Journal of Microbiology

Jin-Kwang Kim

4 Articles

Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity: Jin-Kwang Kim , Myung-Suk Kang , Sung Chul Park , Kyeng-Min Kim , Kangduk Choi , Min-Ho Yoon , Wan-Taek Im; J. Microbiol. 2015;53(7):435-441. Published online June 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5087-3

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The Gram-reaction-negative, strictly aerobic, non-motile, nonspore- forming, and rod-shaped bacterial strain designated BS11T was isolated from the compost and its taxonomic position was investigated by using a polyphasic approach. Strain BS11T grew optimally at 30?7캜 and at pH 7.0 in the absence of NaCl on nutrient agar. Strain BS11T displayed ?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 BS11T was shown to belong to the family Sphingomonadaceae and was related to Sphingosinicella vermicomposti YC7378T (96.3% sequence similarity), S. xenopeptidilytica 3-2W4T (96.2%), S. microcystinivorans Y2T (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 ?c/?t/?2t; 40.6%), C16:0 (22.5%), C17:1 ?c (13.7%) and C17:0 (9.1%). DNA and chemotaxonomic data supported the affiliation of strain BS11T to the genus Sphingosinicella. Strain BS11T 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 BS11T (=KACC 16619T =JCM 18201T).

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Morphological and molecular characterization of Sphingomonas lindongxini sp. nov. and Sphingosinicella wutangchuni sp. nov., isolated from soil in the Qinghai-Tibetan Plateau
Linglin Cao, Hao Zhou, Huimin Zhou, Caixin Yang, Jing Yang, Ji Pu, Yuyuan Huang, Chunmei Liu, Feifei Wang, Jiajia Ma, Qiang Hou, Shuo Ning, Xiaorui Liu, Shan Lu, Jianguo Xu
International Journal of Systematic and Evolutionary Microbiology .2026;[Epub] CrossRef
Sphingosinicella rhizophila sp. nov., Isolated from Oat (Avena sativa L.) Rhizosphere Soil
Yuze Guo, Kai Tang, Ting Yao, Jieyuzheng Zhang, Yang Liu, Jianyu Meng, Fuying Feng
Current Microbiology.2025;[Epub] CrossRef
Genomic-based taxonomic classification of the order Sphingomonadales
Yuan Wang, Hao You, Yan-Hui Kong, Cong Sun, Lin-Huan Wu, Song-Gun Kim, Jung-Sook Lee, Lin Xu, Xue-Wei Xu
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Isolation and characterization of a novel glycoside hydrolase positive bacterial strain named Terrimonas ginsenosidimutans sp. nov. with ginsenoside-converting activity
Muhammad Zubair Siddiqi, Ji Eun Lee, Min Ok Jun, Md. Amdadul Huq, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Evaluation of agricultural soil health after applying pyraclostrobin in wheat/maize rotation field based on the response of soil microbes
Kaixuan Hou, Chengbo Lu, Baihui Shi, Zongyuan Xiao, Xiaole Wang, Jingwen Zhang, Chao Cheng, Junchao Ma, Zhongkun Du, Bing Li, Lusheng Zhu
Agriculture, Ecosystems & Environment.2022; 340: 108186. CrossRef
Sphingosinicella terrae sp. nov. Isolated from a Desert Soil and Reclassification of Sphingomonas deserti as Sphingosinicella deserti comb. nov.
Dong Wang, Lei Dong, Neeli Habib, Feng Liu, Sohail Ahmad Jan, Jian-Yu Jiao, Min Xiao, Nimaichand Salam, Wen-Jun Li
Current Microbiology.2022;[Epub] CrossRef
Histidinibacterium aquaticum sp. nov., Isolated from Salt-Field Sea Water
Kyu-Hang Lee, Jin-Sook Park
Current Microbiology.2022;[Epub] CrossRef
Isolation, characterisation and genome analysis of a novel ginsenosides hydrolysing bacterium Ginsengibacter hankyongi gen. nov., sp. nov. isolated from soil
Muhammad Zubair Siddiqi, Md. Amdadul Huq, Wan-Taek Im
Antonie van Leeuwenhoek.2021; 114(1): 11. CrossRef
Sphingosinicella flava sp. nov., indole acetic acid producing bacteria isolated from maize field soil
Geeta Chhetri, Minchung Kang, Jiyoun Kim, Inhyup Kim, Yoonseop So, Taegun Seo
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Luteimonas granuli sp. nov., Isolated from Granules of the Wastewater Treatment Plant
Muhammad Zubair Siddiqi, Jun Mo Yeon, Hanna Choi, Jae Hag Lee, Sang Yong Kim, Ji-Hyang Wee, Wan Taek Im
Current Microbiology.2020; 77(9): 2002. CrossRef
Hankyongella ginsenosidimutans gen. nov., sp. nov., isolated from mineral water with ginsenoside coverting activity
Muhammad Zubair Siddiqi, Wan-Taek Im
Antonie van Leeuwenhoek.2020; 113(5): 719. CrossRef
Corallincola spongiicola sp. nov., isolated from sponge
Heejae Choi, Wan-Taek Im, Jin-Sook Park
Antonie van Leeuwenhoek.2020; 113(5): 643. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019; 69(5): 1247. CrossRef
Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil
Gyu-Min Choi, Soon-youl Lee, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(1): 125. CrossRef
Tardibacter chloracetimidivorans gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from an agricultural soil from Jeju Island in Republic of Korea
Hyosun Lee, Dong-Uk Kim, Sooyeon Park, Jung-Hoon Yoon, Jae-Hyung Ahn, Jong-Ok Ka
Journal of Microbiology.2018; 56(5): 324. CrossRef
Aquimarina spongiicola sp. nov., isolated from spongin
Kang Duk Choi, Ga-Eun Lee, Jin-Sook Park
International Journal of Systematic and Evolutionary Microbiology.2018; 68(4): 990. CrossRef
Olivibacter ginsenosidimutans sp nov., with ginsenoside converting activity isolated from compost, and reclassification of Pseudosphingobacterium domesticum as Olivibacter domesticus comb. nov
Muhammad Zubair Siddiqi, Qingmei Liu, Soon Youl Lee, kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(8): 2509. CrossRef
Vibrio hannami sp. nov., Isolated from Seawater
Ga-Eun Lee, Wan-Taek Im, Jin-Sook Park
Current Microbiology.2018; 75(3): 278. CrossRef
Ciceribacter azotifigens sp. nov., a nitrogen-fixing bacterium isolated from activated sludge
Muhammad Zubair Siddiqi, Gyu-Min Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(2): 482. CrossRef
Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil
Gyu-Min Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(1): 310. CrossRef
Flavobacterium hankyongi sp. nov., isolated from activated sludge
Qingzhen Liu, Muhammad Zubair Siddiqi, Qingmei Liu, Md. Amdadul Huq, Soon Yeol Lee, Kang-Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2018; 68(5): 1732. CrossRef
Lysobacter spongiae sp. nov., isolated from spongin
Heejae Choi, Wan-Taek Im, Jin-Sook Park
Journal of Microbiology.2018; 56(2): 97. CrossRef
Sphingomonas montis sp. nov., Isolated from Forest Soil of Low-Altitude Mountain
Dhiraj Kumar Chaudhary, Ram Hari Dahal, Jaisoo Kim
Current Microbiology.2018; 75(10): 1299. CrossRef
Brevibacterium hankyongi sp. nov., isolated from compost
Kang Duk Choi, Muhammad Zubair Siddiqi, Qingmei Liu, Siddiqi Muhammad Shafi, Yasser Durrani, Soon Yeol Lee, Myung-Suk Kang, Wan Taek Im
International Journal of Systematic and Evolutionary Microbiology.2018; 68(9): 2783. CrossRef
Bacillus spongiae sp. nov., isolated from sponge of Jeju Island
Ga-Eun Lee, Wan-Taek Im, Jin-Sook Park
Journal of Microbiology.2018; 56(4): 217. CrossRef
Sphingomonas aquatica sp. nov., isolated from tap water
Gyu-min Choi, Jung Hun Jo, Myung-Suk Kang, Minseok S. Kim, Soon-Youl Lee, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2017; 67(4): 845. CrossRef
Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water
Muhammad Zubair Siddiqi, Gyu-Min Choi, Mi-Sun Kim, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2017; 67(8): 2665. CrossRef
Pseudaminobacter granuli sp. nov., isolated from granules used in a wastewater treatment plant
Young Ki Hahn, Minseok S. Kim, Wan-Taek Im
Journal of Microbiology.2017; 55(8): 607. CrossRef
Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil
Muhammad Zubair Siddiqi, Gyu-Min Choi, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2017; 67(12): 4917. CrossRef
Mucilaginibacter ginsenosidivorans sp. nov., Isolated from Soil of Ginseng Field
Minseok M. Kim, Muhammad Zubair Siddiqi, Wan-Taek Im
Current Microbiology.2017; 74(12): 1382. CrossRef
Mucilaginibacter hankyongensis sp. nov., isolated from soil of ginseng field Baekdu Mountain
Qingmei Liu, Muhammad Zubair Siddiqi, Mi-Sun Kim, Sang Yong Kim, Wan-Taek Im
Journal of Microbiology.2017; 55(7): 525. CrossRef
Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field
Muhammad Zubair Siddiqi, Siddiqi Muhammad Shafi, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(10): 4039. CrossRef
Marmoricola ginsengisoli sp. nov. and Marmoricola pocheonensis sp. nov. isolated from a ginseng-cultivating field
Hye-Yeon Lee, Qingmei Liu, Myung-Suk Kang, Soo-Ki Kim, Soon-Youl Lee, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology.2016; 66(5): 1996. CrossRef
Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil
Muhammad Zubair Siddiqi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(9): 3449. CrossRef
Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng
Muhammad Zubair Siddiqi, Qingmei Liu, Myung-Suk Kang, Minseok S. Kim, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(3): 1125x. CrossRef
Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost
Muhammad Zubair Siddiqi, Siddiqi Muhammad Shafi, Kang Duk Choi, Wan-Taek Im, Zubair Aslam
International Journal of Systematic and Evolutionary Microbiology.2016; 66(11): 4433. CrossRef
Compostibacter hankyongensis gen. nov., sp. nov., isolated from compost
Muhammad Zubair Siddiqi, Siddiqi Muhammad Shafi, Kang Duk Choi, Wan-Taek Im
International Journal of Systematic and Evolutionary Microbiology .2016; 66(9): 3681. CrossRef

Characterization of Recombinant β-Glucosidase from Arthrobacter chlorophenolicus and Biotransformation of Ginsenosides Rb1, Rb2, Rc, and Rd: Myung Keun Park , Chang-Hao Cui , Sung Chul Park , Seul-Ki Park , Jin-Kwang Kim , Mi-Sun Jung , Suk-Chae Jung , Mi-Sun Jung , Suk-Chae Jung , Sun-Chang Kim , Wan-Taek Im; J. Microbiol. 2014;52(5):399-406. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-3601-7

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The focus of this study was the cloning, expression, and characterization of recombinant ginsenoside hydrolyzing β-glucosidase from Arthrobacter chlorophenolicus with an ultimate objective to more efficiently bio-transform ginse-nosides. The gene bglAch, consisting of 1,260 bp (419 amino acid residues) was cloned and the recombinant enzyme, over-expressed in Escherichia coli BL21 (DE3), was characterized. The GST-fused BglAch was purified using GST·Bind agarose resin and characterized. Under optimal conditions (pH 6.0 and 37°C) BglAch hydrolyzed the outer glucose and arabino-pyranose moieties of ginsenosides Rb1 and Rb2 at the C20 position of the aglycone into ginsenoside Rd. This was fol-lowed by hydrolysis into F2 of the outer glucose moiety of ginsenoside Rd at the C3 position of the aglycone. Additio-nally, BglAch more slowly transformed Rc to F2 via C-Mc1 (compared to hydrolysis of Rb1 or Rb2). These results in-dicate that the recombinant BglAch could be useful for the production of ginsenoside F2 for use in the pharmaceutical and cosmetic industries.

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Crystal Structure of XoLAP, a Leucine Aminopeptidase, from Xanthomonas oryzae pv. oryzae: Jin-Kwang Kim , Sampath Natarajan , Hanseul Park , Kim-Hung Huynh , Sang Hee Lee , Jeong-Gu Kim , Yeh-Jin Ahn , Lin-Woo Kang; J. Microbiol. 2013;51(5):627-632. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3234-2

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Aminopeptidases are metalloproteinases that degrade N-terminal residues from protein and play important roles in cell growth and development by controlling cell homeostasis and protein maturation. We determined the crystal structure of XoLAP, a leucyl aminopeptidase, at 2.6 Å resolution from Xanthomonas oryzae pv. oryzae, causing the destructive rice disease of bacterial blight. It is the first crystal structure of aminopeptidase from phytopathogens as a drug target. XoLAP existed as a hexamer and the monomer structure consisted of an N-terminal cap domain and a C-terminal peptidase domain with two divalent zinc ions. XoLAP structure was compared with BlLAP and EcLAP (EcPepA) structures. Based on the structural comparison, the molecular model of XoLAP in complex with the natural aminopeptidase inhibitor of microginin FR1 was proposed. The model structure will be useful to develop a novel antibacterial drug against Xoo.

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Mucilaginibacter ginsenosidivorax sp. nov., with Ginsenoside Converting Activity Isolated from Sediment: Jin-Kwang Kim , Tae-Eun Choi , Qing-Mei Liu , Hye-Yoon Park , Tae-Hoo Yi , Min-Ho Yoon , Sun-Chang Kim , Wan-Taek Im; J. Microbiol. 2013;51(3):394-399. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2653-4

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A Gram-reaction-negative, strictly aerobic, non-motile, nonspore-forming, and rod-shaped bacterial strain designated KHI28T was isolated from sediment in Gapcheon (river) and its taxonomic position was investigated using a polyphasic approach. Strain KHI28T grew at 10–42°C and at pH 5.5–8.5 on R2A and nutrient agar without additional NaCl as a supplement. Strain KHI28T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Re (ones of the dominant active components of ginseng) to C-K and Rg2, respectively. On the basis of 16S rRNA gene sequence similarity, strain KHI28T was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter dorajii DR-f4T (97.9% sequence similarity), M. polysacchareus DRP28T (97.3%), and M. lappiensis ANJLI2 T (97.2%). The G+C content of the genomic DNA was 45.8%. 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 C16:0. DNA and chemotaxonomic data supported the affiliation of strain KHI28T to the genus Mucilaginibacter. Strain KHI28T 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 ginsenosidivorax sp. nov. is proposed, with the type strain KHI28T (=KACC 14955T =LMG 25804T).

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