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Chong-Tai Kim, Bong-Soo Kim,
Min-Ji Kim,
Bang Heon Park,
Sujin Kwon,
Hack Young Maeng,
Jangyul Kwak,
Jongsik Chun,
Yong-Jin Cho,
Namsoo Kim,
Chul-Jin Kim,
Jin-Soo Maeng
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ABSTRACT: A bacterium, designated M2-6, was isolated from Korean ginseng, Panax ginseng C. A. Meyer, roots after high-hydrostatic-pressure processing. On the basis of 16 rRNA gene phylogeny, the isolate was presumptively identified as a Bacillus sp. Here we report the draft genome sequence of Bacillus sp. strain M2-6 (= KACC 16563).
Journal of bacteriology 12/2012; 194(24):7003-4. · 3.94 Impact Factor
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ABSTRACT: A bacterium designated M1-1 was isolated from the gills of a Korean rockfish, Sebastes schlegeli Hilgendorf, after high hydrostatic pressure processing. Studies of 16S rRNA phylogeny and comparative genomics demonstrated that the isolate belongs to Staphylococcus saprophyticus subsp. saprophyticus. Here, we report the draft genome sequence of S. saprophyticus subsp. saprophyticus M1-1 (KACC 16562).
Journal of bacteriology 08/2012; 194(16):4441-2. · 3.94 Impact Factor
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ABSTRACT: Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived from the 5' region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and 95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporicAscomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales, Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities in soils.
The Journal of Microbiology 06/2010; 48(3):284-9. · 1.10 Impact Factor
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ABSTRACT: A Gram-reaction-negative, aerobic, yellowish-orange-pigmented bacterial strain, designated JC2436(T), was isolated from tidal-flat sediment of Oi Island in Korea. Comparative 16S rRNA gene sequence analysis indicated its close affiliation to Vitellibacter vladivostokensis, with 96 % sequence similarity to the type strain. Cells grew with 2-6 % NaCl and at 10-41 degrees C. Orange flexirubin pigments were present. The major isoprenoid quinone was MK-6, the DNA G+C content was 48.7 mol% and the predominant fatty acids (>10 %) were iso-C(15 : 0) and iso-C(17 : 0) 3-OH. The data obtained from this polyphasic study support the classification of this isolate within a novel species in the genus Vitellibacter, for which the name Vitellibacter aestuarii sp. nov. is proposed. The type strain is JC2436(T) (=IMSNU 14137(T) =KACC 13727(T) =KCTC 22361(T) =JCM 15496(T)).
International journal of systematic and evolutionary microbiology 10/2009; 60(Pt 9):1989-92. · 2.27 Impact Factor
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ABSTRACT: Two yellow-pigmented, Gram-negative, aerobic bacterial strains, designated FR1087(T) and FR1093(T), were isolated from surface seawater off Jeju Island, Republic of Korea. Both strains required sea salts for growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Sphingopyxis, showing the highest level of sequence similarity with respect to Sphingopyxis flavimaris SW-151(T) (97.9 %). The two isolates shared 98.5 % sequence similarity. DNA-DNA hybridization between the isolates and the type strain of Sphingopyxis flavimaris clearly suggested that strains FR1087(T) and FR1093(T) represent two separate novel species in the genus Sphingopyxis. Several phenotypic characteristics served to differentiate these two isolates from recognized members of the genus Sphingopyxis. The data from the polyphasic study presented here indicated that strains FR1087(T) and FR1093(T) should be classified as representing novel species in the genus Sphingopyxis, for which the names Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., respectively, are proposed. The type strain of Sphingopyxis marina sp. nov. is FR1087(T) (=IMSNU 14132(T)=KCTC 12763(T)=JCM 14161(T)) and the type strain of Sphingopyxis litoris sp. nov. is FR1093(T) (=IMSNU 14133(T)=KCTC 12764(T)=JCM 14162(T)).
International journal of systematic and evolutionary microbiology 11/2008; 58(Pt 10):2415-9. · 2.27 Impact Factor
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ABSTRACT: Dissection of prokaryotic community structure is prerequisite to understand their ecological roles. Various methods are available for such a purpose which amplification and sequencing of 16S rRNA genes gained its popularity. However, conventional methods based on Sanger sequencing technique require cloning process prior to sequencing, and are expensive and labor-intensive. We investigated prokaryotic community structure in tidal flat sediments, Korea, using pyrosequencing and a subsequent automated bioinformatic pipeline for the rapid and accurate taxonomic assignment of each amplicon. The combination of pyrosequencing and bioinformatic analysis showed that bacterial and archaeal communities were more diverse than previously reported in clone library studies. Pyrosequencing analysis revealed 21 bacterial divisions and 37 candidate divisions. Proteobacteria was the most abundant division in the bacterial community, of which Gamma-and Delta-Proteobacteria were the most abundant. Similarly, 4 archaeal divisions were found in tidal flat sediments. Euryarchaeota was the most abundant division in the archaeal sequences, which were further divided into 8 classes and 11 unclassified euryarchaeota groups. The system developed here provides a simple, in-depth and automated way of dissecting a prokaryotic community structure without extensive pretreatment such as cloning.
The Journal of Microbiology 09/2008; 46(4):357-63. · 1.10 Impact Factor
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ABSTRACT: A yellow-pigmented, Gram-negative, aerobic bacterial strain comprising rod-shaped cells devoid of flagellar and gliding motility, designated strain JC2129(T), was isolated from tidal flat sediment of Dongmak on Ganghwa Island, South Korea. Results from a 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae; the highest level of nucleotide sequence similarity (91.9%) occurred with Polaribacter dokdonensis DSW-5(T). The predominant cellular fatty acids were iso-C(15:0) (19.8%), iso-C(15:1) G (14.0%), iso-C(17:0) 3-OH (13.7%) and iso-C(13:0) (6.4%). Flexirubin-type pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content was 43-45 mol%. Data from a polyphasic taxonomy study suggested that the isolate represents a novel genus and species in the family Flavobacteriaceae, for which the name Actibacter sediminis gen. nov., sp. nov. is proposed. The type strain of Actibacter sediminis is JC2129(T) (=KCTC 12704(T) =JCM 14002(T)).
International journal of systematic and evolutionary microbiology 02/2008; 58(Pt 1):139-43. · 2.27 Impact Factor
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ABSTRACT: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25-100%) to sequences from other environments in the public database than did those (75.22-98.46%) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.
The Journal of Microbiology 05/2005; 43(2):144-51. · 1.10 Impact Factor
