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Article
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
  • 2,184 View
  • 96 Download
AbstractAbstract PDFSupplementary Material

Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605T and CBA3606T, 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 CBA3605T and CBA3606T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605T and CBA3606T were 91.7%, and those with strain 382-1T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605T and CBA3606T were 45.0%, and those with strain 382-1T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C16:0, C18:1 ω9c, and summed features 7 (C19:1 ω7c, C19:1 ω6c, C19:0 cyclo ω10c, and/or C19:0 ω6c). The peptidoglycan of both strains CBA3605T and CBA3606T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605T contained aminophosphoglycolipid, which was absent in CBA3606T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605T and CBA3606T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605T (= KACC 81073BPT = JCM 37965T), and CBA3606T (= KACC 81074BPT = JCM 37966T) as the type strains.
Article
Virgibacillus saliphilus sp. nov. and Virgibacillus salidurans sp. nov., isolated from kimchi
Young Joon Oh, Joon Yong Kim, Min-Sung Kwon, Sulhee Lee, Sang-Pil Choi, Hak-Jong Choi
J. Microbiol. 2025;63(1):e.2501001.   Published online January 24, 2025
DOI: https://doi.org/10.71150/jm.2501001
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  • 134 Download
  • 4 Web of Science
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AbstractAbstract PDFSupplementary Material

This study aimed to provide a taxonomic description of two bacterial strains, NKC19-3T and NKC19-16T, isolated from commercially produced kimchi obtained from various regions within the Republic of Korea. Both strains were rod-shaped, gram-stain-positive, facultatively anaerobic, and displayed positive reactions for oxidase and catalase. Additionally, these bacteria were motile, halophilic (salt-tolerant), and proliferated under alkaline conditions. Genetically, both strains showed 98.0% similarity in their 16S rRNA gene sequences and were most closely related to Virgibacillus natechei FarDT, with 96.5 and 96.8% sequence similarity, respectively. ANI values indicated that the two novel strains were distinct from V. natechei FarDT, as they were below the species demarcation threshold. The ANI value between strains NKC19-3ᵀ and NKC19-16ᵀ was 84.64–84.75%, and the values between these strains and other related strains did not exceed 80.0%, further supporting their classification as novel species. Phylogenetic analysis revealed that strains NKC19-3T and NKC19-16T formed a distinct branch within the genus Virgibacillus, clearly distinguishing them from other species in the same genus. Regarding genomic characteristics, the GC content was 38.9% for strain NKC19-3T and 39.5% for strain NKC19-16T. The genome of strain NKC19-3T had a size of approximately 4.1 Mb and contained 3,785 protein-coding genes (CDSs). Strain NKC19-16T had a slightly smaller genome, approximately 3.9 Mb in size and harbored 3,726 CDSs. The polar lipid profiles of strains NKC19-3ᵀ and NKC19-16ᵀ included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), glycolipids (GL), and an unidentified lipid (L). The predominant fatty acids of both strains were anteiso-C15:0 and anteiso-C17:0. Considering the comprehensive analysis encompassing phenotypic, genomic, phylogenetic, and chemotaxonomic data, strains NKC19-3T and NKC19-16T are proposed to represent two novel species within the genus Virgibacillus. The suggested names for these species are Virgibacillus saliphilus sp. nov. (type strain NKC19-3T, also referred to as KACC 22326T and DSM 112707T) and Virgibacillus salidurans sp. nov. (type strain NKC19-16T, also referred to as KACC 22327T and DSM 112708T).

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  • Unraveling volatile and microbial dynamics of Pukeng tea with different storage times using metabolomics, chemometrics, and microbiome analysis
    Fengke Lin, Yuedi Xu, Siyu Lin, Ziqi Zhao, Jingran Zhao, Chunsong Cheng, Binsheng Luo
    Food Chemistry: X.2026; 34: 103692.     CrossRef
  • Complete genome sequence of Virgibacillus sp. KFRI-KCUT25010 isolated from a fermented hairtail ( Trichiurus lepturus ) sauce
    Myunglip Lee, Yukyoung Park, Sunghun Yi, Zhenjiang Zech Xu
    Microbiology Resource Announcements.2026;[Epub]     CrossRef
  • Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, Markus Göker
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
  • Genome-based reclassification of Virgibacillus kapii Daroonpunt et al. 2016 and Virgibacillus massiliensis Khelaifia et al. 2023 as later heterotypic synonyms of Virgibacillus salexigens (Garabito et al. 1997) Heyrman et al. 2003
    Taha Menasria, Nawel Zaatout
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
Article
Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
J. Microbiol. 2024;62(12):1089-1097.   Published online December 2, 2024
DOI: https://doi.org/10.1007/s12275-024-00188-z
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  • 1 Web of Science
  • 1 Crossref
AbstractAbstract PDF
Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01(T) and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5-25 ℃ (optimum, 20 ℃), pH 5-8 (optimum, pH 7) and in the presence of 0-5% (w/v) NaCl (optimum, 1%). Results of 16S rRNA gene-based phylogenetic analyses showed that strains MS01(T) and MS02 shared identical sequences, clustered within the Leuconostoc clade in phylogenetic trees, and were most closely related to Leuconostoc inhae IH003(T) and Leuconostoc gasicomitatum LMG 18811(T) with sequence similarities of 98.74%. The complete whole-genome sequences of strains MS01(T) and MS02 measured 2.04-2.06 Mbp and harbored a 50.6 kb plasmid, with DNA G + C contents of 37.7% for both. Based on average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values, both strains were confirmed to belong to the same species but showed ≤ 85.9% ANI and ≤ 29.9% dDDH values to other Leuconostoc species, indicating that they represent a novel species. Metabolic pathway reconstruction revealed that both strains perform heterolactic acid fermentation, producing lactate, acetate, and ethanol. Chemotaxonomic analyses, including cellular fatty acids, polar lipids, and peptidoglycan amino acid, confirmed the inclusion of both strains within the genus Leuconostoc. Based on the phylogenetic, genomic, and phenotypic characterization, strains MS01(T) and MS02 were considered to represent a novel species within the genus Leuconostoc, for which the name Leuconostoc aquikimchii sp. nov. is proposed with MS01(T) (= KACC 23748(T) = JCM 37028(T)) as the type strain.

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  • Validation List no. 224. Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, Markus Göker
    International Journal of Systematic and Evolutionary Microbiology .2025;[Epub]     CrossRef
Review
Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target
Yurim Yoon, Saemee Song
J. Microbiol. 2024;62(4):261-275.   Published online May 31, 2024
DOI: https://doi.org/10.1007/s12275-024-00137-w
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  • 6 Web of Science
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AbstractAbstract PDF
Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.

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    Veronika Zdarska, Gabriele Arcari, Milan Kolar, Patrik Mlynarcik
    Antibiotics.2026; 15(1): 37.     CrossRef
  • Therapeutic milestones against multidrug resistant Acinetobacter baumannii: from legacy antibiotics to Zosurabalpin
    Jaya Malik, Shilpy Singh, Dharmsheel Shrivastav, Ved Vrat Verma, Ravi Kant Pal, Manoj Kumar Mishra, Varun Kumar Sharma
    Archives of Microbiology.2026;[Epub]     CrossRef
  • Fragaria Nubicola (A Wild Strawberry) from Azad Kashmir: Its Molecular Identification and Screening of Thaumatin-Like and Defensin Ec-Amp-D2-Like Proteins
    Amna Shahid Awan, Ruba Shahid, Zahid Mushtaq
    Biochemical Genetics.2026;[Epub]     CrossRef
  • Genomic and GWAS-Based Insights into Antimicrobial Resistance in Shewanella algae Isolated from Penaeus monodon
    Ponsit Sathapondecha, Wichai Pornthanakasem, Timpika Thepsuwan, Pacharaporn Angthong, Wiyada Chumpol, Kamonwan Lunha, Suganya Yongkiettrakul, Wanilada Rungrassamee
    Antibiotics.2026; 15(4): 405.     CrossRef
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    Dongyang Fan, Meng Li, Zipeng Shen, Ying Li, Jingjing Guo, Dong Wang, Ting Han, Ben Zhong Tang
    Aggregate.2025;[Epub]     CrossRef
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    Annabelle Mathieu-Denoncourt, Marylise Duperthuy
    Applied Microbiology.2025; 5(3): 64.     CrossRef
  • Integrated Omics-Based Discovery of Bioactive Halogenated Metabolites from the Deep-Sea Streptomyces sp. B188M101
    Emmanuel Tope Oluwabusola, Stephen A. Jackson, Cristina Brunati, Stefanie Gackstatter, Hannah Vedder, Marianna Iorio, Gargee Chawande, Lekha Menon Margassery, Giang-Son Nguyen, David J. Clarke, Rainer Ebel, Marcel Jaspars, Alan D. W. Dobson
    Marine Drugs.2025; 23(9): 362.     CrossRef
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Article
miR-135b Aggravates Fusobacterium nucleatum-Induced Cisplatin Resistance in Colorectal Cancer by Targeting KLF13
Wei Zeng , Jia Pan , Guannan Ye
J. Microbiol. 2024;62(2):63-73.   Published online February 24, 2024
DOI: https://doi.org/10.1007/s12275-023-00100-1
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  • 11 Web of Science
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AbstractAbstract PDF
Cisplatin resistance is the main cause of colorectal cancer (CRC) treatment failure, and the cause has been reported to be related to Fusobacterium nucleatum (Fn) infection. In this study, we explored the role of Fn in regulating cisplatin resistance of CRC cells and its underlying mechanism involved. The mRNA and protein expressions were examined by qRT-PCR and western blot. Cell proliferation and cell apoptosis were assessed using CCK8 and flow cytometry assays, respectively. Dual-luciferase reporter gene assay was adopted to analyze the molecular interactions. Herein, our results revealed that Fn abundance and miR-135b expression were markedly elevated in CRC tissues, with a favorable association between the two. Moreover, Fn infection could increase miR-135b expression via a concentration-dependent manner, and it also enhanced cell proliferation but reduced apoptosis and cisplatin sensitivity by upregulating miR-135b. Moreover, KLF13 was proved as a downstream target of miR-135b, of which overexpression greatly diminished the promoting effect of miR-135b or Fn-mediated cisplatin resistance in CRC cells. In addition, it was observed that upstream 2.5 kb fragment of miR-135b promoter could be interacted by β-catenin/TCF4 complex, which was proved as an effector signaling of Fn. LF3, a blocker of β-catenin/TCF4 complex, was confirmed to diminish the promoting role of Fn on miR-135b expression. Thus, it could be concluded that Fn activated miR-135b expression through TCF4/β-catenin complex, thereby inhibiting KLF13 expression and promoting cisplatin resistance in CRC.

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    Critical Reviews in Clinical Laboratory Sciences.2026; 63(2): 147.     CrossRef
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    Frontiers in Molecular Biosciences.2026;[Epub]     CrossRef
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    Non-coding RNA Research.2025; 12: 67.     CrossRef
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Article
Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes
Kang Xiao , Zhengyu Chen , Qin Long
J. Microbiol. 2023;61(5):571-578.   Published online April 21, 2023
DOI: https://doi.org/10.1007/s12275-023-00045-5
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AbstractAbstract PDF
Microbial communities played a vital role in maintaining homeostasis of ocular surface. However, no studies explored the myopia-associated conjunctiva microbiota changes until now. In this study, conjunctival sac swab specimens were collected from 12 eyes of low myopia (LM), and 14 eyes of high myopia (HM) patients. The V3–V4 region of the 16S rRNA gene was amplified and then sequenced. Statistical analysis was performed to investigate differences in the taxonomy and diversity between two groups. Compared to LM, higher Ocular Surface Disease Index (OSDI) scores were observed in HM group. The Shannon index of the HM was lower than that of the LM group (P = 0.017). Principle coordinate analysis and Partial Least Squares Discrimination Analysis showed distinct microbiome composition between two groups. At the phylum level, there were higher relative abundances of Proteobacteria (68.27% vs 38.51%) and lower abundances of Actinobacteria (3.71% vs 9.19%) in HM, compared to LM group (P = 0.031, 0.010, respectively). At the genus level, the abundances of Acinetobacter in HM (18.16%) were significantly higher than the LM (6.52%) group (P = 0.011). Actinobacteria levels were negatively correlated with the myopic spherical equivalent and OSDI scores. Moreover, positive correlations were found between Proteobacteria levels and OSDI scores, Acinetobacter levels were positively correlated with myopic spherical equivalent and OSDI scores. In conclusion, HM Patients have bacterial microbiota imbalance in the conjunctival sac, compared with LM patients. Proteobacteria, Actinobacteria, Acinetobacter may play roles in the HM associated ocular surface irritation.

Citations

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  • Associations between Ocular Surface Microbiome and Refractive Status in Children and Adolescents
    Xiangtian Ling, Yu Peng, Yuzhou Zhang, Charlene C. Yim, Hei-Nga Chan, Yating Yang, Qihang Sun, Xiu-Juan Zhang, Ka Wai Kam, Wai Kit Chu, Patrick Ip, Alvin L. Young, Christopher J. Hammond, Stephen Kwok Wing Tsui, Clement C. Tham, Chi Pui Pang, Li Jia Chen,
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    Frontiers in Ophthalmology.2025;[Epub]     CrossRef
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    Wan E. W. Omar, Gurdeep Singh, Andrew J. McBain, Fiona Cruickshank, Hema Radhakrishnan
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Review
Recent Advances in CRISPR‑Cas Technologies for Synthetic Biology
Song Hee Jeong , Ho Joung Lee , Sang Jun Lee
J. Microbiol. 2023;61(1):13-36.   Published online February 1, 2023
DOI: https://doi.org/10.1007/s12275-022-00005-5
  • 2,941 View
  • 6 Download
  • 43 Web of Science
  • 49 Crossref
AbstractAbstract PDF
With developments in synthetic biology, “engineering biology” has emerged through standardization and platformization based on hierarchical, orthogonal, and modularized biological systems. Genome engineering is necessary to manufacture and design synthetic cells with desired functions by using bioparts obtained from sequence databases. Among various tools, the CRISPR-Cas system is modularly composed of guide RNA and Cas nuclease; therefore, it is convenient for editing the genome freely. Recently, various strategies have been developed to accurately edit the genome at a single nucleotide level. Furthermore, CRISPR-Cas technology has been extended to molecular diagnostics for nucleic acids and detection of pathogens, including disease-causing viruses. Moreover, CRISPR technology, which can precisely control the expression of specific genes in cells, is evolving to find the target of metabolic biotechnology. In this review, we summarize the status of various CRISPR technologies that can be applied to synthetic biology and discuss the development of synthetic biology combined with CRISPR technology in microbiology.

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Protocol
Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method
Jaemin Lee , Minkyung Ryu , Dayeong Bae , Hong-Man Kim , Seong-il Eyun , Jeehyeon Bae , Kangseok Lee
J. Microbiol. 2022;60(7):659-667.   Published online June 22, 2022
DOI: https://doi.org/10.1007/s12275-022-2235-4
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AbstractAbstract PDF
Aptamers are short single-stranded DNA or RNA oligonucleotides capable of binding with high affinity and specificity to target molecules. Because of their durability and ease of synthesis, aptamers are used in a wide range of biomedical fields, including the diagnosis of diseases and targeted delivery of therapeutic agents. The aptamers were selected using a process called systematic evolution of ligands by exponential enrichment (SELEX), which has been improved for various research purposes since its development in 1990. In this protocol, we describe a modified SELEX method that rapidly produces high aptamer screening yields using two types of magnetic beads. Using this method, we isolated an aptamer that specifically binds to an antimicrobial peptide. We suggest that by conjugating a small therapeutic-specific aptamer to a gold nanoparticle-based delivery system, which enhances the stability and intracellular delivery of peptides, aptamers selected by our method can be used for the development of therapeutic agents utilizing small therapeutic peptides.

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  • Recent approaches in the application of antimicrobial peptides in food preservation
    Satparkash Singh, Bhavna Jha, Pratiksha Tiwari, Vinay G. Joshi, Adarsh Mishra, Yashpal Singh Malik
    World Journal of Microbiology and Biotechnology.2024;[Epub]     CrossRef
  • Design and application of microfluidics in aptamer SELEX and Aptasensors
    Shikun Zhang, Yingming Zhang, Zhiyuan Ning, Mengxia Duan, Xianfeng Lin, Nuo Duan, Zhouping Wang, Shijia Wu
    Biotechnology Advances.2024; 77: 108461.     CrossRef
  • Nanogenosensors based on aptamers and peptides for bioelectrochemical cancer detection: an overview of recent advances in emerging materials and technologies
    Babak Mikaeeli Kangarshahi, Seyed Morteza Naghib
    Discover Applied Sciences.2024;[Epub]     CrossRef
  • Recent progress of SELEX methods for screening nucleic acid aptamers
    Chao Zhu, Ziru Feng, Hongwei Qin, Lu Chen, Mengmeng Yan, Linsen Li, Feng Qu
    Talanta.2024; 266: 124998.     CrossRef
  • Aptamer-conjugated gold nanoparticles platform as the intracellular delivery of antibodies for cancer therapy
    Ji-Hyun Yeom, Eunkyoung Shin, Hanyong Jin, Haifeng Liu, Yongyang Luo, Youngwoo Nam, Minkyung Ryu, Wooseok Song, Heeyoun Chi, Jeongkyu Kim, Kangseok Lee, Jeehyeon Bae
    Journal of Industrial and Engineering Chemistry.2023; 126: 480.     CrossRef
  • Regulation of transforming growth factor-β signaling as a therapeutic approach to treating colorectal cancer
    Jana Maslankova, Ivana Vecurkovska, Miroslava Rabajdova, Jana Katuchova, Milos Kicka, Michala Gayova, Vladimir Katuch
    World Journal of Gastroenterology.2022; 28(33): 4744.     CrossRef
Article
The efficacy of a 2,4-diaminoquinazoline compound as an intranasal vaccine adjuvant to protect against influenza A virus infection in vivo
Kyungseob Noh , Eun Ju Jeong , Timothy An , Jin Soo Shin , Hyejin Kim , Soo Bong Han , Meehyein Kim
J. Microbiol. 2022;60(5):550-559.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1661-7
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AbstractAbstract PDF
Adjuvants are substances added to vaccines to enhance antigen- specific immune responses or to protect antigens from rapid elimination. As pattern recognition receptors, Toll-like receptors 7 (TLR7) and 8 (TLR8) activate the innate immune system by sensing endosomal single-stranded RNA of RNA viruses. Here, we investigated if a 2,4-diaminoquinazolinebased TLR7/8 agonist, (S)-3-((2-amino-8-fluoroquinazolin- 4-yl)amino)hexan-1-ol (named compound 31), could be used as an adjuvant to enhance the serological and mucosal immunity of an inactivated influenza A virus vaccine. The compound induced the production of proinflammatory cytokines in macrophages. In a dose-response analysis, intranasal administration of 1 μg compound 31 together with an inactivated vaccine (0.5 μg) to mice not only enhanced virus-specific IgG and IgA production but also neutralized influenza A virus with statistical significance. Notably, in a virus-challenge model, the combination of the vaccine and compound 31 alleviated viral infection-mediated loss of body weight and increased survival rates by 40% compared with vaccine only-treated mice. We suggest that compound 31 is a promising lead compound for developing mucosal vaccine adjuvants to protect against respiratory RNA viruses such as influenza viruses and potentially coronaviruses.

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  • Synthetic Cathepsin B Sensitive Adjuvant‐Peptide Conjugates to Target Intracellular Toll‐Like Receptors 7 and 8
    Marjolein M. E. Isendoorn, Giulia Castello, Nico J. Meeuwenoord, Martijn Verdoes, Jeroen D. C. Codée, Ferry Ossendorp, Dmitri V. Filippov
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    Muhammad Haroon, Sharmin Sultana, Seyedeh A. Najibi, Emily T. Wang, Abbey Michaelson, Pranto S. M. Al Muied, Amy E. Nielsen, Rock J. Mancini
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  • Design, Synthesis, and Biological Evaluation of New 2,6,7-Substituted Purine Derivatives as Toll-like Receptor 7 Agonists for Intranasal Vaccine Adjuvants
    Morgan Kim, Kyungseob Noh, Pyeongkeun Kim, Jae Ho Kim, Byeong Wook Choi, Ravi Singh, Jun-Ho Choi, Soo Bong Han, Seong Soon Kim, Eun-Young Lee, Myung Ae Bae, Daeho Shin, Meehyein Kim, Jin Hee Ahn
    Journal of Medicinal Chemistry.2024; 67(11): 9389.     CrossRef
  • Evaluation of Antiviral Activity of Gemcitabine Derivatives against Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2
    Hyeon-Min Cha, Uk-Il Kim, Soo Bin Ahn, Myoung Kyu Lee, Haemi Lee, Hyungtae Bang, Yejin Jang, Seong Soon Kim, Myung Ae Bae, Kyungjin Kim, Meehyein Kim
    ACS Infectious Diseases.2023; 9(4): 1033.     CrossRef
  • Identification of broad-spectrum neutralizing antibodies against influenza A virus and evaluation of their prophylactic efficacy in mice
    Sumin Son, Soo Bin Ahn, Geonyeong Kim, Yejin Jang, Chunkyu Ko, Meehyein Kim, Sang Jick Kim
    Antiviral Research.2023; 213: 105591.     CrossRef
  • Inhibition of KIF20A suppresses the replication of influenza A virus by inhibiting viral entry
    Hoyeon Jeon, Younghyun Lim, In-Gu Lee, Dong-In Kim, Keun Pil Kim, So-Hee Hong, Jeongkyu Kim, Youn-Sang Jung, Young-Jin Seo
    Journal of Microbiology.2022; 60(11): 1113.     CrossRef
Article
Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds
Lingmin Jiang , Chan Ju Lim , Song-Gun Kim , Jae Cheol Jeong , Cha Young Kim , Dae-Hyuk Kim , Suk Weon Kim , Jiyoung Lee
J. Microbiol. 2020;58(1):24-29.   Published online November 25, 2019
DOI: https://doi.org/10.1007/s12275-020-9346-6
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AbstractAbstract PDF
Strain ATSA2T was isolated from surface-sterilized kimchi cabbage (Brassica rapa subsp. pekinensis) seeds and represents a novel bacterium based on the polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ATSA2T formed a lineage within genus Saccharibacillus and was most closely to Saccharibacillus deserti WLG055T (98.1%) and Saccharibacillus qingshengii H6T (97.9%). The whole-genome of ATSA2T comprised a 5,619,468 bp of circular chromosome with 58.4% G + C content. The DNA-DNA relatedness values between strain ATSA2T and its closely related type strains S. deserti WLJ055T and S. qingshengii H6T were 26.0% and 24.0%, respectively. Multiple gene clusters associated with plant growth promotion activities (stress response, nitrogen and phosphorus metabolism, and auxin biosynthesis) were annotated in the genome. Strain ATSA2T was Gram-positive, endospore-forming, facultatively anaerobic, and rod-shaped. It grew at 15–37°C (optimum 25°C), pH 6.0–10.0 (optimum pH 8.0), and in the presence of 0–5% (w/v) NaCl (optimum 1%). The major cellular fatty acids (> 10%) of strain ATSA2T were anteiso- C15:0 and C16:0. MK-7 was the major isoprenoid quinone. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, and three unknown glycolipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, strain ATSA2T is proposed to represent a novel species of genus Saccharibacillus, for which the name is Saccharibacillus brassicae sp. nov. The type strain is ATSA2T (KCTC 43072T = CCTCC AB 2019223T).

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  • Comprehensive genomic and phenotypic characterization of thermophilic bacterium Sinimarinibacterium thermocellulolyticum sp. nov. HSW-8T, a cellulase-producing bacterium isolated from hot spring water in South Korea
    Yue Jiang, Zhun Li
    Antonie van Leeuwenhoek.2025;[Epub]     CrossRef
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    Yuxin Peng, Dong Hyun Cho, Zalfa Humaira, Yu Lim Park, Ki Hyun Kim, Cha Young Kim, Jiyoung Lee
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    Yue Jiang, Yong Guan, Sungmo Kang, Mi-Kyung Lee, Ki-Hyun Kim, Zhun Li
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T
    Lingmin Jiang, Jiyoon Seo, Yuxin Peng, Doeun Jeon, Soon Ju Park, Cha Young Kim, Pyoung Il Kim, Chul Hong Kim, Ju Huck Lee, Jiyoung Lee
    AMB Express.2023;[Epub]     CrossRef
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    Hyun-Sun Baek, Yong Guan, Min-Ju Kim, Yue Jiang, Mi-Kyung Lee, Ki-Hyun Kim, Jaeyoon Lee, Yuna Shin, Yoon-Ho Kang, Zhun Li
    Antonie van Leeuwenhoek.2023; 116(12): 1317.     CrossRef
  • Identification and genomic analysis of Pseudosulfitobacter koreense sp. nov. isolated from toxin-producing dinoflagellate Alexandrium pacificum
    Yue Jiang, Zhun Li
    Archives of Microbiology.2023;[Epub]     CrossRef
  • Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum
    Yuxin Peng, Lingmin Jiang, Yue Jiang, Jiyoon Seo, Doeun Jeon, Young-Min Kim, Zhun Li, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2023;[Epub]     CrossRef
  • Flavobacterium endoglycinae sp. nov., an endophytic bacterium isolated from soybean (Glycine max L. cv. Gwangan) stems
    Jiyoon Seo, Yuxin Peng, Lingmin Jiang, Sang-Beom Lee, Rae-Dong Jeong, Soon Ju Park, Cha Young Kim, Man-Soo Choi, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii
    Yue Jiang, Yuxin Peng, Hyeon Ho Shin, Hyun Jung Kim, Ki-Hyun Kim, Lingmin Jiang, Jiyoung Lee, Zhun Li
    Archives of Microbiology.2022;[Epub]     CrossRef
  • Flagellatimonas centrodinii gen. nov., sp. nov., a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum
    Yue Jiang, Lingmin Jiang, Yuxin Peng, Ki-Hyun Kim, Hyeon Ho Shin, Young-Min Kim, Jiyoung Lee, Zhun Li
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila
    Yuxin Peng, Lingmin Jiang, Jiyoon Seo, Zhun Li, Hanna Choe, Jae Cheol Jeong, Suk Weon Kim, Young-Min Kim, Cha Young Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
  • Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots
    Lingmin Jiang, Myoung Hui Lee, Jae Cheol Jeong, Dae-Hyuk Kim, Cha Young Kim, Suk Weon Kim, Jiyoung Lee
    International Journal of Systematic and Evolutionary Microbiology .2019;[Epub]     CrossRef
Article
Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
Young Joon Oh , Joon Yong Kim , Hyo Kyeong Park , Ja-Young Jang , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
J. Microbiol. 2019;57(11):997-1002.   Published online October 28, 2019
DOI: https://doi.org/10.1007/s12275-019-9421-z
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AbstractAbstract PDF
A Gram-stain-positive, rod-shaped, alkalitolerant, and halophilic bacterium–designated as strain NKC3-5T–was isolated from kimchi that was collected from the Geumsan area in the Republic of Korea. Cells of isolated strain NKC3-5T were 0.5–0.7􍾘μm wide and 1.4–2.8 μm long. The strain NKC3-5T could grow at up to 20.0% (w/v) NaCl (optimum 10%), pH 6.5–10.0 (optimum pH 9.0), and 25–40°C (optimum 35°C). The cells were able to reduce nitrate under aerobic conditions, which is the first report in the genus Salicibibacter. The genome size and genomic G + C content of strain NKC3-5T were 3,754,174 bp and 45.9 mol%, respectively; it contained 3,630 coding sequences, 16S rRNA genes (six 16S, five 5S, and five 23S), and 59 tRNA genes. Phylogenetic analysis based on 16S rRNA showed that strain NKC- 3-5T clustered with bacterium Salicibibacter kimchii NKC1-1T, with a similarity of 96.2–97.6%, but formed a distinct branch with other published species of the family Bacillaceae. In addition, OrthoANI value between strain NKC3-5T and Salicibibacter kimchii NKC1-1T was far lower than the species demarcation threshold. Using functional genome annotation, the result found that carbohydrate, amino acid, and vitamin metabolism related genes were highly distributed in the genome of strain NKC3-5T. Comparative genomic analysis revealed that strain NKC3-5T had 716 pan-genome orthologous groups (POGs), dominated with carbohydrate metabolism. Phylogenomic analysis based on the concatenated core POGs revealed that strain NKC3-5T was closely related to Salicibibacter kimchii. The predominant polar lipids were phosphatidylglycerol and two unidentified lipids. Anteiso- C15:0, iso-C17:0, anteiso-C17:0, and iso-C15:0 were the major cellular fatty acids, and menaquinone-7 was the major isoprenoid quinone present in strain NKC3-5T. Cell wall peptidoglycan analysis of strain NKC3-5T showed that meso-diaminopimelic acid was the diagnostic diamino acid. The phenotypic, genomic, phylogenetic, and chemotaxonomic properties reveal that the strain represents a novel species of the genus Salicibibacter, for which the name Salicibibacter halophilus sp. nov. is proposed, with the type strain NKC3-5T (= KACC 21230T = JCM 33437T).

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  • Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
    Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
    Journal of Microbiology.2021; 59(5): 460.     CrossRef
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  • 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
Article
Mixed starter of Lactococcus lactis and Leuconostoc citreum for extending kimchi shelf-life
Mi-Ju Kim , Hae-Won Lee , Mo-Eun Lee , Seong Woon Roh , Tae-Woon Kim
J. Microbiol. 2019;57(6):479-484.   Published online May 27, 2019
DOI: https://doi.org/10.1007/s12275-019-9048-0
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AbstractAbstract PDF
To develop a starter culture system for improving the shelflife and quality of kimchi, we prepared a mixed starter composed of Lactococcus lactis and Leuconostoc citreum. Two strains, L. lactis WiKim0098 and Leu. citreum WiKim0096, showed high antimicrobial activity and mannitol productivity, respectively. These lactic acid bacteria (LAB) were introduced as a starter into kimchi following cultivation in foodgrade liquid medium. Two kimchi samples, with and without starter, were fermented for 12 days at 10°C. Compared to the control kimchi without starter, a lower initial pH and higher number of LAB were observed in kimchi with starter at 0 day. However, the starter in kimchi prolonged the period taken by kimchi to reach to pH 4.2 by approximately 1.5-fold compared to that in the control kimchi. To estimate the effect of the starter on the flavor of kimchi, metabolite changes were evaluated by gas chromatography/mass spectrometry. In starter fermented kimchi, the levels of mannitol and amino acid, which are associated with the flavor of kimchi, were increased following fermentation. The amount of mannitol was confirmed by high-performance liquid chromatography analysis, showing concentrations of 3.4 and 5.1 mg/ml for the control and starter fermented kimchi, respectively. Thus, mixed starter inoculated with L. lactis WiKim0098 and Leu. citreum WiKim0096 may extend the shelf-life of kimchi and improve its sensory characteristics.

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Article
Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables
Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh
J. Microbiol. 2019;57(1):30-37.   Published online October 25, 2018
DOI: https://doi.org/10.1007/s12275-019-8487-y
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  • 26 Web of Science
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AbstractAbstract PDF
White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

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Article
Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi
Ja-Young Jang , Young Joon Oh , Seul Ki Lim , Hyo Kyeong Park , Changsu Lee , Joon Yong Kim , Mi-Ai Lee , Hak-Jong Choi
J. Microbiol. 2018;56(12):880-885.   Published online October 25, 2018
DOI: https://doi.org/10.1007/s12275-018-8518-0
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AbstractAbstract PDF
A moderately halophilic and alkalitolerant bacterial strain NKC1-1T was isolated from commercial kimchi in Korea. Strain NKC1-1T was Gram-stain-positive, aerobic, rod-shaped, non-motile, and contained diaminopimelic acid-type murein. Cell growth was observed in a medium containing 0–25% (w/v) NaCl (optimal at 10% [w/v]), at 20–40°C (optimal at 37°C) and pH 6.5–10.0 (optimal at pH 9.0). The major isoprenoid quinone of the isolate was menaquinone-7, and the major polar lipids were phosphatidylglycerol and unidentified phospholipids. Cell membrane of the strain contained iso-C17:0 and anteiso-C15:0 as the major fatty acids. Its DNA G + C content was 45.2 mol%. Phylogenetic analysis indicated the strain to be most closely related to Geomicrobium halophilum with 92.7–92.9% 16S rRNA gene sequence similarity. Based on polyphasic taxonomic evaluation with phenotypic, phylogenetic, and chemotaxonomic analyses, the strain represents a novel species in a new genus, for which the name Salicibibacter kimchii gen. nov., sp. nov. is proposed (= CECT 9537T; KCCM 43276T).

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Article
Effects of heat-killed Lactobacillus plantarum against influenza viruses in mice
Sehee Park , Jin Il Kim , Joon-Yong Bae , Kirim Yoo , Hyunung Kim , In-Ho Kim , Man-Seong Park , Ilseob Lee
J. Microbiol. 2018;56(2):145-149.   Published online February 2, 2018
DOI: https://doi.org/10.1007/s12275-018-7411-1
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AbstractAbstract PDF
The potential use of dietary measures to treat influenza can be an important alternative for those who lack access to influenza vaccines or antiviral drugs. Lactobacillus plantarum (Lp) is one of many lactic acid bacteria that grow in ‘kimchi’, an essential part of Korean meal, and several strains of Lp reportedly show protective effects against influenza. Using heat-killed Lp (nF1) isolated from kimchi, which is known for its immunomodulatory effects, we investigated whether regular oral intake of nF1 could influence the outcome of influenza virus infection in a mouse model. In a lethal challenge with influenza A (H1N1 and H3N2 subtypes) and influenza B (Yamagata lineage) viruses, daily oral administration of nF1 delayed the mean number of days to death of the infected mice and resulted in increased survival rates compared with those of the non-treated mice. Consistent with these observations, nF1 treatment also significantly reduced viral replication in the lungs of the infected mice. Taken together, our results might suggest the remedial potential of heatkilled Lactobacillus probiotics against influenza.

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Article
Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi
Young Joon Oh , Ja-Young Jang , Seul Ki Lim , Min-Sung Kwon , Jieun Lee , NamHee Kim , Mi-Young Shin , Hyo Kyeong Park , Myung-Ji Seo , Hak-Jong Choi
J. Microbiol. 2017;55(12):933-938.   Published online December 7, 2017
DOI: https://doi.org/10.1007/s12275-017-7386-3
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AbstractAbstract PDF
A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2T, was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1- 2T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1T (96.9%), V. sediminis YIM kkny3T (96.8%), and V. salarius SA-Vb1T (96.7%). The isolate grew at pH 6.5–10.0 (optimum, pH 8.5–9.0), 0.0–25.0% (w/v) NaCl (optimum, 10–15% NaCl), and 15–50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C14:0, anteisio-C15:0, iso- C15:0, and iso-C16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2T was 42.5 mol%. On the basis of these findings, strain NKC1- 2T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404T =JCM 32284T). The type strain of Virgibacillus kimchii is NKC1-2T.

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Article
A lactic acid bacterium isolated from kimchi ameliorates intestinal inflammation in DSS-induced colitis
Jin-Soo Park , Inseong Joe , Paul Dong Rhee , Choon-Soo Jeong , Gajin Jeong
J. Microbiol. 2017;55(4):304-310.   Published online January 26, 2017
DOI: https://doi.org/10.1007/s12275-017-6447-y
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AbstractAbstract PDF
Some species of lactic acid bacteria have been shown to be beneficial in inflammatory bowel disease (IBD). In the pre-sent study, a strain of lactic acid bacterium (Lactobacillus paracasei LS2) was isolated from the Korean food, kimchi, and was shown to inhibit the development of experimental colitis induced by dextran sulfate sodium (DSS). To inves-tigate the role of LS2 in IBD, mice were fed DSS in drinking water for seven days along with LS2 bacteria which were administered intragastrically to some of the mice, while phos-phate-buffered saline (PBS) was administered to others (the controls). The administration of LS2 reduced body weight loss and increased survival, and disease activity indexes (DAI) and histological scores indicated that the severity of colitis was significantly reduced. The production of inflammatory cy-tokines and myeloperoxidase (MPO) activity also decreased. Flow cytometry analysis showed that the number of Th1 (IFN-γ) population cells was significantly reduced in the LS2- administered mice compared with the controls. The admini-stration of LS2 induced the increase of CD4+FOXP3+ Treg cells, which are responsible for IL-10. Numbers of macro-phages (CD11b+ F4/80+), and neutrophils (CD11b+ Gr-1+) among lamina propria lymphocytes (LPL) were also reduced. These results indicate that LS2 has an anti-inflammatory effect and ameliorates DSS-induced colitis.

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Article
Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi§
Young Joon Oh , Hae-Won Lee , Seul Ki Lim , Min-Sung Kwon , Jieun Lee , Ja-Young Jang , Hae Woong Park , Young-Do Nam , Myung-Ji Seo , Hak-Jong Choi
J. Microbiol. 2016;54(9):588-593.   Published online August 31, 2016
DOI: https://doi.org/10.1007/s12275-016-6349-4
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AbstractAbstract PDF
A novel halophilic bacterium, strain K7T, was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0–25.0% (w/v) NaCl (optimum 10–15% NaCl), pH 5.5–8.5 (optimum pH 7.0–7.5), and 15–42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone- 7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio- C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7T and Gracilibacillus orientalis XH-63T (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7T is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7T (KACC 18669T; JCM 31344T).

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Article
Lactobacillus curvatus WiKim38 isolated from kimchi induces IL-10 production in dendritic cells and alleviates DSS-induced colitis in mice
Sung-Gang Jo , Eui-Jeong Noh , Jun-Young Lee , Green Kim , Joo-Hee Choi , Mo-Eun Lee , Jung-Hee Song , Ji-Yoon Chang , Jong-Hwan Park
J. Microbiol. 2016;54(7):503-509.   Published online June 28, 2016
DOI: https://doi.org/10.1007/s12275-016-6160-2
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AbstractAbstract PDF
Probiotics such as lactobacilli and bifidobacteria have healthpromoting effects by immune modulation. In the present study, we examined the immunomodulatory properties of Lactobacillus curvatus WiKim38, which was newly isolated from baechu (Chinese cabbage) kimchi. The ability of L. curvatus WiKim38 to induce cytokine production in bone marrow-derived dendritic cells (BMDCs) was determined by enzyme-linked immunosorbent assay. To evaluate the molecular mechanisms underlying L. curvatus Wikim38-mediated IL-10 production, Western blot analyses and inhibitor assays were performed. Moreover, the in vivo anti-inflammatory effects of L. curvatus WiKim38 were examined in a dextran sodium sulfate (DSS)-induced colitis mouse model. L. curvatus WiKim38 induced significantly higher levels of IL- 10 in BMDCs compared with that induced by LPS. NF-κB and ERK were activated by L. curvatus WiKim38, and an inhibitor assay revealed that these pathways were required for L. curvatus WiKim38-induced production of IL-10 in BMDCs. An in vivo experiment showed that oral administration of L. curvatus WiKim38 increased the survival rate of mice with DSS-induced colitis and improved clinical signs and histopathological severity in colon tissues. Taken together, these results indicate that L. curvatus Wikim38 may have health-promoting effects via immune modulation, and may thus be applicable for therapy of various inflammatory diseases.

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Research Support, Non-U.S. Gov't
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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AbstractAbstract PDF
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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Research Support, Non-U.S. Gov't
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
J. Microbiol. 2010;48(6):862-866.   Published online January 9, 2011
DOI: https://doi.org/10.1007/s12275-010-0214-7
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AbstractAbstract PDF
A moderate halophile, strain X50T, was isolated from mustard kimchi, a traditional Korean fermented food. The organism grew under conditions ranging from 0-15.0% (w/v) NaCl (optimum: 3.0%), pH 7.0-10.0 (optimum: pH 9.0) and 15-45°C (optimum: 37°C). The morphological, physiological, and biochemical features and the 16S rRNA gene sequences of strain X50T were characterized. Colonies of the isolate were creamcolored and the cells were rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain X50T belongs to the genus Oceanobacillus and is closely related phylogenetically to the type strain O. iheyensis HTE831T (98.9%) and O. oncorhynchi subsp. oncorhynchi R-2T (97.0%). The cellular fatty acid profiles predominately included anteiso-C15:0 and iso-C15:0. The G+C content of the genomic DNA of the isolate was 37.9 mol% and the major isoprenoid quinone was MK-7. Analysis of the 16S rRNA gene sequences, DNA-DNA relatedness and physiological and biochemical tests indicated genotypic and phenotypic differences among strain X50T and reference species in the genus Oceanobacillus. Therefore, strain X50T was proposed as a novel species and named Oceanobacillus kimchii. The type strain of the new species is X50T (=JCM 16803T =KACC 14914T =DSM 23341T).

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Research Support, Non-U.S. Gov't
Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi
Eun-Jin Park , Ho-Won Chang , Kyoung-Ho Kim , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae
J. Microbiol. 2009;47(6):682-685.   Published online February 4, 2010
DOI: https://doi.org/10.1007/s12275-009-0297-1
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AbstractAbstract PDF
Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45×106 which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.

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Research Support, Non-U.S. Gov't
Microbial Population Dynamics and Temperature Changes during Fermentation of Kimjang Kimchi
Dongyun Lee , Sunjoo Kim , Jinhee Cho , Jeongho Kim
J. Microbiol. 2008;46(5):590-593.   Published online October 31, 2008
DOI: https://doi.org/10.1007/s12275-008-0156-5
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AbstractAbstract PDF
A distinct subset of lactic acid bacteria that are greatly influenced by temperature play an important role during kimchi fermentation. However, microbial population dynamics and temperature control during kimjang kimchi fermentation, which is traditionally fermented underground, are not known. Here we show that Lactobacillus sakei predominates in kimjang kimchi, perhaps due to suitable fermentation (5~9°C) and storage (-2°C) temperatures. The temperature of this kimchi gradually decreased to 3.2°C during the first 20 days of fermentation (-0.3°C/day) and then was stably maintained around 1.6°C, indicating that this simple approach is very efficient both for fermentation and storage. These findings provide important information towards the development of temperature controlling systems for kimchi fermentation.

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Research Support, Non-U.S. Gov't
Detection of Escherichia coli O157:H7, Salmonella spp.,Staphylococcus aureus and Listeria monocytogenes in Kimchi by Multiplex Polymerase Chain Reaction (mPCR)
Yeon Sun Park , Sang Rok Lee , Young Gon Kim
J. Microbiol. 2006;44(1):92-97.
DOI: https://doi.org/2331 [pii]
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AbstractAbstract PDF
We developed an mPCR assay for the simultaneous detection, in one tube, of Escherichia coli O157:H7, Salmonella spp., Staphylococcus aureus and Listeria monocytogenes using species-specific primers. The mPCR employed the E. coli O157:H7 specific primer Stx2A, Salmonella spp. specific primer Its, S. aureus specific primer Cap8A-B and L. monocytogenes specific primer Hly. Amplification with these primers produced products of 553, 312, 405 and 210 bp, respectively. All PCR products were easily detected by agarose gel electrophoresis, and the sequences of the specific amplicons assessed. Potential pathogenic bacteria, in laboratory-prepared and four commercially available kimchi products, were using this mPCR assay, and the amplicons cloned and sequenced. The results correlated exactly with sequences derived for amplicons obtained during preliminry tests with known organisms. The sensitivity of the assay was determined for the purified pathogen DNAs from four strains. The mPCR detected pathogen DNA at concentrations ranging from approximately 0.45 to 0.05 pM/μl. Thus, this mPCR assay may allow for the rapid, reliable and cost-effective identification of four potentially pathogens present in the mixed bacterial communities of commercially available kimchi.
Identification and Characterization of Leuconostoc gelidum, Isolated from Kimchi, a Fermented Cabbage Product
Bong-Joon Kim , Hye-Ja Lee , Sae-Young Park , Jeongho Kim , Hong-Ui Han
J. Microbiol. 2000;38(3):132-136.
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AbstractAbstract PDF
We recently identified Leuconostoc gelidum, a typical psychrophile, as a microbial component from kimchi that has been laboratory-prepared and fermented at 20 C. However, it has been shown that the growth of leuconostocs in food products is highly influenced by fermenting temperature. To determine the distribution of L. gelidum species in kimchi fermented at a lower temperature, 8 C, we characterized a total of 64 dextran-forming strains isolated from kimchi using a polyphasic method including 16S rDNA sequencing and DNA-DNA hybridization. We found that 80% of the isolates were L. gelidum, which has been found mainly at chill-stored meat products. We also found that L. gelidum could be a dominant Leuconostoc species in so-called Kimjang kimchi, which is traditionally prepared at late fall to be preserved during winter in Korea. These results suggest that L. gelidum can be a predominant species in kimchi especially when fermented at low temperature.
Isolation of Dextran-producing Leuconostoc lactis from Kimchi
Bong-Joon Kim , Bong-Hee Min , Jeongho Kim , Hong-Ui Han
J. Microbiol. 2001;39(1):11-16.
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AbstractAbstract PDF
Tentative identification of Leuconostoc lactis IH23 isolated from kimchi (a fermented vegetable product) has been described previously with 16S rDNA sequencing (Choi, I., M. Sc. Thesis Inha Univ. 1999). This strain produced the slime identified as dextran based on IR, 13C- and 1H-NMR spectroscopic results. Further study proved that the isolate IH23 belongs to a homogeneous genetic group with L. lactis DSM 20202T and L. argentinum DSM 8581T. The results showed DNA-DNA homology of 99-100%, 16S rDNA gene sequence similarity (99.7%), and a phylogenetic relationship although L. argentinum DSM 8581T had lower homology (80-91%). These data indicate that L. argentinum DSM 8581T and the isolate IH23 belong to an identical species with L. lactis DSM 20202T at the genetic level, although in carbohydrate fermentation, the isolate IH23 was most closely related to L. argentinum DSM 8581T and quite different from L. lactis DSM 20202T. Here we first report the isolation of consistent phenotypic variation in Leuconostoc lactis. We also emphasize that the nomenclature of subspecies needs to be differentiated into the three strains mentioned above in Leuconostoc lactis.
Journal of Microbiology : Journal of Microbiology
© The Microbiological Society of Korea.
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