1,721,040 research outputs found
Complete genome sequence of Spirosoma sp. strain KCTC 42546, isolated from a reservoir in South Korea
No full textThis study reports on the complete genome sequence of Spirosoma sp. strain KCTC 42546, isolated from fresh water in a reservoir in South Korea. The genome contained genes for various glycosyl hydrolases, which are associated with degrading sugars and DNA-repairing enzymes.
Novosphingobium aquiterrae sp. nov., isolated from ground water
No full textA Gram-staining-negative, strictly aerobic, non-motile, non-spore-forming, yellow and rod-shaped bacterium, designated E-II-3T, was isolated from ground water at Daejeon in Korea. Strain E-II-3T grew between 4 and 45 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0-2.0% (w/v) NaCl, growing optimally with 0.5% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain E-II-3T was shown to belong to the genus Novosphingobium and showed closest phylogenetic similarity to ‘Novosphingobium ginsenosidimutans’ FW-6 (97.7 %), Novosphingobium aromaticivorans F199T (96.9 %) and Novosphingobium subterraneum B0478T (96.5 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18 : 1ω7c (34.0 %), C16 : 1 ω7c and/or iso-C15 : 0 2-OH (23.8 %) and C17 : 1 ω6c (19.3 %). The DNA G+C content of this novel isolate was 62.7 mol%. DNA-DNA relatedness between strain E-II-3T and ‘N. ginsenosidimutans’ KACC 16615, N. aromaticivorans KCTC 2888T and N. capsulatum KCTC 22844T was 38, 33 and 29 %, respectively. On the basis of polyphasic analysis from this study, strain E-II-3T represents a novel species of the genus Novosphingobium for which the name Novosphingobium aquiterrae sp. nov. is proposed. The type strain is E-II-3T (=KACC 17599T=NBRC 109812T=NCAIM B 02537T).open
Sphingobium subterraneum sp. nov., isolated from ground water
No full textA Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, yellow, rod-shaped bacterium, designated S-II-13T, was isolated from ground water at Daejeon in Korea. Strain S-II-13T grew between 15 and 30 6C (optimal growth at 28 6C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0.3？1.5% (w/v) NaCl, growing optimally with 0.5% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain S-II-13T was found to belong to the genus Sphingobium, showing closest phylogenetic similarity to Rhizorhapis suberifaciens CA1T (97.0% 16S rRNA gene sequence similarity), Sphingobium sufflavum HL-25T (96.9%) and Sphingobium vulgare HU1-GD12T (96.6%). The major polar lipids were phosphatidylgly-cerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone was Q-10. The major fatty acids were C18:1v7c, C14:0 2-OH, C16:0 and summed feature 3 (C16:1v7c and/or iso-C15:0 2-OH). The DNA G+C content of strain S-II-13T was 63.5 mol%. DNA？DNA relatedness between strain S-II-13T and Rhizorhapis suberifaciens LMG 17323T, Sphingobium sufflavum KCTC 23953T and Sphingobium vulgare KCTC 22289T was 24, 52 and 55%, respectively. On the basis of evidence from this taxonomic study using a polyphasic approach, strain S-II-13T represents a novel species of the genus Sphingobium for which the name Sphingobium subterraneum sp. nov. is proposed. The type strain is S-II-13T (5KACC 17606T5NBRC 109814T).open
Flavobacterium ustbae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia
No full textA yellow-pigmented bacterial strain, designated T13T, was isolated from the rhizosphere soil of Alhagi sparsifolia collected from Xinjiang, PR China. Cells were rod-shaped, Gram-stain-negative, aerobic and gliding. Strain T13T grew optimally at 25-30？°C？and pH 7.0-8.0 with a NaCl tolerance of 0-2？% on Reasoner's 2A agar. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain T13T belonged to the genus Flavobacterium within the family Flavobacteriaceae and was closely related to Flavobacterium nitrogenifigens KCTC 42884T with a similarity value of 97.4？%. The major polar lipid was phosphatidylethanolamine; the only respiratory quinone was MK-6, and the polyamine profile contained sym-homospermidine as the major polyamine and a trace amount of spermidine. The major fatty acids were iso-C15？:？0, C16？:？ 1ω7c and summed feature 3 (comprising C16？:？1ω7c or C16？:？1ω6c). The G+C content of the genomic DNA was 34.1？mol%. It is concluded from the phenotypic and genotypic data that strain T13T represents a novel species of the genus Flavobacterium, for which the name Flavobacteriumustbae sp. nov. with the type strain T13T (=KCTC 62874T=ACCC 60126T) is proposed.
Dextran-like exopolysaccharide-producing Leuconostoc and Weissella from kimchi and its ingredients
No full textDextran-like exopolysaccharide (EPS)-producing lactic acid bacteria were isolated from kimchi and its ingredients. Analysis of 16S rRNA genes (500-600 bp) of 158 isolates revealed that dextran-like EPS-producing strains were most similar to either Leuconostoc or Weissella. The gene sequence analysis of the strains revealed a similarity to Leuconostoc mesenteroides and Weissella confusa in the samples. The molecular masses of dextranlike polymers from the most isolated Leuconostoc and Weissella strains were 1,176 and 1,158 kDa, respectively. Fourier transform infrared analysis of these polymers showed a similarity to the structure of commercial dextran from Leu. mesenteroides B-512F.open
Arcticibacter pallidicorallinus sp. nov. isolated from glacier ice
No full textA Gram-stain-negative, rod-shaped bacterium (strain Hh36T) was isolated from the No. 1 glacier in Xinjiang, north-west China. Colonies of strain Hh36Twere pink, convex and round on PYG medium plates. Strain Hh36T was able to grow at 4-30 °C and pH 6.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh36T was related to members of the genus Arcticibacter. The major cellular fatty acids of the novel strain were iso-C15: 0, summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) and iso-C17: 0 3-OH. The G+C content of the genomic DNA was 44.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain Hh36T is considered to represent a novel species of the genus Arcticibacter, for which the name Arcticibacter pallidicorallinus sp. nov. is proposed. The type strain is Hh36T (=CGMCC 1.9313T=KCTC 32542T).open
Psychrosphaera aquimarina sp. nov., a marine bacterium isolated from seawater collected from Asan Bay, Republic of Korea
No full textCells of strain SW33T, isolated from the seawater of Asan Bay, Republic of Korea, were characterized as Gram-stainnegative, aerobic, rod-shaped, motile and non-spore-forming. Phylogenetic analysis revealed that strain SW33T belonged to the genus Psychrosphaera and clustered distantly with the other genera in the family Pseudoalteromonadaceae in the phylogenetic tree. The 16S rRNA sequences of strain SW33T revealed high similarities to Psychrosphaera saromensis SA4- 48T (98.7%), Psychrosphaera haliotis KDW4T (97.4%) and Psychrosphaera aestuarii PSC101T (97.3%). The major fatty acids were C16: 0 (27.9%), summed feature 3 (32.2%) and summed feature 8 (17.2%). The predominant quinone was Q-8, and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. The DNA G+C content was 38.3 mol%. The DNA？DNA relatedness values with the three species of Psychrosphaera saromensis KCTC 23240T, Psychrosphaera haliotis KCTC 22500T and Psychrosphaera aestuarii KCTC 32274T were 22, 23 and 18%, respectively. Based on the phenotypic characteristics and taxonomic analyses, we propose that strain SW33T represents a novel species within the genus Psychrosphaera, for which the name Psychrosphaera aquimarina sp. nov. with the type strain SW33T (=KCTC 52743T=CICC 24249T) is proposed
Roseomonas terricola sp. nov., isolated from agricultural soil
No full textA novel strain, designated EM302T, was isolated from a soil sample collected from farmland located in Yesan-gun in the Republic of Korea. The cells were Gram-stain-negative, aerobic, non-motile without flagella and coccobacilli-shaped. Colonies were circular with entire edges, convex, opaque and pink. The strain grew at 15？40 °C (optimum, 35 °C) and pH 6.0？9.0 (optimum, 7.0). The strain grew in R2A medium without the addition of NaCl. Based on 16S rRNA gene sequences analysis, strain EM302T was found to be phylogenetically related to Roseomonas wooponensis WW53T (96.5% 16S rRNA gene sequence similarity), Roseomonas arcticisoli MC 3624T (95.2%), Roseomonas aerilata 5420-30T (94.5%), Roseomonas pecuniae N75T (94.4%) and Roseomonas vinacea CPCC 100056T (94.4%). The major cellular fatty acids were summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) and C16: 0. The predominant respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of the type strain was 65.7 mol%. On the basis of data presented here, strain EM302T is considered to represent a novel species of the genus Roseomonas, for which the name Roseomonas terricola sp. nov. is proposed. The type strain is EM302T (=KACC 13942T=KCTC 42906T=NBRC 111477T).
Mucilaginibacter carri sp. nov., isolated from a car air conditioning system
No full textA Gram-stain-negative, pink bacterial strain, designated PR0008KT, was isolated from an automobile evaporator core in Korea. The cells were obligately aerobic and rod-shaped. The strain grew at 10-40 °C (optimum, 20 °C), at pH 5-8 (optimum, 7), and in the presence of 0-1.5 % (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Mucilaginibacter (93.4-97.0 % 16S rRNA sequence similarities) and showed a high sequence similarity with Mucilaginibacter litoreus BR-18T, Mucilaginibacter lutimaris BR-3T and Mucilaginibacter soli R9-65T (97.0 %, 96.9 % and 96.9 % 16S rRNA sequence similarity, respectively). It contained summed feature 3 (C16: 1ω7c and/or C16: 1ω6c), C16: 0, iso-C17: 0 3-OH and C16: 0 as the predominant fatty acids and MK-7 as the major menaquinone. The polar lipids were phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and two unknown polar lipids. The DNA G+C content of this strain was 47.4 mol%. Based on the phenotypic, genotypic and chemotaxonomic data, strain PR0008KT represents a novel species in the genus Mucilaginibacter, for which the name Mucilaginibacter carri sp. Nov. (=KACC 17938T=NBRC 111539T) is proposed.open
Rational design of a beta-glycosidase with high regiospecificity for triterpenoid tailoring
No full textTriterpenoids with desired glycosylation patterns have attracted considerable attention as potential therapeutics for inflammatory diseases and various types of cancer. Sugar-hydrolyzing enzymes with high substrate specificity would be far more efficient than other methods for the synthesis of such specialty triterpenoids, but they are yet to be developed. Here we present a strategy to rationally design a β-glycosidase with high regiospecificity for triterpenoids. A β-glycosidase with broad substrate specificity was isolated, and its crystal structure was determined at 2.0 A resolution. Based on the product profiles and substrate docking simulations, we modeled the substrate binding modes of the enzyme. From the model, the substrate binding cleft of the enzyme was redesigned in a manner that preferentially hydrolyzes glycans at specific glycosylation sites of triterpenoids. The designed mutants were shown to produce a variety of specialty triterpenoids with high purity.open
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