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Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii
Lee, Jina,Whon, Tae Woong,Shin, Na-Ri,Roh, Seong Woon,Kim, Jandi,Park, Seong-Kyu,Kim, Min-Soo,Shin, Kee-Sun,Lee, Jung-Sook,Lee, Keun Chul,Kim, Young-Ok,Bae, Jin-Woo Microbiology Society 2012 International journal of systematic and evolutiona Vol.62 No.12
<P>A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15<SUP>T</SUP>, was isolated from an ark clam in South Korea. Growth occurred at 10-37 °C, with 1-5 % (w/v) NaCl and at pH 7.0-10.0. Optimal growth occurred at 25-30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15<SUP>T</SUP> exhibited both oxidase and catalase activities. The major fatty acids of strain TW15<SUP>T</SUP> were summed feature 8 (consisting of C18 : 1ω7<I>c</I> and/or C18 : 1ω6<I>c</I>) and 11-methyl C18 : 1ω7<I>c</I>. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15<SUP>T</SUP> comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15<SUP>T</SUP> was most closely related to <I>Ruegeria lacuscaerulensis</I> DSM 11314<SUP>T</SUP> (98.0 % 16S rRNA gene sequence similarity). DNA-DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15<SUP>T</SUP> represents a novel species of the genus <I>Ruegeria</I>, for which the name <I>Ruegeria conchae</I> sp. nov. is proposed. The type strain is TW15<SUP>T</SUP> ( = KACC 15115<SUP>T</SUP> = JCM 17315<SUP>T</SUP>).</P>
Oceanisphaera sediminis sp. nov., isolated from marine sediment
Shin, Na-Ri,Whon, Tae Woong,Roh, Seong Woon,Kim, Min-Soo,Kim, Young-Ok,Bae, Jin-Woo Microbiology Society 2012 International journal of systematic and evolutiona Vol.62 No.7
<P>Two strains, designated TW92<SUP>T</SUP> and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92<SUP>T</SUP> grew optimally in the presence of 2 % (w/v) NaCl (range 1-5 %) while strain TW93 grew optimally in the presence of 1 % (w/v) NaCl (range 0-12 %), and both strains had an optimal growth temperature of 30 °C (range 4-37 °C). Strains TW92<SUP>T</SUP> and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92<SUP>T</SUP> and TW93 were most closely related to <I>Oceanisphaera donghaensis</I> BL1<SUP>T</SUP>, with 98.8 % and 98.7 % similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92<SUP>T</SUP> and TW93 was 99.9 %. The major fatty acids of both strains were summed features 3 (comprising C16 : 1ω7<I>c</I>/iso-C15 2-OH), C16 : 0 and C18 : 1ω7<I>c</I>. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92<SUP>T</SUP> and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA-DNA hybridization of strains TW92<SUP>T</SUP> and TW93 with related species were below 47 % and 31 %, respectively. DNA-DNA hybridization values between strains TW92<SUP>T</SUP> and TW93 were above 85 %. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species, <I>Oceanisphaera</I><I>sediminis</I> sp. nov., with strain TW92<SUP>T</SUP> ( = KACC 15117<SUP>T</SUP> = JCM 17329<SUP>T</SUP>) as the type strain and strain TW93 ( = KACC 15118 = JCM 17330) as an additional strain.</P>
( Dong Wook Hyun ),( Tae Woong Whon ),( Joon Yong Kim ),( Pil Soo Kim ),( Na Ri Shin ),( Min Soo Kim ),( Jin Woo Bae ) 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.12
Oceanobacillus kimchii is a member of the genus Oceanobacillus within the family Bacillaceae. Species of the Oceanobacillus possess moderate haloalkaliphilic features and originate from various alkali or salty environments. The haloalkaliphilic characteristics of Oceanobacillus advocate they may have possible uses in biotechnological and industrial applications, such as alkaline enzyme production and biodegradation. This study presents the draft genome sequence of O. kimchii X50(T) and its annotation. Furthermore, comparative genomic analysis of O. kimchii X 5 0T was performed with two previously reported Oceanobacillus genome sequences. The 3,822,411 base-pair genome contains 3,792 protein-coding genes and 80 RNA genes with an average G+C content of 35.18 mol%. The strain carried 67 and 13 predicted genes annotated with transport system and osmoregulation, respectively, which support the tolerance phenotype of the strain in high-alkali and high-salt environments.
Comparative Viral Metagenomics of Environmental Samples from Korea
Kim, Min-Soo,Whon, Tae Woong,Bae, Jin-Woo Korea Genome Organization 2013 Genomics & informatics Vol.11 No.3
The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se, but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples. This review considers the current state of viral metagenomics, based on examples from Korean viral metagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere. Viral metagenomics has become widespread due to various methodological developments, and much attention has been focused on studies that consider the intrinsic role of viruses that interact with their hosts.
Park, Seong-Kyu,Roh, Seong Woon,Whon, Tae Woong,Bae, Jin-Woo American Society for Microbiology 2011 Journal of Bacteriology Vol.193 No.22
<P>Brachybacterium squillarumM-6-3<SUP>T</SUP>was isolated from salt-fermented seafood in Korea and belongs to theDermabacteraceae, a rather isolated family within the actinobacterial suborderMicrococcineae. Here, we present the draft genome sequence of the type strainBrachybacterium squillarumM-6-3<SUP>T</SUP>(3,191,479 bp), a Gram-positive bacterium with high (72.8%) G+C content.</P>
Yun, Ji-Hyun,Roh, Seong Woon,Whon, Tae Woong,Jung, Mi-Ja,Kim, Min-Soo,Park, Doo-Sang,Yoon, Changmann,Nam, Young-Do,Kim, Yun-Ji,Choi, Jung-Hye,Kim, Joon-Yong,Shin, Na-Ri,Kim, Sung-Hee,Lee, Won-Jae,Bae, American Society for Microbiology 2014 Applied and environmental microbiology Vol.80 No.17
<P>Insects are the most abundant animals on Earth, and the microbiota within their guts play important roles by engaging in beneficial and pathological interactions with these hosts. In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes. In total, 174,374 sequence reads were obtained, identifying 9,301 bacterial operational taxonomic units (OTUs) at the 3% distance level from all samples, with an average of 84.3 (±97.7) OTUs per sample. The insect gut microbiota were dominated by <I>Proteobacteria</I> (62.1% of the total reads, including 14.1% <I>Wolbachia</I> sequences) and <I>Firmicutes</I> (20.7%). Significant differences were found in the relative abundances of anaerobes in insects and were classified according to the criteria of host environmental habitat, diet, developmental stage, and phylogeny. Gut bacterial diversity was significantly higher in omnivorous insects than in stenophagous (carnivorous and herbivorous) insects. This insect-order-spanning investigation of the gut microbiota provides insights into the relationships between insects and their gut bacterial communities.</P>