- Volume 67, Issue 7, 2017
Volume 67, Issue 7, 2017
- Validation List no. 176
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- Notification List
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- List of Changes in Taxonomic Opinion no. 26
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- New Taxa
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- Actinobacteria
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Arcanobacterium wilhelmae sp. nov., isolated from the genital tract of a rhinoceros (Rhinoceros unicornis)
A taxonomic study using a polyphasic approach was performed on an unidentified Arcanobacterium -like Gram-stain-positive bacterium isolated from the genital tract of a rhinoceros. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strains of Arcanobacterium canis (98.8 % 16S rRNA gene sequence similarity), Arcanobacterium phocisimile (97.8 %), Arcanobacterium phocae (97.7 %), Arcanobacterium haemolyticum (97.4 %), Arcanobacterium hippocoleae (96.6 %), Arcanobacterium pinnipediorum (96.4 %) and Arcarnobacterium pluranimalium (95.4 %). DNA–DNA hybridization values between strain 647T and Arcanobacterium canis DSM 25104T were very low, 13.4 % (reciprocal 15.9 %). The genomic DNA G+C content of strain 647T was 58.7 mol%. The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium . The polar lipid profile consisted of the major components diphosphatidylglycerol, phosphatidylcholine and an unidentified phosphoglycolipid. The results of physiological and biochemical testing clearly distinguished the unknown bacterium from other species of the genus Arcanobacterium . Based on these tests, it is proposed that the unknown bacterium should be classified as a representative of a novel species of the genus Arcanobacterium named Arcanobacterium wilhelmae sp. nov. The type strain is 647T (=DSM 102162T=LMG 29418T).
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Leucobacter corticis sp. nov., isolated from symptomatic bark of Populus × euramericana canker
More LessA Gram-stain-positive, aerobic, non-motile, rod-shaped bacterial strain, designated 2C-7T, was isolated from symptomatic bark of a Populus × euramericana canker. Growth occurred between 10 and 37 °C and between pH 6 and 10, with optimal growth at 30 °C and pH 7.0–8.0. Growth was present under 0–8 % (w/v) salinity conditions (optimum 1–2 %). Growth occurred in the presence of 10 mM chromium (Cr6+). The major fatty acids (≥10 %) of the novel strain were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid, glycolipid and two unknown lipids. The major respiratory quinone was menaquinone MK-11. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid and glycine. Strain 2C-7T was most similar to Leucobacter celer subsp . celer NAL101T (97.2 % 16S rRNA gene sequence similarity), ‘ Leucobacter kyeonggiensis ’ F3-P9T (97.1 %) and Leucobacter chromiireducens L-1T (97.1 %). In the phylogenetic tree, the isolate formed a single distinct branch separate from those of L. celer subsp . celer NAL101T, ‘ L. kyeonggiensis’ F3-P9T and Leucobacter chironomi DSM 19883T. The DNA–DNA hybridization values between the novel strain and the reference strains were lower than the accepted bacterial threshold level of 70 % for species delineation. The DNA G+C content of strain 2C-7T was 70.0 mol%. Based on the data, strain 2C-7T represents a novel species in the genus Leucobacter , for which the name Leucobacter corticis sp. nov. is proposed. The type strain is 2C-7T (=CFCC 11901T=KCTC 39643T).
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Mobilicoccus caccae sp. nov., isolated from the faeces of the primate Rhinopithecus roxellanae
More LessA novel actinobacterium, designated YIM 101593T, was isolated from the faeces of a primate (Rhinopithecus roxellanae) living in Yunnan Wild Animal Park in Yunnan province, south-west China. The isolate was Gram-stain-positive, facultatively anaerobic, coccus-shaped, oxidase-negative and motile. The cell wall contained meso-diaminopimelic acid as its diagnostic diamino acid, and mannose, ribose, glucose, galactose and arabinose were detected as the main whole-cell sugars. The predominant menaquinone was MK-8(H2). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids, three unidentified phospholipids and two unidentified lipids. The major fatty acids were C17 : 1ω8c, C15 : 0 and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I). The DNA G+C content was 69.8 mol%. The 16S rRNA gene sequence similarity between strain YIM 101593T and Mobilicoccus pelagius was 97.9 %, and the two strains formed a distinct lineage stably on the basis of phylogenetic analysis. In addition, DNA–DNA relatedness between the two strains was 49.0±5.1 %. On the basis of chemotaxonomical and physiological characteristics and the phylogenetic analysis, strain YIM 101593T should be considered to represent a novel species of the genus Mobilicoccus , for which we propose the name Mobilicoccus caccae sp. nov., with the type strain YIM 101593T (=DSM 27611T=CCTCC AB 2013229T).
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Nocardioides litoris sp. nov., isolated from the Taean seashore
A novel Gram-stain-positive, irregularly rod-shaped actinomycete, designated strain 002-2T, was isolated from sand beach sediment collected from the Taean seashore, Republic of Korea. Cells were aerobic, oxidase-negative and catalase-positive. Colonies of cells were bright yellow, circular, smooth and convex. The diagnostic diamino acid in the cell wall was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid and two unknown amino phospholipids. The major fatty acids were iso-C16 : 0 and C17 : 1ω8c. The DNA G+C content was 68.8 mol%. 16S rRNA gene sequence analysis revealed that strain 002-2T belongs to the family Nocardioidaceae and formed a cluster with Nocardioides rubroscoriae Sco-A25T (98.1 % sequence similarity) and Nocardioides plantarum NCIMB 12834T (97.6 %). On the basis of the phenotypic and phylogenetic data, strain 002-2T (=KCTC 39838T=DSM 103718T) is considered to represent a novel species of the genus Nocardioides , for which the name Nocardioides litoris sp. nov. is proposed.
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Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa)
Fresh samples of intestinal contents of three wild pigs originating from the Central Bohemia region were examined for the presence of bifidobacterial strains. During the study, we isolated many fructose-6-phosphate phosphoketolase-positive, strictly anaerobic, irregular rod-shaped bacterial isolates. Three of them were preliminarily identified as representing a novel species of the genus Bifidobacterium because their 16S rRNA gene sequence similarity with the closest relatives of thermophilic bifidobacteria ( Bifidobacterium boum DSM 20432T, Bifidobacterium thermophilum DSM 20210T, Bifidobacterium thermacidophilum subsp. porcinum LMG 21689T, Bifidobacterium thermacidophilum subsp. thermacidophilum DSM 15837T) was in the range of 97.9 – 98.4 %. All three bacterial isolates had identical 16S rRNA, dnaJ1, fusA, gyrB and rplB gene sequences. Isolate RP115T was chosen as a representative of the bacterial group and DNA G+C content (mol%) determination, biochemical tests and analyses of physiological and morphological characteristics, habitat and chemotaxonomic traits (peptidoglycan structure, cellular fatty acids and polar lipids profile) were performed. The DNA–DNA hybridization analyses of RP115T and species representing the group of thermophilic bifidobacteria revealed values in the range from 33 to 53 %. This fact, together with relatively low sequence similarities of particular phylogenetic markers among examined bacterial strains and the phenotyping and chemotaxonomy results obtained, indicated that the evaluated bacterial isolate should be classified as representing a separate taxon within the specific group of thermophilic bifidobacteria. The name Bifidobacterium apri (of boar) sp. nov. has been proposed for the representative strain RP115T (=CCM 8605T=DSM 100238T=LMG 28779T).
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Lentzea cavernae sp. nov., an actinobacterium isolated from a karst cave sample, and emended description of the genus Lentzea
A novel actinobacterial strain, designated SYSU K10001T, was isolated from a limestone sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive. On the basis of 16S rRNA gene sequence analysis, strain SYSU K10001T was most closely related to the type strains of the genus Lentzea , Lentzea albida NBRC 16102T (98.8 % similarity) and Lentzea waywayandensis NRRL B-16159T (98.6 %), and is therefore considered to represent a member of the genus Lentzea . DNA–DNA hybridization values between strain SYSU K10001T and related type strains of the genus Lentzea were less than 70 %. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were arabinose, fructose, mannose and xylose. The major isoprenoid quinone was MK-9(H4), while the major fatty acids (>10 %) were iso-C16 : 0 and C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10001T was 69.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10001T represents a novel species of the genus Lentzea , for which the name Lentzea cavernae sp. nov. is proposed. The type strain is SYSU K10001T (=KCTC 39804T=CGMCC 4.7367T=NBRC 112394T).
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Puzihella rosea gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from freshwater
More LessTwo Gram-stain-positive, aerobic, pink, curved, rod-shaped, non-motile bacterial strains, designated MI-28T and SKY-11, were isolated from freshwater samples taken from a river and fish pond, respectively. Based on characterization using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic profiles. They demonstrated 99.9 % 16S rRNA gene sequence similarity and a 93–95 % DNA-DNA relatedness value, suggesting that they represent a single genomic species. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strains MI-28T and SKY-11 form a distinct lineage with respect to closely related genera within the family Microbacteriaceae of the class Actinobacteria , which is most closely related to Rhodoluna and Pontimonas, and levels of 16S rRNA gene sequence similarity with the type species of related genera were less than 95 %. Cell-wall analysis showed that the peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized glycolipid and an uncharacterized aminophospholipid. The major polyamine was putrescine. The major isoprenoid quinone was MK-10. The G+C content of DNA was between 62.6 and 62.9 mol%. On the basis of the genotypic and phenotypic data, strains MI-28T and SKY-11 represent a novel genus and species of the family Microbacteriaceae , for which the name Puzihella rosea gen. nov., sp. nov. is proposed. The type strain of the type species is MI-28T (=BCRC 80688T=LMG 27848T=KCTC 29239T).
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Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica)
More LessBacteria with potential probiotic applications are not yet sufficiently explored, even for animals with economic importance. Therefore, we decided to isolate and identify representatives of the family Bifidobacteriaceae , which inhabit the crop of laying hens. During the study, a fructose-6-phosphate phosphoketolase-positive strain, RP51T, with a regular/slightly irregular and sometimes an S-shaped slightly curved rod-like shape, was isolated from the crop of a 13 -month-old Hisex Brown hybrid laying hen. The best growth of the Gram-stain-positive bacterium, which was isolated using Bifidobacterium -selective mTPY agar, was found out to be under strictly anaerobic conditions, however an ability to grow under microaerophilic and aerobic conditions was also observed. Sequencing of the almost complete 16S rRNA gene (1444 bp) showed Alloscardovia omnicolens CCUG 31649T and Bombiscardovia coagulans BLAPIII/AGVT to be the most closely related species with similarities of 93.4 and 93.1 %, respectively. Lower sequence similarities were determined with other scardovial genera and other representatives of the genus Bifidobacterium . Taxonomic relationships with A. omnicolens and other members of the family Bifidobacteriaceae were also demonstrated, based on the sequences of dnaK, fusA, hsp60 and rplB gene fragments. Low sequence similarities of phylogenetic markers to related scardovial genera and bifidobacteria along with unique features of the bacterial strain investigated within the family Bifidobacteriaceae ( including the lowest DNA G+C value (44.3 mol%), a unique spectrum of cellular fatty acids and polar lipids, cellular morphology, the wide temperature range for growth (15–49 °C) and habitat) clearly indicate that strain RP51T is a representative of a novel genus within the family Bifidobacteriaceae for which the name Galliscardovia ingluviei gen. nov., sp. nov. (RP51T=DSM 100235T=LMG 28778T=CCM 8606T) is proposed.
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- Archaea
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Natrinema soli sp. nov., a novel halophilic archaeon isolated from a hypersaline wetland
An extremely halophilic archaeon, designated strain 5-3T, was isolated from a soil sample of Meighan wetland in Iran. Strain 5-3T was strictly aerobic, catalase-positive and oxidase-negative. Cells were Gram-stain-negative, non-motile and ovoid. Colonies of strain 5-3T were cream-coloured. The isolate showed optimum growth at 4.0 M NaCl, 40 °C and pH 7.0. The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two unknown phospholipids and three glycolipids (including one that was chromatographically identical to S2-DGD). The major respiratory quinone was menaquinone MK-8. The G+C content of the genomic DNA was 61.5 mol%. The closest relative was Natrinema salaciae JCM 17869T with 97.3 % similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB′ gene sequences indicated that strain 5-3T is a member of the genus Natrinema in the family Natrialbaceae and forms a distinct cluster. On the basis of phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, a novel species of the family Natrialbaceae , Natrinema soli sp. nov., is proposed. The type strain is 5-3T (=IBRC-M 11063T=LMG 29247T).
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Salinarchaeum chitinilyticum sp. nov., a chitin-degrading haloarchaeon isolated from commercial salt
Two chitin-degrading halophilic archaeal strains, MC-74T and MC-23, were isolated from commercial salt samples. Cells were motile, rod-shaped and stained Gram-negative. Colonies were vermillion-pigmented. Strains MC-74T and MC-23 were able to grow with 1.5–5.1 M NaCl (optimum, 2.6–3.1 M) at pH 6.0–10.0 (optimum, pH 7.0) and at 20–50 °C (optimum, 40 °C). The orthologous 16S rRNA gene sequence similarity between the two strains was 99.8 %, and the closest phylogenetic relative was Salinarchaeum laminariae JCM 17267T with 99.3–99.5 % similarity. The level of DNA–DNA relatedness between the two strains was 93 and 94 % (reciprocally), and those between the two strains and Salinarchaeum laminariae JCM 17267T were 35–36 % and 38–39 % (reciprocally). The polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Glycolipids were not detected. Based on the phenotypic and phylogenetic analyses, the strains represent a novel species of the genus Salinarchaeum , for which the name Salinarchaeum chitinilyticum sp. nov. is proposed. The type strain is MC-74T (=JCM 19597T=KCTC 4262T), isolated from solar salt produced in France. Strain MC-23, isolated from a commercial solar salt sample produced in China, is an additional strain of the species.
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- Bacteroidetes
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Parapedobacter deserti sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems
More LessStrain N5SSJ16T, a Gram-negative-staining, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from Haloxylon ammodendron stems. The strain grew in the presence of 0–4 % (w/v) NaCl (optimum growth in the absence of NaCl), at pH 7–9 (optimum: pH 8) and at 12–50 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N5SSJ16T was related phylogenetically to Parapedobacter composti 4M40T (96.5 %) and Parapedobacter luteus 4M29T (95.9 %). The cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c) and iso-C17 : 0 3-OH. MK-7 was the respiratory quinone. The main polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and two unknown lipids. The G+C content of the DNA was 45.8 mol%. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain N5SSJ16T represents a novel species of the genus Parapedobacter , for which the name Parapedobacter deserti sp. nov. is proposed. The type strain is N5SSJ16T (=ACCC 19928T=KCTC 52416T).
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Flavobacterium keumense sp. nov., isolated from freshwater
More LessA yellow-pigmented, oxidase-positive, catalase-negative, Gram-stain-negative, rod-shaped, aerobic and non-motile bacterial strain designated K3R-10T was isolated from a freshwater source. The strain grew over a temperature range from 4 to 35 °C (optimum, 30 °C), pH range pH 6–8 (optimum, pH 7) and in the presence of 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain K3R-10T belonged to the genus Flavobacterium and shared close similarities with Flavobacterium succinicans LMG 10402T (97.0 %), Flavobacterium chungangense LMG 26729T (96.4 %), Flavobacterium branchiophilum IFO 15030T (96.4 %) and Flavobacterium piscis 412R-09T (96.3 %), but formed a distinct phylogenetic line of its own in the phylogenetic trees. The polar lipids consisted of phosphatidylethanolamine, an unidentified aminolipid and three unidentified phospholipids. The DNA G+C content was 35.4 mol%, MK-6 was the major isoprenoid quinone, and homospermidine was the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 3-OH, iso-C15 : 0, a summed feature comprising C16 : 1ω7c and/or C16 : 1ω6c and iso-C15 : 1 G. The absence of aminophospholipid, acid production from carbohydrates, DNA G+C content and colony morphology differentiated strain K3R-10T from related species of the genus Flavobacterium . Thus, on the basis of phenotypic, chemotaxonomic and phylogenetic features, strain K3R-10T evidently represents a novel species in the genus Flavobacterium , for which the name Flavobacterium keumense sp. nov. is proposed. The type strain is K3R-10T (=JCM 31220T=KCTC 52563T).
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Hymenobacter tenuis sp. nov., isolated from wastewater of an acidic water neutralization facility
More LessA non-motile, red–pink-coloured, rod-shaped bacterium, designated strain POB6T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The strain contained menaquinone MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine. The DNA G+C content was 61 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain POB6T forms a distinct evolutionary lineage within the radiation enclosing the members of the genus Hymenobacter , sharing the highest similarity with Hymenobacter rigui WPCP131T (97.5 %) followed by Hymenobacter xinjiangensis X2-1gT (97.2 %), Hymenobacter perfusus A1-12T (97.2 %) and Hymenobacter gelipurpurascens Txg-1T (97.1 %). A number of phenotypic characteristics distinguished strain POB6T from related members of the genus Hymenobacter . On the basis of the evidence presented in this study, a novel species, Hymenobacter tenuis sp. nov., is proposed, with POB6T (=KCTC 52271T=JCM 31659T) as the type strain.
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Algibacter aquaticus sp. nov., a slightly alkaliphilic marine Flavobacterium isolated from coastal surface water
A rod-shaped, pale yellow-pigmented, aerobic, Gram-staining-negative strain with gliding motility, designated as strain SK-16T, was isolated from the coastal surface water of a semi-enclosed coastal inlet in Misaki, Japan. Analysis of 16S rRNA gene sequences revealed that SK-16T represented a member of the family Flavobacteriaceae and was closely related to the genus Algibacter , with sequence similarities ranging from 95.9 to 94.3 % to the type strains of species of the genus Algibacter . The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 G and iso-C15 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, an aminophospholipid and an unidentified phospholipid. The DNA G+C content of SK-16T was 32.3 mol% and MK-6 was the only predominant isoprenoid quinone. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic studies, it was suggested that SK-16T represents a novel species within the genus Algibacter , with the newly proposed name Algibacter aquaticus. The type strain is SK-16T (=NBRC 110220T=KCTC 32974T).
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Olleya algicola sp. nov., a marine bacterium isolated from the green alga Ulva fenestrata
More LessA strictly aerobic, Gram-stain-negative, rod-shaped, motile by gliding and yellow-pigmented bacterium, designated strain 3Alg 18T, was isolated from the Pacific green alga Ulva fenestrata. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was affiliated to the family Flavobacteriaceae of the phylum Bacteroidetes , being most closely related to the type strains of recognized species of the genus Olleya , with 16S rRNA gene sequence similarity of 97.9–99.3 %. Strain 3Alg 18T grew in the presence of 0.5–5 % (w/v) NaCl and at 4–37 °C, and hydrolysed aesculin, casein, gelatin, starch and Tweens 20, 40 and 80. The prevalent fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C15 : 0 3-OH, iso-C16:0 2-OH, iso-C17 : 0 3-OH, summed feature 3, iso-C16 : 0 3-OH, anteiso-C15 : 0 and C15 : 0. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. The major respiratory quinone was menaquinone MK-6. The genomic DNA G+C content was 34.6 mol%. On the basis of 16S rRNA gene sequence data, and chemotaxonomic and phenotypic characteristics, strain 3Alg 18T represents a novel species of the genus Olleya , for which the name Olleya algicola sp. nov. is proposed. The type strain is 3Alg 18T (=KCTC 22024T=KMM 6133T).
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Flavobacterium olei sp. nov., a novel psychrotolerant bacterium isolated from oil-contaminated soil
More LessDuring a study of psychrophilic hydrocarbon-degrading bacteria, two yellow, Gram-staining-negative, non-motile, and rod shaped bacteria, designated R-10-9T and K-4-2 were isolated from oil-contaminated soil from Ulaanbaatar, Mongolia. Both strains were able to grow at 0–32 °C, pH 5.0–9.5, and 0–1 % (w/v) NaCl concentration. These strains were taxonomically characterized by a polyphasic approach. On the basis of the results of 16S rRNA gene sequence analysis, R-10-9T and K-4-2 belong to the genus Flavobacterium and are closely related to Flavobacterium oncorhynchi 631-08T (97.80 and 98.09 % sequence similarity, respectively). The pairwise sequence similarity between R-10-9T and K-4-2 was observed to be 99.72 %. In both strains, the predominant respiratory quinone was menaquinone-6; the major polar lipid was phosphatidylethanolamine; and the major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 0 3-OH, antesio-C15 : 0, C16 : 0, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH. The genomic DNA G+C contents of R-10-9T and K-4-2 were 35.9 and 35.4 mol%, respectively. The DNA–DNA relatedness between R-10-9T and K-4-2 was higher than 70 % but relatedness values with closely related reference strains were less than 35 %. The morphological, physiological, chemotaxonomic, and phylogenetic analyses clearly distinguished R-10-9T from its closest phylogenetic neighbours. Thus, R-10-9T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium olei sp. nov. is proposed. The type strain is R-10-9T (=KEMB 9005-447T=KACC 18997T=JCM 31673T), and strain K-4-2 as an additional strain.
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Flavitalea antarctica sp. nov., isolated from Fildes Peninsula, Antarctica
A bright-yellow, Gram-stain-negative, rod-shaped, gliding and aerobic bacterium, designated strain AQ6-291T, was isolated from the Fildes Peninsula, Antarctica, and its taxonomic position was investigated by genotypic, phenotypic and chemotaxonomic analyses. Growth occurred at 4–28 °C (optimum 20 °C) and at pH 5.0–8.0 (optimum pH 7.0). Strain AQ6-291T contained iso-C15 : 1 G, iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) as the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown phospholipids, five unknown aminolipids and two unknown polar lipids. MK-7 was the major respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain AQ6-291T belonged to the genus Flavitalea . The DNA G+C content was 48.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain AQ6-291T is considered to represent a novel species of the genus Flavitalea , for which the name Flavitalea antarctica sp. nov. is proposed. The type strain is AQ6-291T (=CCTCC AB 2016109T=KCTC 52491T).
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Bizionia sediminis sp. nov., isolated from coastal sediment
More LessA Gram-stain-negative, aerobic, non-gliding, rod-shaped and orange-coloured bacterium, designated strain P131T, was isolated from marine sediment of the coast of Weihai, China, and subjected to a polyphasic study. Strain P131T was found to grow optimally at 28–30 °C, at pH 7.0–7.5 and in the presence of 2–3 % (w/v) NaCl. In a phylogenetic analysis based on 16S rRNA gene sequences, strain P131T was found to belong to the genus Bizionia and exhibited 94.6–97.0 % 16S rRNA gene sequence similarity with recognized Bizionia species. The dominant cellular fatty acids of strain P131T were identified as iso-C15 : 0, iso-C15 : 0 G, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The predominant polar lipids were phosphatidylethanolamine, phospholipid, two aminolipids and two unidentified lipids. The predominant respiratory quinone was menaquinone MK-6 and the DNA G+C content was 36.7 mol%. On the basis of the phylogenetic and phenotypic evidence presented, strain P131T represents a novel species of the genus Bizionia , for which the name Bizionia sediminis sp. nov. is proposed. The type strain is P131T (=KCTC 42587T=MCCC 1H00124T).
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Parafilimonas rhizosphaerae sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.)
A bacterial strain, designated T16E-198T, was isolated from the rhizosphere of tomato plant collected from a farm on Buyeo-gun, Chungcheongnam-do, South Korea. The strain was aerobic, Gram-stain-negative, rod-shaped, non-flagellated and yellow-pigmented. Strain T16E-198T was mesophilic, catalase- and oxidase-positive and with flexirubin-type pigments. A phylogenetic tree based on 16S rRNA gene sequences showed that strain T16E-198T formed a lineage with Parafilimonas terrae 5GHs7-2T, sharing highest sequence similarity of 98.4 % with it and less than 93 % with all the other validly published species. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The predominant menaquinone was MK-7. The polar lipids were phosphatidylethanolamine, one unknown aminophospholipid, five unknown aminolipids and five unknown lipids. The DNA G+C content was 41.2 mol%. On the basis of the phenotypic, phylogenetic and chemotaxonomic data presented, strain T16E-198T is considered to represent a novel species of the genus Parafilimonas , for which the name Parafilimonas rhizosphaerae sp. nov. is proposed; the type strain is T16E-198T (=KACC 18786T=JCM 31601T).
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Sphingobacterium soli sp. nov., isolated from soil
A Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated YIM X0211T, was isolated from a soil sample of Shiling County, Yunnan Province, south-west China. The new isolate was characterized taxonomically by using a polyphasic approach. The strain grew optimally at 30 °C, at pH 7.0 and with 0–3 % (w/v) NaCl. It was positive for catalase and oxidase but negative for H2S production. Comparative 16S rRNA gene sequence analysis showed that strain YIM X0211T fell within the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii DSM 11724T (97.93 % similarity). The G+C content of the genomic DNA was 41.2 mol%. The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0 2-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The polar lipids consisted of phosphatidylethanolamine, sphingolipid, and several unknown phospholipids or lipids. The DNA–DNA hybridization value between strain YIM X0211T and S. mizutaii DSM 11724T was 42.3±0.4 %, which is below the 70 % limit for species delineation. These chemotaxonomic data supported the affiliation of strain YIM X0211T to the genus Sphingobacterium . Based on the recorded phenotypic and genotypic characteristics, it is determined that the isolate represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium soli sp. nov. is proposed. The type strain is YIM X0211T (=KCTC 42696T=CGMCC 1.15966T).
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Flaviramulus aestuariivivens sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and ovoid or rod-shaped bacterium, designated OITF-51T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-51T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain OITF-51T forms a cluster with the type strains of three species of the genus Flaviramulus . Strain OITF-51T exhibited 16S rRNA gene sequence similarity values of 97.0, 95.8 and 95.8 % to the type strains of Flaviramulus ichthyoenteri , Flaviramulus basaltis and Flaviramulus aquimarinus , respectively, and of less than 96.5 % to the type strains of other recognized species. Strain OITF-51T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain OITF-51T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain OITF-51T was 33.4 mol%, and its mean DNA–DNA relatedness value with the type strain of F. ichthyoenteri was 13 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OITF-51T is separated from recognized species of the genus Flaviramulus . On the basis of the data presented, strain OITF-51T is considered to represent a novel species of the genus Flaviramulus , for which the name Flaviramulus aestuariivivens sp. nov. is proposed. The type strain is OITF-51T (=KCTC 52657T=NBRC 112707T).
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Algoriphagus marinus sp. nov., isolated from marine sediment and emended description of the genus Algoriphagus
More LessA Gram-stain-negative, facultatively anaerobic coccobacilli approximately 0.4–0.5×0.5–1.1 µm, non-motile, orange-pigmented bacterial strain, designated am2T, was isolated from the coastal area of Weihai, PR China (121° 57′ E, 37° 29′ N). The temperature, pH and NaCl ranges for growth were 4–40 °C, pH 6.5–8.5 and 0.0–6.0 % (w/v) NaCl. The results of phylogenetic analyses based on 16S rRNA gene sequences revealed that am2T was phylogenetically related to members of the genus Algoriphagus and was closely related to Algoriphagus boritolerans , Algoriphagus namhaensis and Algoriphagus antarcticus with 96.4, 96.2 and 95.8 % sequence similarities, respectively. The quinone system contained menaquinone MK-7 as the predominant component. The dominant fatty acids were iso-C17 : 1ω9c,iso-C16 : 1H and iso-C15 : 0. The major polar lipids consisted of one phospholipid, phosphatidylethanolamine and six unknown lipids. The DNA G+C content was 40.6 mol%. On the basis of morphological, physiological and molecular properties as well as on phylogenetic distinctiveness, am2T should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus marinus sp. nov. is proposed. The type strain is am2T (=KCTC 52549T=MCCC 1H00178T).
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Flavobacterium soyangense sp. nov., a psychrotolerant bacterium, isolated from an oligotrophic freshwater lake
More LessA bacterial strain, designated IMCC26223T, was isolated from an oligotrophic freshwater lake, Lake Soyang, Korea. Cells of strain IMCC26223T were Gram-staining negative, strictly aerobic, non-motile and short-rod-shaped. Growth occurred at pH 6–8 (optimum, pH 7.0), at 4–25 °C (optimum, 15 °C) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain IMCC26223T was identified as a member of the genus Flavobacterium and most closely related to Flavobacterium fluvii H7T (97.6 %), Flavobacterium segetis AT1048T (97.5 %) and Flavobacterium weaverense AT1042T (97.2 %). DNA–DNA relatedness between strain IMCC26223T and F. fluvii H7T was 41.5–51.7 % in the reciprocal hybridization. Strain IMCC26223T contained MK-6 as the major respiratory quinone. The major cellular fatty acids consisted of C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), and the polar lipids were phosphatidylethanolamine, an unidentified aminolipid and two unidentified lipids. The DNA G+C content of strain IMCC26223T was 34.5 mol%. On the basis of 16S rRNA gene phylogeny and phenotypic characterization, strain IMCC26223T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium soyangense sp. nov., is proposed. The type strain is IMCC26223T (=KCTC 52245T=JCM 31384T).
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Muricauda marina sp. nov., isolated from marine snow of Yellow Sea
More LessA Gram-staining-negative, long rod-shaped, non-motile, strictly aerobic bacterial strain, designated H19-56T, was isolated from a surface marine snow sample collected from the Yellow Sea near China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that H19-56T represented a member of the genus Muricauda and showed the highest sequence similarity to Muricauda ruestringensis B1T (96.9 %). H19-56T grew optimally at pH 8.0, 32 °C and in the presence of 3 % (w/v) NaCl. The DNA G+C content was 43.6 mol%. H19-56T contained MK-6 as the predominant respiratory quinone and had iso-C15 : 0 and iso-C15 : 1G as the major cellular fatty acids. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. On the basis of the results of the polyphasic analyses, this isolate was considered to represent a novel species of the genus Muricauda , for which the name Muricauda marina sp. nov. is proposed. The type strain is H19-56T (CGMCC 1.15774T=JCM 31456T=MCCC 1K03196T=KCTC 52374T).
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- Firmicutes and Related Organisms
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Sporosarcina terrae sp. nov., isolated from orchard soil
A Gram-stain-positive, motile and rod-shaped bacterium, designated strain LZ2T, was isolated from a sample of orchard soil from Laizhou city, Shandong province, PR China. On the basis of 16S rRNA gene sequence analysis, strain LZ2T was closely related to members of the genus Sporosarcina , sharing highest levels of sequence similarity with Sporosarcina pasteurii NCIMB 8841T (98.8 %), Sporosarcina soli I80T (95.9 %). The value for the DNA-DNA relatedness between strain LZ2T and Sporosarcina pasteurii NCIMB 8841T was 39.8±1.7 %. Growth occurred at 10–44 °C (optimum, 30–35 °C), pH 5.0–11.0 (optimum pH 9.0–10.0); NaCl concentrations of up to 7.0 % (w/v) were tolerated. The dominant respiratory quinone was MK-7 and the G+C content was 39.2 mol%. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The major polar lipids of strain LZ2T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. Based on phenotypic and chemotaxonomic characteristics, and phylogenetic data strain LZ2T represents a novel species of the genus Sporosarcina , for which the name Sporosarcina terrae sp. nov. (type strain LZ2T=KACC 18822T=MCCC 1K03174T) is proposed.
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Megasphaera hexanoica sp. nov., a medium-chain carboxylic acid-producing bacterium isolated from a cow rumen
More LessStrain MHT, a strictly anaerobic, Gram-stain-negative, non-spore-forming, spherical coccus or coccoid-shaped microorganism, was isolated from a cow rumen during a screen for hexanoic acid-producing bacteria. The microorganism grew at 30–40 °C and pH 5.5–7.5 and exhibited production of various short- and medium-chain carboxylic acids (acetic acid, butyric acid, pentanoic acid, isobutyric acid, isovaleric acid, hexanoic acid, heptanoic acid and octanoic acid), as well as H2 and CO2 as biogas. Phylogenetic analysis based on 16S rRNA gene sequencing demonstrated that MHT represents a member of the genus Megasphaera , with the closest relatives being Megapsphaera indica NMBHI-10T (94.1 % 16S rRNA sequence similarity), Megasphaera elsdenii DSM 20460T (93.8 %) and Megasphaera paucivorans DSM 16981T (93.8 %). The major cellular fatty acids produced by MHT included C12 : 0, C16 : 0, C18 : 1 cis 9, and C18 : 0, and the DNA G+C content of the MHT genome is 51.8 mol%. Together, the distinctive phenotypic and phylogenetic characteristics of MHT indicate that this microorganism represents a novel species of the genus Megasphaera , for which the name Megasphaera hexanoica sp. nov. is herein proposed. The type strain of this species is MHT (=KCCM 43214T=JCM 31403T).
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Paenibacillus polysaccharolyticus sp. nov., a xylanolytic and cellulolytic bacteria isolated from leaves of Bamboo Phyllostachys aureosulcata
A novel xylanolytic and cellulolytic strain, BL9T, was isolated from leaves of the Bamboo plants maintained at the Tamil Nadu Agricultural University Campus, Coimbatore, India. On the basis of the results of 16S rRNA gene analysis, it was determined to be phylogenetically close to the type strains of Paenibacillus amylolyticus NRRL NRS-290T (98.3 %), Paenibacillus barcinonensis BP-23T (98.1 %), Paenibacillus tundrae A10bT (98.0 %) and Paenibacillus xylanexedens B22aT (97.6 %). The strain stained Gram variable and was aerobic, motile and catalase- and oxidase-positive, with rod-shaped cells. Based upon the genome sequence, the average nucleotide identity with the related species ranged from 66 % to 72 %, and the digital DNA–DNA hybridization value ranged from 13 % to 27 %. The DNA G+C content was 45.6 mol%, meso-diaminopimelic acid was identified as the predominant component of the cell wall, and MK-7 was the only menaquinone in cell membranes. The whole-cell fatty acid profile included C16 : 0, iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0. The polar lipids identified were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and diphosphtidylglycerol. On the basis of these polyphasic taxonomic traits, BL9T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus polysaccharolyticus sp. nov. is proposed. The type strain is BL9T (=NBRC 105191T=ICMP 17623T).
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Bacillus mangrovi sp. nov., isolated from a sediment sample from a mangrove forest
A facultatively anaerobic, endospore forming, alkali-tolerant, Gram-stain-positive, motile, rod-shaped bacterium, designated strain AK61T, was isolated from a sediment sample collected from Coringa mangrove forest, India. Colonies were circular, 1.5 mm in diameter, shiny, smooth, yellowish and convex with entire margins after 48 h growth at 30 °C. Growth occurred at 15–42 °C, with 0–3 % (w/v) NaCl and at pH 6–9. AK61T was positive for amylase activity and negative for oxidase, catalase, aesculinase, caseinase, cellulase, DNase, gelatinase, lipase and urease activities. The fatty acids were dominated by branched types with iso- and anteiso- saturated fatty acids with a high abundance of iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0; the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid; and MK-7 was the major menaquinone. DNA–DNA hybridization between AK61T and Bacillus indicus MTCC 4374T and between AK61T and Bacillus indicus KCTC 3880 showed relatedness of 37.99 and 33.32 % respectively. The DNA G+C content of AK61T was 44 mol%. The results of a blast sequence similarity search based on 16S rRNA gene sequences indicated that Bacillus cibi and Bacillus indicus were the nearest phylogenetic neighbours, with a pair-wise sequence similarity of 97.69 and 97.55 % respectively. The results of phylogenetic analysis indicated that AK61T was clustered with Bacillus idriensis and Bacillus indicus . On the basis of its phenotypic characteristics and phylogenetic inference, AK61T represents a novel species of the genus Bacillus , for which the name Bacillus mangrovi sp. nov. is proposed. The type strain is AK61T (=JCM 31087T=MTCC 12015T=KCTC 33872T).
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A proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences
More LessThe type strains of four subspecies of Leuconostocmesenteroides , L. mesenteroides subsp. mesenteroides , L. mesenteroides subsp. cremoris , L. mesenteroides subsp. dextranicum and L. mesenteroides subsp. suionicum , and strain DRC1506T, used as a starter culture for commercial kimchi production in Korea, were phylogenetically analyzed on the basis of their complete genome sequences. Although the type strains of the four L. mesenteroides subspecies and strain DRC1506T shared very high 16S rRNA gene sequence similarities (>99.72 %), the results of analysis of average nucleotide identity (ANI), in silico DNA–DNA hybridization (DDH) and core-genome-based relatedness indicated that they could form five different phylogenetic lineages. The type strains of L. mesenteroides subsp. mesenteroides , L. mesenteroides subsp. cremoris and L. mesenteroides subsp. dextranicum and DRC1506T shared higher ANI and in silico DDH values than the thresholds (95–96 % and 70 %, respectively) generally accepted for different species delineation, whereas the type strain of L. mesenteroides subsp. suionicum (DSM 20241T) shared lower ANI (<94.1 %) and in silico DDH values (<57.0 %) with the other four L. mesenteroides lineage strains, indicating that DSM 20241T couldn be reclassified as representing a different species. Here, we report that DRC1506T represents a novel subspecies within the species Leuconostoc mesenteroides , for which the name Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. is proposed. The type strain is DRC1506T (=KCCM 43249T=JCM 31787T). In addition, L. mesenteroides subsp. suionicum is also reclassified as Leuconostoc suionicum. sp. nov. (type strain DSM 20241T=ATCC 9135T=LMG 8159T=NCIMB 6992T).
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Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone
A novel bacterial strain, designated S5H2222T, was isolated form the screen of a cellular phone. The cells were Gram-stain-positive, rod-shaped, aerobic and motile, and endospores are formed. S5H2222T grew as pale white colonies on trypticase soy agar and the best growth was observed at 37 °C (10–55 °C) and at pH 7.0 (5.0–9.0). S5H2222T could tolerate up to 10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within the genus Lysinibacillus and it exhibited high 16S rRNA gene sequence similarity to Lysinibacillus halotolerans LAM612T (97.8 %), Lysinibacillus chungkukjangi 2RL3-2T (97.4 %) and Lysinibacillus sinduriensis BLB-1T (97.2 %). The DNA–DNA relatedness of the strain with L. halotolerans JCM 19611T, L. chungkukjangi KACC 16626T and L. sinduriensis KACC 16611T was 57, 64 and 55 % respectively. The genomic DNA G+C content was 39.8 mol%. The major fatty acids of S5H2222T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. MK-7 was the only menaquinone and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, four unidentified polar lipids were also present. The diagnostic amino acids in the cell wall peptidoglycan contained Lys–Asp (type A4α). On the basis of the results of the phenotypic and genotypic characterizations, it was concluded that S5H2222T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus telephonicus sp. nov. is proposed. The type strain is S5H2222T (=MCC 3065T=KACC 18714T=LMG 29294T).
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Paenibacillus tritici sp. nov., isolated from wheat roots
A bacterial strain designated RTAE36T was isolated from wheat roots in northern Spain. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Paenibacillus with its closest relative being Paenibacillus borealis DSM 13188T with 97.7 % sequence similarity. Cells of the isolate were facultatively anaerobic, Gram-stain-positive, motile and sporulating rods. Catalase and oxidase were positive. Gelatin, casein and starch were not hydrolysed. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected, and anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C16 : 0 were the major fatty acids. The polar lipids profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, two unidentified phospholipids, three unidentified phosphoaminolipids, one unidentified glycolipid and one unidentified lipid. m eso-Diaminopimelic acid was detected in the cell-wall peptidoglycan. Strains RTAE36T and P. borealis DSM 13188T had an mean DNA–DNA relatedness of 39 % and differed in several phenotypic and chemotaxonomic characteristics, confirming that strain RTAE36T should be considered as a representative of a novel species of the genus Paenibacillus , for which the name Paenibacillus tritici sp. nov. is proposed. The type strain is RTAE36T (=LMG 29502T=CECT 9125T).
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Clostridium tepidum sp. nov., a close relative of Clostridium sporogenes and Clostridium botulinum Group I
Obligately anaerobic, Gram-stain-positive, spore-forming bacteria indistinguishable by pulsed-field gel electrophoresis were isolated from non-dairy protein shakes in bloated bottles. One of the isolates, strain IEH 97212T, was selected for further study. The strain was closely related to Clostridium sporogenes and Clostridium botulinum Group 1 based on 16S rRNA gene sequence similarities. Phylogenetic analysis also showed that strain IEH 97212T and strain PE (=DSM 18688), a bacterium isolated from solfataric mud, had identical 16S rRNA gene sequences. Strains IEH 97 212T and DSM 18 688 were relatively more thermophilic (temperature range for growth: 30–55 °C) and less halotolerant [growth range: 0–2.5 % (w/v) NaCl] than C. sporogenes and C. botulinum . They were negative for catalase, oxidase, urease and l-pyrrolidonyl-arylamidase and did not produce indole. The strains produced acid from d-glucose, maltose and trehalose, and hydrolysed gelatin, but did not hydrolyse aesculin. The end-products of growth included acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, isovaleric acid, isocaproic acid, phenylpropionic acid, 2-piperidinone, 2-pyrrolidinone and gas(es). The predominant fatty acids were C14 : 0, C16 : 0 and C18 : 1ω9c. The genomic DNA G+C content of strains IEH 97212T and DSM 18688 was 26.9 and 26.7 mol%, respectively. According to the digital DNA–DNA hybridization data, the relatedness of these strains was 98.4 %, while they showed only 35.7–36.0 % relatedness to C. sporogenes . Based on the results of this polyphasic study, these strains represent a novel species, for which the name Clostridium tepidum sp. nov. is proposed, with the type strain IEH 97212T (=NRRL B-65463T=DSM 104389T).
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Paenibacillus konkukensis sp. nov., isolated from animal feed
More LessA Gram-stain-positive, oxidase- and catalase-positive, aerobic, rod-shaped bacterium, designated strain SK-3146T, was isolated from animal feed. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that the strain formed a distinct lineage within the genus Paenibacillus that was closely related to Paenibacillus yunnanensis JCM 30953T (98.6 %), Paenibacillus vulneris CCUG 53270T (98.0 %) and Paenibacillus chinjuensis DSM 15045T (96.9 %). Cells were non-motile, endospore-forming and formed milky colonies on NA and R2A agar media. Growth of strain SK-3146T occurred at temperatures of 18–45 °C, at pH 6.0–9.5 and between 0.5–3.0 % NaCl (w/v). The major menaquinone was MK-7, with lesser amounts of MK-6 present. The cell wall peptidoglycan of strain SK-3146T contained meso-diaminopimelic acid. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 53.8 mol% and the DNA–DNA hybridization relatedness values between strain SK-3146T and P . yunnanensis JCM 30953T and P . vulneris CCUG 53270T were 26.13±0.8 % and 38.7±0.6 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that strain SK-3146T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus konkukensis sp. nov. is proposed. The type strain is SK-3146T (=KACC 18876T=LMG 29568T).
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Sporolactobacillus shoreicorticis sp.nov., a lactic acid-producing bacterium isolated from tree bark
A Gram-stain-positive, lactic acid-producing bacterium designed strain MK21-7T, was isolated from tree bark collected from the north east of Thailand. This strain was a facultatively anaerobic spore-forming rod that was catalase-negative. It contained meso-diaminopimelic acid in the cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. Major fatty acids of MK21-7T were anteiso-C17 : 0, iso-C16 : 0, anteiso-C15 : 0 and C18 : 1ω9c. Polar lipids were phosphatidglycerol, diphosphatidylglycerol, an unknown phospholipid, three unknown glycolipids and an unknown lipid. The results of 16S rRNA gene sequence analysis indicated that it represented a member of the genus Sporolactobacillus . MK21-7T showed the highest 16S rRNA gene sequence similarity to Sporolactobacillus terrae NBRC 101527T with 98.4 % similarity and exhibited 97.6 % similarity with Sporolactobacillus kofuensis NRIC 0334T, 97.5 % with Sporolactobacillus laevolacticus NRIC 0361T, 97.3 % with Sporolactobacillus nakayamae subsp. nakayamae NRIC 0347T and 97.1 % with Sporolactobacillus nakayamae subsp. racemicus NBRC 101524T. Analysis of the phylogenetic relationship based on 16S rRNA and gyrB gene sequencing revealed that the position of MK21-7T was clearly separated from all related species of the genus Sporolactobacillus . It had low DNA–DNA relatedness (22.8–57.2 %) with S. terrae NBRC 101527T and related type strains. The DNA G+C content was 43.1 mol%. On the basis of the results of the phenotypic, genotypic and chemotaxonomic studies, MK21-7T should be classified as representing a novel species of the genus Sporolactobacillus for which the name Sporolactobacillus shoreicorticis sp. nov. is proposed. The type strain is MK21-7T (=NBRC 111517T=LMG 29111T=TISTR 2466T).
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Merdimonas faecis gen. nov., sp. nov., isolated from human faeces
More LessA strictly anaerobic Gram-stain-positive, non-motile and non-spore-forming bacterial strain, BR31T, was isolated from a faecal sample of a healthy human. Bacterial colonies were ivory-coloured on GAM agar and composed of rod-shaped cells with rounded ends approximately 1.4–2.1×0.5–0.6 µm in size. According to comparative analysis based on 16S rRNA gene sequences, strain BR31T formed a distinct phylogenetic lineage that reflects a new genus within Clostridium cluster XIVa in the family Lachnospiraceae , with highest similarity to Eubacterium contortum DSM 3982T (94.6 %). The DNA G+C content was calculated to be 47.0 mol% from whole genome sequencing. Predicted genes associated with synthesis of teichuronic acid, polyamines, polar lipids and diaminopimelic acid were detected. The peptidoglycan contained meso-diaminopimelic acid and the main polar lipid detected was phosphatidylglycerol. The major metabolic end product of glucose was acetic acid, which was in agreement with those of most members of the family. However, the profile of major cellular fatty acids (C16 : 0, C14 : 0, summed feature 4 and C13 : 0) and overall enzyme activity demonstrated phenotypic differentiation of strain BR31T from other closely related genera. Thus, based on distinct phenotypic, phylogenetic, genotypic and chemotaxonomic characteristics, strain BR31T is considered to represent a novel species of a new genus, for which the name Merdimonas faecis gen. nov., sp. nov. is proposed. The type strain of Merdimonas faecis is BR31T (=KCTC 15482T=JCM 30748T).
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- Other Bacteria
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Treponema rectale sp. nov., a spirochete isolated from the bovine rectum
A Gram-stain-negative, obligatory anaerobic spirochete, CHPAT, was isolated from the rectal tissue of a Holstein–Friesian cow. On the basis of 16S rRNA gene comparisons, CHPAT was most closely related to the human oral spirochete, Treponema parvum , with 88.8 % sequence identity. Further characterisation on the basis of recA gene sequence analysis, cell morphology, pattern of growth and physiological profiling identified marked differences with respect to other recognised species of the genus Treponema . Microscopically, the helical cells measured approximately 1–5 µm long and 0.15–0.25 µm wide, with two to five irregular spirals. Transmission electron microscopy identified four periplasmic flagella in a 2 : 4 : 2 arrangement. CHPAT grew independently of serum, demonstrated no evidence of haemolytic activity and possessed an in vitro enzyme activity profile that is unique amongst validly named species of the genus Treponema , exhibiting C4 esterase, α-galactosidase and β-galactosidase activity. Taken together, these data indicate that CHPAT represents a novel species of the genus Treponema , for which the name Treponema rectale is proposed. The type strain of Treponema rectale is CHPAT (=DSM 103679T=NCTC 13848T).
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Herpetosiphon gulosus sp. nov., a filamentous predatory bacterium isolated from sandy soil and Herpetosiphon giganteus sp. nov., nom. rev.
More LessThree filamentous gliding bacteria from the German Collection of Microorganisms and Cell Cultures, Hp g11, Hp g471 and Hp g472, were subjected to a phylogenetic analysis. These organisms had previously been classified as members of the genus Herpetosiphon based on their growth physiology and morphology. However, a taxonomic assignment at the species level had not been carried out. Analysis of 16S rRNA sequences now confirmed the close relationship of strain Hp g472 to Herpetosiphon aurantiacus DSM 785T (98.6 % nucleotide identity) and Herpetosiphon geysericola DSM 7119T (97.7 %). The results of DNA–DNA hybridization experiments further implied that strain Hp g472 should be classified as a distinct species. The DNA G+C content of strain Hp g472 was 49.9 mol%. The major quinone was MK-10 and the predominant cellular fatty acids were C18 : 1, C16 : 1 and C16 : 0. Based on phenotypic, chemotaxonomic and phylogenetic data it was concluded that strain Hp g472 represents a novel species of the genus Herpetosiphon , for which the name Herpetosiphon gulosus sp. nov. is proposed. The type strain is Hp g472T (=DSM 52871T=NBRC 112829T). In contrast to Hp g472T, the strains Hp g11 and Hp g471 exhibited closest 16S rRNA gene sequence similarity (>99 %) with ‘Herpetosiphon giganteus’ Hp a2. The distinctive genotypic and phenotypic properties of the latter supported the revival of the name as Herpetosiphon giganteus (ex Reichenbach & Golecki, 1975) sp. nov., nom. rev. We propose the previously deposited reference strain DSM 589T=NBRC 112828T as the type strain.
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- Proteobacteria
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Aliidiomarina sedimenti sp. nov., a haloalkaliphilic bacterium in the family Idiomarinaceae
A novel Gram-staining-negative straight or curved rod-shaped, moderately halophilic and alkaliphilic bacterium, designated strain GBSy1T, was isolated from a sediment sample from the coastal-marine wetland Gomishan in Iran. GBSy1T was motile, and formed non-pigmented, mucoid colonies. Growth occurred with between 1 and 15 % (w/v) NaCl and the isolate grew optimally with 5 % (w/v) NaCl. The optimum pH and temperature for growth were 8.5 and 34 °C, while the strain was able to grow at pH 7.0–10 and 4–40 °C. On the basis of the results of 16S rRNA gene sequence analysis, GBSy1T was shown to represent a member of the genus Aliidiomarina within the class Gammaproteobacteria , family Idiomarinaceae and showed closest phylogenetic similarity to Aliidiomarina marisCF12–14T (97.7 %). The DNA G+C content of GBSy1T was 51.2 mol%. The cells of GBSy1T contained the isoprenoid ubiquinones Q-8, Q-9 and Q-10 (92, 2 and 2 %, respectively). The major cellular fatty acids of the isolate were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The level of DNA–DNA relatedness between GBSy1T and Aliidiomarina maris DSM 22154T was 31 %. All these features confirmed the placement of GBSy1T within the genus Aliidiomarina . On the basis of evidence from this study, a novel species of the genus Aliidiomarina , Aliidiomarina sedimenti sp. nov., is proposed, with GBSy1T (=IBRC-M 10764T=CECT 8340T) as the type strain.
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Rhizobium arenae sp. nov., isolated from the sand of Desert Mu Us, China
A Gram-strain-negative, rod-shaped, motile bacterium, designated MIM27T, was isolated from the sand of the Mu Us Desert, PR China. The strain could grow at 4–45 °C (optimum, 37 °C), at pH 6.6–9.0 (optimum, 8.0) and in the presence of 0–3 % (w/v) NaCl (optimum, 0 % in RNA liquid medium). The results of phylogenetic analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Rhizobium , with the highest similarity (96.5 %) to Rhizobium pakistanense BN-19T. The results of analysis of the sequences of the nitrogen fixation gene nifH and three housekeeping genes, recA, atpD and glnII, also indicated that MIM27T was most closely related to the species of the genus Rhizobium with validly published names but the similarities were low (≤90.7 %). MIM27T did not form nodules on Pisum sativum, Vicia faba, Astragalus sinicus and Phaseolus vulgaris. The major respiratory quinone of MIM27T was Q-10. The genomic DNA G+C content was 59.8 mol%. Major fatty acids of MIM27T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 1ω7c 11-methyl, C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 2 (C12 : 0 aldehyde and/or unknown ECL 10.9525). On the basis of the physiological, chemotaxonomic and phenotypic data, MIM27T is suggested to represent a novel species of the genus Rhizobium, for which the name Rhizobium arenae sp. nov. is proposed. The type strain is MIM27T (=KCTC 52299T=MCCC 1K03215T).
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Thioclava nitratireducens sp. nov., isolated from surface seawater
More LessA bacterial strain, designated 25B10_4T, was isolated from surface seawater of the Bering Sea and characterized using a polyphasic taxonomic approach. Cells of strain 25B10_4T were Gram-stain-negative, motile and short-rod-shaped. Growth was observed at 10–43 °C (optimum 28 °C), at pH 6–9 (optimum pH 7) and with 0–12 % NaCl (optimum 3–4 %, w/v). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 25B10_4T formed an independent branch within the genus Thioclava , sharing high similarities with four related type strains, Thioclava atlantica 13D2W-2T (98.9 %), Thioclava pacifica TL 2T (98.5 %), Thioclava dalianensis DLFJ1-1T (98.4 %) and Thioclava indica DT23-4T (96.9 %), and low similarities (less than 96.5 %) with other type strains within the family Rhodobacteraceae . The major fatty acid was identified as summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The quinone was Q-10. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, glycolipid and five unidentified phospholipids. The DNA G+C content was 63.8 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain 25B10_4T and the four above-mentioned type strains were, respectively, 20.5–25.7 % and 77.8–82.4 %. The phenotypic, phylogenetic and chemotaxonomic analyses clearly indicated that strain 25B10_4T represents a novel species within the genus Thioclava , for which the name Thioclava nitratireducens sp. nov. is proposed. The type strain is 25B10_4T (=MCCC 1A07302T=LMG 29614T).
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Proposal to reclassify Ehrlichia muris as Ehrlichia muris subsp. muris subsp. nov. and description of Ehrlichia muris subsp. eauclairensis subsp. nov., a newly recognized tick-borne pathogen of humans
We have previously described a novel taxon of the genus Ehrlichia (type strain WisconsinT), closely related to Ehrlichia muris , that causes human ehrlichiosis among patients with exposures to ticks in the upper midwestern USA. DNA from this bacterium was also detected in Ixodes scapularis and Peromyscus leucopus collected in Minnesota and Wisconsin. To determine the relationship between the E. muris -like agent (EMLA) and other species of the genus Ehrlichia phenotypic, genotypic and epidemiologic comparisons were undertaken, including sequence analysis of eight gene loci (3906 nucleotides) for 39 EMLA DNA samples and the type strain of E. muris AS145T. Three loci were also sequenced from DNA of nine strains of E. muris from mouse spleens from Japan. All sequences from E. muris were distinct from homologous EMLA sequences, but differences between them were less than those observed among other species of the genus Ehrlichia . Phenotypic comparison of EMLA and E. muris revealed similar culture and electron microscopic characteristics, but important differences were noted in their geographic distribution, ecological associations and behavior in mouse models of infection. Based on these comparisons, we propose that type strain WisconsinT represents a novel subspecies, Ehrlichia muris subsp. eauclairensis,subsp. nov. This strain is available through the Centers for Disease Control and Prevention Rickettsial Isolate Reference Collection (CRIRC EMU002T) and through the Collection de Souches de l’Unité des Rickettsies (CSURP2883 T). The subspecies Ehrlichia muris subsp. muris subsp. nov. is automatically created and the type strain AS145T is also available through the same collections (CRIRC EMU001T, CSUR E2T). Included is an emended description of E. muris .
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Acinetobacter colistiniresistens sp. nov. (formerly genomic species 13 sensu Bouvet and Jeanjean and genomic species 14 sensu Tjernberg and Ursing), isolated from human infections and characterized by intrinsic resistance to polymyxins
More LessStrains of the genus Acinetobacter , classified as genomic species 13BJ/14TU have been previously associated with human infections and resistance to colistin. To clarify the taxonomy of this provisional group, we investigated 24 strains that have been isolated from humans since the 1960s in 10 countries. The genus-wide analysis of the rpoB and gyrB sequences of all strains and whole-genome sequences of strains representing different rpoB/gyrB genotypes showed that the 24 strains formed a distinct monophyletic group within the so-called haemolytic clade of the genus Acinetobacter . The distinctness of the group at the species level was supported by the results of the cluster analysis of the whole-cell protein fingerprints generated by matrix-assisted laser desorption ionization-time-of-flight MS. The 24 strains had very similar metabolic features and could be distinguished from other members of the genus by the combination of strong haemolytic and proteolytic activities and the ability to oxidize d-glucose and grow on phenylacetate and/or l-phenylalanine. The minimum inhibitory concentrations of the 24 strains to colistin and polymyxin B ranged from 16 to 64 mgl−1 and from 4 to 32 mgl−1, respectively, so uniformly reaching the current clinical resistance breakpoint (4 mg l−1) for these drugs. Genus-wide comparison revealed that such a consistently high level of resistance to polymyxins is a unique feature among species of the genus Acinetobacter, which occur in humans. We conclude that genomic species 13BJ/14TU represents a biologically meaningful and medically relevant species, for which the name Acinetobacter colistiniresistens sp. nov. is proposed. The type strain is NIPH 2036T (=CCM 8641T=CIP 110478T=CCUG 67966T=CNCTC 7573T).
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Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour
More LessThree heterotrophic, aerobic, brown-pigmented strains, designated P97T, P100 and P104, were isolated from a harbour in the southern North Sea. Phylogenetic analysis of 16S rRNA gene sequences revealed that the isolates are affiliated to the genus Phaeobacter . In silico DNA–DNA hybridization of the genome of strain P97T against those of existing type species indicated that P97T represents a novel species within the genus Phaeobacter , with Phaeobacter inhibens T5T as the closest described organism (29.6 % DNA–DNA relatedness) followed by P. gallaeciensis CIP 105210T (26.4 %). DNA–DNA hybridization demonstrated that the three new strains belong to the same species. The new isolates inhibited Pseudoalteromonas tunicata DSM 14096T, and were Gram-stain-negative, catalase- and oxidase-positive, chemo-organoheterotrophic and motile. Growth occurred at pH 6.5–9.5 (optimum 7.0–8.0) and at 4–30 °C (optimum 20–28 °C). The strains required NaCl for growth. The salinity range was 0.5–6.0 % (w/v) NaCl for P97T and P100, and 0.5–5.0 % for P104, lower than values described for Phaeobacter gallaeciensis and Phaeobacter inhibens . The optimum NaCl concentration for strains P97T and P104 was 2.0–4.0 %, and for P100 was 2.0–3.0 %. Fatty acids (>1 %) comprised 18 : 1ω7c, 16 : 0, 18 : 1 ω7c 11-methyl, 18 : 0, 12 :1, 18 : 2ω7c,12, 10 : 0 3-OH and 12 : 0 3-OH. Polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, one unknown lipid and one additional unknown lipid in strain P97T. The major respiratory quinone was Q10. Based on phylogenetic and phenotypic differences, the strains represent a novel species in the genus Phaeobacter , for which the name Phaeobacter porticola sp. nov. is proposed. The type strain is P97T (=DSM 103148T=LMG 29594T).
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Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead–zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica
More LessA yellow-pigmented bacterial strain, designated 9NM-10T, was isolated from an abandoned lead–zinc mine in Meizhou, Guangdong Province, China. Cells were strictly aerobic, Gram-stain-negative and motile with a polar monotrichous flagellum. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 9NM-10T belongs to the genus Sphingomonas and was most closely related to Sphingomonas yantingensis JCM 19201T and Sphingomonas japonica JCM 15438T. DNA–DNA relatedness values between strain 9NM-10T and these two type strains were 43.6±1.3 and 35.4±0.9 %, respectively. It contained Q-10 as the predominant respiratory quinone and the major cellular fatty acids were C18 : 1ω7c, C16 : 0, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The genomic DNA G+C content of strain 9NM-10T was 68.7±0.2 mol%. The polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and three unidentified lipids. Strain 9NM-10T contained spermidine as the major polyamine. On the basis of phenotypic, phylogenetic and chemotaxonomic analyses, strain 9NM-10T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas spermidinifaciens sp. nov. is proposed. The type strain is 9NM-10T (=GDMCC 1.657T=DSM 27571T). Descriptions of the genus of Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica were also emended in this study.
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Cysteiniphilum litorale gen. nov., sp. nov., isolated from coastal seawater
A taxonomic study was performed on strain SYSU D3-2T, isolated from coastal seawater near the estuary of Pearl River in southern China. The strain was observed to be Gram-reaction-negative, non-motile and non-spore-forming. Cells were found to be of coccobacilli shape. Chemotaxonomic analysis of the plasma membrane revealed ubiquinone-8 as the respiratory quinone, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified aminophospholipid and an unidentified phospholipid as the polar lipids, and anteiso-C15 : 0, C18 : 0 and anteiso-C17 : 0 as the major fatty acids (>10 % of total fatty acids). Comparison of 16S rRNA gene sequences showed that strain SYSU D3-2T shared maximum similarities with Caedibacter taeniospiralis 51T (92.3 %) and Fangia hongkongensis UST040201-002T (90.6 %), while sharing 85.8–90.0 % similarity with species of the genera Allofrancisella and Francisella . Phylogenetic dendrograms based on the 16S rRNA gene sequences showed that the strain clustered within the family Francisellaceae , but formed a separate lineage closely linked to Caedibacter taeniospiralis 51T and F. hongkongensis UST040201-002T. Based on the findings of the polyphasic taxonomic study, strain SYSU D3-2T is proposed to be recognized as a representative of a novel species of a new genus within the order Thiotrichales , with the name Cysteiniphilum litorale gen. nov., sp. nov. The type strain of the type species is SYSU D3-2T (=NBRC 112441T=DSM 101832T=KCTC 52386T=CGMCC 1.15758T).
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Bombella apis sp. nov., an acetic acid bacterium isolated from the midgut of a honey bee
More LessAs part of a study to investigate the microbial diversity in the intestine of Apis mellifera, we isolated strain MRM1T from the midgut. MRM1T was a Gram-stain-negative, strictly aerobic, non-motile, non-spore forming and rod-shaped bacteria. Creamy beige-coloured colonies were circular with entire margins in Lactobacilli MRS agar. The strain grew at 25–37 °C (optimum, 30–37 °C) and at a pH range of 4.0 to 9.0 (optimum pH, 7.0–8.5). The strain tolerated 0–1 % (w/v) NaCl (optimal growth occurred in the absence of NaCl). On the basis of the results of a phylogenetic analysis based on the 16S rRNA gene sequences, we determined that MRM1T represents a member of the genus Bombella with the highest sequence similarity to Bombella intestini LMG 28161T (98.8 %). The major quinone was Q10, and dominant fatty acids (>10 %) were C19 : 0cyclo ω8c (33.6 %), C16 : 0 (22.2 %), C18 : 1ω7c (15.9 %) and C14 : 0 (12.5 %). The polar lipid profile of MRM1T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified phospholipid and four unidentified lipids. The DNA G+C content of MRM1T was 59.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, MRM1T represents a novel species of the genus Bombella , for which the name Bombella apis sp. nov. is proposed with the type strain MRM1T (=KCTC 52452T=JCM 31623T).
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Roseobacter ponti sp. nov., isolated from seawater
More LessA Gram-stain-negative, coccoid to oval-shaped and non-motile bacterial strain, designated MM-7T, was isolated from seawater of the Yellow Sea, South Korea, and was subjected to a polyphasic taxonomic study. Strain MM-7T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MM-7T joins the branch comprising the species of the genus Roseobacter , clustering with the type strains of Roseobacter litoralis and Roseobacter denitrificans , with which it exhibited 97.9 and 96.8 % sequence similarity values, respectively. The DNA G+C content of strain MM-7T was determined to be 60.8 mol%, and its mean DNA–DNA relatedness values with Rsb. litoralis JCM 21268T was 10.3±0.4 %. Strain MM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain MM-7T is distinguishable from other species of the genus Roseobacter . On the basis of the data presented, strain MM-7T is considered to represent a novel species of the genus Roseobacter , for which the name Roseobacter ponti sp. nov. is proposed. The type strain is MM-7T (=KCTC 52469T=NBRC 112431T).
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Thalassotalea crassostreae sp. nov., isolated from Pacific oyster
More LessA Gram-staining-negative, aerobic, rod-shaped bacterial strain, designated LPB0090T, was isolated from the Pacific oyster, Crassostreagigas, collected from the Yeongheung Island, Korea (37° 15′ 16.1″ N; 126° 29′ 46.5″ E). The complete genome sequence of LPB0090T (accession number CP017689) was 3 861 670 bp long with a DNA G+C content of 38.8 mol%. The genome included 3245 protein-coding genes and six copies of rRNA operons. On the basis of the results of 16S rRNA gene sequence analysis, LPB0090T was found to form an independent phyletic line within the genus Thalassotalea , with 94.7–96.0 % sequence similarities to the previously known species of the genus. The isoprenoid quinone (Q-8) and major fatty acids (C16 : 0, C17 : 1 ω8c, and C16 : 1 ω7c and/or C16 : 1 ω6c) of the isolate were similar to those of the other members of the genus Thalassotalea . A number of phenotypic features, however, distinguished LPB0090T from its closest neighbour Thalassotalea ponticola as well as other species of the genus Thalassotalea . On the basis of the phylogenetic, genomic and phenotypic data presented in this study, the strain was classified as representing a novel species of the genus Thalassotalea . Therefore, the name Thalassotalea crassostreae sp. nov. is proposed for the isolate. The type strain is LPB0090T (=KACC 18695T=JCM 31189T).
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Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter
More LessA Gram-stain-negative, rod-shaped, non-spore forming, motile and strictly oxidative bacterium, strain CHU3T, was isolated from fresh water in the Daecheong Reservoir, South Korea. A comparison of the 16S rRNA gene sequence showed that the novel bacterium is closely related to Paucibacter toxinivorans 2C20T (=KCTC 42569T) with a sequence similarity value of 97.8 %, Pelomonas saccharophila DSM 654T (=KCTC 52256T) with 97.4 % similarity and Pelomonas aquatica CCUG 52575T (=KCTC 42961T) with 97.3 % similarity, respectively. The major fatty acids (>10 %) of the isolate were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. Ubiquinone-8 was detected as the respiratory quinone. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and an unidentified aminolipid. The DNA G+C content was 62.5 mol%. DNA–DNA hybridization experiments with Paucibacter toxinivorans KCTC 42569T (=2C20T), Pelomonas saccharophila KCTC 52256T (=DSM 654T) and Pelomonas aquatica KCTC 42961T (=CCUG 52575T) resulted in relatedness values of 20 % (reciprocal 11 %), 16 % (reciprocal 17 %) and 15 % (reciprocal 19 %), respectively. The phylogenetic analysis, DNA–DNA hybridization value, polar lipids, fatty acid composition and other physiological characteristics confirmed that strain CHU3T represents a novel species in the genus Paucibacter for which the name Paucibacter oligotrophus sp. nov. is proposed. The type strain is CHU3T (=KCTC 42519T=CICC 24092T). An emended description of the genus Paucibacter is also proposed on the basis of new data obtained in this study.
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Bradyrhizobium cajani sp. nov. isolated from nodules of Cajanus cajan
Two slow-growing strains, AMBPC1010T and AMBPC1011, were isolated from nodules of Cajanus cajan in the Dominican Republic. 16S rRNA gene analysis placed these strains within the genus Bradyrhizobium , being phylogenetically equidistant to several species of this genus. Analysis of the recA and atpD genes showed that the strains isolated belong to a cluster containing the strains Bradyrhizobium ottawaense OO99T, ‘ Bradyrhizobium americanum' CMVU44 and Bradyrhizobium daqingense CCBAU 15774T, and presented similarity values lower than 96 % for both genes with respect to the strains nodulating C. cajan. DNA–DNA hybridization analysis showed averages of 36, 40 and 39 % relatedness with respect to the representative strains of Bradyrhizobium ottawaense , ‘ Bradyrhizobium americanum' and Bradyrhizobium daqingense , respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Bradyrhizobium . Therefore, based on the data obtained in this study, we propose to classify the strains AMBPC1010T (=LMG 29967T=CECT 9227T) and AMBPC1011 into a novel species named Bradyrhizobium cajani sp. nov.
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Paraglaciecola hydrolytica sp. nov., a bacterium with hydrolytic activity against multiple seaweed-derived polysaccharides
A novel bacterial strain, S66T, was isolated from eelgrass collected on the coastline of Zealand, Denmark. Polyphasic analyses involving phenotypic, phylogenetic and genomic methods were used to characterize strain S66T. The strain was Gram-reaction-negative, rod-shaped, aerobic, and displayed growth at 10–25 °C (optimum 20–25 °C) and at pH 7–9 (optimum pH 7.5). Furthermore, strain S66T grew on seaweed polysaccharides agar, agarose, porphyran, κ-carrageenan, alginate and laminarin as sole carbon sources. Major fatty acids were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The respiratory quinone was determined to be Q-8, and major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was determined to be 42.2 mol%. Phylogenetic analyses based on the 16S rRNA gene and GyrB sequence comparisons showed that the bacterium was affiliated with the genus Paraglaciecola within the family Alteromonadaceae of the class Gammaproteobacteria . The percentage similarity between the 16S rRNA gene and GyrB sequences of strain S66T and other members of the genus Paraglaciecola were 94–95 % and 84–85 %, respectively. Based on the genome sequence of S66T, the average nucleotide identity (ANI) between strain S66T and other members of the genus Paraglaciecola was 77–80 %, and DNA–DNA hybridization prediction showed values of less than 24 % relatedness, respectively, between S66T and other species of the genus Paraglaciecola . The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain S66T represents a novel species of the genus Paraglaciecola , for which the name Paraglaciecola hydrolytica sp. nov. is proposed. The type strain is S66T (=LMG 29457T=NCIMB 15060T=DSM 102834T).
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Thalassotalea litorea sp. nov., isolated from seashore sand
More LessA novel Gram-stain-negative, aerobic and rod-shaped marine bacterium, designated strain HMF4135T, was isolated from a sand sample which was collected from the seashore of the South Sea, Republic of Korea. It required NaCl for growth and exhibited optimal growth at 30 °C, with 2 % (w/v) NaCl and at pH 7–8. Cellular fatty acids were dominated by C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c and C12 : 0 3-OH. The predominant isoprenoid quinone was ubiquinone-8 (Q-8). Polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain HMF4135T formed a distinct species-level lineage within the genus Thalassotalea of the class Gammaproteobacteria and was most closely related to Thalassotalea ponticola GJSW-36T (96.4 % similarity). Based on the distinctive phenotypic characteristics and phylogenetic analysis, it is concluded that strain HMF4135T represents a novel species of the genus Thalassotalea , for which the name Thalassotalea litorea sp. nov. is proposed. The type strain is HMF4135T (=KCTC 52154T=NBRC 112672T).
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Perlucidibaca aquatica sp. nov., isolated from fresh water
More LessA Gram-staining-negative, non-motile, non-pigmented, strictly aerobic and rod-shape bacterium, designated BK296T, was isolated from stream water originating from a limestone cave in Samcheok, Korea. Optimal growth of strain BK296T was observed at 30 °C, pH 7.0–8.0 and without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BK296T belonged to the genus Perlucidibaca , forming a robust clade with a member of the genus, and was most closely related to Perlucidibaca piscinae (97.8 %). The average nucleotide identity value between strain BK296T and Perlucidibaca piscinae IMCC1704T was 79.8 %, and the genome-to-genome distance was 17.5 % on mean. The G+C content of the DNA of strain BK296T was 55.7 mol%. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was ubiquinone Q-8. On the basis of phenotypic, genotypic and phylogenetic analyses, strain BK296T (=KCTC 52162T=JCM 31377T) represents a novel species of the genus Perlucidibaca , for which the name Perlucidibaca aquatica sp. nov. is proposed.
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Mesorhizobium helmanticense sp. nov., isolated from Lotus corniculatus nodules
In this study, three strains belonging to the genus Mesorhizobium , CSLC115NT, CSLC19N and CSLC37N, isolated from Lotus corniculatus nodules in Spain, were characterized. Their 16S rRNA gene sequences were closely related to those of Mesorhizobium metallidurans STM 2683T, Mesorhizobium tianshanense A-1BST, Mesorhizobium tarimense CCBAU 83306T, Mesorhizobium gobiense CCBAU 83330T and Mesorhizobium caraganae CCBAU 11299T with similarity values higher than 99.7 %. The analysis of concatenated recA and glnII genes showed that the most closely related type strains were M. metallidurans STM 2683T, M. tianshanense A-1BST and M. tarimense CCBAU 83306T with 96, 95 and 94 % similarity values in the recA gene and 95, 94 and 94 % in the glnII gene, respectively. M. metallidurans LMG 24485T, M. tianshanense USDA 3592T and M. tarimense LMG 24338T showed means of 44, 41 and 42 % DNA–DNA relatedness, respectively, with respect to strain CSLC115NT. The major fatty acids were those from summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0 and C18 : 1ω7c 11-methyl. The results of phenotypic characterization support that the L. corniculatus nodulating strains analysed in this work belong to a novel species of the genus Mesorhizobium for which the name Mesorhizobium helmanticense sp. nov. is proposed, and the type strain is CSLC115NT (= LMG 29734T=CECT 9168T).
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Rhizobium zeae sp. nov., isolated from maize (Zea mays L.) roots
More LessA bacterial strain designated CRZM18RT was isolated from a root of Zea mays in Spain. The analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Rhizobium , with Rhizobium cellulosilyticum ALA10B2T and Rhizobium yantingense H66T being the most closely related species with 98.3 and 97.9 % sequence similarity, respectively. The analysis of the concatenated recA and atpD genes showed that strain CRZM18RT forms a cluster with these species and also with Rhizobium smilacinae PTYR-5T, but the recA and atpD genes of strain CRZM18RT were phylogenetically distant, with identities lower than 90 and 96 %, respectively. DNA–DNA hybridization analysis showed mean relatedness of 43, 22 and 38 % with respect to R. cellulosilyticum ALA10B2T, R. yantingense LMG 28229T and R. smilacinae LMG 27604T. Phenotypic characteristics also differed from those of the most closely related species of the genus Rhizobium . The major fatty acids were those from summed feature 8 (C18 : 1ω6c/C18 : 1ω7c) and C16 : 0. Based on the genotypic, chemotaxonomic and phenotypic data obtained in this study, we propose to classify strain CRZM18RT in a novel species named Rhizobium zeae sp. nov. (type strain CRZM18RT=LMG 29735T=CECT 9169T).
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Description of a phototrophic bacterium, Thiorhodococcus alkaliphilus sp. nov.
Strain JA878T was purified from a photoheterotrophic enrichment obtained from a sediment sample of a brown pond near Nari Salt Pan, Bhavnagar, Gujarat, India. Cells of the isolate were coccoid, motile by means of single polar flagellum and Gram-stain-negative. The internal photosynthetic membrane architecture was vesicular. Strain JA878T contained bacteriochlorophyll a and spirilloxanthin series of carotenoids with rhodopin (>85 %) as the major component. Strain JA878T grew optimally at pH 10–11, and had no requirement for NaCl (tolerated up to 6 %, w/v) or vitamins for growth. C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c/C18 : 1ω6c and C16 : 0 were identified as the major fatty acids (>10 %). Phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown polar lipid were identified. Q8 was the predominant quinone system in strain JA878T. The DNA G+C content was 62.4 mol%. Highest 16S rRNA gene sequence similarity through EzTaxon-based blast analysis of strain JA878T was found with the type strains of Thiorhodococcus fuscus (99 %), Thiorhodococcus kakinadensis (98.6 %), Thiohalobacter thiocyanaticus (98.4 %), Thiophaeococcus fuscus (97.3 %) and other members of the class Gammaproteobacteria (<97.3 %), revealing a close affiliation to the genera Thiorhodococcus , Thiohalobacter and Thiophaeococcus . However, the phylogenetic treeing firmly placed the strain in the genus Thiorhodococcus . Phenotypic and chemotaxonomic evidence supported the affiliation of strain JA878T to the genus Thiorhodococcus and not to Thiohalobacter , Thiophaeococcus or other known genera of Chromatiaceae . Distinct physiological, genotypic and chemotaxonomic differences indicate that strain JA878T represents a novel species of the genus Thiorhodococcus , for which the name Thiorhodococcus alkaliphilus sp. nov. is proposed. The type strain is JA878T (=KCTC 15531T=JCM 31245T).
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Proposal for transfer of Oceanibulbus indolifex Wagner-Döbler et al. 2004 to the genus Sulfitobacter as Sulfitobacter indolifex comb. nov.
More LessA polyphasic taxonomic study was undertaken to clarify the exact position of type strain HEL-45T of Oceanibulbusindolifex Wagner-Döbler et al. 2004. A combination of physiological properties of HEL-45T were similar to those of its closest relatives, Sulfitobacterdelicatus KMM 3584T and Sulfitobacterdubius KMM 3554T. The results of 16S rRNA gene sequences analysis indicated that HEL-45T and the two relatives shared 99.6 % similarity and formed a coherent cluster in the phylogenetic tree. The close relationship between HEL-45T and the two relatives was underpinned by the results for chemotaxonomic characters, including the fatty acids, quinone and polar lipids. The digital DNA–DNA hybridization values and between HEL-45T and the two relatives were 25.9 and 31.6 %, respectively, which were well below the 70 % threshold value recommended for delineation of bacterial species. The comparative phenotypic and genotypic analyses supported the incorporation of Oceanibulbusindolifex into the genus Sulfitobacter as Sulfitobacter indolifex comb. nov.; the type strain is HEL-45T (=MCCC 1A11773T=DSM 14862T=NCIMB 13983T).
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Isolation and characterization of Kingella negevensis sp. nov., a novel Kingella species detected in a healthy paediatric population
We herein report the isolation and characterization of 21 Gram-stain-negative strains cultivated from the oropharynx of healthy children in Israel and Switzerland. Initially described as small colony variants of Kingella kingae , phenotypic analysis, biochemical analysis, phylogenetic analysis based on sequencing of the partial 16S rRNA gene and five housekeeping genes (abcZ, adk, G6PD, groEL and recA), and whole genome sequencing and comparison between members of the genera Kingella and Neisseria provided evidence for assigning them to the genus Kingella . Cellular fatty acids included important amounts of C12 : 0, C14 : 0, C16 : 0 and C16 : 1n7. Digital DNA–DNA hybridization between the isolates Sch538T and K. kingae ATCC 23330T revealed relatedness of 19.9 %. Comparative analysis of 16S rRNA gene sequences available in GenBank allowed matches to strains isolated in the USA, suggesting a wider geographical distribution. A novel species named Kingella negevensis sp. nov. is proposed, as most strains have been isolated in the Negev, a desert region of southern Israel. The type strain is Sch538T (=CCUG 69806T=CSUR P957).
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Roseomonas suffusca sp. nov., isolated from lagoon sediments
More LessThree light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The strains (S1T, AS3 and AS6) grew aerobically at 13–42 °C (optimum, 30–35 °C) and pH 6.5–9.1 (optimum, pH 7.0–7.5). All three strains were positive for catalase and oxidase activity, and no added NaCl was required for growth. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 0 were the predominant fatty acids (>5 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were the major polar lipids. The genomic DNA G+C content of strains S1T, AS3 and AS6 was 70.5, 70.1 and 70.8 mol%, respectively. Strain S1T showed 16S rRNA gene sequence similarity of 99.1 % with Roseomonas rubra S5T, 98.7 % with Roseomonas rhizosphaerae YW11T, 98.5 % with Roseomonas cervicalis E7107T, 97.8 % with Roseomonas aestuarii JC17T, 97.2 % with Roseomonas oryzae JC288T, 97.2 % with Roseomonas ludipueritiae 170/96Tand <97 % with other members of the genus Roseomonas . Strains AS3 and AS6 shared 99.9 % 16S rRNA gene sequence similarity with strain S1T. DNA–DNA hybridization values among strains S1T, AS3 and AS6 were >89 %, while all the three strains showed <56 % relatedness with the most closely related type strains. Distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa support the classification of strain S1T as a representative of a novel species in the genus Roseomonas , for which the name Roseomonas suffusca sp. nov. is proposed. The type strain is S1T (=KEMB 563-465T=JCM 31176T). Strains AS3 and AS6 serve as additional strains of the newly proposed species.
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Kiloniella antarctica sp. nov., isolated from a polynya of Amundsen Sea in Western Antarctic Sea
A taxonomic study was conducted on strain soj2014T, which was isolated from the surface water of a polynya in the Antarctic Sea. Comparative 16S rRNA gene sequence analysis showed that strain soj2014T belongs to the family Kiloniellaceae and is closely related to Kiloniella spongiae MEBiC09566T, ‘ Kiloniella litopenaei ’ P1-1T and Kiloniella laminariae LD81T (98.0 %, 97.8 % and 96.2 % 16S rRNA gene sequence similarity, respectively). The DNA–DNA hybridization values between strain soj2014T and closely related strains were below 28.6 %. The G+C content of the genomic DNA of strain soj2014T was 45.5 mol%. The predominant cellular fatty acids were summed feature 8 (composed of C18 : 1ω6c/C18 : 1ω7c, 57.0 %) and summed feature 3 (composed of C16 : 1ω6c/C16 : 1ω7c, 23.5 %). Strain soj2014T was Gram-stain-negative, slightly curved, spiral-shaped, and motile with a single polar flagellum. The strain grew at 0–30 °C (optimum, 25 °C), in 1.5–5.1 % (w/v) NaCl (optimum, 2.1–2.4 %) and at pH 5.5–9.5 (optimum, 7.5–8.0). It also had differential carbohydrate utilization traits and enzyme activities compared with closely related strains. Based on these phylogenetic, phenotypic and chemotaxonomic analyses, strain soj2014T represents a distinct species, separable from the reference strains, and is, therefore, proposed as a novel species, Kiloniella antarctica sp. nov. The type strain is soj2014T (=KCTC 42186T=JCM 30386T).
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Novosphingobium fontis sp. nov., isolated from a spring
More LessA bacterial strain designated STM-14T was isolated from a spring in Taiwan and characterized using a polyphasic taxonomic approach. Strain STM-14T was a Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, non-motile, rod-shaped bacterium and formed cream-coloured colonies. Strain STM-14T grew at 15–37 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 6.0) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain STM-14T belonged to the genus Novosphingobium and showed the highest levels of sequence similarity to Novosphingobium naphthae D39T (98.5 %) and Novosphingobium mathurense SM117T (97.6 %). The major fatty acids (>10 %) of strain STM-14T were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C15 : 0 2-OH and C17 : 1ω8c. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine and several uncharacterized lipids. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 66.6 mol%. The DNA–DNA hybridization value for strain STM-14T with N. naphthae JCM 31158T and N. mathurense DSM 23374T was less than 49 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain STM-14T should be classified as representing a novel species of the genus Novosphingobium , for which the name Novosphingobium fontis sp. nov. is proposed. The type strain is STM-14T (=BCRC 80924T=LMG 29290T=KCTC 42983T).
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Paracoccus hibiscisoli sp. nov., isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus)
A Gram-reaction-negative, aerobic, non-motile, short-rod-shaped bacterium (THG-T2.31T) was isolated from the rhizosphere of Mugunghwa (Hibiscus syriacus). Growth occurred at 10–35 °C (optimum 28 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–4.0 % NaCl (optimum 1.0 %). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T2.31T were identified as Paracoccus marcusii DSM 11574T (98.4 %), Paracoccus haeundaensis BC74171T (98.3 %), Paracoccus carotinifaciens E-396T (98.3 %), Paracoccus aestuarii B7T (97.3 %) and Paracoccus seriniphilus MBT-A4T (97.0 %); levels of similarity with the type strains of other species of the genus Paracoccus were lower than 97.0 %. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified phospholipids. The major fatty acids were C16 : 0, C18 : 0, C10 : 0 3-OH, and C18 : 1 ω7c. The quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain THG-T2.31T was 69.1 mol%. DNA–DNA hybridization values between strain THG-T2.31T and P. marcusii DSM 11574T, P. haeundaensis BC74171T, P. carotinifaciens E-396T, P. aestuarii B7T and P. seriniphilus MBT-A4T were 38.9 % (34.9 %, reciprocal analysis), 29.1 % (23.5 %), 28.0 % (19.7 %), 18.9 % (9.3) and 13.1 % (6.2 %). On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain THG-T2.31T represents a novel species of the genus Paracoccus , for which the name Paracoccus hibiscisoli sp. nov. is proposed. The type strain is THG-T2.31T (=KACC 18933T=CCTCC AB 2016182T).
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Erythrobacter xanthus sp. nov., isolated from surface seawater of the South China Sea
A Gram-reaction-negative, aerobic, oxidase- and catalase-positive, yellow-pigmented, non-flagellated, rod-shaped bacterium, designed strain SM1501T, was isolated from surface seawater of the South China Sea. SM1501T grew at 7–42 °C and with 0–11 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that SM1501T represented a member of the genus Erythrobacter , sharing the highest 16S rRNA gene sequence similarity (97.4 %) with Erythrobacter luteus and 94.2–96.5 % 16S rRNA gene sequence similarities to other species of the genus Erythrobacter with validly published names. The average nucleotide identity (ANI) value and in silico DNA–DNA hybridization value between SM1501T and E. luteus were only 74.6 and 20.0 %, respectively. The predominant cellular fatty acids of SM1501T were C17 : 1ω6c, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, diphosphatidylglycerol and phosphatidylcholine and the main respiratory quinone of was Q-10. Polyphasic data presented in this paper support the notion that SM1501T represents a novel species in the genus Erythrobacter , for which the name Erythrobacter xanthus sp. nov. is proposed. The type strain of Erythrobacter xanthus is SM1501T (=KCTC 42669T=CCTCC AB 2015396T).
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- Eukaryotic Micro-organisms
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Nakazawaea todaengensis f.a., sp. nov., a yeast isolated from a peat swamp forest in Thailand
Strain DMKU-PS11(1)T was isolated from peat in a swamp forest in Thailand. DNA sequence analysis showed that it belonged to a novel species that was most closely related to Nakazawaea laoshanensis. However, it differed from the type strain of N. laoshanensis (NRRL Y-63634T) by 2.3 % nucleotide substitutions in the D1/D2 region of the large subunit (LSU) rRNA gene, 1.0 % nucleotide substitutions in the small subunit (SSU) rRNA gene and 8.0 % nucleotide substitutions in the internal transcribed spacer (ITS) region. The phylogenetic analyses based on the combined sequences of the SSU and the D1/D2 region and that of the SSU sequences alone confirmed the placement of the novel species in the Nakazawaea clade and its close affinity with N. laoshanensis. Hence, the species Nakazawaea todaengensis f.a., sp. nov. is proposed. The type strain is DMKU-PS11(1)T (=CBS 14555T=TBRC 6559T). The MycoBank number for Nakazawaea todaengensis f.a., sp. nov. is MB 819513
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Meira siamensis sp. nov., a novel anamorphic ustilaginomycetous yeast species isolated from the vetiver grass phylloplane
More LessTwo strains, DMKU-LV83 and DMKU-LV85, of a novel yeast species were isolated from the phylloplane of vetiver grass collected in Thailand by plating of leaf washings. Analysis of the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene showed that the two strains represent a single novel species and most closely related to Meira miltonrushii. However, the novel species differed from the type strain of M. miltonrushii (MCA 3882T) by 5.5 % nucleotide substitutions in the D1/D2 region and 8.9 % nucleotide substitutions in the ITS region. The phylogenetic analysis based on the D1/D2 region of the LSU rRNA gene confirmed the placement of the novel species in the Meira clade and its close affinity with M. miltonrushii. Therefore, the species Meira siamensis sp. nov. is proposed. The type strain is DMKU-LV83T (=CBS 12860T=BCC 61180T).
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Deakozyma yunnanensis sp. nov., a novel yeast species isolated from rotten wood
More LessThree strains representing a novel yeast species were isolated from rotten wood samples collected in Xishuangbanna Tropical Rainforest in Yunnan Province, PR China. Sequence analysis of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions indicated that the novel species represented a member of the genus Deakozyma. The novel species was related most closely to the type strain of Deakozyma indianensis but they differed by 5.8 % sequence divergence (20 substitutions and 5 gaps) in the D1/D2 domain and by 12.2 % sequence divergence (27 substitutions and 15 gaps) in the ITS region. Interestingly, the novel yeast species was able to ferment glucose and sucrose in Durham tubes, a clear difference from its closest relative D. indianensis, the type species of the genus Deakozyma. The species name of Deakozyma yunnanensis sp. nov. is proposed to accommodate these strains, with NYNU 16742T (=CICC 33160T=CBS 14688T) designated the type strain. As the current description of the genus does not allow the inclusion of sugar fermenting species, the emendation of the diagnosis of the genus Deakozyma Kurtzman and Robnett is proposed.
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Ogataea haglerorum sp. nov., a novel member of the species complex, Ogataea (Hansenula) polymorpha
More LessThree strains representing a novel species of the Ogataea clade were isolated by W. T. Starmer and H. J. Phaff from rotting tissue of Opuntia phaeacantha in Arizona, USA. Analyses of the sequences of the D1/D2 LSU rRNA gene, ITS1-5.8S-ITS2, and translation elongation factor-1α (EF-1 α) showed that this novel species belongs to the Ogataea polymorpha complex formed by Ogataea angusta, Ogataea parapolymorpha and Ogataea polymorpha. The novel species differs from these species by 4–5 nucleotide substitutions in the D1/D2 domain, by 28–29 nucleotide substitutions in the EF-α gene and by 18–24 nucleotide substitutions and 2–5 indels in the ITS–5.8S region. The name Ogataea haglerorum sp. nov. is proposed for this novel species. The type strain is VKPM Y-2583T (=CBS 14645T=UCDFST 17-101T). The Mycobank number is MB 819772.
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- ICSP Matters
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