Journal of Microbiology

Jaisoo Kim

8 Articles

Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae: Tuan Manh Nguyen , Ngoc Hoang Trinh , Jaisoo Kim; J. Microbiol. 2018;56(7):485-492. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8025-3

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Three novel bacterial strains (UCM-2T, UCM-G28T, and UCM-G35T) were obtained while isolating soil bacteria for the development of antibiotics. Cells of these strains were Gram-negative, non-spore forming, motile by means of a single flagellum, and rod shaped. In all strains, the predominant isoprenoid quinone was ubiquinone-8 (Q-8). Cells contained C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and C17:0 cyclo as the major fatty acids, and C10:0 3-OH as the major hydroxy fatty acid. The polar lipid profiles of the three novel strains were dominated by diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C contents of strains UCM-2T, UCM-G28T, and UCMG35T were 67.5, 65.9, and 66.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA sequences showed that strain UCM-2T was most closely related to Variovorax soli NBRC 106424T, whereas strains UCM-G28T and UCM-G35T were most similar to Variovorax ginsengisoli Gsoil 3165T. Values indicating DNA-DNA hybridization between the novel isolates and closely related species in the genus Variovorax were lower than the 70% cut-off point. These phenotypic, chemotaxonomic, and phylogenetic data indicate that the three isolates should be classified as new members of the genus Variovorax, for which the names Variovorax ureilyticus sp. nov., Variovorax rhizosphaerae sp. nov., and Variovorax robiniae sp. nov. are proposed. The type strains are UCM-2T (= KACC 18899T = NBRC 112306T), UCMG28T (= KACC 18900T = NBRC 112307T), and UCM-G35T (= KACC 18901T = NBRC 112308T), respectively.

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Hydrophilobacter chitinilyticus gen. nov., sp. nov., a new member of the family Comamonadaceae isolated from freshwater
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International Journal of Systematic and Evolutionary Microbiology .2026;[Epub] CrossRef
Optimization of a high-throughput single spore DNA extraction protocol for the model species of arbuscular mycorrhizal fungi, Rhizophagus irregularis
Selina A. Spence, Brontë R. Shelton, Diego Yusta Belsham, Joana Larrere, Cassandra E. Bruce, Olivia J. Regush, Miranda M. Hart
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Variovorax atrisoli sp. nov., a novel species isolated from black soil applied with herbicide atrazine in Northeast China
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International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
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International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
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The first reported case of human infection with Variovorax durovernensis; a novel Variovorax sp. Isolated from the prosthetic aortic graft of a shepherd
Lara Payne, Adela Alcolea-Medina, Luke B Snell, Christopher Alder, Themoula Charalampous, Jake D Turnbull, Jonathan D Edgeworth, Rahul Batra, John L Klein, Anna L Goodman
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Variovorax durovernensis sp. nov., a novel species isolated from an infected prosthetic aortic graft in a human
Adela Alcolea-Medina, Luke B. Snell, Lara Payne, Christopher J. Alder, Jake D. Turnbull, Themoula Charalampous, Lisa Bryan, John L. Klein, Jonathan D. Edgeworth, Rahul Batra, Anna L. Goodman
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Variovorax terrae sp. nov. Isolated from Soil with Potential Antioxidant Activity
Chae Yung Woo, Jaisoo Kim
Journal of Microbiology and Biotechnology.2022; 32(7): 855. CrossRef
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Phytobiomes Journal.2021; 5(1): 1. CrossRef
Nitrogen Fertilization Reduces Nitrogen Fixation Activity of Diverse Diazotrophs in Switchgrass Roots
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Phytobiomes Journal.2021; 5(1): 80. CrossRef
Variovorax beijingensis sp. nov., a novel plant-associated bacterial species with plant growth-promoting potential isolated from different geographic regions of Beijing, China
Jun-lian Gao, Yu-chen Sun, Jing Xue, Pengbo Sun, Hui Yan, Mohammad Sayyar Khan, Li-wei Wang, Xiuhai Zhang, Jian-guang Sun
Systematic and Applied Microbiology.2020; 43(6): 126135. 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.2018; 68(11): 3379. CrossRef

Characterization of Flavobacterium aquimarinum sp. nov., a halotolerant bacterium isolated from seawater: Sylvia Kristyanto , Tuan Manh Nguyen , Dhiraj Kumar Chaudhary , Sang-Seob Lee , Jaisoo Kim; J. Microbiol. 2018;56(5):317-323. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7454-3

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Abstract PDF

A novel, aerobic, Gram-stain-negative, non-motile, non-spore forming, rod-shaped bacterium, designated strain Dol 15-39T, was isolated from a seawater sample near Geoje Island in the South Sea, Republic of Korea. The strain was found to be oxidase-negative and catalase-positive. The isolate was observed to grow at temperatures from 4 to 37°C, at salinities of up to 7%, and at pH levels from 6 to 9; moreover, it was not able to degrade starch, DNA, esculin, or tyrosine. Phylogenetic analysis based on 16S rRNA gene sequences showed that Dol 15-39T was most closely related to Flavobacterium jumunjinense HME7102T with a sequence similarity of 97.3%. However, the levels of DNA-DNA relatedness between Dol 15-39T and the most closely related species were much lower than 70%, confirming that they represented distinct genomic species. The genomic DNA G + C content of Dol 15-39T was calculated to be 32.6 mol%. MK-6 was the predominant respiratory quinine, while iso-C15:0 (25.0%), iso- C15:1 G (17.0%), and iso-C17:0 3-OH (10.4%) were the major cellular fatty acids. Phosphatidylethanolamine was identified as a major polar lipid, while various unidentified aminolipids and polar lipids were also detected. Based on polyphasic taxonomic data, Dol 15-39T represents a novel species of the genus Flavobacterium, for which the name F. aquimarinum sp. nov. is proposed. The type strain is accessible under the culture collection numbers (KEMB 9005-617T = JCM 31930T).

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Flavobacterium frigoritolerans sp. nov. and Flavobacterium shii sp. nov., isolated from glaciers on the Tibetan Plateau
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International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
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Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
Journal of Microbiology.2022; 60(9): 890. CrossRef
List of new names and new combinations previously effectively, but not validly, published
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A rapid and simple method for identifying bacterial polar lipid components in wet biomass: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(8):635-639. Published online July 4, 2017; DOI: https://doi.org/10.1007/s12275-017-7092-1

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Abstract PDF

There are marked differences between wet and freeze-dried cells with regard to the identification of polar lipid components. The determination of the polar lipid composition of freeze-dried cells is well established. However, several approaches to identifying polar lipid components in wet cells have met with limited success owing to the presence of non-polar compounds in the extracts, resulting in a lipid composition with a narrow scope. In this study, we surveyed the lipid profiles of the wet biomasses of three Gram-positive (Microbacterium lacticum, Rhodococcus koreensis, and Streptomyces longwoodensis) and two Gram-negative (Pseudomonas aeruginosa and Novosphingobium capsulatum) bacteria; the results were comparable in quality to those obtained using a standard freeze-dried approach. Moreover, our improved method ensures simple lipid extraction. Overall, the results of the analysis showed minor lipid profile differences between the two approaches with regard to quantity, and lipid identification was consistent in both methods for all species.

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Streptomyces lothianensis sp. nov., an Antibiotic‐Producing Strain Isolated From the Indian Sundarbans Mangrove Forest
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Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment
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Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil
Ram Hari Dahal, Jaisoo Kim
Antonie van Leeuwenhoek.2018; 111(11): 2131. CrossRef
Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae
Tuan Manh Nguyen, Ngoc Hoang Trinh, Jaisoo Kim
Journal of Microbiology.2018; 56(7): 485. CrossRef
Characterization of Flavobacterium aquimarinum sp. nov., a halotolerant bacterium isolated from seawater
Sylvia Kristyanto, Tuan Manh Nguyen, Dhiraj Kumar Chaudhary, Sang-Seob Lee, Jaisoo Kim
Journal of Microbiology.2018; 56(5): 317. CrossRef

Limnobacter humi sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from humus soil, and emended description of the genus Limnobacter Spring et al. 2001: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(7):508-513. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6645-7

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Abstract PDF

Three Gram-negative, strictly aerobic, chemolithoheterotrophic bacterial strains, designated UCM-30, UCM-33, and UCM-39T, were isolated in South Korea. Based on their 16S rRNA gene sequences, the three isolated strains were found to be similar to Limnobacter thiooxidans CS-K2T (97.41– 97.68%), Limnobacter litoralis KP1-19T (95.55–95.76%), and various genera belonging to the class Betaproteobacteria (90.34–93.34%). DNA-DNA hybridization showed 79.3–83.9% similarity between the genomic DNA of UCM-39T, UCM-30, and UCM-33, while the sequence similarity between UCM- 39T and L. thiooxidans KACC 13837T or L. litoralis LMG 24869T was 23.7% and 18.6%, respectively. The DNA G+C content of UCM 39T was 59.7 mol%, the major ubiquinone was Q-8, and the optimal oxidation rate was observed at 10 mM thiosulfate. The major fatty acids (≥ 10%) were summed features 3 (C16:1ω7c and/or C16:1ω6c) and 8 (C18:1ω7c and/or C18:1ω6c), and C16:0. The major polar lipids (diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol) were found in all members of genus Limnobacter. Based on phenotypic, physiological, and phylogenetic analyses, the UCM-39T strain was found to be significantly distinct to represent a novel species affiliated to the genus Limnobacter. We propose to name it Limnobacter humi sp. nov. with the type strain UCM-39T (=KACC 18574T =NBRC 111650T).

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Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in South Korea: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(5):330-336. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6519-z

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White and pale yellow coloured bacteria were isolated from the riverside soil, Daejeon, South Korea, and were designated UCM-11T, UCM-F25, and UCM-80T. We found that all strains were able to reduce nitrate, and the cells were aerobic and motile. The DNA G+C contents of UCM-11T, UCM-F25, and UCM-80T were between 68.9 to 71.2 mol% and the main ubiquinone was observed as Q-8. Based on16S rRNA gene sequences, strains UCM-11T and UCM-F25 were found to closely match with Azohydromonas australica IAM 12664T (98.48–98.55%), and the strain UCM-80T was the closest match with Azohydromonas lata IAM 12599T (98.34%). The presence of summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c) as well as twokinds of hydroxyfatty acids consisting of C10:0 3-OH and C12:0 2-OH, and branched fatty acids containing C16:0 iso and C17:0 cyclo were detected in all the strains. Phosphatidy-lethanolamine was a major polar lipid. DNA–DNA related-ness confirmed UCM-11T, UCM-F25 and UCM-80T as novel members of the genus Azohydromonas. Based on the mor-phological, physiological, biochemical and genotypic char-acteristics, we suggest that strains UCM-11T, UCM-F25, and UCM-80T represent novel species within the genus Azohy-dromonas. The names Azohydromonas riparia sp. nov., and Azohydromonas ureilytica sp. nov. are proposed for the type strains UCM-11T (=KACC 18570T =NBRC 111646T) and UCM-80T (=KACC 18576T =NBRC 111658T), respectively.

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Massilia kyonggiensis sp. nov., Isolated from Forest Soil in Korea: Jaisoo Kim; J. Microbiol. 2014;52(5):378-383. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-4010-7

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A Gram-negative, short, rod-shaped bacterium, TSA1T, was isolated from forest soil collected at Kyonggi University, South Korea. Assessment of 16S rRNA gene sequence sim-ilarity indicated that the strain is related to Massilia niastensis 5516S-1T (98.3%), M. haematophila CCUG 38318T (97.9%), M. aerilata 5516S-11T (97.9%), M. tieshanensis TS3T (97.6%), and M. varians CCUG 3529T (97.1%). Colonies grown on Reasoner’s 2A agar at 30°C for 2 days were transparent, white, round, smooth, and glossy. The cells grew at 10–42°C (optimum: 25–37°C) and pH 5–9 (optimum: 5–9) and in 0–2% NaCl (optimum: 0–1%). TSA1T was able to grow on trypticase soy and nutrient agar, but not on Luria-Bertani or MacConkey agar. The strain was catalase- and oxidase- positive and able to degrade starch and casein, but not car-boxymethyl cellulose. The predominant quinone of TSA1T was Q-8, the major fatty acids were summed feature 3 and C16:0, and the DNA G+C content was 66.7 mol%. Given these findings, we propose that this strain is a novel species of the genus Massilia. We suggest the name Massilia kyonggiensis sp. nov. (type strain, KACC 17471T =KEMB 9005-031T =JCM 19189T).

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Isolation of Paenibacillus pinesoli sp. nov. from Forest Soil in Gyeonggi-Do, Korea: Jeongsuk Moon , Jaisoo Kim; J. Microbiol. 2014;52(4):273-277. Published online March 29, 2014; DOI: https://doi.org/10.1007/s12275-014-3622-2

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Using a new culture method for unculturable soil bacteria, strain NB5T was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0–9.5 (optimum, 6.5–9.5) and at temperatures between 15°C and 45°C (optimum, 25–40°C). Growth was possible at 0–5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3T and P. agaridevorans DSM 1355T, respectively. The predominant menaquinone in NB5T was MK-7; the major fatty acids were anteiso-C15:0 and iso-C16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472T =KEMB 9005-025T =JCM 19203T).

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Rummeliibacillus suwonensis sp. nov., Isolated from Soil Collected in a Mountain Area of South Korea: Jihee Her , Jaisoo Kim; J. Microbiol. 2013;51(2):268-272. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-3126-5

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A Gram-positive, facultatively aerobic, rod-shaped, nonmotile, terminal spore-forming bacterium, designated strain G20T, was isolated from soil collected in a mountain region of Suwon, South Korea. On the basis of 16S rRNA gene sequence similarity, this strain was shown to be related to Rummeliibacillus pycnus NBRC 101231T (97.4%) and Rummeliibacillus stabekisii KSC-SF6gT (95.7%). DNA-DNA hybridization studies showed 42% and 50% similarity of strain G20T with R. pycnus NBRC 101231Tand R. stabekisii KSCSF6gT, respectively. The DNA G+C content of G20T was 37.8 mol%, the major cellular fatty acids were iso-C15:0 and anteiso-C15:0, and the predominant menaquinones were MK-7 and MK-8. On the basis of phylogenetic, chemotaxonomic, and phenotypic characteristics, we propose this strain to be a novel species and the third member of genus Rummeliibacillus. We suggest the name Rummeliibacillus suwonensis sp. nov. The type strain is G20T (KACC 17316T =KEMB 9005-003T =JCM 19065T).

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