107 results on '"Im WT"'
Search Results
2. Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity.
- Author
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Keum DH, Yeon JM, Yun CS, Lee SY, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Glycolipids chemistry, Nucleic Acid Hybridization, Phospholipids chemistry, Pigmentation, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Chryseobacterium classification, Chryseobacterium isolation & purification, Ginsenosides metabolism, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped and yellow-pigmented bacterium, designated strain Gsoil 183
T , was isolated from ginseng-cultivation soil sampled in Pocheon Province, Republic of Korea. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 183T grew at 10-37 °C and at pH 5.0-9.0 on tryptic soy agar. Strain Gsoil 183T had β -glucosidase activity, which was responsible for its ability to convert ginsenoside Rb1 (one of the dominant active components of ginseng) to F2. Based on 16S rRNA gene sequencing, strain Gsoil 183T clustered with species of the genus Chryseobacterium and appeared to be closely related to Chryseobacterium sediminis LMG 28695T (99.1 % sequence similarity), Chryseobacterium lactis NCTC 11390T (98.6%), Chryseobacterium rhizoplanae LMG 28481T (98.6%), Chryseobacterium oncorhynchi CCUG 60105T (98.5%), Chryseobacterium viscerum CCUG 60103T (98.4%) and Chryseobacterium joostei DSM 16927T (98.3%). Menaquinone MK-6 was the predominant respiratory quinone and the major fatty acids were iso-C15 : 0 , iso-C17 : 0 -3OH and summed feature 3 (C16 : 1 ω 6 c and/or C16 : 1 ω 7 c ). The polar lipids were phosphatidylethanolamine, six unidentified glycolipids, five unidentified aminolipids and three unidentified lipids. The G+C content of the genomic DNA was 36.6 mol%. Digital DNA-DNA hybridization between strain Gsoil 183T and the type strains of C. sediminis , C. lactis , C. rhizoplanae , C. oncorhynchi , C. viscerum and C. joostei resulted in values below 70 %. Strain Gsoil 183T could be differentiated genotypically and phenotypically from the recognized species of the genus Chryseobacterium . The isolate therefore represents a novel species, for which the name Chryseobacterium panacisoli sp. nov. is proposed, with the type strain Gsoil 183T (=KACC 15033T =LMG 23397T ).- Published
- 2021
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3. Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water.
- Author
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Park Y, Liu Q, Maeng S, Choi WJ, Chang Y, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Genome Size, Nocardioides isolation & purification, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Mineral Waters microbiology, Nocardioides classification, Phylogeny, Soil Microbiology
- Abstract
Two bacterial strains designated as W3-2-3
T and HKS04T were isolated from mineral water and a soil sample, respectively, in the Republic of Korea. The 16S rRNA genes of the two strains shared a sequence similarity of 93.5 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains W3-2-3T and HKS04T formed a distinct lineage within the genus Nocardioides of the family Nocardioidaceae (order Propionibacteriales ). The closely related species of strain W3-2-3T were Nocardioides albidus (98.9 %), Nocardioides caeni (98.8 %), Nocardioides kongjuensis (98.6 %), Nocardioides aromaticivorans (98.5 %), Nocardioides nitrophenolicus (98.4 %), Nocardioides flava (98.2 %) and Nocardioides ginsengisoli (98.1 %). The closest species of strain HKS04T was Nocardioides halotolerans (98.7 %). The genome sizes of strains W3-2-3T and HKS04T were 4741198 and 5 120341 bp, respectively. The genomic DNA G+C contents of strains W3-2-3T and HKS04T were 73.3 and 72.1 mol%, respectively. The main fatty acids of strain W3-2-3T were C17:1 ω 6 c and iso-C16:0 and those of strain HKS04T were iso-C16:0 and iso-C16:0 H. The main polar lipids of both strains were diphosphatidylglycerol and phosphatidylglycerol and the predominant respiratory quinone was MK-8(H4 ), supporting the affiliation of these strains with the genus Nocardioides . Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, Nocardioides convexus W3-2-3T (KACC 21211T =LMG 31251T ) and Nocardioides anomalus HKS04T (KACC 18879T =LMG 31249T ), are proposed.- Published
- 2020
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4. Devosia ginsengisoli sp. nov., isolated from ginseng cultivation soil.
- Author
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Quan XT, Siddiqi MZ, Liu QZ, Lee SM, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Hyphomicrobiaceae isolation & purification, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone analogs & derivatives, Ubiquinone chemistry, Hyphomicrobiaceae classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, strictly aerobic, motile, ivory-coloured and rod-shaped bacterium (designated Gsoil 520
T ) isolated from ginseng cultivation soil was characterized by using a polyphasic approach to clarify its taxonomic position. Strain Gsoil 520T was observed to grow optimally at 30 °C and pH 7.0 on Reasoner's 2A agar medium. The results of phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that Gsoil 520T belongs to the genus Devosia of the family Hyphomicrobiaceae and was most closely related to Devosia epidermidihirudinis E84T (98.0 %), Devosia yakushimensis Yak96BT (97.7 %), Devosia neptuniae J1T (97.7 %) and Devosia chinhatensis IPL18T (96.8 %). The complete genome of strain Gsoil 520T is a presumptive circular chromosome of 4 480 314 base pairs having G+C content of 63.7 mol%. A total of 4 354 genes, 4 303 CDS and 43 rRNA genes were assigned a putative function. The major isoprenoid quinone was Q-10. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminolipids (AL1 and AL3). The predominant fatty acids of strain Gsoil 520T were C18 : 1 ω7 c 11-methyl, C16 : 0 and C18 : 1 ω7 c /C18 : 1 ω6 c (summed feature 8) supporting the affiliation of strain Gsoil 520T to the genus Devosia . The low values of DNA-DNA hybridization distinguished strain Gsoil 520T from the recognized species of the genus Devosia . Thus, the novel isolate represents a novel species of the genus Devosia , for which the name Devosia ginsengisoli sp. nov. is proposed, with the type strain Gsoil 520T (=KACC 19440T =LMG 30329T ).- Published
- 2020
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5. Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.
- Author
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Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids chemistry, Lysobacter isolation & purification, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Ubiquinone chemistry, Lysobacter classification, Phylogeny, Rhizosphere, Soil Microbiology, Nicotiana microbiology
- Abstract
A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain C8-1
T , was isolated from the rhizosphere soil of Nicotiana tabacum L. collected from Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10-40 °C, at pH 6.0-8.0 and in the presence of up to 1 % (w/v) NaCl, with optimal growth at 30 °C and pH 7.0. The predominant isoprenoid quinone was Q-8. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. The genomic DNA G+C content was 70.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C8-1T should be assigned to the genus Lysobacter. 16S rRNA gene sequence similarity analysis showed that strain C8-1T was closely related to Lysobacter cavernae YIM C01544T (98.6 %), Lysobacter soli DCY21T (97.6 %), Lysobacter panacisoli CJ29T (97.3 %), Lysobacter firmicutimachus PB-6250T (97.3 %), Lysobacter niastensis GH41-7T (97.3 %) and Lysobacter gummosus KCTC 12132T (97.1 %). DNA-DNA hybridization data indicated that the isolate may represent a novel genomic species belonging to the genus Lysobacter. Polyphasic taxonomic characteristics indicated that strain C8-1T represents a novel species of the genus Lysobacter, for which the name Lysobacter tabacisoli sp. nov. is proposed. The type strain is C8-1T (=KCTC 62034T =CGMCC 1.16271T ) .- Published
- 2019
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6. Caballeronia ginsengisoli sp. nov., isolated from ginseng cultivating soil.
- Author
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Quan XT, Liu QZ, Siddiqi MZ, and Im WT
- Subjects
- Base Composition, Burkholderiaceae chemistry, Burkholderiaceae genetics, Burkholderiaceae isolation & purification, DNA, Bacterial chemistry, Fatty Acids analysis, Panax, Phospholipids analysis, Phylogeny, RNA, Ribosomal, 16S genetics, Soil, Burkholderiaceae classification, Soil Microbiology
- Abstract
A Gram-stain-negative, strictly aerobic, non-motile, ivory colored and rod-shaped bacterium (designated Gsoil 652
T ) isolated from ginseng cultivating soil, was characterized using a polyphasic approach to clarify its taxonomic position. Strain Gsoil 652T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Phylogenetic analysis, based on 16S rRNA gene sequences similarities, indicated that Gsoil 652T belongs to the genus Caballeronia of the family Burkholderiaceae and was most closely related to Caballeronia choica LMG 22940T (98.9%), Caballeronia udeis LMG 27134T (98.9%), Caballeronia sordidicola LMG 22029T (98.2%) and Caballeronia humi LMG 22934T (98.1%). The DNA G+C content was 62.1 mol% and Q-8 was the major isoprenoid quinone. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipid, and unidentified phospholipid. The predominant fatty acids were C16:0 , C17:0 cyclo and C19:0 cyclo ω8c. The DNA-DNA relatedness value between strain Gsoil 652T and closely related type strains of Caballeronia species were less than 36.0%. Moreover, strain Gsoil 652T could be distinguished phenotypically from the recognized species of the genus Caballeronia. The novel isolate, therefore, represents a novel species, for which the name Caballeronia ginsengisoli sp. nov. is proposed, with the type strain Gsoil 652T (= KACC 19441T = LMG 30326T ).- Published
- 2019
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7. Mesorhizobium hankyongi sp. nov. Isolated from Soil of Ginseng Cultivating Field.
- Author
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Siddiqi MZ, Shah S, Choi KD, Lee SY, Kim SY, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids chemistry, Fatty Acids metabolism, Mesorhizobium classification, Mesorhizobium genetics, Mesorhizobium metabolism, Panax microbiology, Phylogeny, RNA, Ribosomal, 16S genetics, Mesorhizobium isolation & purification, Panax growth & development, Soil Microbiology
- Abstract
A Gram-negative, non-spore-forming and rod-shaped, bacterium (designated Gsoil 531
T ) was isolated from soil of a ginseng field. On the basis of 16S rRNA gene sequence, strain Gsoil 531T clustered with species of the genus Mesorhizobium and was closely related to M. camelthorni CCNWXJ 40-4T (98.9%) and M. alhagi CCNWXJ12-2T (98.7%). The DNA G + C content was 62.9 mol% and the predominant quinone was ubiquinone-10 (Q-10). The major cellular fatty acids were C16:0 , C19:0 cyclo ω8c and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The DNA-DNA hybridization values were less than 35.0% between novel isolate and its closest reference strains M. camelthorni HAMBI 3020T , M. alhagi HAMBI 3019T and M tamadayense LMG 26736T . Physiological, biochemical and low values of DNA-DNA hybridization results enabled strain Gsoil 531T to be differentiated genotypically and phenotypically from all known species of the genus Mesorhizobium. Therefore, strain Gsoil 531T signifies a novel species of the genus Mesorhizobium, for which the name Mesorhizobium hankyongi sp. nov. is proposed. The type strain Gsoil 531T (= KACC 19443T = LMG 30463T ).- Published
- 2018
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8. Phenylobacterium terrae sp. nov., isolated from a soil sample of Khyber-Pakhtun-Khwa, Pakistan.
- Author
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Khan IU, Habib N, Xiao M, Huang X, Khan NU, Im WT, Ahmed I, Zhi XY, and Li WJ
- Subjects
- Alphaproteobacteria chemistry, Alphaproteobacteria genetics, Bacterial Typing Techniques, Molecular Typing, Pakistan, Phenotype, Phylogeny, RNA, Ribosomal, 16S genetics, Alphaproteobacteria classification, Alphaproteobacteria isolation & purification, Soil Microbiology
- Abstract
A Gram-stain negative, aerobic, motile, non-spore-forming and rod-shaped bacterial strain, designated YIM 730227
T , was isolated from a soil sample, collected from Karak district, Khyber-Pakhtun-Khwa, Pakistan. The bacterium was characterized using a polyphasic taxonomic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strain YIM 730227T is closely related to Phenylobacterium lituiforme FaiI3T (97.5% sequence similarity), Phenylobacterium muchangponense A8T (97.4%), Phenylobacterium panacis DCY109T (97.1%), Phenylobacterium immobile ET (97.1%) and Phenylobacterium composti 4T-6T (97.0%), while also sharing 98.0% sequence similarity with Phenylobacterium hankyongense HKS-05T after NCBI blast, showing it represents a member of the family Caulobacteraceae. The major respiratory quinone was Q-10 and the major fatty acids were C16:0, summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), C18:1 ω7c 11-methyl and C17:0 . The polar lipids were phosphatidylglycerol, unidentified glycolipids, phospholipid and unidentified lipid. The G + C content of the genomic DNA was 68.2 mol%. The DNA-DNA relatedness values of strain YIM 730227T with P. hankyongense HKS-05T , P. lituiforme FaiI3T , P. muchangponense A8T , P. panacis DCY109T , P. immobile ET and P. composti 4T-6T were 31.3 ± 0.6, 26.1 ± 0.2, 24.3 ± 0.1, 21.8 ± 0.9, 19.8 ± 0.6 and 18.2 ± 1.1%, respectively, values lower than 70%. Besides the morphological and chemotaxonomic characteristics, phylogenetic analyses of 16S rRNA gene sequences and the biochemical characteristics indicated that the strain YIM 730227T represents a novel member of the genus Phenylobacterium, for which the name Phenylobacterium terrae sp. nov. (type strain YIM 730227T = KCTC62324T = CGMCC 1.16326T ) is proposed.- Published
- 2018
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9. Brevibacterium anseongense sp. nov., isolated from soil of ginseng field.
- Author
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Jung MS, Quan XT, Siddiqi MZ, Liu Q, Kim SY, Wee JH, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, Brevibacterium genetics, Brevibacterium isolation & purification, DNA, Bacterial genetics, Diaminopimelic Acid analysis, Fatty Acids analysis, Phosphatidylglycerols analysis, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Brevibacterium classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
Gram-positive, aerobic, non-motile, pale-yellow, and rodshaped bacterium, designated as Gsoil 188
T , was isolated from the soil of a ginseng field in Pocheon, South Korea. A phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Brevibacterium and was most closely related to B. epidermidis NBRC 14811T (98.4%), B. sediminis FXJ8.269T (98.2%), B. avium NCFB 3055T (98.1%), and B. oceani BBH7T (98.1%), while it shared less than 98.1% identity with the other species of this genus. The DNA G + C content was 68.1 mol%. The predominant quinone was MK-8(H2 ). The major fatty acids were anteiso-C15:0 and anteiso-C17:0 . The cell wall peptidoglycan of strain Gsoil 188T contained meso-diaminopimelic acid. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminolipid. The physiological and biochemical characteristics, low DNA-DNA relatedness values, and taxonomic analysis allowed the differentiation of strain Gsoil 188T from the other recognized species of the genus Brevibacterium. Therefore, strain Gsoil 188T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium anseongense sp. nov. is proposed, with the type strain Gsoil 188T (= KACC 19439T = LMG 30331T ).- Published
- 2018
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10. Actinomadura hankyongense sp. nov. Isolated From Soil of Ginseng Cultivating Field.
- Author
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Siddiqi MZ, Liu Q, Choi KD, Lee SY, Lee JH, and Im WT
- Subjects
- Actinomycetales classification, Actinomycetales genetics, Actinomycetales metabolism, Bacterial Typing Techniques, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids chemistry, Fatty Acids metabolism, Genotype, Panax microbiology, Phylogeny, Actinomycetales isolation & purification, Panax growth & development, Soil Microbiology
- Abstract
A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 556
T ) was isolated from soil of a ginseng field and subjected to its taxonomic position. Based on 16S rRNA gene sequence similarity, strain Gsoil 556T was shown to belong to the genus Actinomadura of the family Thermomonosporaceae and was closely related to A. montaniterrae CYP1-1BT (99.3%), A. nitritigenes DSM 44137T (98.7%), and A. rudentiformis HMC1T (98.5%), while it showed less than 98.4% sequence similarity to the other species of this genus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that it is most closely related to A. rudentiformis HMC1T and A. nitritigenes DSM 44137T . The DNA G+C content was 73.1 mol%. The peptidoglycan was meso-diaminopimelic acid and the whole-cell sugar contained fucose, galactose, glucose, mannose, and ribose. The predominant menaquinone (KK) was MK-9(H8 ) [55%] and MK-9(H6 ) [45%]. The major cellular fatty acids were C14:0 , C16:0 , C18:1 ω9c and summed feature 3 (C16:1 ω6c/C16:1 ω7c). All these data supported the affiliation of strain Gsoil 556T to the genus Actinomadura. The DNA-DNA hybridization between strain Gsoil 556T and its phylogenetically closest relatives were less than 40%. Furthermore, the results of physiological and biochemical tests enabled strain Gsoil 556T to be differentiated genotypically and phenotypically from currently known Actinomadura species. Therefore, strain Gsoil 556T represents a novel species of the genus Actinomadura, for which the name Actinomadura hankyongense sp. nov. is proposed. The type strain Gsoil 556T (=KACC 19438T =LMG 30327T ).- Published
- 2018
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11. Brevibacterium hankyongi sp. nov., isolated from compost.
- Author
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Choi KD, Siddiqi MZ, Liu Q, Muhammad Shafi S, Durrani Y, Lee SY, Kang MS, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, Brevibacterium genetics, Brevibacterium isolation & purification, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Nucleic Acid Hybridization, Peptidoglycan chemistry, Phosphatidylglycerols chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Brevibacterium classification, Composting, Phylogeny, Soil Microbiology
- Abstract
A Gram-positive, strictly aerobic, non-motile, milky-white to creamy coloured and rod-shaped bacterium, designated BS05
T , was isolated from compost. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Brevibacterium and was most closely related to Brevibacterium avium NCFB 3055T (96.3 %), Brevibacterium oceani BBH7T (96.2 %) and Brevibacterium epidermidis NBRC 14811T (96.1 %). The DNA G+C content was 62.3 mol%. The predominant quinone was MK-8(H2). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The cell-wall peptidoglycan of strain BS05T contained meso-diaminopimelic acid. The major polar lipid was phosphatidylglycerol. Moreover, the low sequence similarity of the 16S rRNA gene sequencing, physiological, biochemical and chemotaxonomic analyses allowed the phenotypic and genotypic differentiation of strain BS05T from the recognized species of the genus Brevibacterium. Therefore, strain BS05T represents a novel species of the genus Brevibacterium, for which the name Brevibacteriumhankyongi sp. nov. is proposed, with the type strain BS05T (=KACC 18875T =LMG 29562T ).- Published
- 2018
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12. Olivibacter ginsenosidimutans sp nov., with ginsenoside converting activity isolated from compost, and reclassification of Pseudosphingobacterium domesticum as Olivibacter domesticus comb. nov.
- Author
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Siddiqi MZ, Liu Q, Lee SY, Choi KD, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, Composting, DNA, Bacterial genetics, Fatty Acids chemistry, Ginsenosides metabolism, Phosphatidylethanolamines chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, aerobic and rod-shaped, bacterium designated as strain BS18
T , was isolated from compost and subjected to a polyphasic taxonomic analysis. On the basis of the results of 16S rRNA gene sequence analysis, BS18T represents a member of the genus Olivibacter of the family Sphingobacteriaceaeand is most closely related to Olivibacter oleidegradansTBF2/20.2T (93.7 %), Olivibacter jilunii 14-2AT (93.6 %), Olivibacter ginsengisoli Gsoil 060T (93.6 %), Pseudosphingobacterium domesticumDC186T (93.0 %) and shared ≤93.1 % sequence similarity with the other members of the genus Olivibacter. BS18T contained MK-7 as the predominant quinone, iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), as the major fatty acids and phosphatidylethanolamine (PE) as main polar lipid. BS18T could be distinguished from the other members of the genus Olivibacter by a number of chemotaxonomic and phenotypic characteristics. On the basis of the results of polyphasic taxonomic analysis, BS18T represents a novel species within the genus, for which the name Olivibacter ginsenosidimutans sp. nov. is proposed. The type strain of Olivibacter ginsenosidimutans is BS18T (=KACC 16612T =JCM 18200T ). It is also proposed to transfer Pseudosphingobacterium domesticumto the genus Olivibacter, as Olivibacter domesticus comb. nov. (type strain DC186T =CCUG 54353T =LMG 23837T ).- Published
- 2018
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13. Aeromicrobium panacisoli sp. nov. Isolated from Soil of Ginseng Cultivating Field.
- Author
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Siddiqi MZ, Lee SY, Choi KD, and Im WT
- Subjects
- Actinomycetales classification, Actinomycetales genetics, Actinomycetales metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids chemistry, Fatty Acids metabolism, Phylogeny, Republic of Korea, Actinomycetales isolation & purification, Panax growth & development, Soil Microbiology
- Abstract
A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 137
T ) was isolated from soil of a ginseng field of Pocheon province in South Korea and subjected to a polyphasic approach in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 137T was shown to belong to the family Nocardioidaceae and was closely related to Aeromicrobium ginsengisoli Gsoil 098T (96.7%), Aeromicrobium panaciterrae (96.7%), and Aeromicrobium halocynthiae JCM 15749T (96.6%). Being phylogenetic, it was most closely related to Aeromicrobium halocynthiae JCM 15749T . The G+C content of the genomic DNA was 70.3 mol%. The diagnostic diamino acid of the cell wall peptidoglycan was LL-diaminopimelic acid. The predominant menaquinone was menaquinone MK-8 (H4 ) and MK-7 (H4) was a minor compound. The major cellular fatty acids were C14:0 , C16:0 , C18:1 ω9c and summed feature 4 (C16:1 ω7c/C15:0 iso 2-OH). All these data supported the affiliation of strain Gsoil 137T to the genus Aeromicrobium. The results of physiological and biochemical tests enabled strain Gsoil 137T to be differentiated genotypically and phenotypically from currently known Aeromicrobium species. Therefore, strain Gsoil 137T represents a novel species of the genus Aeromicrobium, for which the name Aeromicrobium panacisoli sp. nov. is proposed. The type strain is Gsoil 137T (= KCTC 19130T = DSM 17940T = CCUG 52475T ).- Published
- 2018
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14. Polaromonas ginsengisoli sp. nov., isolated from ginseng field soil.
- Author
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Choi KD, Siddiqi MZ, Liu Q, Jo JH, Chun SY, Choi GM, Kim SY, Lee SY, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, Comamonadaceae genetics, Comamonadaceae isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Comamonadaceae classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-reaction-negative, strictly aerobic, milky-white and rod-shaped bacterium (designated Gsoil 115
T ) isolated from ginseng field soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gsoil 115T grew optimally at 30 °C and at pH 7.0 on Reasoner's 2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gsoil 115T belongs to the genus Polaromonas and was most closely related to Polaromonaseurypsychrophila B717-2T (98.6 %), Polaromonasvacuolata 34-PT (98.3 %), Polaromonasjejuensis NBRC 106434T (98.1 %), Polaromonas aquatic CCUG 39402T (97.7 %) and Polaromonascryoconiti Cr4-35T (97.5 %). The DNA G+C content was 60.9 mol%. The DNA-DNA hybridization relatedness between strain Gsoil 115T and P. eurypsychrophila B717-2T , P. vacuolata 34-PT , P. jejuensis NBRC 106434T , P. aquatic CCUG 39402T and P. cryoconiti Cr4-35T were 31.2, 21.6, 16.9, 8.7 and 10.1 %, respectively. The major polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE). The sole respiratory quinone was Q-8. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), which supported the affiliation of strain Gsoil 115T to the genus Polaromonas. Moreover, the physiological, biochemical and low level of DNA-DNA relatedness value allowed the phenotypic and genotypic differentiation of strain Gsoil 115T from the recognized species of the genus Polaromonas. Therefore, strain Gsoil 115T represents a novel species of the genus Polaromonas, for which the name Polaromonas ginsengisoli sp. nov. is proposed, with the type strain Gsoil 115T (LMG 23393T =KCTC 12577T ).- Published
- 2018
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15. Terrabacter ginsengisoli sp. nov., isolated from ginseng cultivating soil.
- Author
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Jin MF, Quan XT, Siddiqi MZ, Liu QZ, Yu HS, and Im WT
- Subjects
- Actinobacteria genetics, Actinobacteria physiology, Bacterial Typing Techniques, Base Composition, Cardiolipins analysis, DNA, Bacterial genetics, Fatty Acids analysis, Genotype, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Phenotype, Phosphatidylethanolamines analysis, Phosphatidylglycerols analysis, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Soil, Species Specificity, Actinobacteria classification, Actinobacteria isolation & purification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-positive, strictly aerobic, nonmotile, yellowish, coccus-rod-shaped bacterium (designated Gsoil 653
T ) isolated from ginseng cultivating soil was characterized using a polyphasic approach to clarify its taxonomic position. The strain Gsoil 653T exhibited optimal growth at pH 7.0 on R2A agar medium at 30°C. Phylogenetic analysis based on 16S rRNA gene sequence similarities, indicated that Gsoil 653T belongs to the genus Terrabacter of the family Humibacillus, and was closely related to Terrabacter tumescens DSM 20308T (98.9%), Terrabacter carboxydivorans PY2T (98.9%), Terrabacter terrigena ON10T (98.8%), Terrabacter terrae PPLBT (98.6%), and Terrabacter lapilli LR-26T (98.6%). The DNA G + C content was 70.5 mol%. The major quinone was MK-8(H4 ). The primary polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidyl-ethanolamine. The predominant fatty acids were iso-C15:0 , iso-C16:0 , iso-C14:0 , and anteiso-C15:0 , as in the case of genus Terrabacter, thereby supporting the categorization of strain Gsoil 653T . However, the DNA-DNA relatedness between Gsoil 653T and closely related strains of Terrabacter species was low at less than 31%. Moreover, strain Gsoil 653T could be both genotypically and phenotypically distinguished from the recognized species of the genus Terrabacter. This isolate, therefore, represents a novel species, for which the name Terrabacter ginsengisoli sp. nov. is proposed with the type strain Gsoil 653T (= KACC 19444T = LMG 30325T ).- Published
- 2018
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16. Lysobacter spongiae sp. nov., isolated from spongin.
- Author
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Choi H, Im WT, and Park JS
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids analysis, Lysobacter genetics, Lysobacter physiology, Nucleic Acid Hybridization, Phospholipids analysis, Quinones analysis, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Species Specificity, Lysobacter classification, Lysobacter isolation & purification, Phylogeny, Soil Microbiology
- Abstract
A Gram-negative, motile, aerobic and rod-shaped bacterial strain designated 119BY6-57
T was isolated from spongin. The taxonomic position of the novel isolate was confirmed using the polyphasic approach. Strain 119BY6-57T grew well at 25-30°C on marine agar. On the basis of 16S rRNA gene sequence similarity, strain 119BY6-57T belongs to the family Xanthomonadaceae and is related to Lysobacter aestuarii S2-CT (99.8% sequence similarity), L. maris KMU-14T (97.5%), and L. daejeonensis GH1-9T (97.3%). Lower sequence similarities (97.0%) were found with all of the other recognized members of the genus Lysobacter. The G + C content of the genomic DNA was 69.9 mol%. The major respiratory quinone was Q-8 and the major fatty acids were C16:0 iso, C15:0 iso, summed feature 9 (comprising C17:1 iso ω9c and/or C16:0 10-methyl), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), and C11:0 iso 3-OH. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified phospholipids, and an unidentified polar lipid. DNADNA relatedness values between strain 119BY6-57T and its closest phylogenetically neighbors were below 48.0 ± 2.1%. Based on genotypic and phenotypic characteristics, it is concluded that strain 119BY6-57T is a new member within the genus Lysobacter, for which the name Lysobacter spongiae sp. nov. is proposed. The type strain is 119BY6-57T (= KACC 19276T = LMG 30077T ).- Published
- 2018
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17. Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.
- Author
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An DS, Siddiqi MZ, Kim KH, Yu HS, and Im WT
- Subjects
- Bacteria genetics, Bacteria metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Fatty Acids metabolism, Panax growth & development, Phylogeny, RNA, Ribosomal, 16S genetics, Bacteria classification, Bacteria isolation & purification, Soil Microbiology
- Abstract
A taxonomic study was conducted on BR7-21
T , a bacterial strain isolated from the soil of a ginseng field in Baekdu Mountain. Comparative studies of the 16S rRNA gene sequence showed that the isolate was most closely related to Conexibacter woesei DSM 14684T , Solirubrobacter pauli ATCC BAA-492T , Patulibacter minatonensis JCM 12834T , with 93.8%, 92.4%, and 91.5% sequence similarity, respectively; each genus represented a family in the order Solirubrobacterales. Strain BR7-21T was Gram-reaction positive, non-spore forming, aerobic, non-motile, and short rod-shaped. It grew well on half-strength R2A medium. The G + C content of the genomic DNA was 73.9%. It contained meso-diaminopimelic acid in the cell wall and the major menaquinones were MK-7(H4 ) and MK-8(H4 ). The major fatty acids were summarized as (C16:1 ω7c/iso-C15:0 2-OH), iso-C16:0 , and C17:0 cyclo. On the basis of polyphasic evidence, it was proposed that strain BR7-21T should be placed in a new genus and species, for which the name Baekduia soli gen. nov., sp. nov. was proposed with the type strain BR7-21T (= KCTC 22257T = LMG 24797T ). The family Baekduiaceae fam. nov. is proposed to encompass the genus Baekduia gen. nov.- Published
- 2018
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18. Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil.
- Author
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Choi GM and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, Burkholderiaceae genetics, Burkholderiaceae isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Nitrogen Fixation, Nucleic Acid Hybridization, Oryza, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone chemistry, Burkholderiaceae classification, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated NF2-5-3
T , was isolated from a paddy soil in Anseong city, Republic of Korea. This bacterium was characterized to determine its taxonomic position using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NF2-5-3T had a close relationship with, and was related most closely to, members of the genus Paraburkholderia, namely Paraburkholderia caribensis MWAP64T (98.8 % similarity), P. sabiae Br3407T (98.8 %), P. hospita LMG 20598T (98.5 %), P. terrae NBRC 100964T (98.3 %) and P. phymatum STM815T (98.1 %). Growth of strain NF2-5-3T occurred at 15-37 °C, at pH 6.0-8.0 and at NaCl concentrations of 0-2 % (w/v). The major respiratory quinone was ubiquinone 8 (Q-8) and the major fatty acids were C16 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C17 : 0 cyclo and C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, unidentified aminophospholipids, unidentified aminolipids and unidentified polar lipids. The G+C content of the genomic DNA was 64.2 mol%. DNA-DNA relatedness values between strain NF2-5-3T and its closest phylogenetic neighbours were much lower than 70 %. Strain NF2-5-3T could be differentiated phylogenetically and phenotypically from recognized species of the genus Paraburkholderia. The isolate therefore represents a novel species, for which the name Paraburkholderia azotifigens sp. nov. is proposed, with NF2-5-3T (=KACC 18968T =LMG 29961T ) as the type strain.- Published
- 2018
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19. Mucilaginibacter panaciglaebae sp. nov., isolated from soil of a ginseng field.
- Author
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Lee SY, Siddiqi MZ, Kim SY, Yu HS, Lee JH, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-reaction-negative, strictly aerobic, non-motile and rod-shaped bacterium, designated strain BXN5-31
T , was isolated from soil of a ginseng field, and its taxonomic position was investigated using a polyphasic approach. Strain BXN5-31T grew at 18-37 °C and at pH 6.0-8.0 on R2A medium. Based on 16S rRNA gene sequence similarity, strain BXN5-31T was shown to belong to the genus Mucilaginibacter and was closely related to Mucilaginibactersoyangensis HME6664T , Mucilaginibacterximonensis XM-003T and Mucilaginibacterpuniceus WS71T . The DNA G+C content was 43.6 %. The predominant respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA-DNA hybridization values between strain BXN5-31T and three reference strains (M. soyangensis HME6664T , M. ximonensis XM-003T and M. puniceus WS71T ) were 9.4±1.9, 8.2±1.3 and 5.7±0.7 %, respectively. The DNA G+C content and chemotaxonomic data supported the affiliation of strain BXN5-31T to the genus Mucilaginibacter. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness allowed the phenotypic and genotypic differentiation of strain BXN5-31T from recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter panaciglaebae sp. nov. is proposed. The type strain is BXN5-31T (=KACC 14957T =JCM 17085T ).- Published
- 2018
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20. Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil.
- Author
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Choi GM, Lee SY, Choi KD, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, Caulobacteraceae genetics, Caulobacteraceae isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Glycolipids chemistry, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Transferases (Other Substituted Phosphate Groups) chemistry, Ubiquinone chemistry, Caulobacteraceae classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated HKS-05
T , was isolated from ginseng field soil. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. HKS-05T grew at 10-37 °C and at pH 6.0-8.0 on R2A agar. On the basis of 16S rRNA gene sequence similarity, HKS-05T was shown to represent a member of the family Caulobacteraceaeand to be related to Phenylobacterium lituiforme FaiI3T (98.1 % sequence similarity), 'Phenylobacterium zucineum' HLK1 (97.9 %), Phenylobacterium muchangponense A8T (97.7 %), Phenylobacteriumcomposti 4T-6T (97.2 %) and Phenylobacterium immobile ET (97.1 %). The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids were phosphatidylglycerol, unidentified glycolipids and unidentified polar lipids. The G+C content of the genomic DNA was 70.4 mol%. DNA-DNA relatedness values between HKS-05T and its closest phylogenetically neighbours were low. HKS-05T could be differentiated genotypically and phenotypically from the species of the genus Phenylobacterium with validly published names. The isolate therefore represents a novel species, for which the name Phenylobacteriumhankyongense sp. nov. is proposed, with the type strain HKS-05T (=KACC 18628T =LMG 30081T ).- Published
- 2018
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21. Mucilaginibacter ginsenosidivorans sp. nov., Isolated from Soil of Ginseng Field.
- Author
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Kim MM, Siddiqi MZ, and Im WT
- Subjects
- Aerobiosis, Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes physiology, Base Composition, Cluster Analysis, Cytosol chemistry, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Fatty Acids analysis, Hydrogen-Ion Concentration, Panax growth & development, Phospholipids analysis, Phylogeny, Quinones analysis, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sodium Chloride metabolism, Temperature, beta-Glucosidase metabolism, Bacteroidetes classification, Bacteroidetes isolation & purification, Soil Microbiology
- Abstract
A Gram-reaction-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped bacterial strain designated Gsoil 3017
T was isolated from soil of ginseng field and investigated by phenotypic and phylogenetic analyses. Strain Gsoil 3017T grew at 10-37 °C (optimal growth at 30 °C) and at pH 5.5-8.0 (optimal growth at pH 7) on R2A and nutrient agar without additional NaCl as a supplement. Strain Gsoil 3017T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 , Rc, and Rd (the three dominant active components of ginseng) to F2 and C-K, respectively. Based on 16S rRNA gene phylogeny, the novel strain represents a new branch within the genus Mucilaginibacter family Sphingobacteriaceae, and clusters with Mucilaginibacter frigoritolerans FT22T (95.6%) and Mucilaginibacter gotjawali SA3-7T (95.6%). The G+C content of the genomic DNA was 48.7%. The predominant respiratory quinone was MK-7, and the major fatty acids were iso-C15:0 , iso-C17:0 3-OH, and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major polar lipid was phosphatidylethanolamine. Strain Gsoil 3017T could be differentiated genotypically and phenotypically from other type strains of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter ginsenosidivorans sp. nov. is proposed, with the type strain Gsoil 3017T (=KACC 14954T = JCM 17081T ).- Published
- 2017
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22. Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.
- Author
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Siddiqi MZ, Choi GM, Choi KD, and Im WT
- Subjects
- Bacterial Typing Techniques, Cell Wall chemistry, DNA, Bacterial genetics, DNA, Ribosomal genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Nucleic Acid Hybridization, Paenibacillus genetics, Paenibacillus isolation & purification, Peptidoglycan chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Nitrogen Fixation, Paenibacillus classification, Phylogeny, Soil Microbiology
- Abstract
A nitrogen-fixing bacterium, designated NF2-4-5
T , was isolated from a paddy soil in Anseong City, Korea. Cells of strain NF2-4-5T were Gram-staining-positive, motile rods and aerobic. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus and was closely related to Paenibacillus graminis RSA19T (98.7 %), Paenibacillus jilunlii Be17T (98.6 %), Paenibacillus salinicaeni LAM0A28T (98.6 %) and Paenibacillus riograndensis SBR5T (98.6 %). Growth of strain NF2-4-5T occurs at temperatures of 18-37 °C, at pH 6.0-8.5 and between 0.5% and 2 % NaCl (w/v). The only respiratory quinone was MK-7. The cell wall peptidoglycan of strain NF2-4-5T contained meso-diaminopimelic acid. The main cellular fatty acids were C16 : 0 and anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The DNA G+C content was 56.36 mol%. The DNA-DNA hybridization relatedness between strain NF2-4-5T and four reference strains, Paenibacillus graminis RSA19T , Paenibacillus jilunlii Be17T , Paenibacillus sonchi X19-5T and Paenibacillus riograndensis SBR5T , was 22.0±0.3, 20.1±0.7, 18.3±0.3 and 12.6±0.5 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that the strain NF2-4-5T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus azotifigens sp. nov. is proposed. The type strain is NF2-4-5T (=KACC 18967T =LMG 29963T ).- Published
- 2017
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23. Sphingomonas agri sp. nov., a bacterium isolated from soil.
- Author
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Siddiqi MZ, Choi GM, Kim SY, Choi KD, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonas genetics, Sphingomonas isolation & purification, Ubiquinone chemistry, Phylogeny, Soil Microbiology, Sphingomonas classification
- Abstract
A Gram-reaction-negative, aerobic, non-motile, white (translucent) and rod-shaped bacterium (designated HKS-06
T ) isolated from soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain HKS-06T was observed to grow optimally at 30 °C and at pH 6.5-7.0 on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HKS-06T belongs to the genus Sphingomonas and is most closely related to Sphingomonas lutea JS5T (97.4 % similarity). The G+C content of the genomic DNA was 64.1 mol%. Chemotaxonomic data [major quinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, unknown polar lipid) and major fatty acids (summed feature 8, comprising C18 : 1ω7c/ω6c and/or C18 : 1ω6c, C18 : 0 3-OH and C16 : 0)] supported the affiliation of strain HKS-06T to the genus Sphingomonas. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness [between strain HKS06T and S. lutea JS5T (20.24±1.2 %)] allowed the phenotypic and genotypic differentiation of strain HKS-06T from recognized species of the genus Sphingomonas. The new isolate therefore represents a novel species, for which the name Sphingomonas agri sp. nov. is proposed. The type strain is HKS-06T (=KACC 18880T =LMG 29563T ).- Published
- 2017
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24. Phenylobacterium deserti sp. nov., isolated from desert soil.
- Author
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Khan IU, Hussain F, Habib N, Wadaan MAM, Ahmed I, Im WT, Hozzein WN, Zhi XY, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, Caulobacteraceae genetics, Caulobacteraceae isolation & purification, DNA, Bacterial genetics, Fatty Acids chemistry, Glycolipids chemistry, Nucleic Acid Hybridization, Pakistan, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Ubiquinone chemistry, Caulobacteraceae classification, Desert Climate, Phylogeny, Soil Microbiology
- Abstract
A novel bacterial strain, designated YIM 73061
T , was isolated from the Cholistan desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to Phenylobacterium conjunctum FWC21T (97.6 %), Phenylobacterium lituiforme FaiI3T (97.4 %), Phenylobacteriumcomposti 4T-6T (97.0 %) and Phenylobacterium aquaticum W2-3-4T (96.8 %). Cells were Gram-stain-negative, aerobic and motile rods that formed orange colonies. The strain was oxidase- and catalase-positive. Growth occurred at 20-40 °C (optimum, 30-37 °C) at pH 5.0-8.0 (optimum, pH 7.0) and with 0-1 % (w/v) NaCl (optimum, 0-0.5 %). The major cellular fatty acids (>10 %) were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylglycerol and four unidentified glycolipids. The major isoprenoid quinone was ubiquinone-10 (Q-10). The G+C content of the genomic DNA was 66.8 mol%. Strain YIM 73061T showed low levels of DNA-DNA relatedness to P. conjunctum FWC21T (27.2±2.6 %), P. lituiforme FaiI3T (24.6±1.1 %) and P.composti 4T-6T (18.4±3.1 %). On the basis of phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain YIM 73061T should be classified as representing a novel species, for which the name Phenylobacterium deserti sp. nov. is proposed. The type strain is YIM 73061T (=DSM 103871T =CCTCC AB 2016297T ).- Published
- 2017
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25. Mucilaginibacter hankyongensis sp. nov., isolated from soil of ginseng field Baekdu Mountain.
- Author
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Liu Q, Siddiqi MZ, Kim MS, Kim SY, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes enzymology, Bacteroidetes genetics, Base Composition, DNA, Bacterial analysis, Fatty Acids analysis, Genotype, Ginsenosides metabolism, Lipids analysis, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Republic of Korea, Sequence Analysis, DNA, beta-Glucosidase biosynthesis, Bacteroidetes classification, Bacteroidetes isolation & purification, Panax growth & development, Panax metabolism, Soil Microbiology
- Abstract
A Gram-negative, non-motile, aerobic, and rod-shaped bacterial strain designated as BR5-28
T was isolated from the soil of a ginseng field at Baekdu Mountain Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BR5-28T grew at 10-42°C (optimum temperature, 30°C) and pH 5.5-8.5 (optimum pH, 7.0) on R2A agar medium without additional NaCl supplementation. Strain BR5- 28T exhibited β-glucosidase activity, which was responsible for its ability to transform the ginsenosides Rb1 and Rd (the two dominant active components of ginseng) to compound-K. Based on 16S rRNA gene phylogeny, the novel strain showed a new branch within the genus Mucilaginibacter of the family Sphingobacteriaceae, and formed clusters with Mucilaginibacter frigoritolerans FT22T (95.8%) and Mucilaginibacter gotjawali SA3-7T (95.7%). The G+C content of the genomic DNA was 45.1%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c), iso-C15:0 and anteiso-C15:0 . The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain BR5-28T was differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter hankyongensis sp. nov. is proposed, with the type strain BR5-28T (=KCTC 22274T =DSM 21151T ).- Published
- 2017
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26. Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil.
- Author
-
Siddiqi MZ, Aslam Z, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Phosphatidylethanolamines chemistry, Polyamines chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Ginsenosides metabolism, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, non-motile, light yellow and rod-shaped bacterium (designated Gsoil 809T) isolated from soil of ginseng field, was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gsoil 809T was observed to grow optimally at 30 °C and at pH 7.0 on nutrient agar medium. Strain Gsoil 809T possessed β-glucosidase activity, which was responsible for its ability to transform protopanaxatriol-type ginsenoside Rg1 to ginsenoside Rh1. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gsoil 809T belongs to the genus Arachidicoccus of the family Chitinophagaceae and was most closely related to Arachidicoccusrhizosphaerae Vu-144T (98.1 % 16S rRNA gene sequence similarity). The DNA G+C content was 39.4 mol%. The DNA-DNA hybridization value between strain Gsoil 809T and A.rhizosphaerae Vu-144T was 41.27±1.03 %. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3, which supported the affiliation of Gsoil 809T to the genus Arachidicoccus. Strain Gsoil 809T contained homospermidineas the major polyamine. Moreover, the physiological and biochemical test results and low DNA-DNA relatedness value allowed the phenotypic and genotypic differentiation of strain Gsoil 809T from recognized species of the genus Arachidicoccus. Therefore, strain Gsoil 809T represents a novel species of the genus Arachidicoccus, for which the name Arachidicoccus ginsenosidivorans sp. nov. is proposed. The type strain is Gsoil 809T (=KCTC 22820T=JCM 30984T).
- Published
- 2017
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27. Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.
- Author
-
Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT, and Aslam Z
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Sphingobacterium genetics, Sphingobacterium isolation & purification, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Ginsenosides metabolism, Panax microbiology, Phylogeny, Soil Microbiology, Sphingobacterium classification
- Abstract
A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7T) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7T belongs to the genus Sphingobacterium of the family Sphingobacteriaceae and was most closely related to Sphingobacterium yanglingense JCM 30166T (92.6 %), Sphingobacterium psychroaquaticum KACC 18188T (92.6 %), and Sphingobacterium thermophilum KCTC 23708T (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7T were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7T to the genus Sphingobacterium. However, strain GJ30-7T could be distinguished genotypically and phenotypically from species of the genus Sphingobacterium with validly published names. The novel isolate therefore represents a novel species, for which the name Sphingobacterium jejuense sp. nov. is proposed, with the type strain GJ30-7T (=KACC 18625T=JCM 30948T).
- Published
- 2016
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28. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field.
- Author
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Siddiqi MZ, Muhammad Shafi S, Choi KD, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Ginsenosides metabolism, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A ginsenoside-transforming bacterium, designated Gsoil 1550T, was isolated from soil of a ginseng field and subjected to a polyphasic taxonomic analysis. Colonies of strain Gsoil 1550T were yellow, of low convexity and with regular margin. Cells were long rods, 0.5-1.2 µm wide and 1.6-3 µm long. The isolate grew at 10-37 °C and at pH 5-9 on R2A agar medium; maximum growth occurred at 30 °C and pH 6-7. Phylogenetic study based on the 16S rRNA gene sequence positioned Gsoil 1550T in a distinct lineage in the family Chitinophagaceae, sharing 92.5-92.8 % sequence similarity with members of the closely related genera Terrimonas, Parafilimonas, Sediminibacterium and Parasegetibacter. Strain Gsoil 1550T contained menaquinone MK-7 as the predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and iso-C15 : 1 G as major fatty acids. The DNA G+C content was 44.6 mol%. Strain Gsoil 1550T could be distinguished from other members of the family Chitinophagaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipid of strain Gsoil 1550T was phosphatidylethanolamine. Based on this polyphasic taxonomic analysis, strain Gsoil 1150T represents a novel species within a new genus, for which the name Panacibacter ginsenosidivorans gen. nov., sp. nov. is proposed. The type strain of Panacibacter ginsenosidivorans is Gsoil 1550T (=KCTC 12658T=JCM 31452T).
- Published
- 2016
- Full Text
- View/download PDF
29. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil.
- Author
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Siddiqi MZ and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Ginsenosides chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-negative, pseudo-rod, non-spore-forming, oxidase- and catalase-positive, strictly aerobic bacterium, designated Gsoil 221T, was isolated from soil of a ginseng field and subjected to a taxonomic analysis using a polyphasic approach. Strain Gsoil 221T grew at 10-37 °C and at pH 5.0-8.0 on R2A medium. Strain Gsoil 221T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (two dominant active components of ginseng) to ginsenoside F2. Phylogenetic study based on the 16S rRNA gene sequence positioned strain Gsoil 221T in a distinct lineage in the family Chitinophagaceae, sharing less than 94.4 % 16S rRNA gene sequence similarity with all taxa with validly published names. The strain showed the highest sequence similarities with members of the genera Parasegetibacter,Flavitalea,Niastella and Terrimonas. Strain Gsoil 221T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G as major fatty acids. The DNA G+C content was 47.1 mol%. Strain Gsoil 221T could be distinguished from the other members of the family Chitinophagaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipids of strain Gsoil 221T were diphosphatidylglycerol, phosphatidylethanolamine and one unidentified polar lipid. Based on these combined data, strain Gsoil 221T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Pseudobacter ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of the type species is Gsoil 221T (=KACC 14278T=DSM 18116T).
- Published
- 2016
- Full Text
- View/download PDF
30. Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost.
- Author
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Siddiqi MZ, Muhammad Shafi S, Choi KD, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Phosphatidylethanolamines chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Phylogeny, Soil Microbiology
- Abstract
A novel bacterial strain, designated strain BS27T, was isolated from mushroom compost and subjected to a taxonomic study using a polyphasic approach. Colonies of BS27T were milky-white, circular with regular fringes and opaque. Cells were short rods, 0.3-0.5 µm wide and 1.2-2.0 µm long. Phylogenetic study based on the 16S rRNA gene sequence placed BS27T in a distinct lineage in the family Chitinophagaceae, sharing 90.1-90.9 % sequence similarity with members of the closely related genera Chitinophaga, Flavitalea, Flavihumibacter, Lacibacter and Flavisolibacter. The novel isolate showed the highest sequence similarities with the members of the genus Chitinophaga. BS27T contained MK-7 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1I and/or anteiso-C17 : 1B (summed feature 4) as major fatty acids. The DNA G+C content was 53.0 mol%. The major polar lipids of BS27T were phosphatidylethanolamine (PE) and five unidentified polar lipids (L1, L2, L5, L6 and L7). The results of physiological and biochemical tests allowed phenotypic differentiation of BS27T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate BS27T represents a novel genus and species in the family Chitinophagaceae for which the name Compostibacter hankyongensisgen. nov., sp. nov. is proposed. The type strain is BS27T (=KACC 18745T=JCM 17664T).
- Published
- 2016
- Full Text
- View/download PDF
31. Mucilaginibacter pocheonensis sp. nov., with ginsenoside-converting activity, isolated from soil of a ginseng-cultivating field.
- Author
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Zhao Y, Lee HG, Kim SK, Yu H, Jin F, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Ginsenosides metabolism, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-reaction-negative, aerobic, heterotrophic, non-motile, non-spore-forming, rod-shaped bacterial strain, designated Gsoil 032T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain Gsoil 032T grew at 10-42 °C and at pH 5.0-10.0 on R2A agar medium. Strain Gsoil 032T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to compound K. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 032T was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter sabulilitoris SMS-12T (97.6 % sequence similarity) and Mucilaginibacter lappiensis ANJLI2T (97.1 %) The G+C content of the genomic DNA was 44.4 mol%. The predominant respiratory quinone was menaquinone MK-7 and the major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipid detected was phosphatidylethanolamine, while the minor polar lipids were various unidentified aminophospholipids, unidentified phospholipids and unidentified polar lipids. DNA and chemotaxonomic data supported the affiliation of strain Gsoil 032T to the genus Mucilaginibacter. Strain Gsoil 032T could be differentiated genotypically and phenotypically from recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter pocheonensis sp. nov. is proposed, with the type strain Gsoil 032T (=KCTC 12641T=LMG 23495T).
- Published
- 2016
- Full Text
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32. Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field.
- Author
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Siddiqi MZ and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids analysis, Panax growth & development, Phylogeny, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Lysobacter classification, Lysobacter genetics, Lysobacter isolation & purification, Panax microbiology, Soil Microbiology
- Abstract
A Gram-staining-negative, non-spore-forming, non-flagellated, rod-shaped, catalase- and oxidase-negative bacterium, designated as Gsoil 193(T), was isolated from the soil of ginseng field in Pocheon province, South Korea. 16S rRNA gene sequence analysis showed that strain Gsoil 193(T) belonged to family Xanthomonadaceae and was most closely related to Lysobacter daecheongensis KCTC 12,600(T) (96.4 %), Lysobacter panaciterrae KCTC 12601(T) (96.3 %), Lysobacter dokdonensis DSM 17958(T) (96.3 %) and Lysobacter oligotrophicus JCM 18257(T) (95.6 %). Strain Gsoil 193(T) grew at temperatures between 20 and 30 °C with an optimum of 30 °C. The pH range for growth was 5-9 pH (optimum 6-7 pH). The predominant respiratory quinone was ubiquinone Q-8 and a fatty acid profile with iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl) as the major fatty acids supported the affiliation of strain Gsoil 193(T) to the genus Lysobacter. The genomic DNA G+C content was 64.8 mol %. On the basis of the genotypic analysis, physiological and chemotaxonomic results indicate that strain Gsoil 193(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter pocheonensis sp. nov. is proposed. The type strain is Gsoil 193(T) (= DSM 18338(T) = KCTC 12624(T)).
- Published
- 2016
- Full Text
- View/download PDF
33. Humibacter soli sp. nov., isolated from soil.
- Author
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Park J, Kim YR, Kim MK, Jo JH, Im WT, and Kim SB
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Aminobutyrates chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall chemistry, DNA, Bacterial genetics, Fatty Acids chemistry, Peptidoglycan chemistry, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 chemistry, Actinomycetales classification, Phylogeny, Soil Microbiology
- Abstract
A novel actinobacterial strain, designated R1-20
T , was isolated during a study of the bacterial diversity of the soil at a white heron nesting site. The isolate was non-motile, Gram-stain-positive and short rod-shaped. Colonies were dull white and convex with entire margin during the early stages of growth, and gradually became yellow. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter of the family Microbacteriaceae, as sequence similarity with its nearest neighbours was 97.16 % with Humibacter antriD7-27T and 96.44 % with Humibacter albusDSM 18994T . However, the combination of cultural and physiological as well as chemotaxonomic properties clearly distinguished strain R1-20T from other Humibacter species. The DNA G+C content of strain R1-20T was 65.5 mol%, and the major respiratory isoprenoid quinone was menaquinone MK-11. The acyl group of the peptidoglycan was of acetyl type, and the diagnostic diamino acid was 2,4-diaminobutyric acid. Glutamic acid, alanine and glycine were also present in the cell wall. The major fatty acids of strain R1-20T were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain R1-20T merits recognition as a representative of a novel species of the genus Humibacter, for which the name Humibacter soli sp. nov. is proposed. The type strain is R1-20T (=KCTC 39614T =JCM 31015T ).- Published
- 2016
- Full Text
- View/download PDF
34. Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field.
- Author
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Lee HY, Liu Q, Kang MS, Kim SK, Lee SY, and Im WT
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, DNA, Ribosomal genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Actinomycetales classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
Two novel actinobacteria, designated strains Gsoil 097T and Gsoil 818T, isolated from soil of a ginseng field, South Korea, were characterized by a polyphasic approach to clarify their taxonomic positions. They were Gram-reaction-positive, aerobic, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Marmoricola and were related most closely to Marmicola solisilvae KIS18-7T (99.1 and 98.3 % similarity, respectively), Marmicola terrae JOS5-1T (97.9 and 97.9 %), Marmicola scoriae Sco-D01T (97.8 and 97.1 %) and Marmicola aequoreus SST-45T (97.5 and 97.0 %). The G+C content of the genomic DNA was 68.8 and 70.0 mol%, respectively. Both strains were characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and C17 : 1ω6c, C18 : 1ω9c, C18 : 0 10-methyl and iso-C16 : 0 as major fatty acids. These chemotaxonomic data supported the affiliation of both strains to the genus Marmoricola. However, levels of DNA-DNA relatedness between the two strains and closely related type strains of Marmoricola species were less than 30 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 097T and Gsoil 818T from other Marmoricola species with validly published names. Therefore, the two isolates represent two novel species, for which the names Marmoricola ginsengisoli sp. nov. (type strain Gsoil 097T = KACC 14267T = DSM 22772T) and Marmoricola pocheonensis sp. nov. (type strain Gsoil 818T = KACC 14275T = DSM 22773T) are proposed.
- Published
- 2016
- Full Text
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35. Flavisolibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from soil used for cultivating ginseng.
- Author
-
Zhao Y, Liu Q, Kang MS, Jin F, Yu H, and Im WT
- Subjects
- Bacteroidetes genetics, Bacteroidetes isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Molecular Sequence Data, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacteroidetes classification, Ginsenosides metabolism, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A Gram-reaction-negative, aerobic, non-motile and rod-shaped bacterial strain designated Gsoil 636T was isolated from soil of a ginseng cultivation field in Pocheon Province, South Korea and its taxonomic position was investigated using a polyphasic approach. Gsoil 636T grew at 18-30 °C and at pH 6.0-8.0 on R2A medium. Gsoil 636T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (ones of the dominant active components of ginseng) to F2. On the basis of 16S rRNA gene sequence similarity, Gsoil 636T was shown to belong to the family Chitinophagaceae and to be related to Flavisolibacter ginsengiterrae Gsoil 492T (96.7 % sequence similarity), Flavisolibacter ginsengisoli Gsoil 643T (96.6 %) and Flavisolibacter rigui 02SUJ3T (96.6 %). The G+C content of the genomic DNA was 48.9 %. The predominant respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. DNA and chemotaxonomic data supported the affiliation of Gsoil 636T to the genus Flavisolibacter. Gsoil 636T could be differentiated genotypically and phenotypically from the species of the genus Flavisolibacter with validly published names. The isolate therefore represents a novel species, for which the name Flavisolibacter ginsenosidimutans sp. nov. is proposed, with the type strain Gsoil 636T (KCTC 22818T = JCM 18197T = KACC 14277T).
- Published
- 2015
- Full Text
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36. Niabella ginsenosidivorans sp. nov., isolated from compost.
- Author
-
Yi KJ, Im WT, Kim DW, Liu QM, and Kim SK
- Subjects
- Bacteroidetes metabolism, Base Composition, DNA, Bacterial, Fatty Acids chemistry, Genotype, Ginsenosides metabolism, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Soil, Bacteroidetes classification, Bacteroidetes genetics, Bacteroidetes isolation & purification, Soil Microbiology
- Abstract
A Gram-reaction negative, strictly aerobic, non-motile, orange colored, and rod-shaped bacterium (designated BS26(T)) isolated from compost, was characterized by a polyphasic approach to clarify its taxonomic position. Strain BS26(T) was observed to grow optimally at 25-30 °C and at pH 7.0 on R2A and nutrient media. Strain BS26(T) showed ß-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the active components of ginseng) to ginsenoside compound-K (C-K). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BS26(T) belongs to the genus Niabella of family Chitinophagaceae and was most closely related to Niabella soli DSM 19437(T) (94.5% similarity), N. yanshanensis CCBAU 05354(T) (94.3%), and N. aurantiaca DSM 17617(T) (93.8%). The G+C content of genomic DNA was 47.3 mol%. Chemotaxonomic data [predominant isoprenoid quinone-MK-7, major fatty acids-iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH, and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c)] supported the affiliation of strain BS26(T) to the genus Niabella. However, strain BS26(T) could be differentiated genotypically and phenotypically from the recognized species of the genus Niabella. The novel isolate therefore represents a novel species, for which the name Niabella ginsenosidivorans sp. nov. is proposed, with the type strain BS26(T) (=KACC 16620(T) =JCM 18199(T)).
- Published
- 2015
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37. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil.
- Author
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Lee JJ, Kang MS, Joo ES, Kim MK, Im WT, Jung HY, and Srinivasan S
- Subjects
- Altitude, Bacterial Typing Techniques, Base Composition, Cytophagaceae growth & development, Cytophagaceae radiation effects, DNA, Ribosomal genetics, Phenotype, Phylogeny, RNA, Ribosomal, 16S genetics, Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Cytophagaceae classification, Cytophagaceae isolation & purification, Gamma Rays, Soil Microbiology, Ultraviolet Rays
- Abstract
A Gram-negative, yellow-pigmented, long-rod shaped bacterial strain designated DY10(T) was isolated from a soil sample collected at Mt. Deogyusan, Jeonbuk province, South Korea. Optimum growth observed at 30°C and pH 7. No growth was observed above 1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain DY10(T) belonged to the genus Spirosoma and was distantly related to Spirosoma arcticum R2-35(T) (91.0%), Spirosoma lingual DSM 74(T) (90.8%), Spirosoma endophyticum EX36(T) (90.7%), Spirosoma panaciterrae DSM 21099(T) (90.5%), Spirosoma rigui WPCB118(T) (90.2%), Spirosoma spitsbergense DSM 19989(T) (89.8%), Spirosoma luteum DSM 19990(T) (89.6%), Spirosoma oryzae RHs22(T) (89.6%), and Spirosoma radiotolerans DG5A(T) (89.1%). Strain DY10(T) showed resistance to gamma and ultraviolet radiation. The chemotaxonomic characteristics of strain DY10(T) were consistent with those of the genus Spirosoma, with the quinone system with MK-7 as the predominant menaquinone, iso-C15:0, C16:1 ω5c, and summed feature3 (C16:1 ω7c/C16:1 ω6c), and phosphatidylethanolamine as the major polar lipid. The G+C content of the genomic DNA was 53.0 mol%. Differential phenotypic properties with the closely related type strains clearly distinguished strain DY10(T) from previously described members of the genus Spirosoma and represents a novel species in this genus, for which the name Spirosoma montaniterrae sp. nov. is proposed. The type strain is DY10(T) (=KCTC 23999(T) =KEMB 9004-162(T) =JCM 18492(T)).
- Published
- 2015
- Full Text
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38. Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity.
- Author
-
Kim JK, Kang MS, Park SC, Kim KM, Choi K, Yoon MH, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition genetics, DNA, Ribosomal genetics, Fatty Acids chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Soil, Sphingomonadaceae classification, Sphingomonadaceae genetics, Vitamin K 2 analysis, beta-Glucosidase metabolism, Ginsenosides metabolism, Soil Microbiology, Sphingomonadaceae isolation & purification, Sphingomonadaceae metabolism
- Abstract
The Gram-reaction-negative, strictly aerobic, non-motile, nonspore-forming, and rod-shaped bacterial strain designated BS11(T) was isolated from the compost and its taxonomic position was investigated by using a polyphasic approach. Strain BS11(T) grew optimally at 30-37°C and at pH 7.0 in the absence of NaCl on nutrient agar. Strain BS11(T) displayed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to Rd. On the basis of 16S rRNA gene sequence similarity, strain BS11(T) was shown to belong to the family Sphingomonadaceae and was related to Sphingosinicella vermicomposti YC7378(T) (96.3% sequence similarity), S. xenopeptidilytica 3-2W4(T) (96.2%), S. microcystinivorans Y2(T) (96.1%), and S. soli KSL-125(T) (95.9%). The G+C content of the genomic DNA was 64.9%. The major menaquinone was Q-10 and the major fatty acids were summed feature 7 (comprising C18:1 ω7c/ω9t/ω12t; 40.6%), C16:0 (22.5%), C17:1 ω6c (13.7%) and C17:0 (9.1%). DNA and chemotaxonomic data supported the affiliation of strain BS11(T) to the genus Sphingosinicella. Strain BS11(T) could be differentiated genotypically and phenotypically from the recognized species of the genus Sphingosinicella. The novel isolate therefore represents a novel species, for which the name Sphingosinicella ginsenosidimutans sp. nov. is proposed, with the type strain BS11(T) (=KACC 16619T =JCM 18201(T)).
- Published
- 2015
- Full Text
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39. Nocardioides panaciterrulae sp. nov., isolated from soil of a ginseng field, with ginsenoside converting activity.
- Author
-
Kim JK, Liu QM, Park HY, Kang MS, Kim SC, Im WT, and Yoon MH
- Subjects
- Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial genetics, Diaminopimelic Acid analysis, Fatty Acids analysis, Molecular Sequence Data, Phylogeny, Propionibacteriaceae classification, Propionibacteriaceae genetics, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analysis, beta-Glucosidase metabolism, Ginsenosides metabolism, Panax microbiology, Propionibacteriaceae isolation & purification, Propionibacteriaceae metabolism, Soil Microbiology
- Abstract
A Gram-positive, coccoid to rod-shaped, non-spore-forming bacterium, designated Gsoil 958(T), was isolated from soil of a ginseng field located in Pocheon province in South Korea. This bacterium was characterized in order to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 958(T) was observed to grow well at 25-30 °C and at pH 7.0 on R2A and nutrient agar without NaCl supplementation. Strain Gsoil 958(T) was determined to have β-glucosidase activity and the ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to F2 via gypenoside XVII and Rd. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 958(T) was shown to belong to the family Nocardioidaceae and related most closely to Nocardioides koreensis MSL-09(T) (97.6 % 16S rRNA gene sequence similarity), Nocardioides aquiterrae GW-9(T) (97.0 %), and Nocardioides sediminis MSL-01(T) (97.0 %). The sequence similarities with other validly named species within the genus Nocardioides were less than 96.8 %. Strain Gsoil 958(T) was characterized chemotaxonomically as having LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone, and iso-C16:0, iso-C16:1 H, iso-C14:0, iso-C15:0 were identified as the major fatty acids. The G + C content of genomic DNA was determined to be 70.8 mol %. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 958(T) to the genus Nocardioides. The results of both physiological and biochemical tests allowed for differentiation of strain Gsoil 958(T) from the recognized Nocardioides species. Therefore, strain Gsoil 958(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides panaciterrulae sp. nov. is proposed, with the type strain Gsoil 958(T) (KACC 14271(T) = KCTC 19471(T) = DSM 21350(T)).
- Published
- 2013
- Full Text
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40. Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov.
- Author
-
An DS, Liu QM, Lee HG, Jung MS, Kim SC, Lee ST, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids analysis, Glycosphingolipids analysis, Molecular Sequence Data, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Sphingomonas genetics, Sphingomonas isolation & purification, Ubiquinone analysis, Geologic Sediments microbiology, Panax microbiology, Phylogeny, Soil Microbiology, Sphingomonas classification
- Abstract
Two novel bacteria, designated strains Gsoil 634(T) and Dae 20(T), were isolated in South Korea from soil of a ginseng field and freshwater sediment, respectively and were characterized by a polyphasic approach to clarify their taxonomic positions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that, although they probably represented two distinct species (indicated by a sequence similarity of 96.6 %), both strain Gsoil 634(T) and strain Dae 20(T) belonged to the genus Sphingomonas and were most closely related to 'Sphingomonas humi' PB323 (97.8 % and 96.7 % sequence similarity, respectively), Sphingomonas kaistensis PB56(T) (96.8 % and 96.7 %), Sphingomonas astaxanthinifaciens TDMA-17(T) (96.6 % and 95.4 %) and Sphingomonas jaspsi TDMA-16(T) (95.6 % and 95.8 %). For both novel strains, the major ubiquinone was Q-10, the major polyamine was homospermidine, the major cellular fatty acids included summed feature 7 (C(18 : 1)ω7c, C(18 : 1)ω9t and/or C(18 : 1)ω12t), C(17 : 1)ω6c and C(16 : 0), and the polar lipids included sphingoglycolipid. These chemotaxonomic data supported the affiliation of both strains to the genus Sphingomonas. However, the DNA-DNA relatedness value between strain Gsoil 634(T) and 'Sphingomonas humi' PB323(T) was 31 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 634(T) and Dae 20(T) from established members of the genus Sphingomonas. Based on these data, the two isolates represent two novel species in the genus Sphingomonas, for which the names Sphingomonas ginsengisoli sp. nov. (type strain Gsoil 634(T) = KCTC 12630(T) = DSM 18094(T) = LMG 23739(T)) and Sphingomonas sediminicola sp. nov. (type strain Dae 20(T) = KCTC 12629(T) = DSM 18106(T) = LMG 23592(T)) are proposed.
- Published
- 2013
- Full Text
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41. Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes.
- Author
-
Im WT, Hu ZY, Kim KH, Rhee SK, Meng H, Lee ST, and Quan ZX
- Subjects
- Bacteria genetics, Bacteria metabolism, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids metabolism, Molecular Sequence Data, Panax growth & development, Phylogeny, RNA, Ribosomal, 16S genetics, Bacteria classification, Bacteria isolation & purification, Soil Microbiology
- Abstract
Strain Gsoil 348(T) was isolated from a ginseng field soil sample by selecting micro-colonies from one-fifth strength modified R2A agar medium after a long incubation period. 16S rRNA gene sequence analysis indicated that the strain is related to members of the phylum Armatimonadetes (formerly called candidate phylum OP10). Strain Gsoil 348(T) is mesophilic, strictly aerobic, non-motile and rod-shaped. It only grows in low nutrient media. The major respiratory quinones are menaquinones MK-11 and MK-10, and the main fatty acids are iso-C(15:0), iso-C(17:0), C(16:0) and C(16:1) ω11c. The G+C content is 61.4 mol%. The 16S rRNA gene sequences in public databases belonging to the phylum Armatimonadetes were clustered here into 6 groups. Five of these groups constituted a coherent cluster distinct from the sequences of other phyla in phylogenetic trees that were constructed using multiple-outgroup sequences from 49 different phyla. On the basis of polyphasic taxonomic analyses, it is proposed that strain Gsoil 348(T) (= KACC 14959(T) = JCM 17079(T)) should be placed in Fimbriimonas ginsengisoli gen. nov., sp. nov., as the cultured representative of the Fimbriimonadia class. nov., corresponding with Group 4 of the phylum Armatimonadetes.
- Published
- 2012
- Full Text
- View/download PDF
42. Streptomyces panacagri sp. nov., isolated from soil of a ginseng field.
- Author
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Cui Y, Baek SH, Wang L, Lee HG, Cui C, Lee ST, and Im WT
- Subjects
- Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Republic of Korea, Streptomyces genetics, Streptomyces isolation & purification, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Panax microbiology, Phylogeny, Soil Microbiology, Streptomyces classification
- Abstract
A Gram-positive, spore-forming, aerobic actinomycete, strain Gsoil 519T, was isolated from soil of a ginseng field of Pocheon province in South Korea. The closest phylogenetic relatives were Streptomyces marinus Sp080513GE-26T (97.94 % 16S rRNA gene sequence similarity), Streptomyces albiaxialis NRRL B-24327T (97.84 %), Streptomyces albus subsp. albus DSM 40313T (97.84 %), Streptomyces almquistii NBRC 13015T (97.81 %), Streptomyces gibsonii NBRC 15415T (97.81 %), Streptomyces rangoonensis NBRC 13078T (97.81 %), Streptomyces sodiiphilus YIM 80305T (97.77 %) and Streptomyces flocculus NBRC 13041T (97.67 %). The G+C content of the genomic DNA was 71.8 mol%. The chemotaxonomic data [MK-9(H6) and MK-9(H8) as the major menaquinones; ll-diaminopimelic acid as a component of the cell-wall peptidoglycan; ribose, xylose, mannose and glucose as the major cell-wall sugars; and anteiso-C15:0, iso-C15:0, iso-C17:0, anteiso-C17:0 and C16:0 as the major fatty acids] supported the affiliation of strain Gsoil 519T to the genus Streptomyces. The physiological and biochemical characteristics and the low level of DNA-DNA relatedness differentiated the isolate genotypically and phenotypically from recognized members of the genus Streptomyces. The isolate, therefore, represents a novel species, for which the name Streptomyces panacagri sp. nov. is proposed, with Gsoil 519T (=KCTC 19139T=DSM 41871T) as the type strain.
- Published
- 2012
- Full Text
- View/download PDF
43. Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field.
- Author
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Lee SH, Liu QM, Lee ST, Kim SC, and Im WT
- Subjects
- Actinomycetales genetics, Actinomycetales physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Diaminopimelic Acid analysis, Fatty Acids analysis, Molecular Sequence Data, Panax growth & development, Peptidoglycan chemistry, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analysis, Actinomycetales classification, Actinomycetales isolation & purification, Soil Microbiology
- Abstract
A Gram-reaction-positive, rod-shaped, non-motile, non-spore-forming bacterium (strain BX5-10(T)) was isolated from the soil of a ginseng field on Baekdu Mountain in Jilin district, China. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain BX5-10(T) was shown to belong to the family Nocardioidaceae and to be most closely related to Nocardioides plantarum NCIMB 12834(T) (96.5% sequence similarity), Nocardioides dokdonensis KCTC 19309(T) (96.2%) and Nocardioides fonticola NAA-13(T) (95.1%). Strain BX5-10(T) was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in its cell-wall peptidoglycan, MK-8(H(4)) as the predominant menaquinone and C(18:1)ω9c, C(16:0) and C(17:1)ω8c as its major fatty acids. The G+C content of the genomic DNA was 70.3 mol%. The novel strain could be differentiated genotypically and phenotypically from all recognized species of the genus Nocardioides. Based on the results of the phylogenetic analyses and the genotypic and phenotypic data, a novel species, Nocardioides ginsengagri sp. nov., is proposed. The type strain is BX5-10(T) (=KCTC 19467(T)=DSM 21362(T)).
- Published
- 2012
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44. Ramlibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity.
- Author
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Wang L, An DS, Kim SG, Jin FX, Kim SC, Lee ST, and Im WT
- Subjects
- Biotransformation, China, Comamonadaceae genetics, Molecular Sequence Data, Panax growth & development, Panax microbiology, Phylogeny, Comamonadaceae isolation & purification, Comamonadaceae metabolism, Ginsenosides metabolism, Soil Microbiology
- Abstract
A novel beta-proteobacterium, designated BXN5-27(T), was isolated from soil of a ginseng field of Baekdu Mountain in China, and was characterized using a polyphasic approach. The strain was Gram-staining-negative, aerobic, motile, non-spore-forming, and rod shaped. Strain BXN5-27(T) exhibited beta-glucosidase activity that was responsible for its ability to transform ginsenoside Rb₁ (one of the dominant active components of ginseng) to compound Rd. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belonged to the family Comamonadaceae; it was most closely related to Ramlibacter henchirensis TMB834(T) and Ramlibacter tataouinensis TTB310(T) (96.4% and 96.3% similarity, respectively). The G+C content of the genomic DNA was 68.1%. The major menaquinone was Q-8. The major fatty acids were C₁₆:₀, summed feature 4 (comprising C₁₆:₁ omega7c and/or iso-C₁₅:₀ 2OH), and C₁₇:₀ cyclo. Genomic and chemotaxonomic data supported the affiliation of strain BXN5-27(T) to the genus Ramlibacter. However, physiological and biochemical tests differentiated it phenotypically from the other established species of Ramlibacter. Therefore, the isolate represents a novel species, for which the name Ramlibacter ginsenosidimutans sp. nov. is proposed, with the type strain being BXN5-27(T) (= DSM 23480(T) = LMG 24525(T) = KCTC 22276(T)).
- Published
- 2012
- Full Text
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45. Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.
- Author
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Wang L, An DS, Kim SG, Jin FX, Lee ST, and Im WT
- Subjects
- DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids metabolism, Molecular Sequence Data, Panax growth & development, Panax metabolism, Phylogeny, RNA, Ribosomal, 16S genetics, Xanthomonadaceae genetics, Xanthomonadaceae metabolism, Ginsenosides metabolism, Soil Microbiology, Xanthomonadaceae classification, Xanthomonadaceae isolation & purification
- Abstract
A novel gammaproteobacterium, designated LnR5-47(T), was isolated from soil of a ginseng field in Liaoning province, China. The isolate was a Gram-negative, aerobic, non-motile, non-spore-forming rod. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LnR5-47(T) belonged to the genus Rhodanobacter. The isolate was most closely related to Rhodanobacter ginsengisoli GR17-7(T), Rhodanobacter terrae GP18-1(T), Dyella ginsengisoli Gsoil 3046(T), Rhodanobacter soli DCY45(T), Dyella soli JS12-10(T) and Dyella japonica IAM 15069(T) (98.0, 97.9, 97.7, 97.3, 97.2 and 97.1% 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C(16:0), iso-C(17:1)ω9c and iso-C(15:0) as the major fatty acids) also supported the affiliation of strain LnR5-47(T) with the genus Rhodanobacter. However, DNA-DNA relatedness between strain LnR5-47(T) and its closest phylogenetic neighbours was <25.8%. Moreover, physiological and biochemical tests phenotypically differentiated the isolate from other members of the genus Rhodanobacter. Therefore, strain LnR5-47(T) represents a novel species, for which the name Rhodanobacter panaciterrae sp. nov. is proposed; the type strain is LnR5-47(T) (=KACC 12826(T)=KCTC 22232(T)=LMG 24460(T)).
- Published
- 2011
- Full Text
- View/download PDF
46. Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field.
- Author
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An DS, Wang L, Kim MS, Bae HM, Lee ST, and Im WT
- Subjects
- Actinobacteria genetics, Actinobacteria metabolism, Base Composition, China, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids metabolism, Ginsenosides metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S genetics, Actinobacteria classification, Actinobacteria isolation & purification, Panax microbiology, Soil Microbiology
- Abstract
A Gram-reaction-positive, non-motile, non-spore-forming, aerobic rod, designated BXN5-15(T), was isolated from the soil of a ginseng field on Baekdu Mountain in China. Strain BXN5-15(T) grew optimally at 30 °C and pH 6.0-7.0 in the absence of NaCl on R2A agar. Strain BXN5-15(T) displayed β-glucosidase activity, which allowed it to transform ginsenoside Rb(1) (one of the dominant active components of ginseng) via Rd to minor ginsenoside F(2). On the basis of 16S rRNA gene sequence analysis, strain BXN5-15(T) was shown to belong to the genus Solirubrobacter. The closest phylogenetic relatives were Solirubrobacter soli Gsoil 355(T) (98.4 % 16S rRNA gene sequence similarity) and Solirubrobacter pauli B33D1(T) (96.4 %). Lower sequence similarities (<96.0 %) were found with all of the other recognized members of the order Solirubrobacterales. The predominant quinone was MK-7(H(4)). The major fatty acids (>10 %) were C(18 : 1)ω9c, iso-C(16 : 0) and C(18 : 3)ω6,9,12c. The G+C content of the genomic DNA was 70.6 mol%. DNA-DNA relatedness between strain BXN5-15(T) and S. soli KCTC 12628(T) was 23.3 %. On the basis of genotypic, phenotypic and chemotaxonomic data, strain BXN5-15(T) represents a novel species within the genus Solirubrobacter, for which the name Solirubrobacter ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-15(T) ( = KACC 20671(T) = LMG 24459(T)).
- Published
- 2011
- Full Text
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47. Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field.
- Author
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Baek SH, Cui Y, Kim SC, Cui CH, Yin C, Lee ST, and Im WT
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids chemistry, Gram-Positive Endospore-Forming Rods genetics, Gram-Positive Endospore-Forming Rods isolation & purification, Molecular Sequence Data, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Gram-Positive Endospore-Forming Rods classification, Panax microbiology, Phylogeny, Soil Microbiology
- Abstract
A gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105(T), was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5(T) (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105(T) had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105(T) represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105(T) ( = KCTC 13942(T) = DSM 18389(T)).
- Published
- 2011
- Full Text
- View/download PDF
48. Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field.
- Author
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Im WT, Yang JE, Kim SY, and Yi TH
- Subjects
- Aerobiosis, Base Composition, Chryseobacterium genetics, Chryseobacterium physiology, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Fatty Acids analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones analysis, RNA, Ribosomal, 16S genetics, Rhus growth & development, Sequence Analysis, DNA, Sodium Chloride metabolism, Temperature, beta-Glucosidase metabolism, Chryseobacterium classification, Chryseobacterium isolation & purification, Ginsenosides metabolism, Soil Microbiology
- Abstract
A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacterial strain, designated THG 15(T), was isolated from soil of a field cultivated with Rhus vernicifera in Okcheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 15(T) grew optimally at 25-30 °C and at pH 7 in the absence of NaCl on nutrient agar. Strain THG 15(T) displayed β-glucosidase (aesculinase) activity that was responsible for its ability to transform ginsenoside Rb(1) (one of the dominant active components of ginseng) into compound K via Rd and F(2). On the basis of 16S rRNA gene sequence similarities, strain THG 15(T) was shown to belong to the family Flavobacteriaceae and was most closely related to Chryseobacterium soldanellicola PSD1-4(T) (97.7 % sequence similarity), Chryseobacterium soli JS6-6(T) (97.5 %) and Chryseobacterium indoltheticum LMG 4025(T) (97.3 %). The G+C content of the genomic DNA was 35.7 mol%. The major menaquinone was MK-6 and the major fatty acids were iso-C(15 : 0) (50.3 %), iso-C(17 : 0) 3-OH (21.9 %), summed feature 4 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 9.5 %) and iso-C(17 : 1)ω9c (9.3 %). DNA sequence analysis and chemotaxonomic data supported the affiliation of strain THG 15(T) to the genus Chryseobacterium. DNA-DNA relatedness values between strain THG 15(T) and its closest phylogenetic neighbours were <15 %. Strain THG 15(T) could be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. The isolate therefore represents a novel species, for which the name Chryseobacterium ginsenosidimutans sp. nov. is proposed. The type strain is THG 15(T) ( = KACC 14527(T) = JCM 16719(T)).
- Published
- 2011
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49. Mucilaginibacter composti sp. nov., with ginsenoside converting activity, isolated from compost.
- Author
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Cui CH, Choi TE, Yu H, Jin F, Lee ST, Kim SC, and Im WT
- Subjects
- Bacterial Typing Techniques, Bacteroidetes genetics, Bacteroidetes physiology, Base Composition, DNA, Bacterial genetics, DNA, Ribosomal genetics, Genes, rRNA, Genotype, Phenotype, Phylogeny, RNA, Ribosomal, 16S genetics, Republic of Korea, Sequence Analysis, DNA, Species Specificity, beta-Glucosidase genetics, beta-Glucosidase metabolism, Bacteroidetes classification, Bacteroidetes isolation & purification, Ginsenosides metabolism, Soil, Soil Microbiology
- Abstract
The Gram-negative, strictly aerobic, non-motile, non-spore-forming, rod shaped bacterial strain designated TR6-03(T) was isolated from compost, and its taxonomic position was investigated by using a polyphasic approach. Strain TR6-03(T) grew at 4-42°C and at pH 6.0-8.0 on R2A and nutrient agar without NaCl supplement. Strain TR6-03(T) had β-glucosidase activity, which was responsible for its ability to transform ginsenoside Re (one of the dominant active components of ginseng) to Rg(2). On the basis of 16S rRNA gene sequence similarity, strain TR6-03(T) was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter lappiensis ANJLI2(T) (96.3% sequence similarity), M. dorajii FR-f4(T) (96.1%), and M. rigui WPCB133(T) (94.1%). The G+C content of the genomic DNA was 45.6%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C(16:1) ω7c and/or iso-C(15:0) 20H), iso-C(16:0) and iso-C(17:0) 3OH. DNA and chemotaxonomic data supported the affiliation of strain TR6-03(T) to the genus Mucilaginibacter. Strain TR6-03(T) could be differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter composti sp. nov. is proposed, with the type strain TR6-03(T) (=KACC 14956(T) = KCTC 12642(T) =LMG 23497(T)).
- Published
- 2011
- Full Text
- View/download PDF
50. Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field.
- Author
-
Yang JE, Kim SY, Im WT, and Yi TH
- Subjects
- Aerobiosis, Base Composition, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Fatty Acids analysis, Flavobacterium genetics, Flavobacterium physiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax growth & development, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Temperature, Vitamin K 2 analysis, Flavobacterium classification, Flavobacterium isolation & purification, Ginsenosides metabolism, Soil Microbiology
- Abstract
A Gram-negative, aerobic, non-motile, non-spore-forming, yellow-pigmented, rod-shaped bacterium, designated strain THG 01(T), was isolated from the soil of a ginseng field in Pocheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 01(T) grew well at 25-37 °C and pH 6.0-7.5 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity data, strain THG 01(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium anhuiense D3(T) (97.5 % similarity), Flavobacterium johnsoniae UW101(T) (96.8 %) and Flavobacterium denitrificans ED5(T) (96.7 %). 16S rRNA gene sequence similarities between the novel strain and members of other recognized species within the family Flavobacteriaceae were less than 96.7 %. The G+C content of the genomic DNA of strain THG 01(T) was 32.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone was MK-6 and major fatty acids were iso-C(15 : 0), iso-C(15 : 0) 3-OH and C(16 : 1)ω7c and/or C(16 : 1)ω6c ) supported the affiliation of strain THG 01(T) to the genus Flavobacterium. DNA-DNA hybridization experiments showed that DNA-DNA relatedness values between strain THG 01(T) and its closest phylogenetic neighbours were below 11 %. The results of physiological and biochemical tests enabled strain THG 01(T) to be differentiated genotypically and phenotypically from recognized species of the genus Flavobacterium. The isolate therefore represents a novel species, for which the name Flavobacterium ginsenosidimutans sp. nov. is proposed, with THG 01(T) ( = KACC 14525(T) = JCM 16720(T)) as the type strain.
- Published
- 2011
- Full Text
- View/download PDF
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