
More LessA bacterial strain was isolated from the water of Lake Martel in Mallorca (Spain). The isolate, designated MACL11T, was halotolerant and strictly aerobic. The cells were non-motile, non-spore-forming, Gram-negative short rods. Comparative 16S rRNA gene sequence analysis revealed that MACL11T represents a separate line of descent within the order ‘Rhizobiales’ of the class ‘Alphaproteobacteria’. Strain MACL11T was most closely related to the genera Rhizobium (93·3 % sequence similarity to Rhizobium rhizogenes), Aurantimonas (90·3 % sequence similarity to Aurantimonas coralicida) and Fulvimarina (90·3 % sequence similarity to Fulvimarina pelagi). Chemotaxonomically, strain MACL11T was characterized by the presence of Q-10 as the major respiratory lipoquinone. The major fatty acids detected were C19 : 0 cycloω8c, C18 : 1 ω7c, C16 : 0 and 11-methyl C18 : 1 ω7c. The G+C content of the DNA was 57·4 mol%. Oxidase and catalase activities were present. Growth with many different carbohydrates as the sole carbon source was observed. The data from this polyphasic study suggest that this bacterium belongs to a novel genus of the order ‘Rhizobiales’ and is not associated with any of the known families of this order. It is proposed that isolate MACL11T should be classified in a novel genus and species, Martelella mediterranea gen. nov., sp. nov., with MACL11T (=LMG 22193T=CECT 5861T) as the type strain.
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- Gram-Positive Bacteria
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Biochemical and genetic evidence for the transfer of Enterococcus solitarius Collins et al. 1989 to the genus Tetragenococcus as Tetragenococcus solitarius comb. nov.
More LessPhylogenetic analysis of 16S rRNA gene sequences revealed that Enterococcus solitarius is not a member of the genus Enterococcus, but is related to species of the genus Tetragenococcus. On a phylogenetic tree, E. solitarius clustered with Tetragenococcus halophilus and Tetragenococcus muriaticus, with which it showed the highest 16S rRNA gene sequence similarity level (about 94 %). Phenotypic studies indicated that E. solitarius was also unable to produce acid from lactose, providing further evidence of its affiliation to the genus Tetragenococcus. DNA hybridization studies indicated that E. solitarius was clearly a separate species, different from T. halophilus and T. muriaticus (reassociation levels of about 23 and 54 %, respectively). As suggested in previous studies, E. solitarius is closely related to but clearly distinct from T. halophilus. Based upon properties that taxonomically distinguish it from species of the genus Enterococcus, it is proposed that E. solitarius be transferred to the genus Tetragenococcus and reclassified as Tetragenococcus solitarius comb. nov. (type strain, 885/78T=ATCC 49428T=CCUG 29293T=CIP 103330T=DSM 5634T=JCM 8736T=LMG 12890T=NCTC 12193T).
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Pseudonocardia dioxanivorans sp. nov., a novel actinomycete that grows on 1,4-dioxane
More LessAn actinomycete strain (CB1190T) was previously isolated from industrial sludge contaminated with 1,4-dioxane. The cells of this culture are Gram-positive and exhibit branching aerial and vegetative mycelium. Analysis of the 16S rRNA gene sequence indicates that the strain belongs to the genus Pseudonocardia, closely related to Pseudonocardia hydrocarbonoxydans, P. sulfidoxydans and P. halophobica. Physiological and biochemical characteristics of CB1190T are different from those of other known Pseudonocardia species. The novel organism described here is distinguished by its ability to grow on 1,4-dioxane, which is a probable human carcinogen. This culture can also grow on tetrahydrofuran, gasoline aromatics and several other toxic environmental contaminants. Strain CB1190T is capable of fixing dinitrogen. The predominant fatty acids are 16 : 0 iso, 16 : 1 iso cis9 and 17 : 1 iso cis9. The major phospholipid fatty acids are 16 : 0 iso, 16 : 0 10-Me and 17 : 0 10-Me. The peptidoglycan belongs to type A1γ, meso-diaminopimelic acid. The major menaquinone is MK-8 (H4). Mycolic acids are absent. The G+C content is 74 mol%. Based on morphological, physiological, chemotaxonomic and phylogenetic evidence, it is proposed that strain CB1190T (=ATCC 55486T=DSM 44775T) be classified as the type strain of a novel species, Pseudonocardia dioxanivorans sp. nov. Further studies with this organism will provide insights into metabolic pathways, responsible enzymes, kinetics and the fate of 1,4-dioxane in the environment.
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Lactobacillus acidifarinae sp. nov. and Lactobacillus zymae sp. nov., from wheat sourdoughs
Three heterofermentative lactic acid bacteria, obtained from Greek and Belgian artisanal wheat sourdoughs, were preliminarily identified as Lactobacillus brevis-like after screening using whole-cell protein fingerprinting and 16S rRNA gene sequence analysis. The three sourdough isolates showed nearly identical sequences (>99·7 % sequence similarity), and highest similarities of 98·2 and 97·6 % were obtained to the species Lactobacillus spicheri and Lactobacillus brevis, respectively. Growth characteristics, biochemical features, amplified fragment length polymorphism fingerprinting, DNA–DNA hybridizations and DNA G+C contents demonstrated that the isolates represent two novel Lactobacillus species. The names Lactobacillus acidifarinae sp. nov. and Lactobacillus zymae sp. nov. are proposed and the type strains are LMG 22200T (=R-19065T=CCM 7240T) and LMG 22198T (=R-18615T=CCM 7241T), respectively.
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Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria
More LessA taxonomic study of two crude-oil-degrading, Gram-positive bacterial strains, designated BAS69T and BNP48T, revealed that they represent two novel Microbacterium species. 16S rRNA gene sequence similarity to their closest phylogenetic neighbours was 98·5 % for BAS69T (Microbacterium paraoxydans DSM 15019T and Microbacterium saperdae DSM 20169T) and 99 % for BNP48T (Microbacterium luteolum DSM 20143T). Levels of DNA–DNA relatedness to the closest phylogenetic neighbours of both strains were between 11 and 38 %. According to phylogenetic analysis, the two strains are distinguishable from all recognized species of Microbacterium. Morphological and physiological characteristics of strains BAS69T and BNP48T were different from those of phylogenetically closely related Microbacterium species. The diamino acid in the cell-wall peptidoglycan of BAS69T is lysine and of BNP48T is ornithine. The major menaquinones are MK-11 and MK-12 for both strains. Based on their ability to degrade crude oil, the name Microbacterium oleivorans sp. nov. is proposed for strain BAS69T (=DSM 16091T=NCIMB 14003T) and Microbacterium hydrocarbonoxydans is proposed for strain BNP48T (=DSM 16089T=NCIMB 14002T).
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Microbacterium natoriense sp. nov., a novel d-aminoacylase-producing bacterium isolated from soil in Natori, Japan
A rod-shaped, Gram-positive bacterium, strain TNJL143-2T, having N-acyl-d-amino acid amidohydrolase (d-aminoacylase) activity, was isolated from a soil sample from Natori, Japan. It was a non-spore-forming, strictly aerobic bacterium without motility, showing a temperature optimum for growth of 30 °C and a pH optimum for growth of 5–7. The 16S rRNA gene sequence of the strain showed the highest similarities to members of the genus Microbacterium, in particular, Microbacterium aerolatum, Microbacterium foliorum and Microbacterium phyllosphaerae. The chemotaxonomic characteristics, including the compositions of cellular menaquinones, cellular fatty acids and cell-wall amino acids, were consistent with those described for the genus Microbacterium. The G+C content of the genomic DNA was determined as 69·1 mol%. DNA–DNA hybridization studies using type strains of M. aerolatum, M. foliorum and M. phyllosphaerae showed only low levels of relatedness (11–12 %). On the basis of these phenotypic and genotypic results, a novel species, Microbacterium natoriense sp. nov., is proposed, with TNJL143-2T (=JCM 12611T=ATCC BAA-1032T) as the type strain.
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Guggenheimella bovis gen. nov., sp. nov., isolated from lesions of bovine dermatitis digitalis
More LessDermatitis digitalis is an economically important ulcerative disease of undetermined aetiology affecting the hooves of cattle. Material was examined from two independent cases of this disease in Switzerland. Cultures from the advancing front of both lesions yielded large numbers of closely related short, mesophilic, non-motile, non-spore-forming, anaerobic, proteolytic, Gram-positive rods. The 16S rRNA gene sequences of strains OMZ 913T and OMZ 915 were identical and indicate Tindallia magadiensis and Eubacterium saphenum as their closest relatives. Phenotypically, the novel isolates are clearly distinguished from related bacteria by protein and antigen patterns, by cellular fatty acids and by API ZYM activities. The diamino acid of the Gram-positive cell wall is ornithine and the G+C content of OMZ 913T DNA is 44·4 mol%. The phylogenetic distance from recognized taxa in the phylum Firmicutes is sufficient to place these bovine isolates into a novel genus and species, for which the name Guggenheimella bovis gen. nov., sp. nov. is proposed, with OMZ 913T (=CIP 108087T=DSM 15657T) as the type strain.
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Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999
The name of the species Gordonia nitida is validly published but its type strain DSM 44499T shares high similarity based on 16S rRNA gene sequences with Gordonia alkanivorans DSM 44369T and Gordonia westfalica DSM 44215T. These three species obviously build up a distinct cluster within the genus Gordonia. In the present paper, data from the literature concerning the three Gordonia species were reviewed and the genetic similarity of G. nitida DSM 44499T and G. alkanivorans DSM 44369T was further investigated by DNA–DNA-hybridization experiments, revealing approximately 80 % DNA–DNA relatedness. Even though the two type strains could be differentiated by automated ribotyping, it is proposed that, according to the rules of priority, G. nitida is a later synonym of G. alkanivorans.
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Planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of Planococcus psychrophilus and Planococcus alkanoclasticus to Planomicrobium as Planomicrobium psychrophilum comb. nov. and Planomicrobium alkanoclasticum comb. nov.
More LessAn aerobic, motile, Gram-positive strain, DX3-12T, was isolated from coastal sediment of the Eastern China Sea in Fujian Province, China, and was identified by means of polyphasic taxonomy. On the basis of 16S rRNA gene sequence similarity, strain DX3-12T was closely related to members of the genera Planomicrobium and Planococcus. 16S rRNA gene sequence similarities between strain DX3-12T and Planomicrobium mcmeekinii, Planomicrobium koreense, Planomicrobium okeanokoites, Planococcus psychrophilus and Planococcus alkanoclasticus were 97·8, 97·8, 97·1, 97·5 and 96·4 %, respectively. Chemotaxonomic and physiological properties of strain DX3-12T supported its affiliation to the genus Planomicrobium. Strain DX3-12T and Planomicrobium mcmeekinii exhibited common phenotypic properties such as the ability to reduce nitrate, but they could be distinguished from each other by physiological and biochemical tests, e.g. acid production from glucose, growth temperature and NaCl concentration requirements. DNA–DNA hybridization further distinguished strain DX3-12T from Planomicrobium mcmeekinii at the species level. Therefore, it is proposed that strain DX3-12T (=AS 1.3454T=JCM 12466T) represents a novel species, Planomicrobium chinense sp. nov. Based on 16S rRNA gene sequence similarities, signature nucleotides, cell morphology and physiological and biochemical properties, Planococcus psychrophilus and Planococcus alkanoclasticus have been transferred to the genus Planomicrobium as Planomicrobium psychrophilum comb. nov. (type strain DSM 14507T=MTCC 3812T) and Planomicrobium alkanoclasticum comb. nov. (type strain NCIMB 13489T=CIP 107718T), respectively.
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Actinomadura napierensis sp. nov., isolated from soil in South Africa
More LessAn actinomycete, strain B60T, was isolated from a soil sample in Napier, Western Cape province of South Africa. Based on 16S rRNA gene sequence analysis and chemotaxonomy, strain B60T was identified as a member of the genus Actinomadura. Strain B60T produced an antibiotic with activity against Escherichia coli, Enterococcus faecium and Mycobacterium aurum, but not against Mycobacterium tuberculosis. Significant differences in morphological and physiological characteristics indicate that strain B60T represents a novel species of the genus Actinomadura. The name Actinomadura napierensis sp. nov. is proposed. The type strain is B60T (=DSM 44846T=NRRL B-24319T).
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Kitasatospora viridis sp. nov., a novel actinomycete from soil
The taxonomic position of a rhizosphere isolate, strain 52108aT, was determined using a polyphasic approach. The strain was found to have chemical and morphological properties consistent with its assignment to the genus Kitasatospora. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Kitasatospora and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the Kitasatospora clade and was most closely related to Kitasatospora arboriphila (98·9 %), Kitasatospora kifunensis (99·0 %), Kitasatospora paracochleata (98·4 %) and Kitasatospora terrestris (98·2 %), but was readily distinguished from representatives of these species using a combination of phenotypic properties. The combined genotypic and phenotypic data show that the strain should be classified in the genus Kitasatospora as a novel species. The name proposed is Kitasatospora viridis sp. nov., with the type strain 52108aT (=AS 4.1878T=DSM 44826T).
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Streptosporangium yunnanense sp. nov. and Streptosporangium purpuratum sp. nov., from soil in China
More LessTwo strains of Streptosporangium were isolated from Yunnan Province, a region of China with specific geographical conditions that contribute to its great microbiological diversity. They were identified using a polyphasic approach employing phenotypic, genotypic and phylogenetic techniques, such as study of morphological and physiological properties, cell chemistry, G+C content of the genomic DNA, DNA–DNA hybridization and phylogenetic analysis. The strains belong to two novel species of Streptosporangium on the basis of 16S rRNA gene sequencing. The results of morphological, physiological and biochemical investigations and DNA–DNA hybridization indicated that the two strains are different from known members of the genus Streptosporangium. The names Streptosporangium yunnanense sp. nov. (type strain CY-11007T=CCTCC AA 97009T=CCRC 16307T=DSM 44663T) and Streptosporangium purpuratum sp. nov. (type strain CY-15110T=CCTCC AA 97010T=CCRC 16308T=DSM 44688T) are proposed. They have been deposited in CCTCC in Wuhan.
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Asanoa iriomotensis sp. nov., isolated from mangrove soil
More LessDuring a study of the distribution of actinomycetes in a mangrove zone, a strain forming spore chains borne on the tip of short sporophores arising directly from the agar surface was isolated from soil. The isolate contained glutamic acid, glycine, alanine and meso-diaminopimelic acid as cell-wall amino acids, menaquinone MK-10(H6, H8), fatty acid type 2d and xylose in the whole-cell hydrolysate. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the members of the genus Asanoa in the family Micromonosporaceae. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA hybridization, a novel species of the genus Asanoa is proposed for strain TT 97-02T (=NBRC 100142T=DSM 44745T), Asanoa iriomotensis sp. nov.
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Reclassification of Streptomyces nigrifaciens as a later synonym of Streptomyces flavovirens; Streptomyces citreofluorescens, Streptomyces chrysomallus subsp. chrysomallus and Streptomyces fluorescens as later synonyms of Streptomyces anulatus; Streptomyces chibaensis as a later synonym of Streptomyces corchorusii; Streptomyces flaviscleroticus as a later synonym of Streptomyces minutiscleroticus; and Streptomyces lipmanii, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces willmorei as later synonyms of Streptomyces microflavus
More LessA DNA–DNA hybridization survey was performed on 13 Streptomyces species and two subspecies, dispersed over five genotypically defined clusters as delineated by Lanoot et al. [Syst Appl Microbiol 27 (2004), 84–92] . Within each of the latter clusters, strains shared DNA–DNA relatedness values above 70 %. On the basis of published recommendations, the following eight Streptomyces species with validly published names are considered as later synonyms: Streptomyces nigrifaciens as a synonym of Streptomyces flavovirens; Streptomyces citreofluorescens, Streptomyces chrysomallus subsp. chrysomallus and Streptomyces fluorescens as synonyms of Streptomyces anulatus; Streptomyces chibaensis as a synonym of Streptomyces corchorusii; Streptomyces flaviscleroticus as a synonym of Streptomyces minutiscleroticus; and Streptomyces lipmanii, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces willmorei as synonyms of Streptomyces microflavus. Emended descriptions are proposed.
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Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood
More LessA Gram-variable, motile, endospore-forming, halotolerant bacillus, strain JG-30T, was isolated from the traditional Korean fermented seafood jeotgal, and was subjected to a polyphasic taxonomic study. This organism grew optimally at 37 °C and in the presence of 0–1 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain JG-30T forms a distinct phylogenetic lineage within the evolutionary radiation encompassed by the genus Bacillus. Strain JG-30T was characterized chemotaxonomically as having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C15 : 0 and iso-C14 : 0 as the major fatty acids. The DNA G+C content was 45 mol%. Strain JG-30T exhibited levels of 16S rRNA gene sequence similarity of less than 95·7 % to Bacillus species with validly published names. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JG-30T (=KCTC 3880T=DSM 16189T) was classified within the genus Bacillus as a novel species, for which the name Bacillus cibi sp. nov. is proposed.
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Paenibacillus hodogayensis sp. nov., capable of degrading the polysaccharide produced by Sphaerotilus natans
More LessSphaerotilus natans is a sheathed bacterium often found in activated sludge that has a bulking problem. A bacterial strain that is able to degrade the extracellular polysaccharide produced by S. natans was isolated. The isolate was a spore-forming, aerobic, rod-shaped bacterium. The Gram reaction was variable or negative. The optimum growth temperature was 30 °C and the optimum pH was 8. The G+C content of the DNA was 55 mol%. The major cellular fatty acid and respiratory quinone were anteiso-C15 : 0 and MK-7, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the genus Paenibacillus. The nearest relative, with a similarity of 94·2 %, was Paenibacillus koleovorans, a bacterium capable of degrading the sheath of S. natans. The phenotypic characteristics of the isolate were apparently different from those of related species in the genus Paenibacillus. It is proposed that the isolate be designated Paenibacillus hodogayensis sp. nov. The type strain is SGT (=JCM 12520T=KCTC 3919T).
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Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera
More LessA bacterial strain, designated PALXIL04T, was isolated from the phyllosphere of Phoenix dactylifera. Phylogenetic analysis placed the isolate within the genus Paenibacillus with the closest relatives being Paenibacillus curdlanolyticus and Paenibacillus kobensis. DNA–DNA hybridization measurements showed low DNA relatedness (15–20 %) between the isolate and its closest relatives. Cells were Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced by the organism. Cellulose, starch, aesculin and xylan were hydrolysed. Growth was supported by many carbohydrates as the carbon source. MK-7 was the predominant menaquinone and anteiso-C15 : 0 the major fatty acid. The G+C content of the DNA was 50·7 mol%. Phylogenetic, DNA–DNA relatedness and phenotypic analyses indicated that strain PALXIL04T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus phyllosphaerae sp. nov. is proposed. The type strain is PALXIL04T (=LMG 22192T=CECT 5862T).
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Lactobacillus hammesii sp. nov., isolated from French sourdough
Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38T and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA–DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38T (=DSM 16381T=CIP 108387T=TMW 1.1236T).
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Syntrophomonas erecta sp. nov., a novel anaerobe that syntrophically degrades short-chain fatty acids
More LessTwo novel anaerobes, strains GB4-38T and SB9-1, were isolated from an upflow anaerobic sludge blanket reactor for treating bean-curd farm wastewater and lotus field mud, respectively. The strains degraded straight-chain fatty acids with 4–8 carbon atoms in syntrophic association with methanogens and converted 1 mol butyrate into about 2 mol acetate and presumably 2 mol H2. None of the branched-chain fatty acids tested could be degraded. Benzoate was not degraded. Fumarate, sulfate, thiosulfate, sulfur and nitrate did not serve as electron acceptors for butyrate degradation. In the absence of a methanogen partner, strain GB4-38T grew on crotonate in pure culture; the generation time was about 5 h at 37 °C. However, strain SB9-1 grew on butyrate plus pentenoate, but not crotonate, in pure culture and the generation time was 18 h at 37 °C. Cells of GB4-38T and SB9-1 were straight rods and stained Gram-negative. The major cellular fatty acids of GB4-38T were C14 : 0 (29·74 %), C16 : 0 (17·00 %), C16 : 1 ω5c (16·63 %) and isoC17 : 1 I (15·34 %). ll-Diaminopimelic acid existed in the cellular peptidoglycan. The genomic DNA G+C content of strain GB4-38T was 43·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences supported clustering of the two strains with syntrophic bacterial species of the genus Syntrophomonas (89·6–92·4 % sequence similarity), but phenotypic, chemotaxonomic and genetic characters differentiated the two strains from members of this genus. Therefore, it is proposed that the two strains are representatives of a novel species, Syntrophomonas erecta sp. nov. The type strain is GB4-38T (=CGMCC 1.5013T=DSM 16215T).
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Polyphasic taxonomic study of strain CCM 2783 resulting in the description of Arthrobacter stackebrandtii sp. nov.
Strain CCM 2783, previously classified as representing Arthrobacter aurescens, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis and chemotaxonomic characteristics such as peptidoglycan type A3α Lys–Ala2, major menaquinone MK-9(H2) and fatty acid composition confirmed assignment of the strain to the genus Arthrobacter. The results of phylogenetic analysis, DNA–DNA relatedness experiments and physiological and chemotaxonomic characteristics indicate that CCM 2783 differs from its nearest phylogenetic relative Arthrobacter psychrolactophilus and from other recognized Arthrobacter species. Therefore, a novel species, Arthrobacter stackebrandtii sp. nov., is proposed with the type strain CCM 2783T (=DSM 16005T).
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Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea
More LessFour Gram-positive, rod- or coccus-shaped bacterial strains, KSL-1T, KSL-9, KSL-10 and KSL-12, were isolated from an alkaline serpentinite soil in Korea, and their taxonomic positions were investigated in a polyphasic study. The four strains exhibited no difference in their 16S rRNA gene sequences. Phylogenetic analyses based on 16S rRNA gene sequences showed that the four strains were phylogenetically affiliated to the genus Nocardioides. The four strains had cell-wall peptidoglycan based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone detected in the four strains was MK-8(H4). The major fatty acid components were iso-C16 : 0, 10-methyl-C18 : 0, C18 : 1 ω9c and C17 : 1 ω6c. The DNA G+C contents were 72·4–73·6 mol%. The four strains exhibited 16S rRNA gene sequence similarity levels of 94·0–96·3 % to the type strains of Nocardioides species with validly published names. DNA–DNA relatedness levels between the four strains were 85–91 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genotypic relatedness, strains KSL-1T, KSL-9, KSL-10 and KSL-12 were classified in the genus Nocardioides as members of a novel species, Nocardioides alkalitolerans sp. nov. The type strain is strain KSL-1T (=KCTC 19037T=DSM 16699T).
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Streptococcus castoreus sp. nov., isolated from a beaver (Castor fiber)
More LessA previously undescribed, Gram-positive, catalase-negative, Streptococcus-like organism originating from a European beaver (Castor fiber) was subjected to a taxonomic study. The organism displayed β-haemolytic activity and gave a positive reaction with Lancefield group A antisera. Based on the results of biochemical testing, the organism was tentatively identified as a member of the genus Streptococcus, but it did not correspond phenotypically to any recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed this assignment, with the bacterium forming a hitherto unknown subline within the genus. Sequence divergence values of greater than 3 % from other reference streptococcal species, however, demonstrated that the unidentified coccus-shaped organism represents a hitherto unknown species. Based on phenotypic and molecular phylogenetic evidence, it is therefore proposed that the unknown organism from a beaver be classified as a novel species, Streptococcus castoreus sp. nov. The type strain is M605815/03/2T (=CCUG 48115T=CIP 108205T).
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Nonomuraea kuesteri sp. nov.
More LessA Gram-positive, aerobic, non-motile actinomycete, strain GW 14-1925T, that formed branched substrate and aerial mycelium was studied using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strain GW 14-1925T was shown to belong to the genus Nonomuraea, being most closely related to Nonomuraea longicatena (97·9 %), Nonomuraea turkmeniaca (98·9 %), Nonomuraea helvata (98·6 %), Nonomuraea polychroma (98·5 %), Nonomuraea salmonaea (98·3 %), Nonomuraea roseoviolacea subsp. roseoviolacea (98·1 %) and Nonomuraea roseoviolacea subsp. carminata (97·7 %). The 16S rRNA gene sequence similarity to other Nonomuraea species was <97·5 %. Chemotaxonomic data [major menaquinones of the MK-9 series with minor amounts of MK-8(H4); major polar lipids of phospholipid type IV; fatty acids with major amounts of iso- and anteiso- and 10-methyl-branched fatty acids in combination with iso-branched 2-hydroxy fatty acids] supported allocation of the strain to the genus Nonomuraea. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW 14-1925T from closely related species; thus, GW 14-1925T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea kuesteri sp. nov. is proposed, with GW 14-1925T (=DSM 44753T=NRRL B-24325T) as the type strain.
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Fastidiosipila sanguinis gen. nov., sp. nov., a new Gram-positive, coccus-shaped organism from human blood
Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6 % O2. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al., Int J Syst Bacteriol 44 (1994), 812–826 ]. Sequence divergence values of 15 % or more were observed between the unidentified bacterium and all other recognized species within this and related rRNA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp. nov. The type strain of Fastidiosipila sanguinis is CCUG 47711T (=CIP 108292T).
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Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs
A polyphasic study was carried out to clarify the taxonomic positions of three Gram-positive isolates from the Catacombs of Domitilla, Rome (Italy). 16S rRNA gene sequence comparisons placed these strains within the genus Agromyces. The morphological and chemotaxonomic characteristics of these isolates were consistent with the description of the genus Agromyces. The three isolates could be readily distinguished from one another and from representatives of all Agromyces species with validly published names by a broad range of phenotypic characteristics and DNA–DNA relatedness studies. Therefore, these isolates are proposed to represent three novel species of the genus Agromyces, Agromyces italicus sp. nov. (type strain CD1T=HKI 0325T=DSM 16388T=NCIMB 14011T), Agromyces humatus sp. nov. (type strain CD5T=HKI 0327T=DSM 16389T=NCIMB 14012T) and Agromyces lapidis sp. nov. (type strain CD55T=HKI 0324T=DSM 16390T=NCIMB 14013T).
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Micromonospora mirobrigensis sp. nov.
An actinomycete strain was recovered from a pond where radon is known to be dissolved. A polyphasic study was undertaken to identify the new isolate. The 16S rRNA gene sequence of strain WA201T showed closest similarity to the type strains of Micromonospora carbonacea (98·5 %) and Micromonospora matsumotoense (98·1 %). The chemotaxonomic results confirmed the taxonomic position of the isolate in the genus Micromonospora. DNA–DNA relatedness values supported the classification of this isolate as a novel species. A number of physiological and biochemical tests were able to distinguish strain WA201T from its closest phylogenetic neighbours. Therefore, it is proposed that isolate WA201T (=DSM 44830T=LMG 22229T) be considered the type strain representing a novel species, Micromonospora mirobrigensis sp. nov.
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Jiangella gansuensis gen. nov., sp. nov., a novel actinomycete from a desert soil in north-west China
More LessA novel actinomycete strain, designated YIM 002T, was isolated from a desert soil sample in Gansu Province, north-west China. This actinomycete isolate formed well-differentiated aerial and substrate mycelia. In the early stages of growth, the substrate mycelia fragmented into short or elongated rods. Chemotaxonomically, it contained ll-2,6-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose and glucose. Phospholipids present were phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol. MK-9(H4) was the predominant menaquinone. The major fatty acids were anteiso C15 : 0 (35·92 %), anteiso C17 : 0 (15·84 %), iso C15 : 0 (10·40 %), iso C16 : 0 (7·07 %) and C17 : 1 ω8c (9·37 %). The G+C content of the DNA was 70 mol%. Phylogenetic analysis and signature nucleotide data based on 16S rRNA gene sequences showed that strain YIM 002T is distinct from all recognized genera of the family Nocardioidaceae in the suborder Propionibacterineae. On the basis of the phenotypic and genotypic characteristics, it is proposed that isolate YIM 002T be classified as a novel species in a new genus, Jiangella gansuensis gen. nov., sp. nov. The type strain is YIM 002T (=DSM 44835T=CCTCC AA 204001T=KCTC 19044T).
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Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
More LessThree Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.
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Bacillus bogoriensis sp. nov., a novel alkaliphilic, halotolerant bacterium isolated from a Kenyan soda lake
More LessStrain LBB3T isolated from Bogoria soda lake in Kenya is an alkaliphilic, Gram-positive, strictly aerobic, non-motile, spore-forming bacterium. It was identified as a member of the genus Bacillus on the basis of phenotypic and phylogenetic analyses. The organism grows optimally at 37 °C and pH 10. The G+C content of the genomic DNA is 37·5 mol%. 16S rRNA gene sequence analysis showed 95 and 96 % sequence similarity with Bacillus pseudofirmus (DSM 8715T) and Bacillus alcalophilus (DSM 485T), respectively. Furthermore, DNA–DNA hybridization against these two Bacillus species showed 39·0 and 55·5 % similarity, respectively. Based on our observations, strain LBB3T is proposed to represent a novel species of the genus Bacillus, for which the name Bacillus bogoriensis sp. nov. is proposed. The type strain of B. bogoriensis is LBB3T (=ATCC BAA-922T=LMG 22234T).
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Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile
More LessA halophilic and halotolerant, facultatively alkaliphilic strain, K11T, was isolated from soil obtained from Oshyamanbe, Oshima, Hokkaido, Japan. The isolate grew at pH 7–10. It was non-motile, Gram-positive and aerobic. Cells comprised straight rods and produced ellipsoidal spores. The isolate grew in 0–20 % NaCl, with optimum growth at 7 % NaCl, and hydrolysed casein, gelatin, starch, DNA and Tweens 20, 40, 60 and 80. The major isoprenoid quinone was menaquinone-7, and the cellular fatty acid profile consisted of significant amounts of C15 branched-chain acids, iso C15 : 0 and anteiso C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain K11T was a member of group 6 [ Nielsen et al., FEMS Microbiol Lett 117 (1994), 61–66 ] (alkaliphiles) of the genus Bacillus. DNA–DNA hybridization revealed a low relatedness (14 %) of the isolate to its closest phylogenetic neighbour, Bacillus clausii. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA–DNA relatedness data, it was concluded that K11T (=JCM 12663T=NCIMB 14023T) merits classification as the type strain of a novel species, for which the name Bacillus oshimensis sp. nov. is proposed.
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Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta
A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10–40 °C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C15 : 0. Comparison of 16S rRNA gene sequences showed that strain BP-23T fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97·4 %), Paenibacillus pabuli (97·1 %) and Paenibacillus amylolyticus (96·9 %). The DNA–DNA relatedness of strain BP-23T with respect to these three species was very low (32·7, 31·6 and 23·0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23T should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23T (=CECT 7022T=DSM 15478T).
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Reclassification of ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus
Comparative analysis of 16S rRNA gene sequences, DNA–DNA hybridization data and phenotypic properties revealed that ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 is not a member of the genus Sulfobacillus. Phylogenetically, strain K1 is closely related to unclassified strains of the genus Alicyclobacillus: the 16S rRNA gene sequence of strain K1 is similar to that of Alicyclobacillus sp. AGC-2 (99·6 %), Alicyclobacillus sp. 5C (98·9 %) and Alicyclobacillus sp. CLG (98·6 %) and bacterium GSM (99·1 %). The 16S rRNA gene sequence similarity values for strain K1 and species of the genus Alicyclobacillus with validly published names were in the range 92·1–94·6 %, and for S. thermosulfidooxidans VKM B-1269T the value was 87·7 %. Sulfobacillus disulfidooxidans SD-11T was also phylogenetically related to strain K1 (92·6 % sequence similarity) and thus belonged to the genus Alicyclobacillus. Chemotaxonomic data, such as the major cell-membrane lipid components of strains K1 and SD-11T (ω-alicyclic fatty acids) and the major isoprenoid quinone (menaquinone MK-7) of strain K1, supported the affiliation of strains K1 and SD-11T to the genus Alicyclobacillus. Physiological and molecular biological tests allowed genotypic and phenotypic differentiation of strains K1 and SD-11T from the nine Alicyclobacillus species with validly published names. The G+C content of the DNA of strain K1 was 48·7±0·6 mol%; that of strain SD-11T was 53±1 mol%. DNA–DNA reassociation studies showed low relatedness (22 %) between strains K1 and SD-11T, and even lower relatedness (3–5 %) between these strains and Alicyclobacillus acidocaldarius subsp. acidocaldarius ATCC 27009T, DSM 446T. DNA reassociation of strains K1 and SD-11T with Alicyclobacillus cycloheptanicus DSM 4006T gave values of 15 and 21, respectively. Based on the phenotypic and phylogenetic characteristics of strains K1 and SD-11T, Alicyclobacillus tolerans sp. nov. (type strain, K1T=VKM B-2304T=DSM 16297T) and Alicyclobacillus disulfidooxidans comb. nov. (type strain, SD-11T=ATCC 51911T=DSM 12064T) are proposed.
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Salinibacillus aidingensis gen. nov., sp. nov. and Salinibacillus kushneri sp. nov., moderately halophilic bacteria isolated from a neutral saline lake in Xin-Jiang, China
More LessThree Gram-positive, moderately halophilic, heterotrophic bacterial strains were isolated from a neutral saline lake in the Xin-Jiang area of China. The strains, designated 8-2T, W11-1 and 25-7T, were motile, spore-forming, aerobic rods and contained meso-diaminopimelic acid in their cell walls. Their DNA G+C contents were 37·4, 37·2 and 39·9 mol%, respectively. The main fatty acids in the cellular membranes of these novel strains were C15 and C17 methyl-branched. No species with validly published names showed 16S rRNA gene sequence similarity of more than 95 % with respect to these novel isolates; the most closely related species was a halophilic denitrifier, Bacillus halodenitrificans (94·6 %). Polyphasic taxonomic studies revealed that these strains belong to the Bacillaceae and are distantly related to other genera of the family. It is proposed that a new genus, Salinibacillus, should be created, with Salinibacillus aidingensis (type strain, 25-7T=AS 1.3565T=JCM 12389T) as the type species. Another species, Salinibacillus kushneri, is also proposed, with 8-2T (=AS 1.3566T=JCM 12390T) as the type strain.
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High genetic similarity of Streptococcus agalactiae and Streptococcus difficilis: S. difficilis Eldar et al. 1995 is a later synonym of S. agalactiae Lehmann and Neumann 1896 (Approved Lists 1980)
More LessThe genetic relationship between Streptococcus agalactiae and Streptococcus difficilis was studied. S. difficilis was originally described as serologically non-typable but was later reported to be a group B, type Ib streptococcus. Upon comparative analysis of five gene sequences, it was found that S. agalactiae and S. difficilis are closely related. Sequence similarity values between these two species were 100·0 % for 16S rRNA, 99·6 % for gyrB, 98·6 % for sodA, 99·5 % for gyrA and 99·8 % for parC genes. These data strongly suggest that S. agalactiae and S. difficilis are synonyms. The biochemical characteristics of S. difficilis, which differ slightly from those of typical S. agalactiae, are similar to those of other group B, type Ib streptococci isolated from fish and frogs. Whole genome DNA–DNA hybridization values between the type strains of both species were greater than 78·6 %. On the basis of these data, it is proposed that S. difficilis is a later synonym of S. agalactiae.
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- Unicellular Eukaryotes
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Candida digboiensis sp. nov., a novel anamorphic yeast species from an acidic tar sludge-contaminated oilfield
More LessTwo strains (TERI-6T and TERI-7) of a novel yeast species were isolated from acidic tar sludge-contaminated soil samples collected from Digboi Refinery, Assam, India. These two yeast strains were morphologically, physiologically and phylogenetically identical to each other. No sexual reproduction was observed on corn meal, malt, Gorodkowa, YM or V8 agars. Physiologically, the novel isolates were most closely related to Candida blankii, but differed in eight physiological tests. The prominent differences were the ability of the isolates to assimilate melibiose and inulin and their inability to assimilate d-glucuronate, succinate and citrate. Phylogenetic analysis using the D1/D2 variable domain showed that the closest relative of these strains is C. blankii (2·8 % divergence). Other related species are Zygoascus hellenicus and Candida bituminiphila. The isolates differed from C. blankii by 11 base substitutions in the 18S rRNA gene sequence and by 58 base substitutions in the internal transcribed spacer sequences. The physiological, biochemical and molecular data support the contention that strains TERI-6T and TERI-7 represent a novel species, for which the name Candida digboiensis sp. nov. is proposed. The type strain is TERI-6T (=MTCC 4371T=CBS 9800T=JCM 12300T).
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Description of Komagataella phaffii sp. nov. and the transfer of Pichia pseudopastoris to the methylotrophic yeast genus Komagataella
More LessThe new methanol-assimilating yeast species Komagataella phaffii Kurtzman sp. nov. (type strain NRRL Y-7556T=CBS 2612T) is described. Of the four known strains of this species, two were isolated from black oak trees in California, USA, one from an Emory oak in Arizona, USA, and one from an unidentified source in Mexico. The species forms hat-shaped ascospores in deliquescent asci and appears to be homothallic. Analysis of nucleotide sequences from domains D1/D2 of large-subunit (26S) rDNA separates the new species from Komagataella pastoris, the type species of the genus, and from Pichia pseudopastoris, which is here renamed Komagataella pseudopastoris (Dlauchy, Tornai-Lehoczki, Fülöp & Péter) Kurtzman comb. nov. (type strain NRRL Y-27603T=CBS 9187T=NCAIM Y 01541T). On the basis of D1/D2 26S rDNA sequence analysis, the three species now assigned to the genus Komagataella represent a clade that is phylogenetically isolated from other ascomycetous yeast genera.
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- Evolution, Phylogeny And Biodiversity
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Benthic cyanobacteria of the genus Nodularia are non-toxic, without gas vacuoles, able to glide and genetically more diverse than planktonic Nodularia
More LessDiversity and ecological features of cyanobacteria of the genus Nodularia from benthic, periphytic and soil habitats are less well known than those of Nodularia from planktonic habitats. Novel benthic Nodularia strains were isolated from the Baltic Sea and their morphology, the presence of gas vacuoles, nodularin production, gliding, 16S rRNA gene sequences, rpoB, rbcLX and ndaF genes, and gvpA-IGS regions were examined, as well as short tandemly repeated repetitive sequence fingerprints. Strains were identified as Nodularia spumigena, Nodularia sphaerocarpa or Nodularia harveyana on the basis of the size and shape of the different types of cells and the presence or absence of gas vacuoles. The planktonic strains of N. spumigena mostly had gas vacuoles and produced nodularin, whereas the benthic strains of N. sphaerocarpa and N. harveyana lacked gas vacuoles and did not produce nodularin (except for strain PCC 7804). The benthic strains were also able to glide on surfaces. In the genetic analyses, the planktonic N. spumigena and benthic N. sphaerocarpa formed monophyletic clusters, but the clusters were very closely related. Benthic strains determined as N. harveyana formed the most diverse and distant group of strains. In addition to phylogenetic analyses, the lack of the gvpA-IGS region and ndaF in N. sphaerocarpa and N. harveyana distinguished these species from the planktonic N. spumigena. Therefore, ndaF can be considered as a potential diagnostic tool for detecting and quantifying Baltic Sea bloom-forming, nodularin-producing N. spumigena strains. The data confirm that only one morphologically and genetically distinct planktonic species of Nodularia, N. spumigena, and at least two benthic species, N. sphaerocarpa and N. harveyana, exist in the Baltic Sea.
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16S–23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas
More LessThe 16S–23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260T divided the sequences into two clusters, of which one was α-fucosidase-positive (like the type strain) while the other was α-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of ‘Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called ‘Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of α-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.
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Extension of the species Helicobacter bilis to include the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Finnish canine and feline flexispira strains
More LessThe evolution and taxonomy of enterohepatic Helicobacter species with flexispira morphology were studied by a polyphasic approach including phenotypic characterization, analysis of 16S rRNA and ureB gene sequences and dot-blot DNA–DNA hybridization of whole genomic DNA. In addition, available phylogenetic data on the HSP60 gene were used in the analysis. The study included 14 Finnish canine and feline flexispira strains, the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Helicobacter bilis ATCC 51630T. Phenotypically, all canine and feline strains were similar to H. bilis. Analysis of 16S rRNA gene sequences of these strains revealed a similarity of 97–99·5 %. Similarity of ureB nucleotide and amino acid sequences within the studied flexispira group was 97–100 % and 99–100 %, respectively, revealing close relatedness. ureB sequences of Helicobacter hepaticus had only 64–66 % similarity to the flexispira group. The similarity to Helicobacter trogontum was 81·5–82·1 %. High levels of DNA–DNA hybridization between the strains were found in dot-blot tests. Polyphasic analysis of the phenotypic and genotypic characteristics of the Finnish flexispira strains and the reference strains of taxa 2, 3 and 8 showed that they differed from other Helicobacter species and are members of the previously described species H. bilis. In addition, canine strain F56 differed in all phylogenetic analyses from the H. bilis group and probably represents a novel Helicobacter species.
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- International Committee On Systematics Of Prokaryotes
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