- Volume 69, Issue 8, 2019
Volume 69, Issue 8, 2019
- Notification List
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- New taxa
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- Actinobacteria
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Streptomyces cyaneochromogenes sp. nov., a blue pigment-producing actinomycete from manganese-contaminated soil
More LessA novel actinomycete isolate, designated strain MK-45T, was isolated from soil sampled at a manganese-contaminated area in Xiangtan, China. The isolate formed extensively branched substrate mycelia and aerial mycelia that differentiated into tightly coiled or spiral spore chains with smooth-surfaced spores. The cell-wall hydrolysates contained ll-diaminopimelic acid and traces of meso-diaminopimelic acid. The major menaquinones consisted of MK-9(H4), MK-9(H6) and MK-9(H8). The major polar lipids contained diphosphatidylgycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphotidylinositol and phosphotidylinositol mannosides. The predominant cellular fatty acids were iso-C16 : 0, C16 : 0 and summed feature 3. Phylogenetic analysis based on the 16S rRNA gene sequences and concatenated partial sequences of the five protein-coding genes indicated that strain MK-45T was a member of the genus Streptomyces and most closely related to Streptomyces caeruleatus GIMN4.002T (99.5 % similarity), Streptomyces curacoi CGMCC 4.1680T (99.5 %), Streptomyces shaanxiensis CCNWHQ 0031T (99.4 %) and Streptomyces cinnabarinus NRRL B12382T (98.9 %), respectively. However, the digital DNA–DNA hybridization values, the average nucleotide identity values and MLSA evolutionary distances between strain MK-45T and them showed that it belonged to a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of strain MK-45T from the four closely related type strains mentioned above and other species of the genus Streptomyces with which this strain has 98.0–99.2 % 16S rRNA gene sequence similarity. Therefore, it is concluded that strain MK-45T represents a novel species of the genus Streptomyces , for which the name Streptomyces cyaneochromogenes sp. nov. is proposed, with MK-45T (=CICC 11045T=KCTC 49099T) as the type strain.
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Transfer of Streptomyces catbensis Sakiyama et al. 2014 and Streptomyces seranimatus Wang et al. 2012 to Yinghuangia catbensis comb. nov. and Yinghuangia seranimata comb. nov.
More LessPhylogenetic analysis of Streptomyces catbensis VN07A0015T and Streptomyces seranimatus YIM 45720T based on 16S rRNA gene sequences suggested that these two strains are related to the genus Yinghuangia rather than Streptomyces . The strains form smooth spores in their spore chains and possessed ll-diaminopimelic acid in cell walls. Their main whole-cell sugars are arabinose, glucose, rhamnose and ribose, or ribose, mannose and galactose, respectively. The menaquinones are MK-9(H8), MK-9(H6) and MK-9(H4). The major polar lipids contain phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol. These characteristics are consistent with the description of the genus Yinghuangia . Physiological, biochemical and chemotaxonomic data clarified that these two strains can be differentiated each other and also from Yinghuangia . aomiensis, only the valid species of the genus Yinghuangia . Therefore, S. catbensis Sakiyama et al. 2014 and S. seranimatus Wang et al. 2012 should be transferred to the genus Yinghuangia and be affiliated to different species, for which the names Yinghuangia catbensis comb. nov. (type strain VN07A0015T=NBRC 107860T=VTCC-A-1889T=VTCC 41889T) and Yinghuangia seranimata comb. nov. (type strain YIM 45720T=CCTCC AA 206006T=DSM 41883T=BCRC 16903T) are proposed.
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Streptomyces huasconensis sp. nov., an haloalkalitolerant actinobacterium isolated from a high altitude saline wetland at the Chilean Altiplano
Streptomyces strain HST28T isolated from the Salar de Huasco, an athalassohaline and poly-extreme high altitude saline wetland located in northern Chile, was the subject of a polyphasic taxonomic study. Strain HST28T showed morphological and chemotaxonomic features in line with its classification in the genus Streptomyces . Optimal growth of strain HST28T was obtained at 28 °C, pH 8–9 and up to 10 % (w/v) NaCl. Single (16S rRNA) and multi-locus gene sequence analyses showed that strain HST28T had a distinct phylogenetic position from its closest relatives, the type strains of Steptomyces aureus and Streptomyces kanamyceticus . Digital DNA–DNA hybridization (23.3 and 31.0 %) and average nucleotide identity (79.3 and 85.6 %) values between strain HST28T and its corresponding relatives mentioned above were below the threshold of 70 and 96 %, respectively, defined for assigning a prokaryotic strains to the same species. Strain HST28T was characterised by the presence of ll-diaminopimelic acid in its peptidoglycan layer; galactose, glucose, ribose and traces of arabinose and mannose as whole-cell sugars; phosphatidylmethylethanolamine, phosphatidylinositol, aminolipid, glycophospholipid and an unidentified lipid as polar lipids; and the predominating menaquinones MK-9(H6), MK-9(H8) and MK-9(H4) (>20 %) as well as anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids (>15 %). Based on the phenotypic and genetic results, strain HST28T (DSM 107268T=CECT 9648T) merits recognition as a new species named Streptomyces huasconensis sp. nov.
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Olsenella faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces
A novel actinobacterial strain, designated KGMB04489T, was isolated from the faeces of a healthy Korean. Cells of the strain were strictly anaerobic, Gram-stain-positive and short-rod-shaped. On the basis of 16S rRNA gene sequence similarity, strain KGMB04489T belonged to the genus Olsenella and was most closely related to Olsenella scatoligenes SK9K4T (94.3 %), Olsenella uli ATCC 49627T (93.5 %), Olsenella umbonata lac31T (93.4 %) and Olsenella profusa D315A-29T (93.3 %). The major end product was lactic acid. The DNA G+C content was 65.5 mol%. The major cellular fatty acids of strain KGMB04489T were C18 : 1 cis9, C18 : 1 cis9 DMA and C16 : 0. Strain KGMB04489T contained meso-diaminopimelic acid as the diamino acid in the peptidoglycan. The polar lipids consisted of an unidentified phospholipid, six unidentified glycolipids and an unidentified lipid. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain KGMB04489T is considered to represent a novel species within the genus Olsenella , for which the name Olsenella faecalis sp. nov. is proposed. The type strain is KGMB04489T (=KCTC 15699T=CCUG 72345T).
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Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China
More LessA novel Gram-stain-positive, non-motile, rod-shaped, non-spore-forming bacterium, designated HLT2-9T, was isolated from the ice tongue surface of Hailuogou Glacier in Sichuan Province, PR China. Colonies of cells were cream yellow, convex and round. Growth occurred at 0–27 °C (optimum, 20 °C), pH 7.0–10.0 (pH 7.0) and in the presence of 0–2.0 % (w/v) NaCl (0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HLT2-9T belonged to the genus Nocardioides . The highest level of sequence similarities were found to Nocardioides glacieisoli CGMCC1.11097T (99.24 %), Nocardioides oleivorans CGMCC 4.6882T (98.54 %) and Nocardioides ganghwensis CGMCC 4.6875T (98.54 %). However, the low average nucleotide identity (85.6–87.9 %) and digital DNA–DNA hybridization values (26.4–30.2 %) of strain HLT2-9T to its three closest relatives demonstrated that it represents a novel species of the genus Nocardioides . The major cellular fatty acids of strain HLT2-9T were C17 : 1 ω8c and iso-C16 : 0. Strain HLT2-9T contained ll-2,6-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinone is MK-8(H4). The G+C content of the genomic DNA was 70.65 mol%. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Nocardioides zhouii sp. nov. is proposed, with HLT2-9T (=CGMCC 1.11084T=NBRC 109783T) as the type strain.
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Streptomyces rhizosphaericola sp. nov., an actinobacterium isolated from the wheat rhizosphere
A novel actinobacterium, designated strain 1AS2cT, was isolated from the wheat rhizosphere collected from the Brazilian Cerrado biome. A polyphasic approach, including phenotypic characterization and phylogenetic multilocus sequence analysis (MLSA), was used to determine the taxonomic position of this strain. Analysis of the 16S rRNA gene sequence indicated that the novel strain is closely related to Streptomyces cavourensis NBRC 13026T, Streptomyces albolongus NBRC 13465T and Streptomyces araujoniae ASBV-1T, sharing a similarity value of 98.2, 98.1 and 97.9 %, respectively. Additionally, MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed evolutionary distances beyond the 0.007 threshold, as well as low DNA–DNA relatedness between strain 1AS2cT and its closest phylogenetic neighbours ( S. cavourensis NBRC 13026T, S. albolongus NBRC 13465T and S. araujoniae ASBV-1T: 56, 62.5 and 63.0 %, respectively), indicating a new phylogenetic lineage. The phylogenetic, chemotaxonomic and phenotypic characteristics support the assignment of strain 1AS2cT to the genus Streptomyces , representing a novel species. It is concluded that strain 1AS2cT (=CMAA 1679T=NRRL B-65479T=DSM 105299T) can be classified as the type strain of a novel species of the genus Streptomyces , for which the name Streptomyces rhizosphaericola sp. nov. is proposed.
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Thermomonospora catenispora sp. nov., isolated from mushroom compost
Hao Wu, Jinfan Wei and Bin LiuA novel thermophilic actinomycete, designated strain 3-22-3T, was isolated from mushroom compost collected in Nanning, Guangxi Province, China. The organism produced white aerial mycelium and short spore chains of non-motile oval spores with a ridged surface on the aerial mycelium. Strain 3-22-3T contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars were galactose, glucose, madurose and ribose. Major fatty acids were iso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. MK-9(H6) and MK-9(H4) were the predominant menaquinones. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, ninhydrin-positive glycophospholipids, glycolipids and unidentified phospholipids. The G+C content of the genomic DNA was 72.5 mol%. The 16S rRNA gene sequence analysis indicated that strain 3-22-3T belonged to the genus Thermomonospora and showed the highest sequence similarity to Thermomonospora curvata DSM 43183T (96.3 %). On the 16S rRNA gene tree of closely related species and type species of all genera in the family Thermomonosporaceae , strain 3-22-3T formed a distinct phyletic line together with Thermomonospora curvata DSM 43183T. Furthermore, the chemotaxonomic characteristics of strain 3-22-3T were congruent with the description of the genus Thermomonospora , but the morphological characteristics of strain 3-22-3T were significantly different from T hermomonospora curvata . Based on the phenotypic and phylogenetic data, strain 3-22-3T represents a novel species of the genus Thermomonospora , and the name Thermomonospora catenispora sp. nov. is proposed. The type strain is 3-22-3T (=CGMCC 4.7155T=DSM 46802T=ATCC BAA-2627T).
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Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus)
A novel Bifidobacterium strain, MRM 9.3T, was isolated from a faecal sample of a baby common marmoset (Callithrixjacchus). Cells were Gram-stain-positive, non-motile, non-sporulating, non-haemolytic, facultatively anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, clpC, dnaJ and dnaG genes) and the core genomes revealed that strain MRM 9.3T exhibited phylogenetic relatedness to Bifidobacterium myosotis DSM 100196T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B.ifidobacterium myosotis DSM 100196T (95.6 %). The average nucleotide identity, amino acid average identity and in silico DNA–DNA hybridization values between MRM 9.3T and DSM 100196T were 79.9, 72.1 and 28.5 %, respectively. Phenotypic and genotypic features clearly showed that the strain MRM 9.3T represents a novel species, for which the name Bifidobacterium jacchi sp. nov. is proposed. The type strain is MRM 9.3T (=DSM 103362T =JCM 31788T).
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Desertihabitans aurantiacus gen. nov., sp. nov., a novel member of the family Propionibacteriaceae
More LessThe taxonomic position of an actinobacterium isolated from a desert soil sample collected from Badain Jaran Desert, designated as CPCC 204711T, was established using a polyphasic approach. Cells of the isolate were Gram-staining-positive, aerobic, non-motile cocci. Good growth was observed at 28 °C (range 20–40 °C), pH 7.0 (range pH 6.0–8.0) and 0–1 % NaCl concentration (range 0–5 %, w/v). Galactose, arabinose and ribose were detected as the sugar compositions in the whole cell hydrolysates. The peptidoglycan type was A3gamma (ll-Dpm-Gly). MK-9(H4) was detected as the predominant menaquinone, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, several unidentified glycolipids, and one unidentified amino-glycolipid were detected as the major polar lipids. The predominant fatty acid was anteiso-C15 : 0. The genomic DNA G+C content was 73.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204711T affiliated to the family Propionibacteriaceae , in which the strain formed a distinct phylogenetic lineage next to the genus Mariniluteicoccus , with the highest 16S rRNA gene sequence similarity of 96.0 % to Mariniluteicoccus endophyticus YIM 2617T. Both phylogenetic analysis and phenotypic characteristics supported that strain CPCC 204711T represents a novel species of a new genus in the family Propionibacteriaceae , for which the name Desertihabitans aurantiacus gen. nov., sp. nov. is proposed, with CPCC 204711T (=KCTC 39977T=DSM 105431T) as the type strain.
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Glaciihabitans arcticus sp. nov., a psychrotolerant bacterium isolated from Arctic soil
More LessA non-motile, Gram-stain-positive, rod-shaped bacterium, designated RP-3-7T, was isolated from soil sampled at the Arctic region in Cambridge Bay, NU, Canada. Cells were strictly aerobic, non-spore-forming, catalase-positive and oxidase-positive. Colonies on Reasoner's 2A agar plates were pale yellow-coloured. Strain RP-3-7T was psychrotolerant and grew optimally at 15–20 °C. Strain RP-3-7T assimilated d-glucose, d-mannitol, l-arabinose and l-proline; tolerated only 0.5 % NaCl (w/v). Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RP-3-7T formed a lineage within the family Microbacteriaceae and clustered with members of the genus Glaciihabitans . The closest member was Glaciihabitans tibetensis MP203T (98.26 % sequence similarity). The major respiratory quinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 1 A. The diagnostic amino acid was 2,4-diaminobutyric acid and whole-cell sugars were xylose, rhamnose and mannose. The DNA G+C content of strain RP-3-7T was 66.9 mol%. The average nucleotide identity and in silico DNA–DNA relatedness values between strain RP-3-7T and Glaciihabitans tibetensis MP203T were 73.79 and 20.1 %, respectively. Based on the polyphasic, genomic and phylogenetic data, strain RP-3-7T represents a novel species of the genus Glaciihabitans , for which the name Glaciihabitans arcticus sp. nov. is proposed. The type strain is RP-3-7T (=KEMB 9005-731T=KACC 21151T=NBRC 113769T).
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Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970
A polyphasic approach was used for evaluating the taxonomic status of strain HST21T isolated from Salar de Huasco in the Atacama Desert. The results of 16S rRNA gene and multilocus sequence phylogenetic analyses assigned strain HST21T to the genus Streptomyces with Streptomyces albidochromogenes DSM 41800Tand Streptomyces flavidovirens DSM 40150T as its nearest neighbours. Digital DNA–DNA hydridization (dDDH) and average nucleotide identity (ANI) values between the genome sequences of strain HST21T and S. albidochromogenes DSM 41800T (35.6 and 88.2 %) and S. flavidovirens DSM 40105T (47.2 and 88.8 %) were below the thresholds of 70 and 95–96 % for prokaryotic conspecific assignation. Phenotypic, chemotaxonomic and genetic results distinguished strain HST21T from its closest neighbours. Strain HST21T is characterized by the presence of ll-diaminopimelic acid in its peptidoglycan layer; glucose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, glycophospholipids, unknown lipids and phospholipids as polar lipids; and anteiso-C15 : 0 (21.6 %) and anteiso-C17 : 0 (20.5 %) as major fatty acids (>15 %). Based on these results, strain HST21T merits recognition as a novel species, for which the name Streptomyces altiplanensis sp. nov. is proposed. The type strain is HST21T =DSM 107267T=CECT 9647T. While analysing the phylogenies of strain HST21T, Streptomyces chryseus DSM 40420T and Streptomyces helvaticus DSM 40431T were found to have 100 % 16S rRNA gene sequence similarity with digital DNA–DNA hydridization (dDDH) and average nucleotide identity (ANI) values of 95.3 and 99.4 %, respectively. Therefore, S. helvaticus is considered as a later heterotypic synonym of S. chryseus and, consequently, we emend the description of S. chryseus .
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Gordonibacter faecihominis is a later heterotypic synonym of Gordonibacter urolithinfaciens
More LessIn this study, the phylogenetic position of Gordonibacter faecihominis and Gordonibacter urolithinfaciens was investigated using phenotypic and molecular (rep-PCR, ARDRA, 16S rRNA gene sequencing and whole-genome sequencing) methods. Our results show that G ordonibacter faecihominis cannot be distinguished from G ordonibacter urolithinfaciens on the basis of the results of this polyphasic approach. Therefore, it is proposed that the two species G ordonibacter faecihominis and G ordonibacter urolithinfaciens belong to the same species.
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Kribbella turkmenica sp. nov., isolated from the Karakum Desert
More LessA novel actinobacterial strain, designated 16K104T, was isolated from desert soil collected from the Karakum Desert and characterized using a polyphasic approach to clarify its taxonomic position. Strain 16K104T was found to have chemotaxonomic and morphological properties consistent with classification in the genus Kribbella . The strain shared the highest 16S rRNA gene sequence similarity with Kribbella albertanoniae BC640T (99.2 %), and formed a branch with Kribbella antibiotica YIM 31530T in the 16S rRNA gene phylogenetic tree. Multilocus sequence analysis (MLSA) using five housekeeping genes (gyrB, rpoB, relA, recA and atpD) for comparing the strain with all Kribbella type strains showed that the MLSA distances of strain 16K104T to the closely related type strains of the genus were much higher than the 0.04 threshold. The organism was found to contain ll-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were identified as ribose and glucose. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0, anteiso-C15:0, iso-C15 : 0 and iso-C17 : 0. The results of digital DNA–DNA hybridization and average nucleotide identity analyses, in addition to MLSA phylogenetic distances, confirmed that the strain represents a novel species of the genus Kribbella , for which the name Kribbella turkmenica sp. nov. is proposed. The type strain is 16K104T (=JCM 32914T=KCTC 49224T).
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Reclassification of Streptomyces rimosus subsp. paromomycinus as Streptomyces paromomycinus sp. nov.
More LessStreptomyces rimosus is currently composed of two subspecies: Streptomyces rimosus subsp. rimosus and Streptomyces rimosus subsp. paromomycinus . The 16S rRNA gene similarity between type strains of these two subspecies is 99.03 %, whereas that between S. rimosus subsp. paromomycinus and Streptomyces chrestomyceticus is 100 %. To assess the taxonomic status of S. rimosus subsp. paromomycinus , genome sequencing was performed on the type strains of S. rimosus subsp. paromomycinus and S. chrestomyceticus . Digital DNA–DNA hybridization values between S. rimosus subsp. paromomycinus NBRC 15454T and S. rimosus subsp. rimosus ATCC 10970T and between S. rimosus subsp. paromomycinus NBRC 15454T and S. chrestomyceticus NBRC 13444T were 35.4 and 59.9 %, respectively, which are less than the thresholds for bacterial species delineation and indicate that S. rimosus subsp. paromomycinus is not S. rimosus , but an independent species different from S. rimosus and S. chrestomyceticus . In addition, phenotypic data also support that S. rimosus subsp. paromomycinus is distinct from S. chrestomyceticus . Therefore, S. rimosus subsp. paromomycinus should be reclassified as a novel species, for which we propose the name Streptomyces paromomycinus sp. nov. The type strain is NBRC 15454T (=ATCC 14827T=DSM 41429T=JCM 4541T=JCM 4871T=NRRL 2455T=VKM Ac-605T).
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Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content
More LessA novel propionate producing bacterium, strain JV5T, was isolated from the rumen fibrous content of a Holstein Friesian dairy cow. Cells of strain JV5T were Gram-stain-positive, non-motile and aerotolerant. Growth occurred between 35 and 45 °C, with an optimum at 39 °C. The pH range for growth was 6.5–8, with an optimum at pH 7. The 16S rRNA gene sequence of strain JV5T was 98.4 and 96.5 % identical to those of Propionibacterium australiense DSM 15818T and Propionibacterium acidifaciens DSM 21887T, respectively. Genome wide average nucleotide identity and digital DNA–DNA hybridization values were 88.3 and 35.5 %, respectively, against P. australiense DSM 15818T. The G+C content of strain JV5T was 68.9 mol%. Strain JV5T did not produce urease and was able to metabolize glutamate, but not aspartate and glycine. Strain JV5T was able to ferment a range of substrates including certain simple and complex carbohydrates, sugar alcohols and amino acids. Chemotaxonomic analysis of strain JV5T revealed the presence of meso-diamino pimelic acid isomers similar those found in P. australiense , but different from P. acidifaciens . The observed major (>10 %) cellular fatty acids in strain JV5T (C18 : 1 ω9c, anteiso-C15 : 1, C16 : 0, C17 : 0 and C16 : 0 alcohol) were also different from those observed in P. australiense and P. acidifaciens . Based on these findings, a novel species is proposed within the genus Propionibacterium , Propionibacterium ruminifibrarum sp. nov. (type strain JV5T=DSM 106771T=TISTR 2629T).
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Amycolatopsis suaedae sp. nov., an endophytic actinomycete isolated from Suaeda maritima roots
More LessAn actinomycete strain, designated 8-3EHSuT, was isolated from surface-sterilised roots of Suaeda maritima, collected from Petchburi province, Thailand. Taxonomic position of strain 8-3EHSuT was studied using a polyphasic approach. Phylogenetic determination based on the 16S rRNA gene sequence similarity showed that strain 8-3EHSuT belongs to the genus Amycolatopsis , with the highest sequence similarity to Amycolatopsis jiangsuensis KLBMP 1262T (96.9 %). The colony of strain 8-3EHSuT was yellowish white. Long straight mycelium breaking down into fragments were observed. Growth occurred at temperatures 15–45 °C and at pH 6.0–10.0. The strain contained meso-diaminopimelic acid, arabinose, galactose and mannose in whole-organism hydrolysates. The predominant menaquinone was MK-9(H4). The major fatty acids were C16 : 0, iso-C16 : 0 and iso-C15 : 0. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, two unknown amino lipids and an unknown lipid. The G+C content of genomic DNA was 71.8 mol%. A phylogenetic tree based on 16S rRNA sequences showed that the strain 8-3EHSuT formed a distinct evolutionary linage within the genus Amycolatopsis . Based on analysis results of physiological, biochemical and chemotaxonomic data, strain 8-3EHSuT represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis suaedae sp. nov. is proposed. The type strain is 8-3EHSuT (=TBRC 8488T=NBRC 113449T).
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- Bacteroidetes
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Flavobacterium amnicola sp. nov., isolated from a sub-tropical stream
More LessStrain LLJ-11T, isolated from water sampled from a freshwater stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain LLJ-11T were Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain LLJ-11T is affiliated with species in the genus Flavobacterium . Strain LLJ-11T was most closely related to Flavobacterium amniphilum KYPY10T with 98.0 % 16S rRNA gene sequence identity. The DNA–DNA relatedness of strain LLJ-11T with respect to Flavobacterium species was less than 35 %. Average nucleotide identity and digital DNA–DNA hybridization values between strain LLJ-11T and the type strains of other closely related Flavobacterium species were 70.0–76.3 % and 21.1–23.9 %, respectively. Strain LLJ-11T contained iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0) as the predominant fatty acids. The major isoprenoid quinone was MK-6. The polar lipid profile consisted of phosphatidylethanolamine, three uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine was homospermidine. The DNA G+C content was 34.8 mol%. On the basis of the phylogenetic inference and phenotypic data, strain LLJ-11T is considered a representative of a novel species within the genus Flavobacterium . The name Flavobacterium amnicola sp. nov. is proposed, with strain LLJ-11T (=BCRC 81124T=LMG 30599T=KCTC 62514T) as the type strain.
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Paracnuella aquatica gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring
More LessA Gram-stain-negative, rod-shaped bacterium (designated strain N24T) with gliding motility was isolated from thermal spring water sampled at Xi’an, PR China. Cells were 0.4–0.8 µm wide and 1.8–7.8 µm long. Optimal growth occurred at 33 °C and pH 7.0 on Reasoner's 2A (R2A) agar. Strain N24T could produce exopolysaccharide on R2A agar at 33 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain N24T formed a distinct phyletic lineage within the family Chitinophagaceae and was most closely related to members of the genera Flavisolibacter , Cnuella , Niveitalea , Flavitalea , Flaviaesturariibacter and Niastella with 91.7–93.9 % 16S rRNA gene sequence similarities. The major fatty acids of strain N24T were iso-C15 : 0 (31.8 %), iso-C17 : 0 3-OH (16.1 %) and iso-C15 : 1 G (12.9 %). The polar lipid profile consisted of phosphatidylethanolamine, two aminolipids and six unknown lipids; the quinone system consisted of menaquinone-7 (MK-7). The genomic G+C content was 49.3 mol%. On the basis of the evidence presented in this study, strain N24T represents a novel species of a new genus in the family Chitinophagaceae , for which the name Paracnuella aquatica gen. nov., sp. nov. is proposed. The type species is N24T (=KCTC 62083T=MCCC 1H00301T).
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Flavobacterium stagni sp. nov., isolated from a freshwater reservoir
More LessStrain WWJ-16T was isolated from a freshwater reservoir in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain WWJ-16T is affiliated with the species in the genus Flavobacterium . Strain WWJ-16T was most closely related to Flavobacterium fontis MIC3010T (97.9 % 16S rRNA gene sequence identity) and Flavobacterium squillarum CMJ-5T (97.6 %). Strain WWJ-16T showed 77.4 % average nucleotide identity and 20.6 % digital DNA–DNA hybridization identity with F. fontis MIC3010T. Cells of strain WWJ-16T were Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in 0.5–1 % NaCl (w/v). Strain WWJ-16T contained iso-C15 : 1 G and iso-C15 : 0 as predominant fatty acids. The major hydroxyl fatty acids were iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids and four uncharacterized phospholipids. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The genomic DNA G+C content of strain WWJ-16T was 39.4 mol%, as determined by genome sequencing. The genotypic and phenotypic characteristics indicate that strain WWJ-16T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium stagni sp. nov. is proposed. The type strain is WWJ-16T (=BCRC 81125T =LMG 30600T=KCTC 62515T).
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Chryseobacterium pennipullorum sp. nov., isolated from poultry feather waste
Strain 7_F195T was previously isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic approach was followed to determine if strain 7_F195T belongs to the genus Chryseobacterium and if the organism can be classified as a new species. The nearest neighbours, based on 16S rRNA gene sequence similarity values (indicated in parentheses), were Chryseobacterium flavum KCTC 12877T (98.42 %), Chryseobacterium indologenes LMG 8337T (98.24 %) and Chryseobacterium gleum ATCC 35910T (97.71 %). Genome sequencing revealed a genome size of 4 796 535 bp and a DNA G+C content of 38.6 mol%. The ANI values of strain 7_F195T compared to C. flavum , C. indologenes and C. gleum were 81.45, 81.86 and 82.38 %, respectively. The digital DNA–DNA hybridization values for strain 7_F195T with C. flavum , C. indologenes and C. gleum were 23.7, 23.7 and 24.9 %, respectively. Notable phenotypic differences include the presence of urease activity in C. indologenes LMG 8337T and C. gleum NCTC 11432T, but not in strain 7_F195T or C. flavum KCTC 12877T. The predominant fatty acids of strain 7_F195T were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH and the most abundant polar lipid was phosphatidylethanolamine. Menaquinone-6 was the only respiratory quinone. Based on the data generated from this polyphasic study, strain 7_F195T represents a novel Chryseobacterium species for which the name Chryseobacterium pennipullorum sp. nov. is proposed. The type strain is 7_F195T (=LMG 30781T=KCTC 62760T).
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Maribellus luteus gen. nov., sp. nov., a marine bacterium in the family Prolixibacteraceae isolated from coastal seawater
More LessA facultatively anaerobic, Gram-stain-negative, non-motile and straight to slightly curved long rod-shaped bacterial strain, designated XSD2T, was isolated from coastal seawater of Xiaoshi Island, PR China. The cells were catalase-positive, oxidase-negative and non-flagellated. Strain XSD2T was found to grow at 20–40 °C (optimum, 33 °C), at pH 6.0–8.5 (pH 7.0–7.5) and with 1–5 % (w/v) NaCl (3 %). Carotenoid pigments were produced. The major cellular fatty acids (>10.0 %) were iso-C15 : 0, iso-C16 : 0 3-OH and C17 : 1ω6c and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and three unidentified polar lipids. The sole respiratory quinone was MK-7 and the genomic DNA G+C content was 44.1 mol%. The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this organism to the order Marinilabiliales , family Prolixibacteraceae , with Mariniphaga sediminis SY21T as its closest relative with only 93.6 % sequence similarity. On the basis of physiological, biochemical and chemotaxonomic characteristics, we propose that strain XSD2T (=KCTC 62994T=MCCC 1H00347T) represents a novel species of a novel genus in the family Prolixibacteraceae , for which the name Maribellus luteus gen. nov., sp. nov. is proposed.
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- Firmicutes and Related Organisms
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When treated as heterotypic synonyms the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) have priority over the names Planococcaceae Krasil'nikov 1949 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980), respectively
More LessThe International Code of Nomenclature of Prokaryotes provides rules that govern the way names are to be selected based on priority of valid publication when two or more alternatives (synonyms) are available. However, these rules are not always followed. In the case of the name Caryophanaceae Peshkoff 1939 (Approved Lists 1980), when its nomenclatural type Caryophanon Peshkoff 1939 (Approved Lists 1980) is placed in the same taxon as Planococcus Migula 1894 (Approved Lists 1980), the nomenclatural type of Planococcaceae Krasil'nikov 1949 (Approved Lists 1980), then the two are considered to be heterotypic synonyms and the name which has priority is Caryophanaceae Peshkoff 1939 (Approved Lists 1980). Similarly in the case of the name Caryophanales Peshkoff 1939 (Approved Lists 1980) when its nomenclatural type Caryophanon Peshkoff 1939 (Approved Lists 1980) is placed in the same taxon as Bacillus Cohn 1872 (Approved Lists 1980), the nomenclatural type of Bacillales Prévot 1953 (Approved Lists 1980), then the two are considered to be heterotypic synonyms and the name which has priority is Caryophanales Peshkoff 1939 (Approved Lists 1980) While the rules of the International Code of Nomenclature of Prokaryotes are unambiguous in determining the correct names despite the fact that the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) are rarely used.
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Lactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili
More LessStrain HBUAS52074T is a Gram-positive staining, aerobic bacterium that was isolated from Zha-Chili, a traditional fermented food made in China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HBUAS52074T is a member of the genus Lactobacillus and closely related to Lactobacillus nantensis DSM 16982T (98.9 %), Lactobacillus heilongjiangensis DSM 28069T (98.8 %), Lactobacillus formosensis NBRC 1095009T (98.6 %), Lactobacillus futsaii JCM 17355T (98.5 %), Lactobacillus farciminis KCTC 3681T (98.5 %), Lactobacillus musae NBRC 112868T (98.5 %) and Lactobacillus crustorum LMG 23699T (98.4 %). The DNA G+C content is 36.3 mol%. The major cellular fatty acids are C16 : 0 (28.2 %), C18 : 1ω9c (30.5 %) and summed feature 7 (C19 : 1ω6c, and/or C19 : 1ω7c; 14.9 %). Average nucleotide identity and DNA–DNA hybridization (GGDC) values based on genomic comparisons between HBUAS52074T and related type species showed that the bacterium was significantly different from its closest relatives. Using polyphasic taxonomic analysis, we have shown that strain HBUAS52074T is a new species in the genus Lactobacillus , for which we propose the name Lactobacillus zhachilii sp. nov. The type strain is HBUAS52074T (=GDMCC 1.1417T=KCTC 21106T).
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Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis
More LessStrain S04009T, a Gram-stain-positive, coagulase-negative staphylococcus, was isolated from bovine mastitis in France. 16S rRNA gene analysis revealed it to be closely related to the coagulase-negative species Staphylococcus xylosus , Staphylococcus saprophyticus , Staphylococcus caeli and Staphylococcus edaphicus . At the whole-genome level, strain S04009T had an average nucleotide identity value <95 % and an inferred DNA–DNA hybridization value <70 % when compared to these species. Furthermore, phenotypic characteristics distinguished S04009T from those species. From these related species only strain S04009T and S. xylosus are able to ferment xylose and these two can be distinguished by the inability of strain S04009T to express urease activity. Based on the genotypic and phenotypic results, it is proposed that this isolate is a novel species, with the name Staphylococcus pseudoxylosus sp. nov. The type strain is S04009T (=DSM 107950T=CCUG 72763T=NCTC 14184T).
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Staphylococcus debuckii sp. nov., a coagulase-negative species from bovine milk
A novel type strain, designated SDB 2975T (=CECT 9737T=DSM 105892T), of the novel species Staphylococcus debuckii sp. nov. isolated from bovine milk is described. The novel species belongs to the genus Staphylococcus and showed resistance to tetracycline and was oxidase- and coagulase-negative, catalase-positive, and Gram-stain-positive. Phylogenetic relationships of Staphylococcus debuckii SDB 2975T to other staphylococcal species were inferred from 16S rRNA gene and whole-genome-based phylogenetic reconstruction. The 16S rRNA gene comparisons showed that the strain is closely related to Staphylococcus condimenti (99.73 %), Staphylococcus piscifermentans (99.66 %), Staphylococcus carnosus (99.59 %) and Staphylococcus simulans (98.03 %). Average nucleotide identity (ANI) values between S.taphylococcus debuckii SDB 2975T and its closely related Staphylococcus species were 83.96, 94.5, 84.03 and 78.09 %, respectively, and digital DNA–DNA hybridization (dDDH) values were 27.70, 58.02, 27.70 and 22.00 %, respectively. The genome of Staphylococcus debuckii SDB 2975T was sequenced with PacBio and Illumina technologies and is 2 691 850 bp long, has a G+C content of 36.6 mol% and contains 2678 genes and 80 RNAs, including six copies of each5S rRNA, 16S rRNA and 23S rRNA genes. Biochemical profiling and a newly developed PCR assay enabled differentiation of Staphylococcus debuckii SDB 2975T and three other SDB strains from its closest staphylococcal species. Differentiation was also achieved by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Genes unique to Staphylococcus debuckii were identified and a PCR-based assay was developed to differentiate Staphylococcus debuckii from other staphylococcal species. In conclusion, the results of phylogenetic analysis along with the ANI values <95 %, and dDDH values <70 % from closely related species along with the phenotypic and biochemical characteristics and specific MALDI-TOF profiles demonstrated that Staphylococcus debuckii SDB 2975T represents a novel species within the genus Staphylococcus , named Staphylococcus debuckii sp. nov. (SDB 2975T=CECT 9737T=DSM 105892T).
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Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound
Two unusual catalase-negative, Gram-stain-positive, Vagococcus -like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus . Strain SS1994T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1 %), followed by SS1994T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA–DNA hybridization <28 % to any other Vagococcus species. The names Vagococcus bubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcus vulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.
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Bacillus antri sp. nov., isolated from cave soil
A Gram-stain-positive, strictly aerobic, rod-shaped, motile, endospore-forming strain, SYSU K30001T, was isolated from a soil sample collected from a cave in Xingyi county, Guizhou province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU K30001T belonged to the genus Bacillus , with the highest sequence similarity to the type strain of Bacillus panaciterrae (98.1 %). Growth occurred at pH 6.0–9.0 (optimum, pH 7.0), at 28–55 °C (optimum, 28 °C) and in the presence of 0–3 % (w/v) NaCl (optimum in the absence of NaCl). Strain SYSU K30001T contained meso-2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-7 as the only isoprenoid quinone present. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The major fatty acids were iso-C15 : 0, iso-C17 : 1 ω10c, anteiso-C14 : 0 and iso-C17 : 0. The genome G+C content was 39.8 mol%. The average nucleotide identity values between SYSU K30001T and B. panaciterrae DSM 19096T were 72.1 % (ANIb) and 83.1 % (ANIm), which were below the cut-off level (95–96 %) for species delineation. Based on phenotypic, chemotaxonomic and molecular characterizations, strain SYSU K30001T represents a novel species of the genus Bacillus , for which the name Bacillus antri sp. nov. is proposed. The type strain is SYSU K30001T (=KCTC 33954T=CGMCC 1.13871T).
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Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis sp. nov. and Lactobacillus mulengensis sp. nov., isolated from Chinese traditional pickle
More LessThirty Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle. The strains were characterized using a polyphasic taxonomic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, determination of average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH), determination of average amino acid identity (AAI) and an analysis of phenotypic features. The data demonstrated that the 30 strains represented 11 novel species belonging to the genus Lactobacillus , strains 159-4T, 47-3T, 257-1T, 187-3T, 220-4T, 151-2BT, 137-3T, 244-4T, 218-10T, 218-6T and 112-3T were designated as the type strains. Strains 159-4T and 47-3T were related to the type strains of Lactobacillus porcinae , Lactobacillus manihotivorans , Lactobacillus nasuensis , Lactobacillus camelliae , Lactobacillus pantheris , Lactobacillus thailandensis , Lactobacillus sharpeae and Lactobacillus songhuajiangensis , having 92.0–98.9 % 16S rRNA gene sequence similarities, 58.1–84.7 % pheS gene sequence similarities and 61.4–90.3 % rpoA gene sequence similarities. Strains 257-1T and 187-3T were related to the type strains of Lactobacillus coryniformis , Lactobacillus iwatensis , Lactobacillus backii , Lactobacillus rennini and Lactobacillus bifermentans , having 93.5–99.3 % 16S rRNA gene sequence similarities, 67.7–81.8 % pheS gene sequence similarities and 77.0–96.2 % rpoA gene sequence similarities. Strains 220-4T, 151-2BT, 137-3T, 244-4T, 218-10T, 218-6T and 112-3T were closely related to the type strains of Lactobacillus paucivorans , Lactobacillus brevis , Lactobacillus hammesii , Lactobacillus senmaizukei , Lactobacillus parabrevis , Lactobacillus yonginensis , Lactobacillus koreensis and Lactobacillus cerevisiae , having 95.6–99.9 % 16S rRNA gene sequence similarities, less than 93.9 % pheS gene sequence similarities and 87.0–99.7 % rpoA gene sequence similarities. ANI, isDDH and AAI values between strains 159-4T, 47-3T, 257-1T, 187-3T, 220-4T, 151-2BT, 137-3T, 244-4T, 218-10T, 218-6T, 112-3T and type strains of phylogenetically related species were less than 92.7, 48.4 and 96.6 %, respectively, confirming that they represent 11 novel species within the genus Lactobacillus . Based upon the data of polyphasic characterization obtained in the present study, eleven novel species, Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis sp. nov. and Lactobacillus mulengensis sp. nov., are proposed and the type strains are 159-4T (=NCIMB 15175T=CCM 8911T), 47-3T (=NCIMB 15165T=CCM 8903T=LMG 31064T), 257-1T (=NCIMB 15166T=CCM 8904T=LMG 31065T), 187-3T (=NCIMB 15172T =CCM 8910T), 220-4T (=NCIMB 15163T =CCM 8902T=KCTC 21136T), 151-2BT (=NCIMB 15164T=CCM 8913T=KCTC 21129T=LMG 31063T), 137-3T (=NCIMB 15170T=CCM 8907T=KCTC 21125T=LMG 31053T), 244-4T (=NCIMB 15168T=CCM 8906T=KCTC 21137T=LMG 31052T), 218-10T (=NCIMB 15167T=CCM 8905T=KCTC 21135T =LMG 31055T), 218-6T (=NCIMB 15171T=CCM 8908T=KCTC 21134T =LMG 31067T) and 112-3T (=NCIMB 15174T=CCM 8909T=KCTC 21123T=LMG 31049T), respectively.
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Paenibacillus luteus sp. nov., isolated from soil
More LessA novel Gram-stain-positive, strictly aerobic, motile, spore-forming and rod-shaped bacterial strain, designated R-3T, was isolated from a soil sample obtained from the shore of Lake Panyang, Sichuan Province, PR China. Strain R-3T hydrolysed starch and casein. It could not assimilate d-glucose as a carbon source, or produce acid from d-glucose and l-arabinose. Phylogenetic, phenotypic, chemotaxonomic and molecular studies were performed on the new isolate. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R-3T was a member of the genus Paenibacillus , exhibiting the highest sequence similarity to Paenibacillus sinopodophylli TEGR-3T (98.4 %). The organism grew at 4–38 °C (optimum, 28–30 °C), at pH 6.0–10.0 (pH 7.0–7.5) and with 0–2.5 % (w/v) NaCl (1 %). The predominant menaquinone was MK-7. Anteiso-C15 : 0 (60.7 %) and C16 : 0 (15.5 %) were the major fatty acids. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The DNA G+C content of strain R-3T was determined to be 47.0 mol%. The DNA–DNA relatedness between strain R-3T and P. sinopodophylli TEGR-3T was 21.2 %. Based on the results obtained in this study, strain R-3T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus luteus sp. nov. is proposed. The type strain is R-3T (=CGMCC 1.16135T=KCTC 33912T).
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Enterococcus florum sp. nov., isolated from a cotton flower (Gossypium hirsutum L.)
A Gram-stain-positive and catalase negative coccus, designated strain Gos25-1T, isolated from a cotton flower (Gossypium hirsutum L.) collected from Khao Wong district, Kalasin province, Thailand. The taxonomic position of this strain was systematically studied based upon polyphasic taxonomic methods. The strain was facultatively anaerobic and produced l-lactic acid from glucose. The predominant cellular fatty acids were the straight-chain fatty acids C18 : 1ω9c and C16 : 0. According to 16S rRNA and phenylalanyl-tRNA synthase alpha subunit (pheS) gene sequence similarity, this strain was closely related to Enterococcus pallens NBRC 100697T, E. hermanniensis CIP 108559T, E. avium NBRC 100477T and E. raffinosus NBRC 100492T with 98.9–99.1 % and 77.0–82.0 % sequence similarities, respectively. Phylogenetic analysis indicated that strain Gos25-1T was clearly distinguished from closely related species of the genus Enterococcus . Draft genome of Gos25-1T had a size of 3.99 Mb which was contained 3788 coding sequences with in silico G+C content of 42.4 mol%. The ANIb and a digital DNA–DNA hybridisation (dDDH) values between strain Gos25-1T and the closest related species, E. pallens NBRC 100697T were 73.65 and 21.10 %, respectively. According to polyphasic characterisation, this strain represents a novel species of the genus Enterococcus , for which the name Enterococcus florum sp. nov. is proposed. The type strain is Gos25-1T (=CIP 110956T=LMG 29007T=NBRC 111461T=TISTR 2382T).
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Chengkuizengella marina sp. nov., isolated from deep-sea sediment of the Pacific Ocean
More LessA taxonomic study was carried out on strain YPA3-1-1T, which was isolated from deep-sea sediment of the Pacific Ocean. The bacterium was Gram-stain-positive, oxidase-positive, catalase-negative, rod-shaped and spore-forming. Growth was observed at salinities of 1.0–6.0 % and at temperatures of 10–40 °C. The isolate could degrade gelatin and aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YPA3-1-1T belonged to the genus Chengkuizengella , with the highest sequence similarity to the only typespecies, Chengkuizengella sediminis J15A17T (98.5 %). The estimated average nucleotide identity and DNA–DNA hybridization values between strain YPA3-1-1T and C. sediminis J15A17T were 88.1 and 35.0 %, respectively. The cell wall of strain YPA3-1-1T contained meso-diaminopimelic acid. The principal fatty acids (>10 %) were iso-C16 : 0 (35.5 %) and anteiso-C15 : 0 (17.5 %). The G+C content of the chromosomal DNA was 33.1 mol%. The respiratory quinone was determined to be MK-7 (100 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid and three unidentified phospholipids. The combined genotypic and phenotypic data show that strain YPA3-1-1T represents a novel species within the genus Chengkuizengella , for which the name Chengkuizengella marina sp. nov. is proposed, with the type strain YPA3-1-1T (=MCCC 1A14042T=KCTC 43019T).
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Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site
More LessA pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19T, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing blast analysis indicated that the strain is a member of the family Planococcaceae with the highest sequence similarity to Planomicrobium soli XN13T (96.1 %), followed by Planococcus maitriensis S1T (95.6 %), Planococcus plakortidis DSM 23997T (95.6 %), Planomicrobium flavidum ISL-41T (95.6 %), Planococcus rifietoensis M8T (95.5 %), Planococcus salinus LCB217T (95.5 %) and Planococcus maritimus DSM 17275T (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family Planococcaceae . Strain S5-TSA-19T had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on l-Lys-d-Asp, iso-C15 : 0 as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera Planococcus and Planomicrobium , thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19T was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2–4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19T is proposed as the type strain of a novel species in a novel genus for which the name Indiicoccus explosivorum gen. nov., sp. nov. is proposed (=JCM 31737T=KCTC 33871T=MTCC 12608T).
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- Other Bacteria
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Tautonia sociabilis gen. nov., sp. nov., a novel thermotolerant planctomycete, isolated from a 4000 m deep subterranean habitat
A novel aerobic bacterium, designated as strain GM2012T, was isolated from a microbial mat proliferating under the flow of thermal water dissipating from the wall of a 4000 m deep mine in South Africa. The cells were non-motile cocci, capable of budding, occurred in single or gathered in aggregates. The organism is a strictly aerobic chemoorganoheterotroph, preferring simple sugars and polysaccharides as growth substrates. The optimal growth occurred at 42 °C and pH 7.5–7.7. The predominant fatty acids were palmitate, stearate and oleate. The G+C content of the DNA was 70.1 mol%. The 16S rRNA gene sequence analysis placed strain GM2012T within the family Isosphaeraceae of the order Planctomycetales with 88–89 % sequence identity to Isosphaera pallida , Aquisphaera giovannonii, Singulisphaera acidiphila , Paludisphaera borealis and Tundrisphaera lichenicola type strains. Based on the genotypic and phenotypic distinctive features of the new strain, we propose a novel genus and species Tautonia sociabilis gen. nov., sp. nov. with the type strain GM2012T (=VKM B-2860,=KCTC 72013).
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- Proteobacteria
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Description of novel members of the family Sphingomonadaceae: Aquisediminimonas profunda gen. nov., sp. nov., and Aquisediminimonas sediminicola sp. nov., isolated from freshwater sediment
Two Gram-stain-negative bacterial strains, DS48-3T and CH68-4T, were isolated from freshwater sediment taken from the Daechung Reservoir, Republic of Korea. Cells of strains DS48-3T and CH68-4T were aerobic, non-motile, non-spore-forming and rod-shaped. Strain DS48-3T was isolated from a sediment surface sample at a depth of 48 m from the Daechung Reservoir and was most closely related to the genus Sphingopyxis according to 16S rRNA gene sequence analysis (94.5–95.9 % similarity). Strain CH68-4T was isolated from the very bottom of a 67-cm-long sediment core collected from Daechung Reservoir at a water depth of 17 m and was most closely related to the genus Sphingopyxis (16S rRNA gene sequence similarity of 93.7–95.0 %). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the two strains formed a separate lineage within the order Sphingomonadales showing similarity values below 95.9 % with their closest phylogenetic neighbours, and sharing 97.3 % similarity with each other. The combined genotypic and phenotypic data showed that strains DS48-3T and CH68-4T could be distinguished from all genera within the family Sphingomonadaceae and represented two distinct species of a novel genus, Aquisediminimonas profunda gen. nov., sp. nov. (type strain DS48-3T=KCTC 52068T=CCTCC AB 2018061T) and Aquisediminimonas sediminicola sp. nov. (type strain CH68-4T=KCTC 62205T=CCTCC AB 2018062T).
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Vibrio echinoideorum sp. nov., isolated from an epidermal lesion on the test of a green sea urchin (Strongylocentrotus droebachiensis)
More LessA Gram-stain-negative, facultatively anaerobic Vibrio strain, designated NFH.MB010T, was isolated from an epidermal lesion on the test (hard shell skeleton) of a green sea urchin (Strongylocentrotus droebachiensis) collected from northern Norway. Cells of strain NFH.MB010T were rod shaped and motile by means of a single, long polar flagellum. Growth was observed at 1–5% NaCl (w/v) and at 4 °C, but not above 28 °C. Phylogenetic analyses based on eight-gene multilocus sequence analysis (16S rRNA, atpA, gyrB, mreB, pyrH, recA, rpoA and rpoD) suggested novelty at the species level. In silico DNA–DNA hybridization and orthologous average nucleotide identity estimates showed percentage genomic resemblances to its closest relative, Vibrio splendidus , that were well below the established same species threshold values. Phenotypically, utilization of glycogen and gentiobiose, inability of acetoin production, and undetectable valine arylamidase and trypsin activity discriminated strain NFH.MB010T from the closely related reference strains. Protein spectra generated by maldi-tof mass spectrometry further consolidated the species level uniqueness of strain NFH.MB010T. Based on the described polyphasic approach, strain NFH.MB010T therefore appears as a novel species within the Splendidus clade of the genus Vibrio , and the name Vibrio echinoideorum sp. nov. is proposed, with NFH.MB010T (=DSM 107264T=LMG 30656T) as the type strain.
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Hydrocarboniclastica marina gen. nov., sp. nov., a marine hydrocarbonoclastic bacterium isolated from an in situ enriched hydrocarbon-degrading consortium in sea sediment
More LessA Gram-stain-negative, motile, non-spore-forming, aerobic and rod-shaped bacterial strain, Soil36-7T, was isolated from an in situ enriched hydrocarbon-degrading consortium in South China Sea sediment. Strain Soil36-7T grew at 4–40 °C (optimum 28–32 °C), at pH 5–10 (pH 7–8) and in the presence of 1–12 % (w/v) NaCl (3–6 %). Phylogenetic analyses based on 16S rRNA gene sequences and a genome-based approach using UBCGs (up-to-date bacterial core genes) showed Soil36-7T formed a distinct branching lineage within the family Alteromonadaceae . 16S rRNA gene sequence similarity was 92.9, 92.1 and >88.3 % between strain Soil36-7T and the type species of the genera Marinobacter , Tamilnaduibacter and the other genera of the family Alteromonadaceae , respectively. The major fatty acids in Soil36-7T were C16 : 0, C16 : 1ω6/7c, C16 : 0 10-methyl, C18 : 1ω7c, C12 : 0 and C18 : 0. The predominant respiratory quinone was Q-9, with a minor amount of Q-10 (3.5 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and various unidentified glycolipids, phospholipids, aminophospholipids and other polar lipids. The DNA G+C content was 57.9 mol%. On the basis of phylogenetic, genomic, phenotypic and chemotaxanomic characteristics, strain Soil36-7T could be classified as representing a novel species of a new genus within the family Alteromonadaceae , for which the name Hydrocarboniclastica marina gen. nov., sp. nov. is proposed. The type strain of the type species is Soil36-7T (=MCCC 1A12105T=KCTC 62334T).
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Marinicauda salina sp. nov., isolated from a marine solar saltern
More LessA novel Gram-stain-negative, aerobic, oxidase-positive, motile, dimorphic rod bacterium, with a polar flagellum or a polar prostheca, designated as strain WD6-1T, was isolated from a sediment sample collected from a marine solar saltern located in Weihai, PR China. Growth of strain WD6-1T was observed at 15–45 °C (optimum, 37–40 °C). The pH range for growth was pH 6.0–9.5 (optimum, pH 7.0–7.5) while the NaCl concentration was 1.0–16.0 % (w/v; optimum, 5.0 %). The most closely related species was Marinicauda algicola (97.0 % 16S rRNA gene sequence similarity). The DNA G+C content of strain WD6-1T was 69.5 mol% and the sole respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>10 %) of strain WD6-1T included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 and C17 : 0, and the major polar lipids were glucuronopyranosyldiglyceride, monoglycosyldiglyceride and sulfo-quinovosyl diacylglycerol. Based on the results of phylogenetic, genotypic and phenotypic analyses, the isolate is representative of a new member of the genus Marinicauda , for which the name Marinicauda salina sp. nov. is proposed. The type strain is WD6-1T (=KCTC 62348T=MCCC 1H00282T).
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Oleisolibacter albus gen. nov., sp. nov., isolated from an oil-contaminated soil
More LessA Gram-stain-negative, aerobic, flagellated, rod-shaped bacterium, designated strain NAU-10T, was isolated from an oil-contaminated soil collected in PR China. Strain NAU-10T could grow at 10–42 °C (optimum, 30 °C), pH 5.0–9.0 (pH 7.0) and in the presence of 0–2.5 % (w/v) NaCl (0.5 % in Luria–Bertani broth). The major fatty acids were C18 : 1 ω 7c (38.6 %), C17 : 1 ω 6c (9.8 %), C18 : 1 2-OH (9.1 %), summed feature 3 (8.7 %), C16 : 0 3-OH (7.2 %) and C16 : 0 (6.7 %). The major respiratory quinones were Q9 and Q10. The total polar lipids were lipid, aminolipid, phospholipid, phosphatidylglycerol and phosphatidylethanolamine. Strain NAU-10T shared the highest 16S rRNA gene sequence similarities with Rhodocista pekingensis 3-pT (95.9 %), Niveispirillum cyanobacteriorum TH16T (95.3 %) and Niveispirillum fermenti CC-LY736T (95.3 %), and constituted a sub-cluster within the family Rhodospirillaceae . The DNA G+C content of strain NAU-10T was 68.2 mol% based on its draft genome sequence. Genome annotation of strain NAU-10T predicted the presence of 4309 genes, of which 4237 are coding proteins and 72 are RNA genes. Based on its phenotypic and chemotaxonomic characteristics, as well as the analysis of the 16S rRNA gene sequences, it was concluded that strain NAU-10T represents a novel genus, for which the name Oleisolibacter gen. nov., is proposed. The type species of this genus is Oleisolibacter albus with the type strain NAU-10T (=KCTC 62417T=CCTCC AB 2018015T).
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Sphingomonas lenta sp. nov., a slowly growing bacterium isolated from an abandoned lead–zinc mine
A novel slowly growing member of the genus Sphingomonas , designated 1PNM-20T, was isolated from an abandoned lead–zinc mine in Meizhou, Guangdong Province, PR China. A polyphasic taxonomic study was performed to characterize the novel strain. Growth occurred on Reasoner’s 2A (R2A) agar and peptone–yeast extract (PYE) agar, but not in liquid R2A or PYE media. Cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with a polar flagellum (monotrichous). 16S rRNA gene sequence comparison showed that it shared the highest similarity with Sphingomonas carri PR0302T (97.2 %), followed by Sp hingomonas spermidinifaciens 9NM-10T (97.0 %), Sphingomonas floccifaciens FQM01T (97.0 %) and other species of Sphingomonas (<97 %). Phylogenetic analyses clearly showed that strain 1PNM-20T fell into the cluster of Sphingomonas , and was most closely related to S. carri . The draft genome sequence was 3.76 Mb in length with a DNA G+C content of 69.8 mol%. Major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and 11-methyl C18 : 1 ω7c, with C14 : 0 2-OH as the main hydroxy fatty acid. Ubiquinone 10 (Q-10) was the predominant respiratory quinone, and sym-homospermidine was displayed as the major polyamine. The polar lipids were composed of sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid and an unidentified glycolipid. The phenotypic, phylogenetic and chemotaxonomic results supported the hypothesis that strain 1PNM-20T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas lenta sp. nov. is proposed. The type strain is 1PNM-20T (=GDMCC 1.660T=DSM 27572T).
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Corallincola holothuriorum sp. nov., a facultative anaerobe isolated from sea cucumber intestine
More LessStrain C4T, isolated from sea cucumber intestine in Weihai, Shandong, PR China, is a novel Gram-stain-negative, facultatively anaerobic, amphitrichously flagellated, short rod that grows as creamy white bacterial colonies on plates. Optimal growth of the strain was observed at 28–30 °C, pH 6.5–7.0 and at a concentration of 3 % NaCl. The G+C content of the genomic DNA was 49.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain C4T is a member of the genus Corallincola and was most similar to Corallincola platygyrae JLT2006T. The major cellular fatty acids of strain C4T were C16 : 1ω7c/iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The sole respiratory quinone was Q-8. The predominant polar lipids in strain C4T were phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. Based on morphology and physiological characteristics, strain C4T should be classified as a novel species in the genus Corallincola, for which Corallincola holothuriorum is proposed. The type strain is C4T (=ATCC BAA-2611T=CICC 10839T).
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Neisseria weixii sp. nov., isolated from rectal contents of Tibetan Plateau pika (Ochotona curzoniae)
Three independent isolates (10022T, 10 009 and 10011) of a novel catalase-positive, Gram-stain-negative coccus in the genus Neisseria were obtained from the rectal contents of plateau pika on the Qinghai–Tibet Plateau, PR China. Based on 16S rRNA gene sequence analysis, our newly identified organisms were most closely related to Neisseria iguanae , Neisseria flavescens and Neisseria perflava with similarities ranging from 98.02 to 98.45 %, followed by seven other species in the genus Neisseria . Phylogenetic analysis based on 16S rRNA and rplF genes showed that our three novel isolates group with members of the genus Neisseria . Results of the average nucleotide identity (ANI) analysis confirmed that our isolates are of the same species, and the ANI values between type strain 10022T and other Neisseria species are 74.12–85.06 %, lower than the threshold range of 95–96 %. The major cellular fatty acids for our novel species are C16 : 0 and C16:1ω7c/C16:1ω6c, which along with their phenotypic characteristics can distinguish our isolates from other Neisseria species. On the basis of polyphasic analyses, our isolates are proposed to represent a novel species in genus Neisseria , with the name Neisseria weixii sp. nov. The type strain is 10022T (=DSM 103441T=CGMCC 1.15732T).
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Reclassification of Ochrobactrum lupini as a later heterotypic synonym of Ochrobactrum anthropi based on whole-genome sequence analysis
The genus Ochrobactrum belongs to the family Brucellaceae and its members are known to be adapted to a wide range of ecological niches. Ochrobactrum anthropi ATCC 49188T and Ochrobactrum lupini LUP21T are strains isolated from human clinical and plant root nodule samples, respectively, which share high similarity for phylogenetic markers (i.e 100 % for 16S rRNA, 99.9 % for dnaK and 99.35 % for rpoB). In this work, multiple genome average nucleotide identity (ANI) approaches, digital DNA–DNA hybridization (dDDH) and phylogenetic analysis were performed in order to investigate the taxonomic relationship between O. anthropi ATCC 49188T, O. lupini LUP21T, and other five type strains from the genus Ochrobactrum . Whole-genome comparisons demonstrated that O. lupini LUP21T and the Ochrobactrum genus type species, O. anthropi ATCC 49188T, share 97.55 % of ANIb, 98.25 % of ANIm, 97.99 % of gANI, 97.94 % of OrthoANI and 83.9 % of dDDH, which exceed the species delineation thresholds. These strains are also closely related in phylogenies reconstructed from a concatenation of 1193 sequences from single-copy ortholog genes. A review of their profiles revealed that O. anthropi ATCC 49188T and O. lupini LUP21T do not present pronounced differences at phenotypic and chemotaxonomic levels. Considering phylogenetic, genomic, phenotypic and chemotaxonomic data, O. lupini should be considered a later heterotypic synonym of O. anthropi .
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Yersinia kristensenii subsp. rochesterensis subsp. nov., isolated from human feces
More LessA single bacterial isolate, EPLC-04T, was isolated from human feces and identified as representing a member of the genus Yersinia on the basis of phenotypic characteristics, matrix assisted laser desorption ionization time-of-flight mass spectrometry and partial 16S rRNA gene sequencing. The isolate’s phenotypic profile differed from that described for the most closely related species, Yersinia kristensenii , by exhibiting lipase production and lacking pyrazinamidase activity. Multiple genetic targets, including the complete (1465 bp) 16S rRNA gene sequence and partial sequences of groEL (539 bp), gyrB (935 bp), glnA (525 bp) and recA (535 bp) indicated that the isolate exhibited 98.91, 92.16, 90.81, 92.78 and 89.01 % identity with Yersinia aldovae , 98.98, 91.99, 90.17, 89.77 and 89.55 % identity with Yersinia intermedia , and 99.66, 98.11, 98.50, 98.49 and 98.51 % identity with Y. kristensenii , respectively. Phylogenetic reconstructions based on the combination of the four housekeeping genes indicated that the isolate formed a unique branch, supported by a bootstrap value of 100 %. Digital DNA–DNA homology and 16S rRNA gene sequencing identified EPLC-04T as representing Y. kristensenii . However, the unique phenotypic traits and results of phylogenetic analysis indicate that it represents a novel subspecies of Y. kristensenii . The name Yersinia kristensenii subsp. rochesterensis subsp. nov. is proposed for this novel taxon (type strain EPLC-04T=ATCC BAA-2637T, DSMZ 28595T).
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Aquincola rivuli sp. nov., isolated from a freshwater stream
More LessStrain KYPY4T, isolated from a water sample taken from the Funglin stream in Taiwan, was characterized using a polyphasic taxonomic approach. The 16S rRNA gene sequence of strain KYPY4T was closely related to Ideonella dechloratans CCUG 30898T (97.1 %) followed by Aquincola tertiaricarbonis L10T (96.9 %) and Kinneretia asaccharophila KIN192T (96.8 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KYPY4T belonged to the genus Aquincola and formed a distinct phyletic line with A. tertiaricarbonis L10T and Aquincola amnicola TTM-94T. The draft genome of strain KYPY4T was approximately 4.93 Mb in size with a G+C content of 70.1 mol%. Strain KYPY4T showed 73.4–76.9 % average nucleotide identity and 21.3–22.5 % digital DNA–DNA hybridization identity with the strains of other related species in the Rubrivivax-Roseateles–Leptothrix–Ideonella-Aquabacterium group. Cells of strain KYPY4T were Gram-stain-negative, aerobic, motile, surrounded by a thick capsule and formed light orange colonies. Optimal growth occurred at 30 °C, pH 7 and 0 % NaCl. Strain KYPY4T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized polar lipids. The major respiratory quinone was Q-8. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KYPY4T should be classified as a novel species of the genus Aquincola , for which the name Aquincola rivuli sp. nov. is proposed. The type strain is KYPY4T (=BCRC 81010T=KCTC 52441T).
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Kineobactrum sediminis gen. nov., sp. nov., isolated from marine sediment
More LessA novel Gram-stain-negative, rod-shaped marine bacterium, designated strain F02T, was isolated from a marine saltern in Weihai, PR China. The cells of strain F02T were approximately 0.8–1.0×3.0–4.0 µm and motile by means of a polar flagellum. Strain F02T grew optimally at 33–35 °C, pH 7.5 and in the presence of 3.0 % (w/v) NaCl. Strain F02T showed oxidase- and catalase-positive activities. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain F02T belonged to the family Halieaceae and exhibited 16S rRNA gene sequence similarities of 96.6 and 96.4 % to the type strains of Chromatocurvus halotolerans and Parahaliea mediterranea , respectively. The major cellular fatty acids of strain F02T were C18 : 1ω7c, C16 : 1ω7c, C15 : 0 and C18 : 1ω9c. The major polar lipids of strain F02T were phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Strain F02T contained Q-8 as the sole respiratory quinone. The genomic DNA G+C content was 58.4 mol%. The genome sequences of strain F02T and Chromatocurvus halotolerans DSM 23344T had an OrthoANI value of 70.5 %, and the average amino acid identity value between the two genomes was 62.6 %. The sequence similarity value between the rpoB genes of strain F02T and Chromatocurvus halotolerans DSM 23344T was 79.5 %. On the basis of polyphasic analysis, strain F02T represents a novel species in a new genus, for which the name Kineobactrum sediminis gen. nov., sp. nov. is proposed. The type strain is F02T (=KCTC 52616T=MCCC 1H00224T).
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Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge
The creamy white to beige, aerobic, non-motile, ovoid to rod-shaped, Gram-stain-negative strain, Cd-10T, was isolated from heavy-metal-contaminated sludge from a decantation basin of a heavy metal processing factory based on its ability to tolerate CdCl2 in the cultivation medium. In the reconstruction of its phylogeny based on 16S rRNA gene sequences, strain Cd-10T clustered with species of the genera Gemmobacter , Xinfangfangia, Tabrizicola and Rhodobacter within the family Rhodobacteraceae . Its 16S rRNA gene sequence exhibited 96.32 % pairwise similarity to the type strain of Xinfangfangia soli , 95.3 % to that of Gemmobacter intermedius , followed by Tabrizicola fusiformis (95.10 %), Rhodobacter sediminis (94.88 %), Gemmobacter nectariphilus and Rhodobacter capsulatus (both 94.81 %). The major respiratory quinone was Q-10 accompanied by Q-9, the fatty acid profile consisted predominantly of C18 : 1ω7c, C18 : 0, C16 : 0 and C16 : 1ω7c, the major polar lipids were phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and diphosphatidylglycerol. An analysis of the percentage of conserved proteins deduced from draft or complete genomic sequences of strain Cd-10T and representatives of its closest relatives suggested that strain Cd-10T is a member of a novel genus within the Rhodobacteraceae family for which we propose the name Pseudogemmobacter. Strain Cd-10T (=DSM 103618T=NCCB 100645T) is the type strain of Pseudogemmobacter bohemicus gen. nov., sp. nov., the type species of the genus Pseudogemmobacter gen. nov.
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Altererythrobacter aquimixticola sp. nov., isolated from sediment sampled at the junction between the ocean and a freshwater spring
More LessA Gram-stain-negative, aerobic, non-motile and coccoid-, ovoid- or rod-shaped bacterial strain, designated SSKS-13T, was isolated from sediment sampled at the junction between the ocean and a freshwater spring at Jeju island, Republic of Korea. Strain SSKS-13T grew optimally at 37 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain SSKS-13T fell within the clade comprising the type strains of Altererythrobacter species, clustering with the type strains of Altererythrobacter lauratis , Altererythrobacter palmitatis and Altererythrobacter buctensis having 16S rRNA gene sequence similarities of 97.2–97.6 %. Strain SSKS-13T exhibited 16S rRNA gene sequence similarities of less than 97.0 % to the type strains of the other recognized species. Strain SSKS-13T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain SSKS-13T were phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain SSKS-13T was 64.6 mol%. The mean DNA–DNA relatedness values of strain SSKS-13T with the type strains of A. lauratis , A. palmitatis and A. buctensis were 11.7–25.3 %. Differential phenotypic properties, together with the phylogenetic and genetic data, proved that strain SSKS-13T is distinct from recognized Altererythrobacter species. On the basis of the data presented here, strain SSKS-13T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter aquimixticola sp. nov. is proposed. The type strain is SSKS-13T (=KACC 19863T=KCTC 62900T=NBRC 113545T).
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Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia
Strains 2B12T, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA–DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai . Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947T (=CFBP 8607T) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12T (=CFBP 8650T=LMG 30903T) as the type strain.
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Shewanella psychromarinicola sp. nov., a psychrophilic bacterium isolated from pelagic sediment of the Ross Sea (Antarctica), and reclassification of Shewanella arctica Kim et al. 2012 as a later heterotypic synonym of Shewanella frigidimarina Bowman et al. 1997
More LessTwo Gram-stain-negative, rod-shaped, facultatively anaerobic, iron-reducing bacterial strains, designated M2T and R106, were isolated from pelagic surface-sediment of the Ross Sea, Antarctica. The 16S rRNA gene sequence analysis revealed that strains M2T and R106 were affiliated to the genus Shewanella and formed a distinct subline in a robust clade encompassing Shewanella vesiculosa , Shewanella livingstonensis , Shewanella arctica and Shewanella frigidimarina with a range of sequence similarities of 98.1–98.9 %. Overall genome relatedness indices indicated that M2T and R106 represented a single genomic species, which was clearly distinguishable from the phylogenetically close relatives with lower values of species delineation thresholds. Cells of M2T grew optimally at 10–15 °C and pH 6.5 in the presence of 3.0–4.0 % (w/v) sea salts. The polar lipids of M2T comprised phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified aminolipid and an unidentified phospholipid. Quinones were Q-7, Q-8, MK-7 and MMK-7. The major cellular fatty acids (>10 %) were C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and C17 : 1ω8c. The DNA G+C content was 42.2 mol%. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic features, we propose the name Shewanella psychromarinicola sp. nov. with the type strain M2T (=KCCM 43257T =JCM 32090T) and the reclassification of S. arctica as a later heterotypic synonym of S. frigidimarina .
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Inhella crocodyli sp. nov., isolated from a crocodile pond
More LessStrain CCP-18T, isolated from a freshwater pond in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CCP-18T belongs to the genus Inhella and has the highest levels of sequence similarity with respect to Inhella inkyongensis IMCC1713T (98.9 %) and Inhella fonticola TNR-25T (98.0 %). Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed white-coloured colonies. Optimal growth occurred at 25 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-18T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, an unidentified phospholipid, an unidentified aminolipid and an unidentified lipid. The predominant polyamine was putrescine. The major isoprenoid quinone was Q-8. The draft genome was approximately 3.76 Mb in size with a G+C content of 68.9 mol%. The DNA–DNA hybridization values for strain CCP-18Twith I. inkyongensis IMCC1713T and I.nhella fonticola TNR-25T were less than 40 %. Based on the phylogenetic and phenotypic data, strain CCP-18T should be classified within the genus Inhella as a representative of a novel species, named Inhella crocodyli sp. nov. The type strain is CCP-18T (=BCRC 81120T=LMG 30595T=KCTC 62511T).
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Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov.
More LessA Gram-stain-negative, aerobic, non-motile, short-rod bacterium, strain MS2-2T, was isolated from mangrove sediment sampled at Jiulong River Estuary, Fujian province, PR China. 16S rRNA gene sequence similarity analysis showed that strain MS2-2T was most closely related to Defluviimonas indica 20V17T (97.41 %) and Defluviimonas pyrenivorans PrR001T (96.18 %). Phylogenetic trees based on 16S rRNA genes and genome sequences both revealed that strain MS2-2T formed a distinct cluster with D. indica 20V17T and D. pyrenivorans PrR001T within family Rhodobacteracea, quite separate from other type species in the genus Defluviimonas . The average nucleotide identity value between strain MS2-2T and D. indica 20V17T was 78.35 %. Growth of strain MS2-2T was observed at 16–41 ° C (optimum, 34 ° C), pH 3.6–7.5 (pH 6.0) and 0.5–10.0 % (w/v) NaCl (4.0 %). The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 0. Ubiquinone 10 was the sole quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 67.9 mol%. The combined genotypic and phenotypic data show that strain MS2-2T represents a novel species of a novel genus in the family Rhodobacteraceae , for which the name Acidimangrovimonassediminis gen. nov., sp. nov. is proposed, with the type strain MS2-2T (=MCCC 1K02682T=NBRC 112978T). We also propose the reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov.
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Chakrabartia godavariana gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Godavari River, India
A Gram-stain-negative, aerobic, yellow-pigmented, oxidase-positive and rod-shaped bacterium, designated PRB40T, was isolated from the Godavari River in India during the course of ‘Kumbh Mela’, the world’s largest mass gathering event. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRB40T formed a lineage within the family Sphingomonadaceae and was distinct from the most closely related genera Sphingorhabdus , Novosphingobium and Sphingomonas with sequence similarity values ≤95.2 %. Growth of strain PRB40T occurred at 10–40 °C (optimum 30 °C), at pH 6.0–9.0 (pH 7.0) and with 0–0.5 % (w/v) NaCl concentration (0 %). The major respiratory quinone was ubiquinone-10 (Q-10). It contained C17 : 1ω6c, C14 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) as the major cellular fatty acids. The predominant polar lipids were phospholipid, phosphatidylethanolamine and sphingoglycolipid. It took sym-homospermidine as the major polyamine. The DNA G+C content based on its draft genome sequence was 63.7 mol%. The polyphasic taxonomic analyses indicated that strain PRB40T represents a novel species of a novel genus within the family Sphingomonadaceae , for which the name Chakrabartia godavariana gen. nov., sp. nov. is proposed. The type strain of Chakrabartia godavariana is PRB40T (=MCC 3406T=GDMCC 1.1197T=KCTC 52678T=LMG 29985T).
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Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil
More LessA Gram-stain-negative, strictly aerobic bacterial strain, designated EO9T, was isolated from gasoline-contaminated soil in the Republic of Korea. Cells were non-motile short rods showing catalase- and oxidase-positive reactions. Growth was observed at 10–37 °C (optimum, 30 °C), at pH 6.0–9.0 (pH 6.5) and in the presence of 0–0.5 % (w/v) NaCl (0 %). Ubiquinone-10 (Q-10) and spermidine were identified as the predominant respiratory quinone and polyamine, respectively. Summed feature 8 (comprising C18:1ω7c/C18:1ω6c), summed feature 3 (comprising C16:1ω7c/C16:1ω6c), C16:0 and C14:0 2-OH were identified as major cellular fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol and an unidentified phospholipid. The G+C content of the genomic DNA was 62.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EO9T formed a tight phylogenetic lineage with Sphingobium xenophagum NBRC 107872T and Sphingobium hydrophobicum C1T within the genus Sphingobium . Strain EO9T was most closely related to S. xenophagum NBRC 107872T (97.2 %) and S. hydrophobicum C1T (97.2 %), but DNA–DNA relatedness levels between strain EO9T and the type strains of S. xenophagum and S. hydrophobicum were 37.1 and 36.8 % , respectively. Based on its phenotypic, chemotaxonomic and molecular features, strain EO9T clearly represents a novel species of the genus Sphingobium , for which the name Sphingobium terrigena sp. nov. is proposed. The type strain is EO9T (=KACC 19523T=JCM 32762T).
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Pseudomonas nitrititolerans sp. nov., a nitrite-tolerant denitrifying bacterium isolated from a nitrification/denitrification bioreactor
More LessA nitrite-tolerant denitrifying bacterium, strain GL14T, was isolated from the nitrification/denitrification bioreactor in our laboratory. Strain GL14T was Gram-stain-negative, rod-shaped, non-spore-forming, facultatively anaerobic and motile by means of a single polar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences indicated that it was assigned to the genus Pseudomonas with highest 16S rRNA gene sequence similarity (98.77 %) to Pseudomonas xanthomarina DSM 18231T and Pseudomonas songnenensis NEAU-ST5-5T, followed by Pseudomonas stutzeri ATCC 17588T (98.42 %), Pseudomonas kunmingensis HL22-2T (98.29 %) and Pseudomonas zhaodongensis NEAU-ST5-21T (98.22 %). Phylogenetic analysis based on both concatenated sequences of the 16S rRNA gene and two housekeeping genes (gyrB and rpoD) and genome sequences further clarified the intrageneric phylogenetic position of strain GL14T. The DNA G+C content of GL14T was 63.1 mol%. The results of digital DNA–DNA hybridization (highest 24.2 % of DNA–DNA relatedness) based on the Genome-to-Genome Distance Calculator and average nucleotide identity analyses (highest 80.23 %) confirmed that the strain was distinctly delineated from known species of the genus Pseudomonas . The major fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C17 : 0cyclo and C12 : 0. The respiratory quinone was ubiquinone Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the phylogenetic, genomic, phenotypic and chemotaxonomic analyses, it was concluded that strain GL14T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas nitrititolerans sp. nov. is proposed. The type strain is GL14T (=CGMCC 1.13874T=NBRC 113853T).
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Pseudopuniceibacterium sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from sediment
More LessA novel Gram-stain-negative bacterium, strain CY03T, was isolated from sediment of the Yellow Sea, PR China. Cells of strain CY03T were rods, aerobic and non-flagellated. Growth occurred at 5–40 °C (optimum, 30 °C), pH 5.5–9.5 (pH 7.5) and with 0.5–9.0 % NaCl (1.5–2.0 %). The 16S rRNA gene sequence comparison showed affiliation to the family Rhodobacteraceae with Puniceibacterium confluentis (97.0 %) as the most closely related species, followed by members of the genus Pseudooceanicola , Pseudooceanicola antarcticus (96.8 %) and Pseudooceanicola nitratireducens (96.7 %). The major cellular fatty acids were cyclo-C19 : 0 ω8c, C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and 11-methyl C18 : 1 ω7c. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, one unidentified phospholipid, one unidentified aminolipid and five unidentified lipids. The predominant respiratory quinone was Q-10. The DNA G+C content of the type strain was 62.8 mol%. Based on the results of the polyphasic characterization for strain CY03T, it represents a novel species of a novel genus of the family Rhodobacteraceae , for which the name Pseudopuniceibacterium sediminis gen. nov., sp. nov. is proposed. The type strain is CY03T (=CCTCC AB 2017195T=KCTC 62198T).
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Alteromonas fortis sp. nov., a non-flagellated bacterium specialized in the degradation of iota-carrageenan, and emended description of the genus Alteromonas
More LessStrain 1T, isolated in the 1970s from the thallus of the carrageenophytic red algae, Eucheuma spinosum, collected in Hawaii, USA, was characterized using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, ovoid or rod-shaped and grew optimally at 20–25 °C, at pH 6–9 and with 2–4 % NaCl. Strain 1T used the seaweed polysaccharides ι-carrageenan, laminarin and alginic acid as sole carbon sources. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2OH) with significant amounts (>6 %) of C16 : 0 N alcohol and 10 methyl C17 : 0. The respiratory quinone was Q-8 and major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unknown aminolipid. Phylogenetic analyses showed that the bacterium is affiliated to the genus Alteromonas (family Alteromonadaceae , class Gammaproteobacteria ). Strain 1T exhibited 16S rRNA gene sequence similarity values of 98.8 and 99.2 % to the type strains of Alteromonas mediterranea and Alteromonas australica respectively, and of 95.2–98.6 % to other species of the genus Alteromonas . The DNA G+C content of strain 1T was determined to be 43.9 mol%. Digital DNA–DNA hybridization predictions by the ANI and GGDC methods between strain 1T and other members of the genus Alteromonas showed values below 83 % and 30 %, respectively. The phenotypic, phylogenetic and genomic analyses show that strain 1T is distinct from species of the genus Alteromonas with validly published names and that it represents a novel species of the genus Alteromonas , for which the name Alteromonas fortis sp. nov. is proposed. The type strain is 1T (=ATCC 43554T=RCC 5933T=CIP 111645T=DSM 106819T).
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Parvularcula marina sp. nov., isolated from surface water of the South China Sea, and emended description of the genus Parvularcula
A Gram-stain-negative, aerobic, flagellated, rod-shaped bacterial strain, SM1705T, was isolated from a surface seawater sample collected from the South China Sea. The strain grew at 10–40 °C and with 0.5–13.0 % (w/v) NaCl. It hydrolysed Tweens 20, 40 and 60, but did not hydrolyse starch or Tween 80 nor reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1705T was affiliated with the genus Parvularcula , sharing the highest sequence similarity (96.0 %) with type strain of Parvularcula bermudensis and forming a coherent branch together with the latter within the clade of Parvularcula . The major cellular fatty acids were identified as summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C18 : 0. Polar lipids included three unidentified glycolipids and one unidentified lipid. The major respiratory quinone of strain SM1705T was Q10. The genomic DNA G+C content of strain SM1705T was 59.3 mol%. Based on the polyphasic evidence presented in this paper, strain SM1705T represents a novel Parvularcula species, for which the name Parvularcula marina sp. nov. is proposed. The type strain is SM1705T (=KCTC 62795T=MCCC 1K03505T=CCTCC AB 2018345T).
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Croceibacterium gen. nov., with description of Croceibacterium ferulae sp. nov., an endophytic bacterium isolated from Ferula sinkiangensis K. M. Shen and reclassification of Porphyrobacter mercurialis as Croceibacterium mercuriale comb. nov.
A novel endophytic bacterium, designated strain SX2RGS8T, was isolated from the surface-sterilized roots of an endangered medicinal plant (Ferula sinkiangensis K. M. Shen) collected from Xinjiang, north-western PR China. The taxonomic position of the candidate was investigated using a polyphasic approach. Strain SX2RGS8T was found to be aerobic, Gram-stain-negative, oxidase-negative, catalase-positive and axiolitic-shaped. Strain SX2RGS8T grew at 4–45 °C (optimum, 28 °C), pH 4.0–10.0 (pH 7.0) and in the presence of 0–5 % (w/v) NaCl. The polar lipids detected for strain SX2RGS8T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified phosphoglycolipids, an unidentified phospholipid and unidentified lipids. The major respiratory quinone of strain SX2RGS8T was ubiquinone 10 and the major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was determined to be 66.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 99.2 % ( Porphyrobacter mercurialis ), 95.5 % ( Porphyrobacter donghaensisi) and 95.4 % ( Porphyrobacter colymbi ) similarities to its closest relatives. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic, genotypic and phylogenetic data, strain SX2RGS8T represents a novel species of a novel genus in the family Erythrobacteraceae , for which the name Croceibacterium ferulae gen. nov., sp. nov. is proposed. The type strain is SX2RGS8T (=CGMCC 1.16402T=KCTC 62090T). In addition, Porphyrobacter mercurialis Coil et al. 2016 is proposed to be transferred to this new genus as Croceibacterium mercuriale comb. nov.
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Tabrizicola sediminis sp. nov., one aerobic anoxygenic photoheterotrophic bacteria from sediment of saline lake
More LessTwo strains of Gram-stain-negative, non-motile, aerobic, short-rod bacteria, designated as DRYC-M-16T and WMC-M-20, were isolated from sediment samples of two saline lakes in the Tibet of China. Both of the strains were catalase- and oxidase-positive. Optimal growth of strain DRYC-M-16T occurred at 20–25 °C, pH 7.0–7.5 and with 1.5 % (w/v) NaCl concentration. The analysis of 16S rRNA gene sequences indicated that strains DRYC-M-16T and WMC-M-20 belonged to the genus Tabrizicola , and showed the highest similarities to Tabrizicola aquatica KCTC 23724T (96.9 %) and Tabrizicola fusiformis KCTC 62105T (96.7 %). The DNA G+C contents of strains DRYC-M-16T and WMC-M-20 were 63.0 mol% and 62.9 mol%, respectively. The main polar lipids contained phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and several unidentified aminophospholipid (APL), aminolipid (AL), phospholipids (PL) and lipids (L). The predominant respiratory quinone was ubiquinone Q-10. The major cellular fatty acids of the two strains were iso-C18 : 0 and summed feature 8 (comprising C18 : 1 ω7c/C18 : 1 ω6c). Comprehensive analysis of the genotypic, physiological, biochemical and phenotypic characteristics indicated that the two strains should be classified as a novel species of the genus Tabrizicola , proposed as Tabrizicola sediminissp. nov., with the type strain DRYC-M-16T (=CGMCC 1.13881T=KCTC 72105 T).
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- Eukaryotic Micro-Organisms
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Cutaneotrichosporon suis sp. nov., a lipolytic yeast species from food and food-related environment
More LessTwo conspecific yeast strains, which based on DNA sequence comparisons represented an undescribed species in the order Trichosporonales were isolated during two independent studies in Hungary and France. One of them (NCAIM Y.02224) was recovered from minced pork in Hungary while the other one (UBOCC-A-218003) was isolated from the air of a dairy plant in France. The two strains shared identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene and in the internal transcribed spacer (ITS) region. Analysis of the concatenated DNA sequences for the ITS region and D1/D2 domain of the LSU rRNA gene indicated that the novel species belongs to the recently erected genus Cutaneotrichosporon. According to sequence comparisons and phylogenetic analysis, the novel species is most closely related to Cutaneotrichosporon curvatum (formerly Cryptococcus curvatus), which is often associated with humans and warm-blooded animals. The physiological characteristics of this novel species are also very similar to that of Cutaneotrichosporon curvatum. The only clear-cut difference is that, unlike C. curvatum, the novel species does not utilize imidazole as a nitrogen-source. The species name Cutaneotrichosporon suis sp. nov. is proposed to accommodate the above-noted two strains.
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- Evolution, Phylogeny and Biodiversity
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Comments on minutes of the Subcommittee on the Taxonomy of Chlamydiae and the Subcommittee on the Taxonomy of Rhizobia and Agrobacteria
More LessTwo recently published minutes of sub-committees of the International Committee on the Systematics of Prokaryotes contain statements that are potentially misleading with regards the workings of the International Code of Nomenclature of Prokaryotes. These issues need clarification.
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- ICSP Matters
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Rule 29 and combined generic and specific descriptions
More LessRule 29 of the International Code of Nomenclature of Prokaryotes caters for the situation where a new genus containing a single species may have a combined description. However, Rule 29 does not clearly state how this is to be implemented with regard to Rules 16 and 27.
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Clarifying the definition and role of effective publication in the International Code of Nomenclature of Prokaryotes with proposals to make changes
More LessThe term effective publication and the adjectival form effectively published occur at numerous points in the International Code of Nomenclature of Prokaryotes. As defined in Rule 25a the term refers to a form of publication rather than to names or descriptions. Although names are also defined as being effectively published, which is also defined as a status under the International Code of Nomenclature of Prokaryotes, such names are not automatically validly published and only validly published names can have a status under the Code. If one clearly separates the act of publication of scientific works from other elements of the Code then it is possible to clarify the workings of the Code whereby only names included in scientific works that are published in accordance with Rule 25a may have a status under the Code once they are validly published. Similarly names would then be validly published or not validly published, with the latter, irrespective of where they are found, having no status under the International Code of Nomenclature of Prokaryotes.
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The name Bradyrhizobiaceae Garrity et al. 2006 contains Nitrobacter Winogradsky 1892 (Approved Lists 1980), the nomenclatural type of the family Nitrobacteraceae Buchanan 1917 (Approved Lists 1980), is illegitimate and proposals to alter the wording of Rule 54 of the International Code of Nomenclature of Prokaryotes to clarify the fact that the family name Bradyrhizobiaceae Garrity et al. 2006 is replaced by the family name Nitrobacteraceae Buchanan 1917 (Approved Lists 1980) the only correct name
More LessThe new name at the rank of family Bradyrhizobiaceae Garrity et al. 2006 was created to include the genera Afipia Brenner et al. 1992, Agromonas Ohta and Hattori 1985, Blastobacter Zavarzin 1961 (Approved Lists 1980), Bosea Das et al. 1996, Bradyrhizobium Jordan 1982 (the nomenclatural type), Nitrobacter Winogradsky 1892 (Approved Lists 1980), Oligotropha Meyer et al. 1994, Rhodoblastus Imhoff 2001 and Rhodopseudomonas Czurda and Maresch 1937 (Approved Lists 1980). However, Nitrobacter Winogradsky 1892 (Approved Lists 1980) is the nomenclatural type of Nitrobacteraceae Buchanan 1917 (Approved Lists 1980) a name at the rank of family that was validly published prior to the valid publication of Bradyrhizobiaceae Garrity et al. 2006 and has priority. In addition Rule 51b (1) of the International Code of Nomenclature of Prokaryotes rules that under these circumstances Bradyrhizobiaceae Garrity et al. 2006 is an illegitimate name. Illegitimate names may not be used (Rule 51a) and illegitimate names are also not taken into consideration when determining priority (Rule 23a). Nitrobacteraceae Buchanan 1917 (Approved Lists 1980) is the only correct name (Rule 23a). Despite these facts the name Bradyrhizobiaceae Garrity et al. 2006 continues to be used, perhaps because the fact that it is an illegitimate name and the consequences of that status are not fully understood. A revision of Rule 54 would also appear to be appropriate in order to further emphasise the fact that the family name Bradyrhizobiaceae Garrity et al. 2006 must be replaced by the family name Nitrobacteraceae Buchanan 1917 (Approved Lists 1980), which is the oldest legitimate name and is the only correct name that may be used for the taxon that includes Bradyrhizobium Jordan 1982 and Nitrobacter Winogradsky 1892 (Approved Lists 1980).
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Arachnia propionica (Buchanan and Pine 1962) Pine and Georg 1969 (Approved Lists 1980), Propionibacterium propionicum corrig. (Buchanan and Pine 1962) Charfreitag et al. 1988 and Pseudopropionibacterium propionicum (Buchanan and Pine 1962) Scholz and Kilian 2016 and the nomenclatural consequences of changes in the taxonomy of the genus Propionibacterium
More LessIn a recent publication dealing with the classification of species assigned to the genus Propionibacterium , evidence was presented supporting that it would be appropriate to sub-divide the genus into four genera, Propionibacterium Orla-Jensen 1909 (Approved Lists 1980) emend. Scholz and Kilian 2016, Acidipropionibacterium Scholz and Kilian 2016, Cutibacterium Scholz and Kilian 2016 and Pseudopropionibacterium Scholz and Kilian 2016. Of these genera, Pseudopropionibacterium Scholz and Kilian 2016 was proposed to contain a single species Pseudopropionibacterium propionicum (Buchanan and Pine 1962) Scholz and Kilian 2016 that is also the nomenclatural type. The nomenclatural type of Pseudopropionibacterium propionicum (Buchanan and Pine 1962) Scholz and Kilian 2016 is also the nomenclatural type of Propionibacterium propionicum corrig. (Buchanan and Pine 1962) Charfreitag et al. 1988 and Arachnia propionica (Buchanan and Pine 1962) [Pine and Georg 1969 (Approved Lists 1980)] and are consequently homotypic synonyms. Arachnia propionica (Buchanan and Pine 1962) Pine and Georg 1969 (Approved Lists 1980) was the nomenclatural type and only species placed within the genus Arachnia Pine and Georg 1969 (Approved Lists 1980). In the light of this fact, the consequences for the names Arachnia propionica (Buchanan and Pine 1962) Pine and Georg 1969 (Approved Lists 1980), Propionibacterium propionicum corrig. (Buchanan and Pine 1962) Charfreitag et al. 1988 and Pseudopropionibacterium propionicum (Buchanan and Pine 1962) Scholz and Kilian 2016 are discussed together with the correct name for the recently validly published name Pseudopropionibacterium rubrum Saito et al. 2018.
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The status of names whose nomenclatural types are based on strains deposited solely for patent purposes
More LessThe International Code of Nomenclature of Prokaryotes specifically forbids the use of strains deposited solely for patent purposes from serving as nomenclatural types. Despite this ruling there are a number of names at the rank of species where strains deposited solely for patent purposes have been designated as the nomenclatural type. In some cases there is only a single deposit where the strain is deposited solely for patent purposes or there are two or more deposits in culture collections, one (or more) of which is a strain deposited solely for patent purposes. In such instances the requirements of Rule 30 may not be fulfilled and the valid publication of the corresponding names called into question because nomenclatural types have not been deposited in at least two publicly accessible culture collections in different countries.
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The role of incorrect citation of the International Code of Nomenclature of Prokaryotes and subsequent misinterpretation in causing unnecessary nomenclatural confusion
More LessThe list that notifies names published in volume 68, part 1 of the International Journal of Systematic and Evolutionary Microbiology provides the information that a number of names of species in the genus Clavibacter that had previously been treated as names at the rank of subspecies were illegitimate because they contravene Rule 34a and Rule 50a of the International Code of Nomenclature of Prokaryotes. Rule 34a deals with combinations at the same rank and this rule does not apply to names that involve a change in rank. Rule 34a, b and c all fall under the heading new combinations and that in the case of names at the rank of species and subspecies where a change in rank is made Rule 34c applies. Rule 50a applies to names at the rank of subspecies that are elevated to species, but it is unclear why these nomenclatural changes lead to illegitimate names. Fortunately the Code is explicit in stating the role of the Notification Lists is limited to allowing orthographic corrections to be made. It is necessary to publish an interpretation of the status of these names that is consistent with the current wording of the Code.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)