Journal of Microbiology

Che Ok Jeon

16 Articles

Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome: Dong-Wook Hyun , Jae-Yun Lee , Min-Soo Kim , Na-Ri Shin , Tae Woong Whon , Kyung Hyun Kim , Pil Soo Kim , Euon Jung Tak , Mi-Ja Jung , June Young Lee , Hyun Sik Kim , Woorim Kang , Hojun Sung , Che Ok Jeon , Jin-Woo Bae; J. Microbiol. 2021;59(8):793-806.; DOI: https://doi.org/10.1007/s12275-021-1165-x

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Viridans group streptococci are a serious health concern because most of these bacteria cause life-threatening infections, especially in immunocompromised and hospitalized individuals. We focused on two alpha-hemolytic Streptococcus strains (I-G2 and I-P16) newly isolated from an ileostomy effluent of a colorectal cancer patient. We examined their pathogenic potential by investigating their prevalence in human and assessing their pathogenicity in a mouse model. We also predicted their virulence factors and pathogenic features by using comparative genomic analysis and in vitro tests. Using polyphasic and systematic approaches, we identified the isolates as belonging to a novel Streptococcus species and designated it as Streptococcus ilei. Metagenomic survey based on taxonomic assignment of datasets from the Human Microbiome Project revealed that S. ilei is present in most human population and at various body sites but is especially abundant in the oral cavity. Intraperitoneal injection of S. ilei was lethal to otherwise healthy C57BL/6J mice. Pathogenomics and in vitro assays revealed that S. ilei possesses a unique set of virulence factors. In agreement with the in vivo and in vitro data, which indicated that S. ilei strain I-G2 is more pathogenic than strain I-P16, only the former displayed the streptococcal group A antigen. We here newly identified S. ilei sp. nov., and described its prevalence in human, virulence factors, and pathogenicity. This will help to prevent S. ilei strain misidentification in the future, and improve the understanding and management of streptococcal infections.

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Microbiota analysis of perimenopausal women experiencing recurrent vaginitis in conjunction with urinary tract infection
Yingying Bi, Yuezhu Wang, Wu Li, Yuhang Chen, Jinlong Qin, Huajun Zheng
BMC Microbiology.2025;[Epub] CrossRef
Characterization of blood microbial population in beef calves with clinical signs of sepsis using 16S rRNA gene sequencing
Giuliano Borriello, Flaminia Valentini, Sara Ferrini, Giorgia Di Muro, Giulia Cagnotti, Elena Grego, Angela Maria Catania, Maria Cristina Stella, Ugo Ala, Patrizia Nebbia, Antonio D’Angelo, Claudio Bellino, Ulrike Gertrud Munderloh
PLOS One.2025; 20(5): e0324469. CrossRef
Alterations of Gut Microbiome and Serum Short‐Chain Fatty Acids in Children With Enthesitis‐Related Arthritis
Qi Zheng, Yiping Xu, Xubo Qian, Bin Hu, Qian Ma, Li Guo, Robert M. Dorazio, Meiping Lu
International Journal of Rheumatic Diseases.2025;[Epub] CrossRef
Molecular characterization of a novel putative pathogen, Streptococcus nakanoensis sp. nov., isolated from sputum culture
Takeaki Wajima, Takashi Sugawara, Emi Tanaka, Kei-ichi Uchiya, Justin R. Kaspar
Microbiology Spectrum.2024;[Epub] CrossRef
Streptococcus raffinosi sp. nov., isolated from human breast milk samples
Ha Viet Nguyen, Anh Thi Van Trinh, Linh Nguyen Hai Bui, Anh Thi Lan Hoang, Quyen Thi Le Tran, Trung Thanh Trinh
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities
Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae
Journal of Microbiology.2024; 62(11): 973. CrossRef
Valid and accepted novel bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2022
Erik Munson, Arianna Carella, Karen C. Carroll, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef
Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Modulation of gut microbiota and fecal metabolites by corn silk among high-fat diet-induced hypercholesterolemia mice
Lin Ding, Shan Ren, Yaoxin Song, Chuangang Zang, Yuchao Liu, Hao Guo, Wenqing Yang, Hong Guan, Jicheng Liu
Frontiers in Nutrition.2022;[Epub] CrossRef
Reclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis
Sanjeet Kumar, Kanika Bansal, Santosh Kumar Sethi
Archives of Microbiology.2022;[Epub] CrossRef

Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil: Kyeong Ryeol Kim† , Kyung Hyun Kim† , Shehzad Abid Khan , Hyung Min Kim , Dong Min Han , Che Ok Jeon; J. Microbiol. 2021;59(8):709-718. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1156-y

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Two Gram-stain negative, yellow-pigmented, and mesophilic bacteria, designated strains R7T and R19T, were isolated from sandy and forest soil, South Korea, respectively. Both strains were non-motile rods showing catalase- and oxidase-positive activities. Both strains were shown to grow at 10–37°C and pH 6.0–9.0, and in the presence of 0–1.5% (w/v) NaCl. Strain R7T contained iso-C14:0, iso-C15:0, iso-C16:0, and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1 ω9c), whereas strain R19T contained iso-C11:0 3-OH, C16:1 ω7c alcohol, iso-C11:0, iso-C15:0, iso-C16:0, and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1 ω9c) as major cellular fatty acids (> 5%). Both strains contained ubiquinone- 8 as the sole isoprenoid quinone and phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid as the major polar lipids. The DNA G + C contents of strains R7T and R19T calculated from their genomes were 66.9 mol% and 68.9 mol%, respectively. Strains R7T and R19T were most closely related to Lysobacter panacisoli C8-1T and Lysobacter niabensis GH34-4T with 98.7% and 97.8% 16S rRNA sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains R7T and R19T formed distinct phylogenetic lineages within the genus Lysobacter. Based on phenotypic, chemotaxonomic, and molecular features, strains R7T and R19T represent novel species of the genus Lysobacter, for which the names Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. are proposed. The type strains of L. arenosi and L. solisilvae are R7T (= KACC 21663T = JCM 34257T) and R19T (= KACC 21767T = JCM 34258T), respectively.

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Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Saline soil improvement promotes the transformation of microbial salt tolerance mechanisms and microbial-plant-animal ecological interactions
Keyu Yao, Guanghao Wang, Wen Zhang, Qiang Liu, Jian Hu, Mao Ye, Xin Jiang
Journal of Environmental Management.2024; 372: 123360. CrossRef
Optimal Irrigation and Fertilization Enhanced Tomato Yield and Water and Nitrogen Productivities by Increasing Rhizosphere Microbial Nitrogen Fixation
Hongfei Niu, Tieliang Wang, Yongjiang Dai, Mingze Yao, Bo Li, Jiaqi Zheng, Lizhen Mao, Mingyu Zhao, Zhanyang Xu, Feng Zhang
Agronomy.2024; 14(9): 2111. CrossRef
Short-term effect of reclaimed wastewater quality gradient on soil microbiome during irrigation
V. Moulia, N. Ait-Mouheb, G. Lesage, J. Hamelin, N. Wéry, V. Bru-Adan, L. Kechichian, M. Heran
Science of The Total Environment.2023; 901: 166028. CrossRef
Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
Kyeong Ryeol Kim, Jeong Min Kim, Jae Kyeong Lee, Dong Min Han, Lujiang Hao, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Physiological and genomic analyses of cobalamin (vitamin B12)-auxotrophy of Lysobacter auxotrophicus sp. nov., a methionine-auxotrophic chitinolytic bacterium isolated from chitin-treated soil
Akihiro Saito, Hideo Dohra, Moriyuki Hamada, Ryota Moriuchi, Yohei Kotsuchibashi, Koji Mori
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Nitratireductor rhodophyticola sp. nov., isolated from marine red algae
Kyung Hyun Kim, Sylvia Kristyanto, Hyung Min Kim, Kyeong Ryeol Kim, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons)
Qian Liu, Guoying Fan, Kui Wu, Xiangning Bai, Xi Yang, Wentao Song, Shengen Chen, Yanwen Xiong, Haiying Chen
Journal of Microbiology.2022; 60(7): 668. CrossRef
Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef
Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment
Ju Hye Baek, Woonhee Baek, Sang Eun Jeong, Sung Chul Lee, Hyun Mi Jin, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef

Minor and major circRNAs in virus and host genomes: Zhihao Lou , Rui Zhou , Yinghua Su , Chun Liu , Wenting Ruan , Che Ok Jeon , Xiao Han , Chun Lin , Baolei Jia; J. Microbiol. 2021;59(3):324-331. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1021-z

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As a special type of noncoding RNA, circular RNAs (circRNAs) are prevalent in many organisms. They can serve as sponges for microRNAs and protein scaffolds, or templates for protein translation, making them linked to cellular homeostasis and disease progression. In recent years, circRNAs have been found to be abnormally expressed during the processes of viral infection and pathogenesis, and can help a virus escape the immune response of a host. Thus, they are now considered to play important functions in the invasion and development of viruses. Moreover, the potential application of circRNAs as biomarkers of viral infection or candidates for therapeutic targeting deserves consideration. This review summarizes circRNAs in the transcriptome, including their classification, production, functions, and value as biomarkers. This review paper also describes research progress on circRNAs in viral infection (mainly hepatitis B virus, HIV, and some human herpes viruses) and aims to provide new ideas for antiviral therapies targeting circRNAs.

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Omics-based microbiome analysis in microbial ecology: from sequences to information
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Journal of Microbiology.2021; 59(3): 229. CrossRef

RNase G controls tpiA mRNA abundance in response to oxygen availability in Escherichia coli: Jaejin Lee , Dong-Ho Lee , Che Ok Jeon , Kangseok Lee; J. Microbiol. 2019;57(10):910-917. Published online September 30, 2019; DOI: https://doi.org/10.1007/s12275-019-9354-6

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Studies have shown that many enzymes involved in glycolysis are upregulated in Escherichia coli endoribonuclease G (rng) null mutants. However, the molecular mechanisms underlying the RNase G-associated regulation of glycolysis have not been characterized. Here, we show that RNase G cleaves the 5􍿁􀁇untranslated region of triosephosphate isomerase A (tpiA) mRNA, leading to destabilization of the mRNA in E. coli. Nucleotide substitutions within the RNase G cleavage site in the genome resulted in altered tpiA mRNA stability, indicating that RNase G activity influences tpiA mRNA abundance. In addition, we observed that tpiA expression was enhanced, whereas that of RNase G was decreased, in E. coli cells grown anaerobically. Our findings suggest that RNase G negatively regulates tpiA mRNA abundance in response to oxygen availability in E. coli.

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Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6
Younkyung Choi, Minju Joo, Wooseok Song, Minho Lee, Hana Hyeon, Hyun-Lee Kim, Ji-Hyun Yeom, Kangseok Lee, Eunkyoung Shin
Journal of Microbiology.2022; 60(12): 1162. CrossRef
Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Microbial Pathogenesis.2022; 165: 105460. CrossRef
Endoribonuclease-mediated control of hns mRNA stability constitutes a key regulatory pathway for Salmonella Typhimurium pathogenicity island 1 expression
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Trans-acting regulators of ribonuclease activity
Jaejin Lee, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(4): 341. CrossRef
The effect of two ribonucleases on the production of Shiga toxin and stx-bearing bacteriophages in Enterohaemorrhagic Escherichia coli
Patricia B. Lodato
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Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus
Jaejin Lee, Eunkyoung Shin, Jaeyeong Park, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(12): 1133. CrossRef
An alternative miRISC targets a cancer‐associated coding sequence mutation in FOXL2
Eunkyoung Shin, Hanyong Jin, Dae‐Shik Suh, Yongyang Luo, Hye‐Jeong Ha, Tae Heon Kim, Yoonsoo Hahn, Seogang Hyun, Kangseok Lee, Jeehyeon Bae
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The coordinated action of RNase III and RNase G controls enolase expression in response to oxygen availability in Escherichia coli
Minho Lee, Minju Joo, Minji Sim, Se-Hoon Sim, Hyun-Lee Kim, Jaejin Lee, Minkyung Ryu, Ji-Hyun Yeom, Yoonsoo Hahn, Nam-Chul Ha, Jang-Cheon Cho, Kangseok Lee
Scientific Reports.2019;[Epub] CrossRef

Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond: Tingye Feng , Sang Eun Jeong , Jin Ju Lim , Seogang Hyun , Che Ok Jeon; J. Microbiol. 2019;57(4):232-237. Published online January 16, 2019; DOI: https://doi.org/10.1007/s12275-019-8463-6

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A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27T was observed at 20–40°C (optimum, 30°C), pH 5.0–7.0 (optimum, pH 6.0), and 0–0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C16:0, cyclo-C17:0, and cyclo- C19:0 ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27T was most closely related to Paraburkholderia rhynchosiae WSM3937T, Paraburkholderia ginsengiterrae DCY85T, Paraburkholderia fungorum NBRC 102489T, and Paraburkholderia graminis C4D1MT with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27T (KACC 19714 T = JCM 32721T).

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International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021
Seyed Abdollah Mousavi, J. Peter W. Young
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef
Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
Journal of Microbiology.2021; 59(8): 709. CrossRef
The history and distribution of nodulating Paraburkholderia, a potential inoculum for Fynbos forage species
Chrizelle W. Beukes, Stephanus N. Venter, Emma T. Steenkamp
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International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019
Philippe de Lajudie, J. Peter W. Young
International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3563. CrossRef
Flavihumibacter soli sp. nov., Isolated from Soil
Ye Lin Seo, Jaejoon Jung, Shehzad Abid Khan, Kyung Hyun Kim, Che Ok Jeon
Current Microbiology.2020; 77(10): 3179. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi: Jin Seok Moon , Hye Sun Choi , So Yeon Shin , Sol Ji Noh , Che Ok Jeon , Nam Soo Han; J. Microbiol. 2015;53(5):337-342. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5090-8

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Abstract

Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.

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Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches
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Erratum] Deodorization of Pig Slurry and Characterization of Bacterial Diversity Using 16S rDNA Sequence Analysis: Ok-Hwa Hwang , Sebastian Raveendar , Young-Ju Kim , Ji-Hun Kim , Tae-Hun Kim , Dong-Yoon Choi , Che Ok Jeon , Sung-Back Cho , Kyung-Tai Lee; J. Microbiol. 2014;52(12):1056-1056.; DOI: https://doi.org/10.1007/s12275-014-0704-0

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Abstract PDF: In the article by Hwang et al. published in Journal of Microbiology 2014; 52, 918-919. Jung-Woo Choi was omitted as the 5th author of this paper. The authors should be Ok-Hwa Hwang1†, Sebastian Raveendar1†, Young-Ju Kim1, Ji-Hun Kim1, Jung-Woo Choi1, Tae-Hun Kim1, Dong-Yoon Choi1, Che Ok Jeon2*, Sung-Back Cho1*, and Kyung-Tai Lee1*

Deodorization of Pig Slurry and Characterization of Bacterial Diversity Using 16S rDNA Sequence Analysis: Ok-Hwa Hwang , Sebastian Raveendar , Young-Ju Kim , Ji-Hun Kim , Tae-Hun Kim , Dong-Yoon Choi , Che Ok Jeon , Sung-Back Cho , Kyung-Tai Lee; J. Microbiol. 2014;52(11):918-929. Published online October 31, 2014; DOI: https://doi.org/10.1007/s12275-014-4251-5

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The concentration of major odor-causing compounds including phenols, indoles, short-chain fatty acids (SCFAs) and branched chain fatty acids (BCFAs) in response to the addition of powdered horse radish (PHR) and spent mushroom compost (SMC) was compared with control nontreated slurry (CNS) samples. A total of 97,465 rDNAs sequence reads were generated from three different samples (CNS, n = 2; PHR, n = 3; SMC, n = 3) using bar-coded pyrosequencing. The number of operational taxonomic units (OTUs) was lower in the PHR slurry compared with the other samples. A total of 11 phyla were observed in the slurry samples, while the phylogenetic analysis revealed that the slurry microbiome predominantly comprised members of the Bacteroidetes, Firmicutes, and Proteobacteria phyla. The rarefaction analysis showed the bacterial species richness varied among the treated samples. Overall, at the OTU level, 2,558 individual genera were classified, 276 genera were found among the three samples, and 1,832 additional genera were identified in the individual samples. A principal component analysis revealed the differences in microbial communities among the CNS, PHR, and SMC pig slurries. Correlation of the bacterial community structure with the Kyoto Encyclopedia of Genes and Genomes (KEGG) predicted pathways showed that the treatments altered the metabolic capabilities of the slurry microbiota. Overall, these results demonstrated that the PHR and SMC treatments significantly reduced the malodor compounds in pig slurry (P < 0.05).

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Effect of Fumarate Reducing Bacteria on In Vitro Rumen Fermentation, Methane Mitigation and Microbial Diversity: Lovelia Mamuad , Seon Ho Kim , Chang Dae Jeong , Yeon Jae Choi , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2014;52(2):120-128. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3518-1

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Abstract PDF

The metabolic pathways involved in hydrogen (H2) production, utilization and the activity of methanogens are the important factors that should be considered in controlling methane (CH4) emissions by ruminants. H2 as one of the major substrate for CH4 production is therefore should be controlled. One of the strategies on reducing CH4 is through the use of hydrogenotrophic microorganisms such as fumarate reducing bacteria. This study determined the effect of fumarate reducing bacteria, Mitsuokella jalaludinii, supplementation on in vitro rumen fermentation, CH4 production, diversity and quantity. M. jalaludinii significantly reduced CH4 at 48 and 72 h of incubation and significantly increased succinate at 24 h. Although not significantly different, propionate was found to be highest in treatment containing M. jalaludinii at 12 and 48 h of incubation. These results suggest that supplementation of fumarate reducing bacteria to ruminal fermentation reduces CH4 production and quantity, increases succinate and changes the rumen microbial diversity.

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Diversity of the Bacterial Community in the Rice Rhizosphere Managed Under Conventional and No-tillage Practices: Zubair Aslam , Muhammad Yasir , Hwan Sik Yoon , Che Ok Jeon , Young Ryun Chung; J. Microbiol. 2013;51(6):747-756. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-2528-8

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Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culturedependent
method
during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89–97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera.

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Characterization, Metabolites and Gas Formation of Fumarate Reducing Bacteria Isolated from Korean Native Goat (Capra hircus coreanae): Lovelia L. Mamuad , Seon Ho Kim , Sung Sil Lee , Kwang Keun Cho , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2012;50(6):925-931. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2497-3

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Fumarate reducing bacteria, able to convert fumarate to succinate, are possible to use for the methane reduction in rumen because they can compete for H2 with methanogens. In this, we isolated fumarate reducing bacteria from a rumen of Korean native goat and characterized their molecular properties [fumarate reductase A gene (frdA)], fumarate reductase activities, and productions of volatile fatty acids and gas. Eight fumarate reducing bacteria belonging to Firmicutes were isolated from rumen fluid samples of slaughtered Korean black goats and characterized their phylogenetic positions based on 16S rRNA gene sequences. PCR based analyses showed that only one strain, closely related to Mitsuokella jalaludinii, harbored frdA. The growths of M. jalaludinii and Veillonella parvula strains were tested for different media. Interestingly, M. jalaludinii grew very well in the presence of hydrogen alone, while V. parvula grew well in response of fumarate and fumarate plus hydrogen. M. jalaludinii produced higher levels of lactate (P≤0.05) than did V. parvula. Additionally, M. jalaludinii produced acetate, but not butyrate, whereas V. parvula produced butyrate, not acetate. The fumarate reductase activities of M. jalaludinii and V. parvula were 16.8 ± 0.34 and 16.9 ± 1.21 mmol NADH oxidized/min/mg of cellular N, respectively. In conclusion, this showed that M. jalaludinii can be used as an efficient methane reducing agent in rumen.

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Acinetobacter oleivorans sp. nov. Is Capable of Adhering to and Growing on Diesel-Oil: Yoon-Suk Kang , Jaejoon Jung , Che Ok Jeon , Woojun Park; J. Microbiol. 2011;49(1):29-34. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0315-y

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A diesel-oil and n-hexadecane-degrading novel bacterial strain, designated DR1T, was isolated from a rice paddy in Deok-So, South Korea. The strain DR1T cells were Gram-negative, aerobic coccobacilli, and grew at 20-37°C with the optimal temperature of 30°C, and an optimal pH of 6-8. Interestingly, strain DR1T was highly motile (swimming and swarming motility) using its fimbriae, and generated N-acyl homoserine lactones as quorum-sensing signals. The predominant respiratory quinone as identified as ubiquinone-9 (Q-9) and DNA G+C content was 41.4 mol%. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species A. calcoaceticus, A. haemolyticus, A. baumannii, A. baylyi, and A. beijerinckii, with which it evidenced sequence similarities of 98.2%, 97.4%, 97.2%, 97.1%, and 97.0%, respectively. DNA-DNA hybridization values between strain DR1T and other Acinetobacter spp. were all less than 20%. The physiological and taxonomic characteristics with the DNA-DNA hybridization data supported the identification of strain DR1T in the genus Acinetobacter as a novel species, for which the name Acinetobacter oleivorans sp. nov. is proposed. The type strain is DR1T (=KCTC 23045T =JCM 16667T).

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Isolation, Characterization, and Abundance of Filamentous Members of Caldilineae in Activated Sludge: Dae-No Yoon , Soo-Je Park , So-Jeong Kim , Che Ok Jeon , Jong-Chan Chae , Sung-Keun Rhee; J. Microbiol. 2010;48(3):275-283. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9366-8

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Abstract PDF: Chloroflexi are currently believed to serve as backbone forming agents in the activated sludge of wastewater treatment plants (WWTPs). In this study, we isolated and characterized filamentous bacteria in the class Caldilineae of the phylum Chloroflexi in municipal WWTPs. Diversity analysis using Chloroflexi-specific 16S rRNA gene clone libraries showed that 97% of the clones belonged to the subdivision Anaerolineae comprising the two classes Anaerolineae (95%) and Caldilineae (2%). Clones of Caldilineae were related to a thermophilic filament Caldilinea aerophila with 93% 16S rRNA gene sequence similarity. We obtained filamentous isolates classified into the class Caldilineae showing the best match to C. aerophila with 89% 16S rRNA gene sequence similarity. Isolates showed no ability to assimilate glucose or N-acetylglucosamine or to degrade biopolymers which were observed in filamentous Chloroflexi of WWTPs. The assessment of relative abundance based on quantitative PCR of the 16S rRNA gene indicated that members of the class Caldilineae comprised 12-19% of the Chloroflexi in the activated sludge. Additionally, fluorescence in situ hybridization experiments showed that diverse filamentous Caldilineae inhabit the activated sludge of municipal WWTPs. These findings yield insight into the role of filamentous mesophilic Caldilinea in stabilizing flocs of activated sludge in a wide range of WWTPs.

Virgibacillus xinjiangensis sp. nov., Isolated from a Salt Lake of Xin-jiang Province in China: Che Ok Jeon , Jeong Myeong Kim , Dong-Jin Park , Li-Hua Xu , Cheng-Lin Jiang , Chang-Jin Kim; J. Microbiol. 2009;47(6):705-709. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0107-9

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A strictly aerobic Gram-positive, moderately halophilic spore forming bacterium, designated strain SL6-1T, was isolated from a salt lake in Xin-jiang province, China. Growth of strain SL6-1T was observed at NaCl concentrations of 0~20% (w/v) (the optimum being 5~7%, w/v). The peptidoglycan type of strain SL6-1T was A1γ-meso-diaminopimelic acid and its major cellular fatty acids were iso-C14:0 and iso-C16:0 and anteiso-C15:0. The major respiratory isoprenoid quinone was MK-7 and the G+C content of the genomic DNA was 44.5 mol%. The major cellular phospholipids were phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL6-1T formed a phylogenetic lineage within the genus Virgibacillus. Based on 16S rRNA gene sequence similarity, the strain was most closely related to Virgibacillus olivae E308T, Virgibacillus kekensis YIM kkny16T, Virgibacillus marismortui DSM 12325T with 97.1%, 97.1%, and 97.0% gene sequence similarities, respectively and the sequence similarities to other related taxa were less than 96.7%. The DNA relatedness values between strain SL6-1T and V. olivae E308T, V. kekensis YIM kkny16T, V. marismortui DSM 12325T were 16.7%, 51.0%, and 22.8%, respectively. On the basis of physiological, biochemical and phylogenetic properties, strain SL6-1T represents a novel species, for which the name Virgibacillus xinjiangensis sp. nov. is proposed. The type strain is SL6-1T (=KCTC 13128T =DSM 19031T).

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Arthrobacter soli sp. nov., a Novel Bacterium Isolated from Wastewater Reservoir Sediment: Seong Woon Roh , Youlboong Sung , Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Jung-Hoon Yoon , Che Ok Jeon , Hee-Mock Oh , Jin-Woo Bae; J. Microbiol. 2008;46(1):40-44.; DOI: https://doi.org/10.1007/s12275-007-0239-8

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A novel Gram-positive bacterium, designated SYB2T, was isolated from wastewater reservoir sediment, and a polyphasic taxonomic study was conducted based on its morphological, physiological, and biochemical features, as well as the analysis of its 16S rRNA gene sequence. During the phylogenetic analysis of the strain SYB2T, results of a 16S rRNA gene sequence analysis placed this bacterium in the genus Arthrobacter within the family Micrococcaceae. SYB2T and Arthrobacter protophormiae ATCC 19271T, the most closely related species, both exhibited a 16S rRNA gene sequence similarity of 98.99%. The genomic DNA G+C content of the novel strain was found to be 62.0 mol%. The predominant fatty acid composition was anteiso-C15:0, anteiso-C17:0, iso-C16:0, and iso-C15:0. Analysis of 16S rRNA gene sequences and DNA-DNA relatedness, as well as physiological and biochemical tests, showed genotypic and phenotypic differences between strain SYB2T and other Arthrobacter species. The type strain of the novel species was identified as SYB2T (= KCTC 19291T= DSM 19449T).

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International Journal of Systematic and Evolutionary Microbiology.2016; 66(1): 9. CrossRef
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Hye Seon Song, In-Tae Cha, Jin-Kyu Rhee, Kyung June Yim, Ah Yoon Kim, Jong-Soon Choi, Su Jeong Baek, Myung-Ji Seo, Soo-Je Park, Young-Do Nam, Seong Woon Roh
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Isolation and Characterization of vB_ArS-ArV2 – First Arthrobacter sp. Infecting Bacteriophage with Completely Sequenced Genome
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Kyung June Yim, In-Tae Cha, Hae-Won Lee, Hye Seon Song, Kil-Nam Kim, Sung-Jae Lee, Young-Do Nam, Dong-Wook Hyun, Jin-Woo Bae, Sung-Keun Rhee, Myung-Ji Seo, Jong-Soon Choi, Hak-Jong Choi, Seong Woon Roh, Daekyung Kim
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Halococcus sediminicola sp. nov., an extremely halophilic archaeon isolated from a marine sediment
Kyung June Yim, In-Tae Cha, Tae Woong Whon, Hae-Won Lee, Hye Seon Song, Kil-Nam Kim, Young-Do Nam, Sung-Jae Lee, Jin-Woo Bae, Sung-Keun Rhee, Jong-Soon Choi, Myung-Ji Seo, Seong Woon Roh, Daekyung Kim
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Jandi Kim, Joon Yong Kim, Min-Soo Kim, Seong Woon Roh, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_4): 1355. CrossRef
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Journal of Microbiology.2013; 51(3): 312. CrossRef
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International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_10): 3640. CrossRef
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Journal of Microbiology.2013; 51(3): 301. CrossRef
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Jina Lee, Na-Ri Shin, Mi-Ja Jung, Seong Woon Roh, Min-Soo Kim, Jung-Sook Lee, Keun Chul Lee, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_2): 428. CrossRef
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International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_9): 3175. CrossRef
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Jina Lee, Na-Ri Shin, Hae-Won Lee, Seong Woon Roh, Min-Soo Kim, Young-Ok Kim, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_12): 2865. CrossRef
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International Journal of Systematic and Evolutionary Microbiology .2012; 62(Pt_10): 2424. CrossRef
Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food
Jandi Kim, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(12): 2851. CrossRef
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Yun-Ji Kim, Seong Woon Roh, Mi-Ja Jung, Min-Soo Kim, Eun-Jin Park, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(2): 399. CrossRef
Dietzia alimentaria sp. nov., isolated from a traditional Korean food
Jandi Kim, Seong Woon Roh, Jung-Hye Choi, Mi-Ja Jung, Young-Do Nam, Min-Soo Kim, Eun-Jin Park, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2011; 61(9): 2254. CrossRef
Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil
Lars Ganzert, Felizitas Bajerski, Kai Mangelsdorf, André Lipski, Dirk Wagner
International Journal of Systematic and Evolutionary Microbiology .2011; 61(4): 979. CrossRef
Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Eun-Jin Park, Jin-Woo Bae
The ISME Journal.2010; 4(1): 1. CrossRef
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Eun-Jin Park, Seong Woon Roh, Min-Soo Kim, Mi-Ja Jung, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(1): 140. CrossRef
Arthrobacter antarcticus sp. nov., isolated from an Antarctic marine sediment
Pavan Kumar Pindi, Ruth Manorama, Zareena Begum, S. Shivaji
International Journal of Systematic and Evolutionary Microbiology.2010; 60(10): 2263. CrossRef
Oceanobacillus kimchii sp. nov. Isolated from a traditional Korean fermented food
Tae Woong Whon, Mi-Ja Jung, Seong Woon Roh, Young-Do Nam, Eun-Jin Park, Kee-Sun Shin, Jin-Woo Bae
The Journal of Microbiology.2010; 48(6): 862. CrossRef
Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood
Eun-Jin Park, Min-Soo Kim, Seong Woon Roh, Mi-Ja Jung, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(4): 914. CrossRef
Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus
Seong Woon Roh, Myung-Lip Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2010; 60(5): 1187. CrossRef
Agromyces atrinae sp. nov., isolated from fermented seafood
Eun-Jin Park, Min-Soo Kim, Mi-Ja Jung, Seong Woon Roh, Ho-Won Chang, Kee-Sun Shin, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2010; 60(5): 1056. CrossRef
Arthrobacter halodurans sp. nov., a new halotolerant bacterium isolated from sea water
Yi-Guang Chen, Shu-Kun Tang, Yu-Qin Zhang, Zhao-Yang Li, Lang-Bo Yi, Yong-Xia Wang, Wen-Jun Li, Xiao-Long Cui
Antonie van Leeuwenhoek.2009; 96(1): 63. CrossRef
Paracoccus aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, K.-S. Shin, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(4): 790. CrossRef
Haloterrigena jeotgali sp. nov., an extremely halophilic archaeon from salt-fermented food
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, Y. Sung, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(9): 2359. CrossRef
Nocardioides basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 42. CrossRef
Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella
S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(2): 421. CrossRef
Sphingomonas aestuarii sp. nov., isolated from tidal flat sediment
S. W. Roh, K.-H. Kim, Y.-D. Nam, H.-W. Chang, M.-S. Kim, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(6): 1359. CrossRef
Halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood
Seong Woon Roh, Jin-Woo Bae
The Journal of Microbiology.2009; 47(2): 162. CrossRef
Nitratireductor basaltis sp. nov., isolated from black beach sand
K.-H. Kim, S. W. Roh, H.-W. Chang, Y.-D. Nam, J.-H. Yoon, C. O. Jeon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(1): 135. CrossRef
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Seong Woon Roh, Young-Do Nam, Ho-Won Chang, Kyoung-Ho Kim, Min-Soo Kim, Ji-Hwan Ryu, Sung-Hee Kim, Won-Jae Lee, Jin-Woo Bae
Applied and Environmental Microbiology.2008; 74(20): 6171. CrossRef
Marinobacter goseongensis sp. nov., from seawater
S. W. Roh, Z.-X. Quan, Y.-D. Nam, H.-W. Chang, K.-H. Kim, S.-K. Rhee, H.-M. Oh, C. O. Jeon, J.-H. Yoon, J.-W. Bae
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Genomics of biological wastewater treatment
Roland J. Siezen, Marco Galardini
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List of new names and new combinations previously effectively, but not validly, published

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(9): 1993. CrossRef
Luteimonas aestuarii sp. nov., isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 525. CrossRef
Marinomonas basaltis sp. nov., a marine bacterium isolated from black sand
H.-W. Chang, S. W. Roh, K.-H. Kim, Y.-D. Nam, J.-H. Yoon, H.-M. Oh, J.-W. Bae
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2008; 58(12): 2743. CrossRef
Aliihoeflea aestuarii gen. nov., sp. nov., a novel bacterium isolated from tidal flat sediment
Seong Woon Roh, Kyoung-Ho Kim, Young-Do Nam, Ho-Won Chang, Min-Soo Kim, Kee-Sun Shin, Jung-Hoon Yoon, Hee-Mock Oh, Jin-Woo Bae
The Journal of Microbiology.2008; 46(5): 594. CrossRef

Analysis of Microbial Communities Using Culture-dependent and Culture-independent Approaches in an Anaerobic/Aerobic SBR Reactor: Shipeng Lu , Minjeong Park , Hyeon-Su Ro , Dae Sung Lee , Woojun Park , Che Ok Jeon; J. Microbiol. 2006;44(2):155-161.; DOI: https://doi.org/2370 [pii]

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Abstract PDF: Comparative analysis of microbial communities in a sequencing batch reactor which performed enhanced biological phosphorus removal (EBPR) was carried out using a cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63% (137 of 217) in the standard PCR method to about 34% (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: α, β, γ- Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivationbased method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.

Che Ok Jeon

8 Articles

Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov., isolated from kimchi, a traditional Korean fermented food: Min Ji Lee, Jisu Lee, Sohee Nam, Mi-Ja Jung, Yeon Bee Kim, Yujin Kim, Jeong Ui Yun, Seong Woon Roh, Tae Woong Whon, Che Ok Jeon, Se Hee Lee; J. Microbiol. 2025;63(11):e2507007. Published online November 30, 2025; DOI: https://doi.org/10.71150/jm.2507007

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Abstract PDF Supplementary Material: Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605^T and CBA3606^T, were isolated from kimchi, a traditional Korean fermented food. Both strains were oxidase- and catalase-negative, non-spore-forming, non-hemolytic, and non-gas-producing. Optimal growth conditions for the two strains were observed at 30°C, pH 5.0, and 0% NaCl. The two genomes were composed of a circular chromosome and three plasmids and the DNA G + C content of 43.0%, respectively. Strains CBA3605^T and CBA3606^T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1^T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605^T and CBA3606^T were 91.7%, and those with strain 382-1^T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605^T and CBA3606^T were 45.0%, and those with strain 382-1^T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C_16:0, C_18:1 ω9c, and summed features 7 (C_19:1 ω7c, C_19:1 ω6c, C_19:0 cyclo ω10c, and/or C_19:0 ω6c). The peptidoglycan of both strains CBA3605^T and CBA3606^T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605^T contained aminophosphoglycolipid, which was absent in CBA3606^T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605^T and CBA3606^T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605^T (= KACC 81073BP^T = JCM 37965^T), and CBA3606^T (= KACC 81074BP^T = JCM 37966^T) as the type strains.

Retraction: Corrigendum: Staphylococcus parequorum sp. nov. and Staphylococcus halotolerans sp. nov., isolated from traditional Korean soybean foods: Ju Hye Baek, Dong Min Han, Dae Gyu Choi, Chae Yeong Moon, Jae Kyeong Lee, Chul-Hong Kim, Jung-Woong Kim, Che Ok Jeon; J. Microbiol. 2025;63(10):e2510100. Published online October 22, 2025; DOI: https://doi.org/10.71150/jm.2510100; Retracts: J. Microbiol 2025;63(9):e2509100

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Corrigendum: Staphylococcus parequorum sp. nov. and Staphylococcus halotolerans sp. nov., isolated from traditional Korean soybean foods: Ju Hye Baek, Dong Min Han, Dae Gyu Choi, Chae Yeong Moon, Jae Kyeong Lee, Chul-Hong Kim, Jung-Woong Kim, Che Ok Jeon; J. Microbiol. 2025;63(10):e2510101. Published online October 23, 2025; DOI: https://doi.org/10.71150/jm.2510101; Corrects: J. Microbiol 2025;63(8):e2503003

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RETRACTED ARTICLE: Corrigendum: Staphylococcus parequorum sp. nov. and Staphylococcus halotolerans sp. nov., isolated from traditional Korean soybean foods: Ju Hye Baek, Dong Min Han, Dae Gyu Choi, Chae Yeong Moon, Jae Kyeong Lee, Chul-Hong Kim, Jung-Woong Kim, Che Ok Jeon; J. Microbiol. 2025;63(9):e2509100. Published online September 30, 2025; DOI: https://doi.org/10.71150/jm.2509100; Corrects: J. Microbiol 2025;63(8):e2503003 Retraction in: J. Microbiol 2025;63(10):e2510100

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Staphylococcus parequorum sp. nov. and Staphylococcus halotolerans sp. nov., isolated from traditional Korean soybean foods: Ju Hye Baek, Dong Min Han, Dae Gyu Choi, Chae Yeong Moon, Jae Kyeong Lee, Chul-Hong Kim, Jung-Woong Kim, Che Ok Jeon; J. Microbiol. 2025;63(8):e2503003. Published online August 31, 2025; DOI: https://doi.org/10.71150/jm.2503003; Correction in: J. Microbiol 2025;63(9):e2509100 Correction in: J. Microbiol 2025;63(10):e2510101

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Abstract PDF Supplementary Material: Strains Mo2-6^T, S9, KG4-3^T, and 50Mo3-2, identified as coagulase-negative, Gram-stain-positive, halotolerant, non-motile coccoid bacteria, were isolated from traditional Korean soybean foods. Strains Mo2-6^T and S9 were both catalase- and oxidase-negative, whereas KG4-3^T and 50Mo3-2 were catalase-positive but oxidase-negative. The optimal growth conditions for Mo2-6^T and S9 were 30°C, 2% NaCl, and pH 7.0, while KG4-3^T and 50Mo3-2 grew best at 35°C, 2% NaCl, and pH 7.0. All strains contained menaquinone-7 as the predominant isoprenoid quinone, with anteiso-C_15:0 and iso-C_15:0 as the major cellular fatty acids (> 10%). Additionally, anteiso-C_13:0 was a major fatty acid in strain KG4-3^T. The DNA G + C contents of strains Mo2-6^T, S9, KG4-3^T, and 50Mo3-2 were 33.4%, 33.3%, 32.5%, and 32.7%, respectively. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strains Mo2-6^T and S9, as well as KG4-3^T and 50Mo3-2, formed distinct lineages within the genus Staphylococcus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses confirmed that strains Mo2-6^T and S9, as well as KG4-3^T and 50Mo3-2, belonged to the same species. Meanwhile, dDDH and ANI values between strains Mo2-6^T and KG4-3^T, as well as comparisons with other Staphylococcus type strains, were below the species delineation thresholds, indicating they represent novel species. Based on phenotypic, chemotaxonomic, and molecular data, we propose strain Mo2-6^T as the type strain of Staphylococcus parequorum sp. nov. (=KACC 23685^T =JCM 37038^T) and strain KG4-3^T as the type strain of Staphylococcus halotolerans sp. nov. (=KACC 23684^T =JCM 37037^T).

Phycobium rhodophyticola gen. nov., sp. nov. and Aliiphycobium algicola gen. nov., sp. nov., isolated from the phycosphere of marine red algae: Jeong Min Kim, Woonhee Baek, Byeong Jun Choi, Hülya Bayburt, Jae Kyeong Lee, Sung Chul Lee, Che Ok Jeon; J. Microbiol. 2025;63(6):e2503014. Published online June 30, 2025; DOI: https://doi.org/10.71150/jm.2503014

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Abstract PDF Supplementary Material

Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated D3-12ᵀ and G2-2ᵀ, were isolated from the phycosphere of marine red algae. Both strains exhibited catalase- and oxidase-positive activities. Strain D3-12ᵀ grew optimally at 30°C, pH 7.0, and 2.0–3.0% (w/v) NaCl, while strain G2-2ᵀ showed optimal growth at 30°C, pH 7.0, and 2.0% NaCl. Ubiquinone-10 was the sole respiratory quinone in both strains. The major fatty acids (> 5%) in strain D3-12ᵀ were feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), 11-methyl-C_18:1 ω7c, and C_16:0, while strain G2-2ᵀ contained summed feature 8 and C_16:0. The predominant polar lipids in strain D3-12ᵀ were phosphatidylcholine, phosphatidylglycerol, and phosphatidylethanolamine, whereas strain G2-2ᵀ contained phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G + C content was 59.9% for strain D3-12ᵀ and 60.2% for strain G2-2ᵀ. Phylogenetic analyses based on 16S rRNA and whole-genome sequences placed both strains into distinct lineages within the family Roseobacteraceae, separate from previously described genera. Genome-based relatedness metrics, including average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity, and percentage of conserved proteins, further confirmed that these strains represent novel genera. Based on phenotypic, chemotaxonomic, and molecular characteristics, strains D3-12ᵀ and G2-2ᵀ are proposed as novel genera: Phycobium rhodophyticola gen. nov., sp. nov. (D3-12ᵀ = KACC 22712ᵀ = JCM 35528ᵀ) and Aliiphycobium algicola gen. nov., sp. nov. (G2-2ᵀ = KACC 22602ᵀ = JCM 35752ᵀ). Additionally, metabolic features relevant to interactions with marine algae, including genes associated with carbohydrate-active enzymes, vitamin biosynthesis, phenylacetic acid production, and bacterioferritin synthesis, were bioinformatically investigated.

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Aquimarina rhodophyticola sp. nov. and Aquimarina besae sp. nov., Isolated from Marine Red Algae
Jeong Min Kim, Byeong Jun Choi, Hülya Bayburt, Dong Min Han, Che Ok Jeon
Current Microbiology.2025;[Epub] CrossRef
Carotenoid-Producing Qipengyuania algicola sp. nov. and Qipengyuania rhodophyticola sp. nov., Isolated from Marine Algae, and Emended Description of the Genus Qipengyuania Xu et al. 2020
Jae Kyeong Lee, Min Woo Lee, Chae Yeong Moon, Jeong Min Kim, Hülya Bayburt, Byeong Jun Choi, Che Ok Jeon
Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef

Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems: Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park; J. Microbiol. 2024;62(11):933-950. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00172-7

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Abstract PDF

Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.

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Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont
Tzipora Peretz, Esther Cattan‐Tsaushu, Chiara Conti, Benyamin Rosental, Laura Steindler, Sarit Avrani
Environmental Microbiology.2025;[Epub] CrossRef
Public goods-mediated bacterial interplay in aquatic ecosystems
Yerim Park, Wonjae Kim, Jihye Bae, Woojun Park
Water Research.2025; 287: 124310. CrossRef
Horizontal Gene Transfer and Recombination in Cyanobacteriota
Devaki Bhaya, Gabriel Birzu, Eduardo P.C. Rocha
Annual Review of Microbiology .2025; 79(1): 685. CrossRef

Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms: Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park; J. Microbiol. 2024;62(3):249-260. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00115-2

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14 Web of Science
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Abstract PDF

The proliferation of harmful cyanobacterial blooms dominated by Microcystis aeruginosa has become an increasingly serious problem in freshwater ecosystems due to climate change and eutrophication. Microcystis-blooms in freshwater generate compounds with unpleasant odors, reduce the levels of dissolved O₂, and excrete microcystins into aquatic ecosystems, potentially harming various organisms, including humans. Various chemical and biological approaches have thus been developed to mitigate the impact of the blooms, though issues such as secondary pollution and high economic costs have not been adequately addressed. Red clays and H₂O₂ are conventional treatment methods that have been employed worldwide for the mitigation of the blooms, while novel approaches, such as the use of plant or microbial metabolites and antagonistic bacteria, have also recently been proposed. Many of these methods rely on the generation of reactive oxygen species, the inhibition of photosynthesis, and/or the disruption of cellular membranes as their mechanisms of action, which may also negatively impact other freshwater microbiota. Nevertheless, the underlying molecular mechanisms of anticyanobacterial chemicals and antagonistic bacteria remain unclear. This review thus discusses both conventional and innovative approaches for the management of M. aeruginosa in freshwater bodies.

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Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
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