Journal of Microbiology

Journal 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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Abstract: 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.

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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Abstract: 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.

Journal Articles

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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Abstract

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.

Citations

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Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies
Zhuangzhuang Shi, Zhaoming Li, Mingzhi Zhang
Journal of Translational Medicine.2024;[Epub] CrossRef
Fusobacterium nucleatum: a novel regulator of antitumor immune checkpoint blockade therapy in colorectal cancer
Mengjie Luo
American Journal of Cancer Research.2024; 14(8): 3962. CrossRef
Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer
Sevag Hamamah, Andrei Lobiuc, Mihai Covasa
International Journal of Molecular Sciences.2024; 25(16): 9026. CrossRef
Identification of Penexanthone A as a Novel Chemosensitizer to Induce Ferroptosis by Targeting Nrf2 in Human Colorectal Cancer Cells
Genshi Zhao, Yanying Liu, Xia Wei, Chunxia Yang, Junfei Lu, Shihuan Yan, Xiaolin Ma, Xue Cheng, Zhengliang You, Yue Ding, Hongwei Guo, Zhiheng Su, Shangping Xing, Dan Zhu
Marine Drugs.2024; 22(8): 357. CrossRef

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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Abstract

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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Gut Microbiota Profiles in Myopes and Nonmyopes
Wan E. W. Omar, Gurdeep Singh, Andrew J. McBain, Fiona Cruickshank, Hema Radhakrishnan
Investigative Ophthalmology & Visual Science.2024; 65(5): 2. CrossRef

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

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Abstract

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.

Citations

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Pankaj Garg, Gargi Singhal, Siddhika Pareek, Prakash Kulkarni, David Horne, Aritro Nath, Ravi Salgia, Sharad S. Singhal
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.2025; 1880(1): 189233. CrossRef
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Irkham, Abdullahi Umar Ibrahim, Chidi Wilson Nwekwo, Pwadubashiyi Coston Pwavodi, Salma Nur Zakiyyah, Mehmet Ozsoz, Yeni Wahyuni Hartati
Microchemical Journal.2025; 208: 112577. CrossRef
Trends in Aptasensing and the Enhancement of Diagnostic Efficiency and Accuracy
Mohd Afaque Ansari, Damini Verma, Mohd-Akmal Hamizan, Maumita Das Mukherjee, Noor Faizah Mohd-Naim, Minhaz Uddin Ahmed
ACS Synthetic Biology.2025;[Epub] CrossRef
Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations
Mehran khan, Mir Muhammad Nizamani, Muhammad Asif, Ali Kamran, Guandi He, Xiangyang Li, Sanwei Yang, Xin Xie
Journal of Environmental Management.2025; 374: 123969. CrossRef
AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach
Serena Rosignoli, Elisa Lustrino, Alessio Conci, Alessandra Fabrizi, Serena Rinaldo, Maria Carmela Latella, Elena Enzo, Gianni Prosseda, Laura De Rosa, Michele De Luca, Alessandro Paiardini
Nucleic Acids Research.2024; 52(W1): W29. CrossRef
Use of paired Cas9-NG nickase and truncated sgRNAs for single-nucleotide microbial genome editing
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Yu He, Huan Li, Xueming Ju, Bo Gong
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Efficient CRISPR-Cas12f1-Mediated Multiplex Bacterial Genome Editing via Low-Temperature Recovery
Se Ra Lim, Hyun Ju Kim, Sang Jun Lee
Journal of Microbiology and Biotechnology.2024; 34(7): 1522. CrossRef
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Eswar Marcharla, Smarika Chauhan, Sneha Hariharan, Parthipan Punniyakotti, Thanigaivel Sundaram, Swamynathan Ganesan, Woong Kim, Muthusamy Govarthanan
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Irkham Irkham, Abdullahi Umar Ibrahim, Pwadubashiyi Coston Pwavodi, Chidi Wilson Nwekwo, Yeni Wahyuni Hartati
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Ratnesh Singh Kanwar, Kirtida Gambhir, Tanishka Aggarwal, Akash Godiwal, Kuntal Bhadra
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DNA.2024; 4(4): 427. CrossRef
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Sandhya Mishra, Anju Patel, Pankaj Bhatt, Shaohua Chen, Pankaj Kumar Srivastava
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Asiya Nazir, Fathima Hasnain Nadeem Hussain, Afsheen Raza
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Journal Articles

[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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Abstract

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.

Citations

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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

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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Abstract

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.

Citations

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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

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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Abstract

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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Improving plant salt tolerance through Algoriphagus halophytocola sp. nov., isolated from the halophyte Salicornia europaea
Yuxin Peng, Dong Hyun Cho, Zalfa Humaira, Yu Lim Park, Ki Hyun Kim, Cha Young Kim, Jiyoung Lee
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Dasania phycosphaerae sp. nov., isolated from phytoplankton sample from the south coast of the Republic of Korea
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
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Emticicia fluvialis sp. nov., a potential hormone-degrading bacterium isolated from Nakdong River, Republic of Korea
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
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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

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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Abstract

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
The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
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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

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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Abstract

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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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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Abstract

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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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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Abstract

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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Microorganisms.2022; 10(12): 2355. CrossRef
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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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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Abstract

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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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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Abstract

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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Bioprospecting for moderately halophilic eubacteria for potential biotechnological applications from Sambhar Lake, Rajasthan, India
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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
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Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi
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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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Abstract

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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