<i>Terrabacter koreensis</i> sp. nov., isolated from soil of a flowerbed

Won, KyungHwa,Kook, MooChang,Yi, Tae-Hoo International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.10

<P>A Gram-staining-positive, non-spore-forming, rod-shaped, non-motile and aerobic bacterium, strain THG-e54<SUP>T</SUP>, was isolated from soil of a flowerbed in Bucheon, South Korea. The taxonomic position of this bacterium was determined in an investigation based on a polyphasic approach. 16S rRNA gene sequence analysis revealed a clear affiliation of strain THG-e54<SUP>T</SUP> with the genus <I>Terrabacter</I>. Strain THG-e54<SUP>T</SUP> showed the closest phylogenetic relationship with <I>Terrabacter tumescens</I> DSM 20308<SUP>T</SUP> with a 16S rRNA gene sequence similarity of 98.6 %. The G+C content of the genomic DNA was 71.0 mol%. The major cellular fatty acids of strain THG-e54<SUP>T</SUP> were iso-C<SUB>15 : 0</SUB> and iso-C<SUB>16 : 0</SUB>, and the predominant menaquinone was menaquinone MK-8(H<SUB>4</SUB>). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified amino-containing phosphoglycolipid, unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholipid. The cell-wall peptidoglycan type was <SMALL>ll</SMALL>-diaminopimelic acid and the cell-wall sugars were glucose and ribose. DNA–DNA hybridization experiments revealed a low level of DNA–DNA relatedness (less than 35.2 %) between strain THG-e54<SUP>T</SUP> and its five closest relatives. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain THG-e54<SUP>T</SUP> could be clearly distinguished from closely related recognized members of the genus <I>Terrabacter</I>. Therefore the results of this study indicated the existence of a novel species of the genus <I>Terrabacter</I> , for which we propose the name <I>Terrabacter koreensis</I> sp. nov., with strain THG-e54<SUP>T</SUP> ( = KACC 17589<SUP>T</SUP> = JCM 19342<SUP>T</SUP>) as the type strain.</P>

<i>Rhodanobacter koreensis</i> sp. nov., a bacterium isolated from tomato rhizosphere

Won, KyungHwa,Singh, Hina,Ngo, Hien T. T.,Son, HeungMin,Kook, MooChang,Kim, Ki–,Young,Yi, Tae–,Hoo International Union of Microbiological Societies 2015 International journal of systematic and evolutiona Vol.65 No.4

<P>A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated THG-DD7<SUP>T</SUP>, was isolated from tomato plant rhizosphere soil. Strain THG-DD7<SUP>T</SUP> grew optimally at 25–30 °C, at pH 7.0–7.5 and in the presence of 0.5 % (w/v) NaCl. According to the results of 16S rRNA gene sequence comparisons, strain THG-DD7<SUP>T</SUP> was most closely related to <I>Rhodanobacter umsongensis</I> GR24-2<SUP>T</SUP> (98.2 %), <I>Rhodanobacter panaciterrae</I> LnR5-47<SUP>T</SUP> (98.0 %), <I>Rhodanobacter soli</I> DCY45<SUP>T</SUP> (97.9 %), <I>Rhodanobacter terrae</I> GP18-1<SUP>T</SUP> (97.9 %) and <I>Dyella ginsengisoli</I> Gsoil 3046<SUP>T</SUP> (97.7 %). The DNA G+C content was 65.2 mol%. In DNA–DNA hybridization, the DNA relatedness levels between strain THG-DD7<SUP>T</SUP> and its closest phylogenetically neighbours were below 40.0 %. The predominant isoprenoid quinone was ubiquinone Q-8. The major polar lipids were diphosphatidylglycerol, phosphtidylethanolamine, phosphatidyl-<I>N</I>-methylethanolamine and phosphatidylglycerol. The major fatty acids were iso-C<SUB>15 : 0</SUB>, iso-C<SUB>16 : 0</SUB>, iso-C<SUB>17 : 0</SUB>, anteiso-C<SUB>15 : 0</SUB> and iso-C<SUB>17 : 1</SUB>ω9<I>c</I> and/or C<SUB>16 : 0</SUB> 10-methyl (summed feature 9). These data supported the affiliation of strain THG-DD7<SUP>T</SUP> to the genus <I>Rhodanobacter</I> . The results of physiological and biochemical tests enabled strain THG-DD7<SUP>T</SUP> to be differentiated genotypically and phenotypically from the species of the genus <I>Rhodanobacter</I> with validly published names. Therefore, the novel isolate represents a novel species, for which the name <I>Rhodanobacter koreensis</I> sp. nov. is proposed. The type strain is THG-DD7<SUP>T</SUP> ( = KACC 17650<SUP>T</SUP> = JCM 19614<SUP>T</SUP>).</P>

Lysobacter agri sp. nov., a bacterium isolated from soil

Singh, Hina,Won, KyungHwa,Du, Juan,Yang, Jung-Eun,Akter, Shahina,Kim, Ki-Young,Yi, Tae-Hoo Springer-Verlag 2015 Antonie van Leeuwenhoek Vol.108 No.3

<P>A bacterial strain, designated as THG-SKA3(T), was isolated from field soil of Kyung Hee University, South Korea. Cells of the isolate were observed to be Gram-negative, aerobic, rod-shaped and motile by gliding. The strain was found to grow optimally at 28?C, at pH 7 and in absence of NaCl. Based on 16S rRNA gene sequence comparisons, strain THG-SKA3(T) shared highest sequence similarity with Lysobacter niastensis KACC 11588(T) followed by Lysobacter panacisoli KACC 17502(T), Lysobacter enzymogenes LMG 8762(T) and Lysobacter oryzae KCTC 22249(T). The G+C content of THG-SKA3(T) was determined to be 68.9?mol%. The DNA-DNA relatedness values between strain THG-SKA3(T) and its closest phylogenetic neighbors were below 25.0?%.The major polar lipids of strain THG-SKA3(T) were determined to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was identified as ubiquinone 8 (Q-8). The major cellular fatty acids were identified as branched chain iso-C15:0, iso-C16:0 and unsaturated iso-C17:1 ω9c. On the basis of polyphasic data presented, it is evident that strain THG-SKA3(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter agri sp. nov. (type strain THG-SKA3(T)?=?KACC 18283(T)?=?CSCTCC AB 2015126(T)) is proposed.</P>

Response to “Medical Statistics Unlock the Gateway to Further Research: Using Deep Learning to Predict CDKN2A/B Homozygous Deletion in Isocitrate Dehydrogenase-Mutant Astrocytoma”

Park Yae Won,Han Kyunghwa,Kim Se Hoon 대한영상의학회 2023 Korean Journal of Radiology Vol.24 No.12

Phycicoccus soli sp. nov., isolated from soil.

Singh, Hina,Won, KyungHwa,Ngo, Hien T T,Du, Juan,Kook, MooChang,Yi, Tae-Hoo Society for General Microbiology 2015 International journal of systematic and evolutiona Vol.65 No.8

<P>A Gram-stain-positive, non-motile, coccus-shaped bacterium, strain THG-a14T, was isolated from soil of Gyeyang mountain in Incheon, Republic of Korea. The isolate grew optimally at 28?C, at pH?6.5-7.5 and with 0-3?% (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain THG-a14T was closely related to Phycicoccus aerophilus 5516T-20T (97.7?%), P. ginsenosidimutans BXN5-13T (97.6?%), 'P. ochangensis' L1b-b9 (97.4?%) and P. bigeumensis MSL-03 (97.2?%). The DNA G+C content of strain THG-a14T was 71.6?mol%. In DNA-DNA hybridization, the DNA-DNA relatedness between strain THG-a14T and its closest phylogenetically neighbours was below 50.0?%. Strain THG-a14T was characterized chemotaxonomically as having meso-diaminopimelic acid in the cell-wall peptidoglycan. Strain THG-a14T contained glucose and ribose as whole-cell-wall sugars and menaquinone MK-8(H4) as the major isoprenoid quinone. Polar lipids in strain THG-a14T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphoaminoglycolipids, unidentified phospholipids and unidentified lipids. The major fatty acids were iso-C16:0, iso-C15:0 and C17:1ω8c. On the basis of our polyphasic taxonomy study, strain THG-a14T represents a novel species within the genus Phycicoccus, for which the name Phycicoccussoli sp. nov. is proposed. The type strain is THG-a14T (?=?KACC 17892T?=?JCM 19837T).</P>

The occurrence and distribution of polychlorinated naphthalenes (PCNs), focusing on tissue-specific bioaccumulation in crucian carp in South Korea

Kim, Kun-Won,Choo, Gyojin,Cho, Hyeon-Seo,Lee, Byoung-Cheun,Park, Kyunghwa,Oh, Jeong-Eun Elsevier 2019 The Science of the total environment Vol.665 No.-

<P><B>Abstract</B></P> <P>The occurrence and distribution of 41 congeners of polychlorinated naphthalenes (PCNs) were investigated in major tissues of crucian carp (muscle, gonad, liver, and blood) and in river sediment to assess the bioaccumulation potential of PCNs. The total PCN concentrations in sediment ranged from 4.37 to 19.5 pg/g dry weight (dw), mainly comprising CN-13, CN-33/34/37, and CN-38/40. Among fish tissues, higher PCN concentrations were observed in the gonads (29.6 ± 10.3 pg/g wet weight, ww) and liver (25.7 ± 4.35 pg/g ww) of crucian carp than in the muscle (2.17 ± 0.68 pg/g ww). CN-28/43, CN-33/34/37, CN-42, CN-52/60, CN-53/55, and CN-66/67 congeners were detected most frequently and had the highest concentration among all crucian carp tissues. We investigated the association between the PCN concentration in each tissue (muscle, liver, and gonad) and the size of the fish (total length and weight) and found positive correlations between the PCN concentration in the gonads and the total length and weight (<I>p</I> < 0.05, Spearman correlation).</P> <P><B>Highlights</B></P> <P> <UL> <LI> The level and distribution of PCNs were investigated in sediment and fish. </LI> <LI> The PCNs accumulation in sediment was mainly influenced by combustion and Halowax. </LI> <LI> The congeners with PCN-NVC and PCN-DVC structures had high levels in fish tissues. </LI> <LI> PCNs levels in gonad tissue of crucian carp increased as crucian carp grew. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Flavobacterium vireti sp. nov., isolated from soil.

Singh, Hina,Du, Juan,Won, KyungHwa,Yang, Jung-Eun,Akter, Shahina,Kim, Ki-Young,Yi, Tae-Hoo N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.107 No.6

<P>A novel Gram-negative, aerobic, yellow-pigmented, non-motile and rod-shaped bacterium, designated as THG-SM1(T), was isolated from field soil collected from Suwon, South Korea. The strain was found to grow optimally at 28?C, at pH 7.0 and in the absence of NaCl. Based on 16S rRNA gene sequence similarities, strain THG-SM1(T) belongs to the genus Flavobacterium and is most closely related to Flavobacterium terrae KACC 11731(T), followed by Flavobacterium columnare KACC 11683(T) and Flavobacterium enshiense KCTC 23775(T). The DNA G+C content of the novel isolate was determined to be 38.5?mol%. In DNA-DNA hybridization tests, the DNA relatedness between strain THG-SM1(T) and its closest phylogenetic neighbour F. terrae was below 50?%. Flexirubin-type pigments were found to be present. The major polar lipid and isoprenoid quinone were phosphatidylethanolamine and menaquinone 6 (MK-6), respectively. The main cellular fatty acids were identified as iso-C15:1G, iso-C15:0 3OH, iso-C16:0 and iso-C15:0. The DNA-DNA hybridization result and differentiating chemotaxonomic and phenotypic characteristics showed that strain THG-SM1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium vireti sp. nov. is proposed. The type strain is THG-SM1(T) (=KACC 18371(T)?=?CCTCC AB2014312(T)).</P>

Sphingomonas flavus sp. nov. isolated from road soil

Du, Juan,Singh, Hina,Won, KyungHwa,Yang, Jung-Eun,Akter, Shahina,Jin, Feng-Xie,Yi, Tae-Hoo Springer-Verlag 2015 Archives of microbiology Vol.197 No.7

<P>A yellow-colored, Gram-negative, strictly aerobic, non-motile, rod-shaped bacterium, designated THG-MM5(T), was isolated from road soil in Yongin-si, Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence, strain THG-MM5(T) was moderately related to Sphingomonas sediminicola KACC 15039(T) (96.1?%), Sphingomonas ginsengisoli KACC 16858(T) (96.1?%) and Sphingomonas jaspsi KACC 13230(T) (96.0?%). Chemotaxonomic data revealed that strain THG-MM5(T) possesses ubiquinone-10 as the only respiratory quinone, sym-homospermidine as the major polyamine and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C18:1 ω7c and C16:0 as the major fatty acids. The polar lipid profile included sphingoglycolipid. The DNA G?+?C content was 60.7?mol%. These data, together with phenotypic characterization, corroborated the affiliation of strain THG-MM5(T) to the genus Sphingomonas. Thus, the isolate represents a novel species, for which the name Sphingomonas flavus sp. nov. is proposed, with THG-MM5(T) as the type strain (=KACC 18277(T)?=?CCTCC AB 2014320(T)).</P>

Taibaiella yonginensis sp. nov., a bacterium isolated from soil of Yongin city.

Singh, Hina,Du, Juan,Won, KyungHwa,Yang, Jung-Eun,Akter, Shahina,Kim, Ki-Young,Yin, ChangShik,Yi, Tae-Hoo N.V. Swets en Zeitlinger 2015 Antonie van Leeuwenhoek Vol.108 No.3

<P>A novel bacterial strain, designated as THG-SC4(T), was isolated from a soil sample collected from Yongin city in South Korea. Cells of the strain were Gram-negative, aerobic, rod-shaped and non-motile. The strain grew optimally at 28-30?C; at pH 7.0 and in the absence of NaCl. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-SC4(T) was shown to belong to the genus Taibaiella and shares high sequence similarity with Taibaiella smilacinae KCTC 32316(T) (95.4?%), followed by Taibaiella koreensis KACC 17171(T) (94.3?%) and Taibaiella chishuiensis JCM 19637(T) (94.2?%). The DNA G+C content of the novel isolate was determined to be 43.1?mol% and MK-7 was identified as the predominant isoprenoid quinone. The only polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified polar lipid. The predominant fatty acids were identified as iso-C15:0, iso-C15:1 G, C16:0 and iso-C17:03-OH. On the basis of data from this polyphasic taxonomic study, strain THG-SC4(T) is considered to represent a novel species of the genus Taibaiella, for which the name Taibaiella yonginensis sp. nov. is proposed. The type strain is THG-SC4(T) (=KACC 18372(T) = CCTCC AB 2014316(T)).</P>

Selection and Reporting of Statistical Methods to Assess Reliability of a Diagnostic Test: Conformity to Recommended Methods in a Peer-Reviewed Journal

Park, Ji Eun,Han, Kyunghwa,Sung, Yu Sub,Chung, Mi Sun,Koo, Hyun Jung,Yoon, Hee Mang,Choi, Young Jun,Lee, Seung Soo,Kim, Kyung Won,Shin, Youngbin,An, Suah,Cho, Hyo-Min,Park, Seong Ho unknown 2017 KOREAN JOURNAL OF RADIOLOGY Vol.18 No.6

<P><B>Objective</B></P><P>To evaluate the frequency and adequacy of statistical analyses in a general radiology journal when reporting a reliability analysis for a diagnostic test.</P><P><B>Materials and Methods</B></P><P>Sixty-three studies of diagnostic test accuracy (DTA) and 36 studies reporting reliability analyses published in the <I>Korean Journal of Radiology</I> between 2012 and 2016 were analyzed. Studies were judged using the methodological guidelines of the Radiological Society of North America-Quantitative Imaging Biomarkers Alliance (RSNA-QIBA), and COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) initiative. DTA studies were evaluated by nine editorial board members of the journal. Reliability studies were evaluated by study reviewers experienced with reliability analysis.</P><P><B>Results</B></P><P>Thirty-one (49.2%) of the 63 DTA studies did not include a reliability analysis when deemed necessary. Among the 36 reliability studies, proper statistical methods were used in all (5/5) studies dealing with dichotomous/nominal data, 46.7% (7/15) of studies dealing with ordinal data, and 95.2% (20/21) of studies dealing with continuous data. Statistical methods were described in sufficient detail regarding weighted kappa in 28.6% (2/7) of studies and regarding the model and assumptions of intraclass correlation coefficient in 35.3% (6/17) and 29.4% (5/17) of studies, respectively. Reliability parameters were used as if they were agreement parameters in 23.1% (3/13) of studies. Reproducibility and repeatability were used incorrectly in 20% (3/15) of studies.</P><P><B>Conclusion</B></P><P>Greater attention to the importance of reporting reliability, thorough description of the related statistical methods, efforts not to neglect agreement parameters, and better use of relevant terminology is necessary.</P>