40 results on '"Baek K"'
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2. Rhodococcus aerolatus sp. nov., isolated from subarctic rainwater
- Author
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Hwang, C. Y., primary, Lee, I., additional, Cho, Y., additional, Lee, Y. M., additional, Baek, K., additional, Jung, Y.-J., additional, Yang, Y. Y., additional, Lee, T., additional, Rhee, T. S., additional, and Lee, H. K., additional
- Published
- 2015
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3. Fulvivirga lutea sp. nov. , a marine bacterium isolated from seawater.
- Author
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Bae SS, Jung YH, Kwon YM, Chung D, Choi G, Cho K, Yu WJ, and Baek K
- Subjects
- Bacterial Typing Techniques, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 chemistry, Bacteroidetes classification, Phylogeny, Seawater microbiology
- Abstract
A strictly aerobic, Gram-stain-negative, gliding, rod-shaped bacteria, designated strain S481
T , was isolated from a surface seawater sample collected at Gunsan marina, in the West Sea of the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S481T formed a monophyletic clade with members of the genus Fulvivirga , showing 93.7-95.8% sequence similarity to the type strains. Strain S481T has a single circular chromosome of 4.13 Mbp with a DNA G+C content of 37.3 mol%. The values of average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization between strain S481T and all genome-sequenced species of the genus Fulvivirga were below 71.2%, 68.6% and 18.9%, respectively, indicating lower values than the standard cut-offs for species delineation. Growth was observed at 20-42 °C (optimum, 37 °C), at pH 6-8 (optimum, pH 7) and with 0 - 6 % NaCl (optimum, 1-2 %). The major fatty acids (>10%) were iso-C15:0 , iso-C15:1 G and C16:1 ω5 c . The respiratory quinone was MK-7. The major polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids and five unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome-based comparison, strain S481T represents a novel species in the genus Fulvivirga , for which we propose the name Fulvivirga lutea sp. nov. The type strain is S481T (=KCTC 82209T =JCM 34505T ).- Published
- 2022
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4. Ferrimonas lipolytica sp. nov. , a facultatively anaerobic bacterium isolated from seawater.
- Author
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Bae SS, Jung YH, Kwon YM, Chung D, and Baek K
- Subjects
- Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Gammaproteobacteria isolation & purification, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Gammaproteobacteria classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, motile, facultatively anaerobic rod-shaped bacterium with a polar flagellum, designated strain S7
T was isolated from seawater sample collected at Uljin marina, in the East Sea of the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain S7T was affiliated with members of genus Ferrimonas, showing the highest sequence similarities to the type strains Ferrimonas senticii P2S11T (95.7 %), Ferrimonas balearica PATT (95.7 %) and Ferrimonas pelagia CBA4601T (95.1 %). The genome was 4.13 Mbp with a DNA G+C content of 49.4 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between S7T and F. senticii P2S11T and F. balearica PATT yielded ANI values of 71.9 and 70.7 %, and dDDH values of 15.1 and 13.9 %, respectively. The genome of S7T was predicted to encode triacylglycerol lipase, phospholipase A1/A2 and lysophospholipase as well as esterase involved in lipolytic processes. Growth was observed at 8-31 °C (optimum 27 °C), at pH 7-9 (optimum pH 7), and with 1-6 % NaCl (optimum 2 %). The respiratory quinones were MK-7 and Q-7 and the major fatty acids (>10 %) were C16 : 0 , C16 : 1 ω9 c , C17 : 1 ω8 c , and summed feature 3 (C16 : 1 ω7 c and/or C16 : 1 ω6 c ). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, and three unidentified lipids. On the basis of the results of this polyphasic analysis, it was determined that the strain represents a novel species of the genus Ferrimonas , for which the name Ferrimonas lipolytica sp. nov. is proposed. The type strain is S7T (=KCTC 72490T =JCM 33793T ).- Published
- 2021
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5. Clostridium fessum sp. nov., isolated from human faeces.
- Author
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Seo B, Jeon K, Baek I, Lee YM, Baek K, and Ko G
- Subjects
- Bacterial Typing Techniques, Base Composition, Clostridium isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Humans, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Clostridium classification, Feces microbiology, Phylogeny
- Abstract
An obligately anaerobic, Gram-stain-positive and spore-forming strain, SNUG30386
T was isolated from a faecal sample of a healthy Korean subject. The strain formed a round ivory-coloured colony and cells were chained rods with tapered ends, approximately 2.0-2.5×0.6-0.8 μm in size. The taxonomic analysis indicated that strain SNUG30386T was within the family Lachnospiraceae . According to the 16S rRNA gene sequence similarity, the closest species to strain SNUG30386T was Clostridium symbiosum (95.6 %), followed by Enterocloster asparagiformis (94.8 %), Enterocloster clostridioformis (94.8 %) and Enterocloster lavalensis (94.6 %). The evolutionary tree based on 16S rRNA gene sequences demonstrated that strain SNUG30386T had split apart at a unique branch point far from other close relatives. Its DNA G+C content was 48.3 mol% calculated from the whole genome sequence. The major cellular fatty acids were C16 : 0 and C14 : 0 . Compared to those of the closely related species, strain SNUG30386T showed distinct biochemical activities such as being unable to utilize most of carbon sources except d-glucose and l-arabinose. As a result, based on its unique phylogenetic clade and taxonomic characteristics, we conclude that strain SNUG30386T represents a novel species within the genus Clostridium , for which the name Clostridium fessum sp. nov. is proposed. The type strain of the novel species is SNUG30386T (=KCTC 15633T = JCM 32258T ).- Published
- 2021
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6. Lichenicola cladoniae gen. nov., sp. nov., a member of the family Acetobacteraceae isolated from an Antarctic lichen.
- Author
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Noh HJ, Shin SC, Park Y, Choi A, Baek K, Hong SG, Cho YJ, Lee H, and Lee YM
- Subjects
- Acetobacteraceae isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Ubiquinone analogs & derivatives, Ubiquinone chemistry, Acetobacteraceae classification, Lichens microbiology, Phylogeny
- Abstract
Two Gram-stain-negative, facultative anaerobic, chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 26568 and PAMC 26569
T , were isolated from an Antarctic lichen. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains PAMC 26568 and PAMC 26569T belong to the family Acetobacteraceae and the most closely related species are Gluconacetobacter takamatsuzukensis (96.1 %), Gluconacetobacter tumulisoli (95.9 %) and Gluconacetobacter sacchari (95.7 %). Phylogenomic and genomic relatedness analyses showed that strains PAMC 26568 and PAMC 26569T are clearly distinguished from other genera in the family Acetobacteraceae by average nucleotide identity values (<72.8 %) and the genome-to-genome distance values (<22.5 %). Genomic analysis revealed that strains PAMC 26568 and PAMC 26569T do not contain genes involved in atmospheric nitrogen fixation and utilization of sole carbon compounds such as methane and methanol. Instead, strains PAMC 26568 and PAMC 26569T possess genes to utilize nitrate and nitrite and certain monosaccharides and disaccharides. The major fatty acids (>10 %) are summed feature 8 (C18 : 1 ω7 c and/or C18 : 1 ω6 c ; 40.3-40.4 %), C18 : 1 2OH (22.7-23.7 %) and summed feature 2 (C14 : 0 3OH and/or C16 : 1 iso I; 12.0 % in PAMC 26568). The major respiratory quinone is Q-10. The genomic DNA G+C content of PAMC 26568 and PAMC 26569T is 64.6 %. Their distinct phylogenetic position and some physiological characteristics distinguish strains PAMC 26568 and PAMC 26569T from other genera in the family Acetobacteraceae supporting the proposal of Lichenicola gen. nov., with the type species Lichenicola cladoniae sp. nov. (type strain, PAMC 26569T =KCCM 43315T =JCM 33604T ).- Published
- 2020
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7. Antarcticibacterium arcticum sp. nov., a bacterium isolated from marine sediment of the Canadian Beaufort Sea.
- Author
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Lee YM, Baek K, Lee DH, Park Y, Shin SC, and Jin YK
- Subjects
- Bacterial Typing Techniques, Base Composition, Canada, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae isolation & purification, Phospholipids chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, aerobic, yellow-pigmented, flexirubin-negative, rod-shaped and non-motile bacterial strain, PAMC 28998
T , was isolated from a surface sediment sample collected from the Canadian Beaufort Sea. Strain PAMC 28998T grew at 4-37 °C (optimum, 25 °C), at pH 7.0-9.0 (optimum, pH 7.5) and in the presence of 1.0-10.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 28998T belongs to the genus Antarcticibacterium showing the highest sequence similarity (96.8 %) with Antarcticibacterium flavum JB01H24T . The average nucleotide identity and genome-to-genome distance values between PAMC 28998T and the most closely related species ( A. flavum JB01H24T ) were 74.1 and 18.5 %, respectively, indicating that strain PAMC 28998T is clearly distinguished from A. flavum . The genomic DNA G+C content calculated from genome sequences was 39.8 %. The major fatty acids (>10 %) were iso-C15 : 0 (19.5 %), anteiso-C15 : 0 (18.0 %), iso-C16 : 0 (11.6 %) and summed feature 3 (C16:1 ω6 c and/or C16:1 ω7 c ; 11.4 %). The major polar lipids were phosphatidylethanolamine, aminoglycolipid, two unidentified aminolipids, three unidentified phospholipids and four unidentified lipids. The major respiratory quinone was MK-6. Based on the phylogenetic, genomic and phenotypic data presented here, strain PAMC 28998T is considered to represent a novel species of the genus Antarcticibacterium , for which the name Antarcticibacterium arcticum sp. nov. is proposed with the strain PAMC 28998T (=KCCM 43316T =JCM 33514T ).- Published
- 2020
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8. Shewanella maritima sp. nov. , a facultative anaerobic marine bacterium isolated from seawater, and emended description of Shewanella intestini .
- Author
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Bae SS, Jung YH, and Baek K
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Phospholipids chemistry, Quinones chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Shewanella isolation & purification, Phylogeny, Seawater microbiology, Shewanella classification
- Abstract
A Gram-stain-negative, motile, facultative anaerobic rod-shaped marine bacterium, designated strain D4-2
T , was isolated from a sample of seawater collected at Dong-do marina, Dokdo Island, in the East Sea of the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain D4-2T was affiliated with members of genus Shewanella and closely related to Shewanella intestini XMDDZSB0408T (97.4%), followed by Shewanella gelidii RZB5-4T (96.7 %) and Shewanella inventionis KX27T (96.1 %). D4-2T has a single circular chromosome of 4.72 Mbp with a DNA G+C content of 44.5 mol%. Average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values between strain D4-2T and the previously mentioned type strains of species of the genus Shewanella were in range of 69-83.8 % and 20.5-21.7 %, respectively. Growth was observed at 10-36 °C (optimum 29-32 °C), at pH 6-9 (optimum pH 7), and with 1-6% NaCl (optimum 2%). The predominant fatty acids (>10 %) of D4-2T were iso-C15:0 and summed feature 3 (C16:1 ω7 c and/or C16:1 ω6 c ). The respiratory quinones were Q-7, Q-8, MK-7 and MMK-7. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified aminolipid and four unidentified lipids were detected in D4-2T . On the basis of phenotypic, chemotaxonomic and molecular properties, D4-2T represents a novel species of the genus Shewanella , for which the name Shewanella maritima sp. nov. is proposed with D4-2T as the type strain (=KCTC 72040T =JCM 33294T ).- Published
- 2020
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9. Lichenihabitans psoromatis gen. nov., sp. nov., a member of a novel lineage ( Lichenihabitantaceae fam. nov.) within the order of Rhizobiales isolated from Antarctic lichen.
- Author
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Noh HJ, Baek K, Hwang CY, Shin SC, Hong SG, and Lee YM
- Subjects
- Alphaproteobacteria isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Ubiquinone analogs & derivatives, Ubiquinone chemistry, Alphaproteobacteria classification, Lichens microbiology, Phylogeny
- Abstract
Two Gram-stain-negative, facultative anaerobic chemoheterotrophic, pink-coloured, rod-shaped and non-motile bacterial strains, PAMC 29128 and PAMC 29148
T , were isolated from lichen. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strains PAMC 29128 and PAMC 29148T belong to lichen-associated Rhizobiales -1 (LAR1), an uncultured phylogenetic lineage of the order Rhizobiales and the most closely related genera were Methylocapsa (<93.9 %) and Methylosinus (<93.8 %). The results of phylogenomic and genomic relatedness analyses also showed that strains PAMC 29128 and PAMC 29148T were clearly distinguished from other species in the order Rhizobiales with average nucleotide identity values of <71.4 % and genome-to-genome distance values of <22.7 %. Genomic analysis revealed that strains PAMC 29128 and PAMC 29148T did not contain genes involved in atmospheric nitrogen fixation or utilization of carbon compounds such as methane and methanol. Strains PAMC 29128 and PAMC 29148T were able to utilize certain monosaccharides, disaccharides, sugar alcohols and other organic compounds as a sole carbon source. The major fatty acids (>10 %) were summed feature 8 (C18 : 1 ω7 c and/or C18 : 1 ω6 c ; 33.7-39.7 %), summed feature 3 (C16 : 1 ω7 c and/or C16:1 ω 6c ; 25.2-25.4 %) and C19 :0 cyclo ω8 c (11.9-15.4 %). The major respiratory quinone was Q-10. The genomic DNA G+C contents of PAMC 29128 and PAMC 29148T were 63.0 and 63.1 mol%, respectively. Their distinct phylogenetic position and some physiological characteristics support the proposal of Lichenihabitans gen. nov., with the type species Lichenihabitans psoromatis sp. nov. (type strain, PAMC 29148T =KCCM 43293T =JCM 33311T ). Lichenihabitantaceae fam. nov. is also proposed.- Published
- 2019
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10. Faecalibacillus intestinalis gen. nov., sp. nov. and Faecalibacillus faecis sp. nov., isolated from human faeces.
- Author
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Seo B, Jeon K, Baek I, Lee YM, Baek K, and Ko G
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Firmicutes isolation & purification, Humans, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Feces microbiology, Firmicutes classification, Phylogeny
- Abstract
Two long-rod-shaped, Gram-stain-positive, obligately anaerobic and non-spore-forming strains, SNUG30099
T and SNUG30370T , were isolated from faecal samples of healthy Korean subjects. The strains formed circular ivory-coloured colonies on Brain-heart infusion medium supplemented with 0.5% Difco yeast extract (YBHI) agar and cells were approximately 3.5-4.5×0.3-0.4 µm in size. Taxonomic analyses based on 16S rRNA gene sequences distinguished the strains from other species within the family Erysipelotrichaceae. The closest relative of strains SNUG30099T and SNUG30370T was Longibaculum muris (92.9 % and 93.6 % similarity, respectively), followed by Clostridium saccharogumia (92.3 % and 92.2 %). Phylogenetic inference also divided the strains into a unique branch that differed from other related strains that belong to the family Erysipelotrichaceae. DNA G+C contents based on the whole genome sequences of strains SNUG30099T and SNUG30370T were 29.2 and 30.2 mol%, respectively. Both novel strains possessed meso-diaminopimelic acid as the peptidoglycan, and phosphatidylethanolamine was observed as one of the major polar lipids. The major cellular fatty acid composition was different from those of other related taxa. In addition, the profile of biochemical activities advocated that the strains have distinct characteristics in comparison to other strains. Taken together, a novel genus, named Faecalibacillus gen. nov., is proposed, which includes the type species Faecalibacillus intestinalis sp. nov. for strain SNUG30099T and Faecalibacillus faecis sp. nov. for strain SNUG30370T . The type strains of these novel species are SNUG30099T (=KCTC 15631T =JCM 32256T ) and SNUG30370T (=KCTC 15632T =JCM 32257T ).- Published
- 2019
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11. Tamlana carrageenivorans sp. nov., a carrageenan-degrading bacterium isolated from seawater.
- Author
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Jung J, Bae SS, Chung D, and Baek K
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae isolation & purification, Nucleic Acid Hybridization, Phosphatidylethanolamines chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Carrageenan metabolism, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped, agarolytic and carrageenolytic bacterial strain, designated UJ94
T , was isolated from seawater of Uljin in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain UJ94T shared sequence similarities of 98.4, 96.1 and 95.4 % with Tamlana agarivorans JW-26T , Tamlana sedimentorum KMM 9545T and Tamlana crocina HST1-43T , respectively. Growth of strain UJ94T was observed at 4-37 °C and pH 6.5-8.0 in the presence of 2-9 % (w/v) NaCl. The major fatty acids of strain UJ94T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C17 : 0 3-OH; MK-6 was the predominant menaquinone. Phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids were detected as major polar lipids. The whole circular genome comprised 4 116 543 bp and had a G+C content of 35.2 mol%. The ranges of average nucleotide identity and in silico DNA-DNA hybridization estimated by genome-to-genome distance were 90.6-74.2 % and 47.6-14.6 %, respectively, with the type strains of T. agarivorans and T. sedimentorum. The present polyphasic study, including phylogenetic, chemotaxonomic, biochemical and genomic data, suggested that strain UJ94T represents a novel species of the genus Tamlana, for which the name Tamlana carrageenivorans sp. nov. is proposed. The type strain is UJ94T (=KCTC 62451T =NBRC 113234T ).- Published
- 2019
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12. Nibricoccus aquaticus gen. nov., sp. nov., a new genus of the family Opitutaceae isolated from hyporheic freshwater.
- Author
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Baek K, Song J, Cho JC, Chung EJ, and Choi A
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Verrucomicrobia isolation & purification, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Fresh Water microbiology, Phylogeny, Verrucomicrobia classification
- Abstract
A yellow-coloured, Gram-strain-negative, non-motile, cocci-shaped, strictly aerobic bacterium, designated HZ-65
T , was isolated from hyporheic freshwater in the Republic of Korea. Strain HZ-65T grew at 15-37 °C (optimum, 25-30 °C), pH 5.5-9.0 (optimum, pH 7.0) and 0-0.5 % NaCl (w/v; optimum at 0 % NaCl). Phylogenetic analysis based on the 16S rRNA gene showed that strain HZ-65T is a member of family Opitutaceae and is closely related to Opitutus terrae PB90-1T (94.0 % similarity), Cephaloticoccus primus CAG34T (93.0 %), and Cephaloticoccus capnophilus CV41T (92.7 %), while the similarities to other Opitutaceae-type strains were lower than 90.0 %. The DNA G+C content was 62.2 mol% and the quinone present was menaquinone-7. The predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0, C16 : 0, and iso-C16 : 0, representing 70 % of the total fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Analysis of the HZ-65T genome revealed the presence of 300 genes that are involved in carbohydrate-active enzymes, which indicates the metabolic potential to degrade polysaccharides. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain HZ-65T represents a novel species in a new genus within the family Opitutaceae, for which the name Nibricoccus aquaticus gen. nov., sp. nov., is proposed. The type strain of Nibricoccus aquaticus is HZ-65T (KACC 19333T =NBRC 112907T ).- Published
- 2019
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13. Leucothrix arctica sp. nov., isolated from Arctic seawater.
- Author
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Baek K, Choi A, Lee YM, Lee HK, and Cho JC
- Subjects
- Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Thiotrichaceae genetics, Ubiquinone chemistry, Phylogeny, Seawater microbiology, Thiotrichaceae classification
- Abstract
A Gram-stain-negative, non-motile, oxidase- and catalase-positive, rod-shaped bacterium was isolated from a coastal seawater sample from the Arctic Circle and designated strain IMCC9719
T . On the basis of 16S rRNA gene sequence analysis, it was shown that strain IMCC9719T belonged to the genus Leucothrix and was closely related to the type strains of Leucothrix pacifica (97.6 % similarity) and Leucothrix mucor (95.1 %), while the strain shared <90.6 % sequence similarity with other bacterial species. The average nucleotide identity and genome-to-genome distance values between strain IMCC9719T and L. pacifica JCM 18388T were 71.7 and 16.9 %, respectively. The DNA G+C content of strain IMCC9719T was 43.5 mol%. Optimum growth of strain IMCC9719T was observed at 15 °C, at pH 7.5-8.5 and in the presence of 2.0-2.5 % (w/v) NaCl. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. Cells of strain IMCC9719T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid, an unidentified aminophospholipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-8 (Q-8). Based on the taxonomic data collected in this study, strain IMCC9719T represents a novel species of the genus Leucothrix, for which the name Leucothrix arctica sp. nov. is proposed. The type strain is IMCC9719T (=KACC 18010T =NBRC 110382T ).- Published
- 2018
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14. Flavobacterium sediminis sp. nov., a starch-degrading bacterium isolated from tidal flat sediment.
- Author
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Bae SS, Kim MR, Jung Y, Yang SH, Kwon KK, and Baek K
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacterium genetics, Flavobacterium isolation & purification, Nucleic Acid Hybridization, Pigmentation, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacterium classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A yellow-pigmented bacterium with the ability to degrade starch, designated MEBiC07310
T , was isolated from tidal flat sediment collected in Taean County, Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MEBiC07310T was affiliated with the genus Flavobacterium in the phylum Bacteroidetes and showed that the strain was most closely related to Flavobacterium haoranii LQY-7T (96.8 % similarity), followed by Flavobacterium indicum GPTSA 100-9T (95.2 %) and Flavobacterium urocaniciphilum YIT 12746T (94.6 %). Genome-based analysis of the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) of strain MEBiC07310T compared with F. haoranii LQY-7T and F. indicum GPTSA 100-9T yielded ANI values of 77.0 and 73.3 % and DDH values of 18.0±2.7 and 16.1±3.6 %, respectively. The DNA G+C content of strain MEBiC07310T was 35.2 mol%. Cells of the strain were aerobic, Gram-stain-negative and rod-shaped, and negative for flexirubin-type pigments. Growth was observed at 17-43 °C (optimum 32 °C), at pH 5.0-8.0 (optimum pH 7.0) and with 0-3 % (w/v) NaCl (optimum 1 %). The major fatty acids (>10 %) of strain MEBiC07310T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 1 (iso-C15 : 1 H and/or C13 : 0 3-OH) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone was menaquinone MK-6. Based on its phenotypic and genotypic characteristics, strain MEBiC07310T should be classified as representing a novel species of the genus Flavobacterium, for which the name Flavobacterium sediminis sp. nov. is proposed. The type strain is MEBiC07310T (=KCTC 62132T =JCM 32291T ).- Published
- 2018
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15. Deinococcus koreensis sp. nov., a gamma radiation-resistant bacterium isolated from river water.
- Author
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Baek K, Chung EJ, Choi GG, Kim MK, Lim S, and Choi A
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Deinococcus isolation & purification, Deinococcus radiation effects, Fatty Acids chemistry, Glycolipids chemistry, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Deinococcus classification, Gamma Rays, Phylogeny, Rivers microbiology
- Abstract
A gamma radiation-resistant, Gram-stain-negative, rod-shaped bacterial strain, designated SJW1-2
T , was isolated from freshwater samples collected from the Seomjin River, Republic of Korea. The 16S rRNA gene sequence analyses showed that strain SJW1-2T was most closely related to Deinococcus metalli 1PNM-19T (94.3 % sequence similarity) and formed a robust phylogenetic clade with other species of the genus Deinococcus. The optimum growth pH and temperature for the isolate were pH 7.0-7.5 and 25 °C, respectively. Strain SJW1-2T exhibited high resistance to gamma radiation. The predominant respiratory quinone was MK-8. The polar lipid profile consisted of different unidentified glycolipids, two unidentified lipids, two unidentified phospholipids and an unidentified phosphoglycolipid. The major peptidoglycan amino acids were alanine, d-glutamic acid, glycine and l-ornithine. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (25.2 %) and C16 : 0 (21.2 %), and the DNA G+C content was 69.5 mol%. On the basis of phenotypic, genotypic and phylogenetic analyses, strain SJW1-2T (=KACC 19332T =NBRC 112908T ) represents a novel species of the genus Deinococcus, for which the name Deinococcus koreensis sp. nov. is proposed.- Published
- 2018
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16. Self-association and conformational variation of NS5A domain 1 of hepatitis C virus.
- Author
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Beldar S, Manimekalai MSS, Cho NJ, Baek K, Grüber G, and Yoon HS
- Subjects
- Carbamates, Chromatography, Gel, Drug Resistance, Viral, Dynamic Light Scattering, Genotype, Hepacivirus genetics, Protein Domains, Pyrrolidines, Scattering, Small Angle, Valine analogs & derivatives, Viral Nonstructural Proteins antagonists & inhibitors, Viral Nonstructural Proteins genetics, Antiviral Agents pharmacology, Hepacivirus drug effects, Imidazoles pharmacology, Molecular Conformation, Viral Nonstructural Proteins chemistry
- Abstract
Direct-acting antivirals (DAAs) targeting the non-structural 5A (NS5A) protein of the hepatitis C virus (HCV) are crucial drugs that have shown exceptional clinical success in patients. However, their mode of action (MoA) remains unclear, and drug-resistant HCV strains are rapidly emerging. It is critical to characterize the behaviour of the NS5A protein in solution, which can facilitate the development of new classes of inhibitors or improve the efficacy of the currently available DAAs. Using biophysical methods, including dynamic light scattering, size exclusion chromatography and chemical cross-linking experiments, we showed that the NS5A domain 1 from genotypes 1b and 1a of the HCV intrinsically self-associated and existed as a heterogeneous mixture in solution. Interestingly, the NS5A domain 1 from genotypes 1b and 1a exhibited different dynamic equilibria of monomers to higher-order structures. Using small-angle X-ray scattering, we studied the structural dynamics of the various states of the NS5A domain 1 in solution. We also tested the effect of daclatasvir (DCV), the most prominent DAA, on self-association of the wild and DCV-resistant mutant (Y93H) NS5A domain 1 proteins, and demonstrated that DCV induced the formation of large and irreversible protein aggregates that eventually precipitated out. This study highlights the conformational variability of the NS5A domain 1 of HCV, which may be an intrinsic structural behaviour of the HCV NS5A domain 1 in solution.
- Published
- 2018
- Full Text
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17. Marinobacterium aestuarii sp. nov., a benzene-degrading marine bacterium isolated from estuary sediment.
- Author
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Bae SS, Jung J, Chung D, and Baek K
- Subjects
- Bacterial Typing Techniques, Base Composition, Benzene, DNA, Bacterial genetics, Fatty Acids chemistry, Oceanospirillaceae genetics, Oceanospirillaceae isolation & purification, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Estuaries, Geologic Sediments microbiology, Oceanospirillaceae classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, aerobic, motile, flagellated rod-shaped bacterium, designated ST58-10
T , was isolated from an estuarine sediment in the Republic of Korea. The strain was able to degrade benzene. Growth of strain ST58-10T was observed at 4-35 °C (optimum, 20-25 °C), pH 5-9 (optimum, pH 7-8) and 1-8 % NaCl (optimum, 3 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ST58-10T formed a phyletic lineage within the genus Marinobacterium of the family Oceanospirillaceae. Strain ST58-10T was most closely related to Marinobacterium profundum PAMC 27536T (99.6 %) and Marinobacterium rhizophilum CL-YJ9T (98.3 %), and to other members of the genus Marinobacterium(94.5-91.5 %). However, the mean value estimated by using the Genome-to-Genome Distance Calculator was 50.6±7.4 % with M. profundum PAMC 27536T and 30.9±2.8 with M. rhizophilum CL-YJ9T , respectively. An average nucleotide identity value was 89.0 % with M. profundum PAMC 27536T and 85.6 % with M. rhizophilum CL-YJ9T , respectively. The major fatty acids of strain ST58-10T were summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c), summed feature 8 (comprising C18 : 1 ω7c/C18 : 1ω6c), C16 : 0 and C10 : 0 3-OH, and contained ubiquinone (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, an unidentified glycolipid and an unidentified lipid were detected as polar lipids. The DNA G+C content of strain ST58-10T was 58.78 mol%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain ST58-10T represents a novel species of the genus Marinobacterium, for which the name Marinobacterium aestuarii sp. nov. is proposed. The type strain is ST58-10T (=KCTC 52193T =NBRC 112103T ).- Published
- 2018
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18. Parasphingopyxis algicola sp. nov., isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012.
- Author
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Jeong SE, Kim KH, Baek K, and Jeon CO
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonadaceae genetics, Sphingomonadaceae isolation & purification, Ubiquinone chemistry, Phylogeny, Rhodophyta microbiology, Sphingomonadaceae classification
- Abstract
An aerobic, Gram-stain-negative, yellow-pigmented bacterium, designated strain ATAX6-5
T , was isolated from a marine red alga, Asparagopsistaxiformis, in South Korea. Cells were non-motile rods showing catalase- and oxidase-positive reactions. Growth of strain ATAX6-5T was observed at 5-35 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 7.0) and in the presence of 0-6.0 % (w/v) NaCl (optimum, 2 %). Ubiquinone-10 was detected as the sole isoprenoid quinone and C18 : 1ω7c, C16 : 0 and C17 : 1ω6c were identified as the major cellular fatty acids. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, an unknown phospholipid and four unknown glycolipids were detected as polar lipids. The G+C content of the genomic DNA was 60.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ATAX6-5T formed a tight phylogenic lineage with Parasphingopyxis lamellibrachiae JAMH 0132T with a 100 % bootstrap value. Strain ATAX6-5T was most closely related to P. lamellibrachiae JAMH 0132T with a 96.9 % 16S rRNA gene sequence similarity. Based on phenotypic, chemotaxonomic and molecular features, strain ATAX6-5T clearly represents a novel species of the genus Parasphingopyxis, for which the name Parasphingopyxis algicola sp. nov. is proposed. The type strain is ATAX6-5T (=KACC 18993T =JCM 31719T ). An emended description of the genus Parasphingopyxis is also proposed.- Published
- 2017
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19. Planktotalea arctica sp. nov., isolated from Arctic seawater.
- Author
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Baek K, Choi A, Lee YM, Lee HK, and Cho JC
- Subjects
- Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Rhodobacteraceae genetics, Rhodobacteraceae isolation & purification, Sequence Analysis, DNA, Ubiquinone chemistry, Phylogeny, Rhodobacteraceae classification, Seawater microbiology
- Abstract
A Gram-staining-negative, non-motile, non-pigmented, rod-shaped bacterium was isolated from an Arctic coastal seawater sample and was designated strain IMCC9565T. Analysis of the 16S rRNA gene sequence of strain IMCC9565T revealed that the closest phylogenetic neighbours of the strain were members of the genus Planktotalea. Furthermore, the strain formed a robust clade with Planktotalea frisia SH6-1T, with which it shared 97.9 % 16S rRNA gene sequence similarity. Determination of genomic relatedness based on average nucleotide identity and genome-to-genome distance showed that strain IMCC9565T was distantly related to P. frisia, meaning the Arctic strain represents a novel species. Optimum growth of strain IMCC9565T was observed at 20 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and the major polar lipids consisted of phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and two unidentified lipids. The principal fatty acids were C18 : 1ω7c and/or C18 : 1ω6c, C18 : 1ω7c 11-methyl and C16 : 0, and the DNA G+C content was 57.1 mol%. Based on these data, Planktotalea arctica sp. nov. is proposed to accommodate the bacterial isolate and the type strain is IMCC9565T (=KACC 18009T=NBRC 110393T).
- Published
- 2017
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20. Perlucidibaca aquatica sp. nov., isolated from fresh water.
- Author
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Baek K, Han JH, and Lee MH
- Subjects
- Bacterial Typing Techniques, Base Composition, Caves, DNA, Bacterial genetics, Fatty Acids chemistry, Moraxellaceae genetics, Moraxellaceae isolation & purification, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Fresh Water microbiology, Moraxellaceae classification, Phylogeny
- Abstract
A 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 Perlucidibacapiscinae 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.
- Published
- 2017
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21. Roseitalea porphyridii gen. nov., sp. nov., isolated from a red alga, and reclassification of Hoeflea suaedae Chung et al. 2013 as Pseudohoeflea suaedae gen. nov., comb. nov.
- Author
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Hyeon JW, Jeong SE, Baek K, and Jeon CO
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, Phyllobacteriaceae genetics, Phyllobacteriaceae isolation & purification, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Phyllobacteriaceae classification, Phylogeny, Rhodophyta microbiology
- Abstract
A Gram-staining-negative, strictly aerobic bacterial strain, designated MA7-20T, was isolated from a marine alga, Porphyridium marinum, in Korea. Cells showing oxidase-positive and catalase-positive activities were motile rods with bipolar flagella. Growth of strain MA7-20T was observed at 15-45 °C (optimum, 30-37 °C), at pH 6.0-10.5 (optimum, pH 7.0-8.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2-3 %). Strain MA7-20T contained summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), 11-methyl C18 : 1ω7c and C18 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. The G+C content of the genomic DNA was 61.5 mol%. Strain MA7-20T was most closely related to Hoeflea suaedae YC6898T, Oricola cellulosilytica CC-AMH-0T and Nitratireductor basaltis J3T with 96.0, 95.8 and 95.8 % 16S rRNA gene sequence similarities, respectively, but the strain formed a distinct phylogenetic lineage from them within the family Phyllobacteriaceae with a low bootstrap value. H. suaedae also formed a clearly distinct phylogenetic lineage from other members of the genus Hoeflea and closely related genera. On the basis of phenotypic, chemotaxonomic and molecular properties, strain MA7-20T represents a novel species of a new genus of the family Phyllobacteriaceae, for which the name Roseitalea porphyridii gen. nov., sp. nov. is proposed. The type strain is MA7-20T (=KACC 18807T=JCM 31538T). In addition, H. suaedae is also reclassified as Pseudohoeflea suaedae gen. nov., comb. nov. (type strain YC6898T=KACC 14911T=NBRC 107700T).
- Published
- 2017
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22. Lacibacter nakdongensis sp. nov., isolated from river sediment.
- Author
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Han JH, Baek K, and Lee MH
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Geologic Sediments microbiology, Phylogeny, Rivers microbiology
- Abstract
A novel Gram-stain-negative, non-spore-forming, orange-pigmented bacterium, designated strain SS2-56T, was isolated from sediment of the Nakdong River in Sangju-si, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate SS2-56T belongs to the family Chitinophagaceae, and was most closely related to Lacibacter daechungensis H32-4T (96.6 % similarity) and Lacibacter cauensis NJ-8T (96.1 %). Strain SS2-56T contained menaquinone 7 (MK-7) as a respiratory quinone and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as major fatty acids. The major polar lipids of strain SS2-56T were phosphatidylethanolamine, one unidentified aminophospholipid and four unidentified lipids. The DNA G+C content was 43.8 mol%. Phenotypic, chemotaxonomic and phylogenetic evidence clearly indicates that strain SS2-56T represents a novel species of the genus Lacibacter, for which the name Lacibacter nakdongensis sp. nov. is proposed. The type strain is SS2-56T (=KCTC 52160T=JCM 31372T).
- Published
- 2017
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23. Roseovarius confluentis sp. nov., isolated from estuary sediment.
- Author
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Jia X, Kim HR, Jia B, Jeon HH, Baek K, Choi SH, and Jeon CO
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Rhodobacteraceae genetics, Rhodobacteraceae isolation & purification, Sequence Analysis, DNA, Ubiquinone chemistry, Estuaries, Geologic Sediments microbiology, Phylogeny, Rhodobacteraceae classification, Seawater microbiology
- Abstract
A Gram-stain-negative and strictly aerobic bacterium, designated strain SAG6T, was isolated from estuary sediment in South Korea. Cells of strain SAG6T were found to be oxidase- and catalase-positive rods with gliding motility. Cell growth was observed at 15-40 °C (optimum 30 °C), at pH 6.5-10.0 (optimum pH 7.0) and in the presence of 0.5-13.0 % (w/v) NaCl (optimum 2.0 %). Ubiquinone-10 was the only detected respiratory quinone and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C18 : 1ω7c 11-methyl and C12 : 0 were the major fatty acids identified (>5 % of the total fatty acids). The polar lipids of strain SAG6T consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The G+C content of the genomic DNA was 66.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SAG6T formed a tight phyletic lineage within the genus Roseovarius. Strain SAG6T was most closely related to Roseovarius indicus B108T with 97.6 % 16S rRNA gene sequence similarity. Based on phenotypic, chemotaxonomic and molecular features, strain SAG6T clearly represents a novel species of the genus Roseovarius, for which the name Roseovarius confluentis sp. nov. is proposed. The type strain is SAG6T (=KACC 18598T=JCM 31541T).
- Published
- 2017
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24. Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment.
- Author
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Yeon Hwang C, Jung Yoon S, Lee I, Baek K, Mi Lee Y, Yoo KC, Il Yoon H, and Kum Lee H
- Abstract
A Gram-stain-negative, rod-shaped and motile strain, designated PAMC 27536
T , was isolated from deep-sea sediment in the East Sea, Korea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Marinobacterium . Phylogenetic analyses revealed that strain PAMC 27536T was related most closely to Marinobacterium rhizophilum CL-YJ9T with a 16S rRNA gene sequence similarity of 98.5 % and to other members of the genus Marinobacterium (94.0-91.7 %). Genomic relatedness analyses between strain PAMC 27536T and M. rhizophilum KCCM 42386T gave an average nucleotide identity of 85.6 % and an estimated DNA-DNA hybridization of 24.6 % using the genome-to-genome distance calculator, indicating that they represent genomically distinct species. Cells of strain PAMC 27536T grew optimally at 25-30 °C and pH 7.0-7.5 in the presence of 3 % (w/v) sea salts. The major cellular fatty acids were C16 : 1 ω6 c and/or C16 : 1 ω7 c , C18 : 1 ω6 c and/or C18 : 1 ω7 c , and C16 : 0 . The major isoprenoid quinone was Q-8. The genomic DNA G+C content was 56.1-57.2 mol%. Based on the phylogenetic, chemotaxonomic, genomic and phenotypic data presented, a novel species with the name Marinobacterium profundum sp. nov. is proposed, with PAMC 27536T ( = KCCM 43095T = JCM 30410T ) as the type strain.- Published
- 2016
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25. Halocynthiibacter arcticus sp. nov., isolated from Arctic marine sediment.
- Author
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Baek K, Lee YM, Shin SC, Hwang K, Hwang CY, Hong SG, and Lee HK
- Abstract
A Gram-staining-negative, oxidase- and catalase-positive, non-motile, aerobic and rod-shaped bacterium producing white colonies, PAMC 20958
T , was isolated from a marine sediment of the Arctic. PAMC 20958T grew at 10-27 °C (optimally at 21 °C), at pH 5.5-9.5 (optimally at pH 7.0-7.5) and in the presence of 0.5-7.5 % (w/v) (optimally at 2.0 %) NaCl. PAMC 20958T showed 97.5 % 16S rRNA gene sequence similarity with Halocynthiibacter namhaensis KCTC 32362T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain PAMC 20958T and H. namhaensis KCTC 32362T was 79.7 % and the genome-to-genome distance was 13.0 % on average. The genomic DNA G+C content calculated from the genome sequence was 53.2 mol%. The major fatty acids were C18 : 1 ω7 c and/or C18 : 1 ω6 c . The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. On the basis of phylogenetic analysis and genotypic and phenotypic data obtained in this study, it is concluded that strain PAMC 20958T ( = KCTC 42129T = JCM 30530T ) represents the type strain of a novel species of the genus Halocynthiibacter, for which the name Halocynthiibacter arcticus sp. nov. is proposed.- Published
- 2015
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26. Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus.
- Author
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Gyeong HR, Baek K, Hwang CY, Park KH, Kim HM, Lee HK, and Lee YK
- Subjects
- Alaska, Bacillaceae genetics, Bacillaceae isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Molecular Sequence Data, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacillaceae classification, Phylogeny, Soil Microbiology, Tundra
- Abstract
A novel Gram-stain-positive, spore-forming, aerobic, motile and rod-shaped bacterium designated strain PAMC 80007T was isolated from an active layer soil sample of Council, Alaska. Optimal growth of strain PAMC 80007T was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain PAMC 80007T belonged to the genus Domibacillus. This strain was closely related to Domibacillus enclensis (98.3 %), Domibacillus robiginosus (98.3 %) and Domibacillus indicus (97.2 %). Genomic DNA G+C content was 43.5 mol% and genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 80007T is clearly distinguished from the closely related species of the genus Domibacillus. The major fatty acids (>5 %) were iso-C15 : 0 (24.7 %), C16 : 1ω11c (16.8 %), anteiso-C15 : 0 (16.5 %), C16 : 0 (15.6 %) and anteiso-C17 : 0 (8.7 %). The major respiratory isoprenoid quinones were menaquinone-6 (MK-6) and menaquinone-7 (MK-7), and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phospholipid and two unidentified lipids. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan, and the major whole-cell sugar was ribose with a minor quantity of glucose. Results from a polyphasic study suggested that strain PAMC 80007T represents a novel species of the genus Domibacillus for which the name Domibacillus tundrae sp. nov. is proposed. The type strain is PAMC 80007T ( = JCM 30371T = KCTC 33549T = DSM 29572T). An emended description of the genus Domibacillus is also provided.
- Published
- 2015
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27. Aureimonas glaciistagni sp. nov., isolated from a melt pond on Arctic sea ice.
- Author
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Cho Y, Lee I, Yang YY, Baek K, Yoon SJ, Lee YM, Kang SH, Lee HK, and Hwang CY
- Subjects
- Alphaproteobacteria genetics, Alphaproteobacteria isolation & purification, Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Molecular Sequence Data, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Ubiquinone chemistry, Alphaproteobacteria classification, Ice Cover microbiology, Phylogeny, Water Microbiology
- Abstract
A Gram-staining-negative, motile, aerobic and rod-shaped bacterial strain, PAMC 27157T, was isolated from a melt pond on sea ice in the Chukchi Sea. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 27157T revealed an affiliation to the genus Aureimonas with the closest sequence similarity (96.2 %) to that of Aureimonas phyllosphaerae. Strain PAMC 27157T grew optimally at 30 °C and pH 7.0 in the presence of 3.5 % (w/v) NaCl. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, sulfoquinovosyldiacylglycerol and an unidentified aminolipid. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 83.1 %) and the major respiratory quinone was Q-10. The genomic DNA G+C content was 69.1 mol%. The combined phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 27157T could be clearly distinguished from species of the genus Aureimonas with validly published names. Thus, strain PAMC 27157T should be classified as representing a novel species in the genus Aureimonas, for which the name Aureimonas glaciistagni sp. nov. is proposed. The type strain is PAMC 27157T ( = KCCM 43049T = JCM 30183T).
- Published
- 2015
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28. Eionea flava sp. nov., isolated from coastal seawater, and emended description of the genus Eionea.
- Author
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Baek K, Choi A, and Cho JC
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Gammaproteobacteria genetics, Gammaproteobacteria isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Water Microbiology, Gammaproteobacteria classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, non-motile, catalase- and oxidase-positive, facultatively aerobic bacterium, designated IMCC1962(T) was isolated from a surface seawater sample from the Yellow Sea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC1962(T )belonged to the genus Eionea, forming a robust clade with members of the genus, and was most closely related to Eionea nigra (97.3% similarity). DNA-DNA relatedness between strain IMCC1962(T) and Eionea nigra DSM 19752(T) was 21.8-26.3%, which indicated strain IMCC1962(T) represents a novel genomic species of the genus Eionea. The G+C content of the DNA of strain IMCC1962(T) was 48.7 mol%. The major isoprenoid quinone was ubiquinone Q-8 and major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c (43.4%), C18 : 1ω7c and/or C18 : 1ω6c (19.3%) and C16 : 0 (17.2%). The polar lipids found in strain IMCC1962(T) were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, unknown phospholipid, and four unknown polar lipids. Strain IMCC1962(T) and Eionea nigra DSM 19752(T) differed from each other in diverse phenotypic characteristics including motility, colony colour and enzyme activities. On the basis of phenotypic and genotypic data, strain IMCC1962(T) ( = KACC 17481(T)= NBRC 109703(T)) represents a novel species of the genus Eionea, for which the name Eionea flava sp. nov. is proposed. An emended description of the genus Eionea is also provided.
- Published
- 2015
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29. Rheinheimera aestuari sp. nov., a marine bacterium isolated from coastal sediment.
- Author
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Baek K and Jeon CO
- Subjects
- Bacterial Typing Techniques, Base Composition, Chromatiaceae genetics, Chromatiaceae isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Seawater microbiology, Sequence Analysis, DNA, Ubiquinone chemistry, Chromatiaceae classification, Geologic Sediments microbiology, Phylogeny
- Abstract
A Gram-stain-negative, strictly aerobic, non-pigmented, motile bacterium with a single polar flagellum, designated H29T, was isolated from coastal sediment of Jeju Island, South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain H29T was observed at 10-40 °C (optimum, 20-25 °C) and pH 6.0-9.0 (optimum, pH 7.0-8.0), and in the presence of 1-4% (w/v) NaCl (optimum, 2-3%). Strain H29T contained C16 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids and ubiquinone-8 (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 46.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H29T formed a phyletic lineage with Rheinheimera hassiensis E48T within the genus Rheinheimera of the family Chromatiaceae. Strain H29T was most closely related to Rheinheimera pacifica KMM 1406T, Rheinheimera muenzenbergensis E49T, Rheinheimera hassiensis E48T and Rheinheimera baltica OSBAC1T with 97.8%, 97.6%, 97.4% and 97.2% 16S rRNA gene sequence similarities, respectively. However, DNA-DNA hybridization values of strain H29T with type strains of these species were lower than 70%. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain H29T represents a novel species of the genus Rheinheimera, for which the name Rheinheimeraaestuarii sp. nov. is proposed. The type strain is H29T ( = KACC 18251T = JCM 30404T).
- Published
- 2015
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30. Mucilaginibacter vulcanisilvae sp. nov., isolated from a volcanic forest.
- Author
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Baek K and Ok Jeon C
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Molecular Sequence Data, Phosphatidylethanolamines chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Forests, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, strictly aerobic, pale-pink-pigmented bacterium, designated strain G27(T), was isolated from a volcanic forest of Jeju Island, South Korea. Cells were catalase- and oxidase-positive, non-motile rods producing exopolysaccharide and flexirubin-type and pale pink pigments. Growth of strain G27(T) was observed at 4-30 °C (optimum, 25 °C) and pH 5.0-8.0 (optimum, pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain G27(T) formed a phyletic lineage within the genus Mucilaginibacter of the family Sphingobacteriaceae. Strain G27(T) was related most closely to Mucilaginibacter gossypii Gh-67(T) at 96.5% 16S rRNA gene sequence similarity. Strain G27(T) contained menaquinone 7 (MK-7) as the sole isoprenoid quinone and summed feature 3 (comprising C16:1ω7c/C16:1ω6c), iso-C15:0, C16:0, C16:1ω5c and C16:1ω5c as the major cellular fatty acids. Phosphatidylethanolamine was identified as the major polar lipid. The G+C content of the genomic DNA was 46.5 mol%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G27(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter vulcanisilvae sp. nov. is proposed. The type strain is G27(T) ( = KACC 18231(T) = JCM 30363(T)).
- Published
- 2015
- Full Text
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31. Algibacter psychrophilus sp. nov., a psychrophilic bacterium isolated from marine sediment.
- Author
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Jung YJ, Lee YM, Baek K, Hwang CY, Cho Y, Hong SG, Kim JH, and Lee HK
- Subjects
- Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, aerobic, yellow-pigmented, flexirubin-negative, rod-shaped, non-motile and psychrophilic bacterial strain, PAMC 27237T, was isolated from marine sediment of the Ross Sea, Antarctica. Strain PAMC 27237T grew at 0-20 °C (optimally at 17 °C), at pH 5.0-9.5 (optimally at pH 7.0) and in the presence of 0-3.5 % (w/v) NaCl (optimally at 1.5-2.5 %). The major fatty acids (≥5 %) were iso-C17 : 0 3-OH, C17 : 0 2-OH, anteiso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), iso-C15 : 0 3-OH, anteiso-C17 : 1ω9c, anteiso-C15 : 1 A, iso-C16 : 0 3-OH and iso-C15 : 1 G. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, four unidentified lipids and a glycolipid. The major respiratory quinone was MK-6. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 27237T belongs to the genus Algibacter, showing high similarities with the type strains of Algibacter agarivorans (97.2 %), Algibacter agarilyticus (97.0 %) and Algibacter mikhailovii (96.4 %). Average nucleotide identity values between strain PAMC 27237T and the type strains of A. agarivorans and A. agarilyticuswere 83.1 and 84.2 %, respectively, and mean genome-to-genome distances were 22.4-24.2 %, indicating that strain PAMC 27237T is clearly distinguished from the most closely related species of the genus Algibacter. The genomic DNA G+C content calculated from genome sequences was 33.5 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain PAMC 27237T is considered to represent a novel species of the genus Algibacter, for which the name Algibacter psychrophilus sp. nov. is proposed. The type strain is PAMC 27237T ( = KCTC 42130T = JCM 30370T).
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- 2015
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32. Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat.
- Author
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Lo N, Kim KH, Baek K, Jia B, and Jeon CO
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Gammaproteobacteria genetics, Gammaproteobacteria isolation & purification, Hydrocarbons metabolism, Molecular Sequence Data, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Gammaproteobacteria classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, strictly aerobic bacterial strain, designated SM-6T, was isolated from a sea tidal flat of the Dangjin bay, South Korea. Strain SM-6T was able to degrade a broad range of aliphatic hydrocarbons. Cells were catalase- and oxidase-positive and non-motile rods. Growth of strain SM-6T was observed at 10-37 °C (optimum, 20-25 °C), at pH 5.5-9.0 (optimum, pH 6.5-7.5) and in the presence of 0-10 % (w/v) NaCl (optimum, 2-3 %). The only isoprenoid quinone detected was ubiquinone-8 (Q-8). C17:1ω8c, C11:0 3-OH, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), C9:0 3-OH and C10:0 3-OH were observed as the major cellular fatty acids and phosphatidylethanolamine, phosphatidylglycerol and four unidentified lipids were detected as polar lipids. The G+C content of the genomic DNA was 47.5 mol%. Strain SM-6T was most closely related to Pseudomaricurvus alkylphenolicus KU41GT (95.5 %), Maricurvus nonylphenolicus KU41ET (94.4 %) and Pseudoteredinibacter isoporae SW-11T (94.3 %), based on 16S rRNA gene sequences, and phylogenetic analyses showed that strain SM-6T formed a phyletic lineage distinct from the closely related genera. On the basis of phenotypic, chemotaxonomic and molecular features, strain SM-6T represents a novel genus and species of the order Alteromonadales in the class Gammaproteobacteria, for which name Aestuariicella hydrocarbonica gen. nov., sp. nov. is proposed. The type strain is SM-6T ( = KACC 18121T = JCM 30134T).
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- 2015
- Full Text
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33. Sediminicola arcticus sp. nov., a psychrophilic bacterium isolated from deep-sea sediment, and emended description of the genus Sediminicola.
- Author
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Hwang CY, Lee I, Cho Y, Lee YM, Jung YJ, Baek K, Nam SI, and Lee HK
- Subjects
- Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, rod-shaped and non-motile strain, designated PAMC 27266(T), was isolated from deep-sea sediment of the Arctic Ocean. Analysis of the 16S rRNA gene sequence of strain PAMC 27266(T) showed closest affiliation with the genus Sediminicola . Phylogenetic analyses revealed that strain PAMC 27266(T) formed a robust clade with Sediminicola luteus CNI-3(T), with which it shared 98.9% 16S rRNA gene sequence similarity. Genomic relatedness analyses based on the average nucleotide identity and genome-to-genome distance showed that strain PAMC 27266(T) is clearly distinguished from S. luteus . Cells of strain PAMC 27266(T) grew optimally at 15 °C and pH 6.5-7.5 in the presence of 3.5% (w/v) sea salts. The major polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids. The only respiratory quinone was menaquinone-6. The major cellular fatty acids (>10%) were C16 : 1ω6c and/or C16 : 1ω7c and C15 : 0. The genomic DNA G+C content was 37.9 mol%. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data presented, we propose strain PAMC 27266(T) ( =KCCM 43038(T) =JCM 19894(T)) as the type strain of a novel species, with the name Sediminicola arcticus sp. nov., (© 2015 IUMS.)
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- 2015
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34. Mesonia aquimarina sp. nov., a marine bacterium isolated from coastal seawater.
- Author
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Choi A, Baek K, Lee H, and Cho JC
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, aerobic, yellow, non-flagellated, non-gliding, rod-shaped bacterium, designated strain IMCC1021(T), was isolated off the coast of the East Sea. Optimal growth of strain IMCC1021(T) was observed at 25 °C, pH 7.0-7.5 and in the presence of 3.0-3.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain belonged to the genus Mesonia, showing a close relationship with Mesonia mobilis KMM 6059(T) (97.4 % similarity) followed by Mesonia phycicola MDSW-25(T) (96.1 %). DNA-DNA relatedness between strain IMCC1021(T) and M. mobilis KMM 6059(T) was 17.5 % (reciprocal 7.4 %), which indicated that the new isolate represents a novel genomic species of the genus Mesonia. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH, and the G+C content of the genomic DNA was 41.4 mol%. Strain IMCC1021(T) contained menaquinone-6 (MK-6) as the respiratory quinone, and polar lipids comprising phosphatidylethanolamine, two unknown aminolipids and three unknown polar lipids. On the basis of the phylogenetic distinctions and differential phenotypic characteristics, it is suggested that strain IMCC1021(T) ( = KCTC 32320(T) = NBRC 109485(T)) should be assigned to the genus Mesonia as the type strain of a novel species, for which the name Mesonia aquimarina sp. nov. is proposed., (© 2015 IUMS.)
- Published
- 2015
- Full Text
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35. Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment.
- Author
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Baek K, Lee YM, Hwang CY, Park H, Jung YJ, Kim MK, Hong SG, Kim JH, and Lee HK
- Subjects
- Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Geologic Sediments microbiology, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, yellow-pigmented, aerobic, rod-shaped and non-motile bacterium, PAMC 27130(T), was isolated from the marine sediment of the Ross Sea, Antarctica. The temperature, pH and NaCl tolerance ranges for growth were 4-20 °C, pH 6.0-9.0 and 0.5-5.0 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PAMC 27130(T) belonged to the genus Psychroserpens and was closely related to Psychroserpens mesophilus, Psychroserpens damuponensis and Psychroserpens burtonensis with 97.2, 94.7 and 94.2 % sequence similarities, respectively. Genomic relatedness analyses based on average nucleotide identity and genome-to-genome distance showed that strain PAMC 27130(T) could be clearly distinguished from other species of the genus Psychroserpens . The genomic DNA G+C content was 32.7 mol%. The major fatty acids (>10 %) were C20 : 4ω6c (13.2 %), iso-C15 : 0 (12.3 %), iso-C15 : 1 G (11.7 %) and iso-C15 : 0 3-OH (10.0 %). The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified aminophospholipid and three unidentified lipids. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain PAMC 27130(T) represents a novel species of the genus Psychroserpens, for which the name Psychroserpens jangbogonensis sp. nov. is proposed. The type strain is PAMC 27130(T) ( = KCTC 42128(T) = JCM 30228(T))., (© 2015 IUMS.)
- Published
- 2015
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36. Granulosicoccus marinus sp. nov., isolated from Antarctic seawater, and emended description of the genus Granulosicoccus.
- Author
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Baek K, Choi A, Kang I, Im M, and Cho JC
- Subjects
- Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Gammaproteobacteria genetics, Gammaproteobacteria isolation & purification, Molecular Sequence Data, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Ubiquinone chemistry, Gammaproteobacteria classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, motile by flagella, non-pigmented, poly-β-hydroxybutyrate-producing, strictly aerobic and sphere-shaped bacterium, IMCC3490(T), was isolated from a coastal seawater sample from the Antarctic Peninsula. Optimal growth of strain IMCC3490(T) was observed at 20 °C, pH 8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain IMCC3490(T) belonged to the genus Granulosicoccus in the family Granulosicoccaceae. The strain was closely related to Granulosicoccus antarcticus IMCC3135(T) (98.8 % 16S rRNA gene sequence similarity) and Granulosicoccus coccoides Z 271(T) (98.5 %). The DNA-DNA relatedness values between IMCC3490(T) and type strains of the two species of the genus were far lower than 70 %, which indicated strain IMCC3490(T) is a novel genomic species of the genus Granulosicoccus. The major fatty acids of strain IMCC3490(T) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The isoprenoid quinone detected was ubiquinone-8 (Q-8) and predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 61.0 mol%. On the basis of phylogenetic analyses, DNA-DNA relatedness values and phenotypic data, it is suggested that strain IMCC3490(T) represents a novel species of the genus Granulosicoccus, for which the name Granulosicoccus marinus sp. nov. is proposed. The type strain is IMCC3490(T) ( = KACC 17483(T) = NBRC 109704(T)). An emended description of the genus Granulosicoccus is also provided., (© 2014 IUMS.)
- Published
- 2014
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37. Ulvibacter marinus sp. nov., isolated from coastal seawater.
- Author
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Baek K, Jo H, Choi A, Kang I, and Cho JC
- Subjects
- Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-stain-negative, aerobic, chemoheterotrophic, yellow, non-motile and flexirubin-positive bacterium, designated strain IMCC12008(T), was isolated from coastal seawater of the Yellow Sea and subjected to polyphasic taxonomy. Optimal growth was observed at 25 °C, pH 7.0 and in the presence of 2% (w/v) NaCl. Based on 16S rRNA gene sequence analysis and subsequent phylogenetic analyses, strain IMCC12008(T) belonged to the genus Ulvibacter of the family Flavobacteriaceae, with Ulvibacter antarcticus IMCC3101(T) (96.0%) and Ulvibacter litoralis KMM 3912(T) (95.8%) having the highest sequence similaries. The major fatty acids were iso-C(15 : 0) (26.2%) and iso-C(15 : 1) G (10.5%). The DNA G+C content was 38.1 mol%. Strain IMCC12008(T) contained menaquinone-6 (MK-6) as the respiratory quinone, and polar lipids comprising phosphatidylethanolamine, two unidentified aminolipids and an unknown aminophospholipid. On the basis of data collected from this study, strain IMCC12008(T) ( = NBRC 109484(T) = KCTC 32322(T)) represents a novel species of the genus Ulvibacter, for which the name Ulvibacter marinus sp. nov. is proposed., (© 2014 IUMS.)
- Published
- 2014
- Full Text
- View/download PDF
38. Celeribacter marinus sp. nov., isolated from coastal seawater.
- Author
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Baek K, Choi A, Kang I, and Cho JC
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Molecular Sequence Data, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Rhodobacteraceae genetics, Rhodobacteraceae isolation & purification, Sequence Analysis, DNA, Ubiquinone chemistry, Phylogeny, Rhodobacteraceae classification, Seawater microbiology
- Abstract
A Gram-staining-negative, non-motile, non-pigmented and rod-shaped bacterial strain, designated IMCC12053(T), was isolated from coastal surface seawater of the Yellow Sea, Korea. Optimal growth of strain IMCC12053(T) was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. 16S rRNA gene sequence comparisons showed that strain IMCC12053(T) was most closely related to Celeribacter baekdonensis L-6(T) (97.5 % similarity) and Celeribacter neptunius H 14(T) (96.0 %). Strain IMCC12053(T) formed a robust phylogenetic clade with members of the genus Celeribacter. The DNA-DNA relatedness value between IMCC12053(T) and C. baekdonensis was far lower than 70 % (35.7-42.5 %), which indicated that strain IMCC12053(T) is a novel genomic species of the genus Celeribacter. The major respiratory isoprenoid quinone was ubiquinone-10 (Q-10) and major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and aminolipids. The DNA G+C content was 61.0 mol%. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain IMCC12053(T) represents a novel species of the genus Celeribacter, for which the name Celeribacter marinus sp. nov. is proposed. The type strain is IMCC12053(T) ( = KACC 17482(T) = NBRC 109702(T)).
- Published
- 2014
- Full Text
- View/download PDF
39. Formosa arctica sp. nov., isolated from Arctic seawater.
- Author
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Kwon T, Baek K, Lee K, Kang I, and Cho JC
- Subjects
- Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Svalbard, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, gliding, catalase- and oxidase-positive, flexirubin-negative, strictly aerobic bacterium, designated strain IMCC9485(T), was isolated from a seawater sample collected from the Arctic Ocean. Optimal growth of strain IMCC9485(T) was observed at 25 °C, pH 7-8 and in the presence of 1.5-2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC9485(T) belonged to the genus Formosa and was closely related to Formosa algae KCTC 12364(T) (98.2 %) and Formosa agariphila KCTC 12365(T) (98.0 %). DNA-DNA relatedness between the new isolate and F. algae and F. agariphila was far lower than 70 %, which indicated that strain IMCC9485(T) is a novel genomic species of the genus Formosa. The major fatty acids (>10 %) were iso-C15 : 1G (13.7 %), C16 : 1ω7c and/or C16 : 1ω6c (13.4 %) and iso-C15 : 0 (12.3 %). The G+C content of the genomic DNA was 37.6 mol%. Strain IMCC9485(T) contained menaquinone-6 (MK-6) as the respiratory quinone and phosphatidylethanolamine, unknown aminophospholipids and unknown polar lipids as polar lipid constituents. On the basis of phylogenetic analyses and differential phenotypic characteristics, it is suggested that strain IMCC9485(T) ( = KACC 17484(T) = KCCM 42937(T) = NBRC 106080(T)) be assigned to the genus Formosa as the type strain of a novel species, for which the name Formosa arctica sp. nov. is proposed.
- Published
- 2014
- Full Text
- View/download PDF
40. Kordia antarctica sp. nov., isolated from Antarctic seawater.
- Author
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Baek K, Choi A, Kang I, Lee K, and Cho JC
- Subjects
- Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids analysis, Flavobacteriaceae genetics, Flavobacteriaceae isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines analysis, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 analysis, Flavobacteriaceae classification, Phylogeny, Seawater microbiology
- Abstract
A Gram-staining-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC3317(T), was isolated from a coastal seawater sample from the Antarctic Penninsula. Optimal growth of strain IMCC3317(T) was observed at 20 °C, pH 8.0 and in the presence of 2-3 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC3317(T) belonged to the genus Kordia and was closely related to Kordia algicida OT-1(T) (96.7 % sequence similarity) and Kordia periserrulae IMCC1412(T) (96.1 % sequence similarity). The major fatty acids were 10-methyl C16 : 0 and/or iso-C16 : 1ω9c, iso-C17 : 0 3-OH, iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 35.1 mol%. The strain contained menaquinone-6 (MK-6) as the respiratory quinone. The polar lipids detected in the strain were phosphatidylethanolamine and unknown aminophospholipids, aminolipids and polar lipids. On the basis of phylogenetic distinction and differential phenotypic characteristics, it is suggested that strain IMCC3317(T) ( = KCTC 32292(T) = NBRC 109401(T)) be assigned to the genus Kordia as the type strain of a novel species, for which the name Kordia antarctica sp. nov. is proposed.
- Published
- 2013
- Full Text
- View/download PDF
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