Journal of Microbiology

Kihyun Lee

3 Articles

Cytoplasmic molecular chaperones in Pseudomonas species: Hyunhee Kim , Seongjoon Moon , Soojeong Ham , Kihyun Lee , Ute Römling , Changhan Lee; J. Microbiol. 2022;60(11):1049-1060. Published online November 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2425-0

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Pseudomonas is widespread in various environmental and host niches. To promote rejuvenation, cellular protein homeostasis must be finely tuned in response to diverse stresses, such as extremely high and low temperatures, oxidative stress, and desiccation, which can result in protein homeostasis imbalance. Molecular chaperones function as key components that aid protein folding and prevent protein denaturation. Pseudomonas, an ecologically important bacterial genus, includes human and plant pathogens as well as growth-promoting symbionts and species useful for bioremediation. In this review, we focus on protein quality control systems, particularly molecular chaperones, in ecologically diverse species of Pseudomonas, including the opportunistic human pathogen Pseudomonas aeruginosa, the plant pathogen Pseudomonas syringae, the soil species Pseudomonas putida, and the psychrophilic Pseudomonas antarctica.

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Dietary supplementation of Phaffia rhodozyma enhances growth performance, immune response, and modulates gut microbiota in Apostichopus japonicus
Xiaofei Tan, Ailin Tang, Zifan Zhou, Haoyu Guo, Siyu Zhang, Yujia Liu, Jian Che, Bingnan Liu
Aquaculture International.2026;[Epub] CrossRef
Culture-enriched sequencing reveals river confluence sediments as high-risk reservoirs of viable multidrug-resistant pathogens
Yi Li, Huijuan Huang, Bi Luo, Rong Wang, Zhiwei Zhu
Journal of Hazardous Materials.2026; 514: 142756. CrossRef
An innovative utilization approach for by-products of biogas desulfurization：Co-hydrothermal treatment of sulfur with biogas slurry to prepare sulfur-enriched liquid fertilizer
Zhijie Xie, Fang Deng, Yuqin Wan, Yiping Luo, Qin Cao, Yichao Chen, Dong Li
Process Biochemistry.2024; 147: 522. CrossRef
Isolation of Pseudomonas oleovorans Carrying Multidrug Resistance Proteins MdtA and MdtB from Wastewater
Haifeng Wang, Chenyang Sun, Xing Chen, Kai Yan, Hongxuan He
Molecules.2023; 28(14): 5403. CrossRef
Development of heat-shock resistance in Legionella pneumophila modeled by experimental evolution
Jeffrey Liang, Gillian Cameron, Sébastien P. Faucher, Christopher A. Elkins
Applied and Environmental Microbiology.2023;[Epub] CrossRef

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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Abstract PDF

Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

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The Application of artificial intelligence in periprosthetic joint infection
Pengcheng Li, Yan Wang, Runkai Zhao, Lin Hao, Wei Chai, Chen Jiying, Zeyu Feng, Quanbo Ji, Guoqiang Zhang
Journal of Advanced Research.2026; 79: 633. CrossRef
Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective
Lenin García Gutiérrez, Alfonso Méndez-Tenorio, Mario Ángel López-Luis, Sandra Alejandra Ávila-Huerta, Gloria León-Ávila, Santiago R. Castaño-Valencia, Gabriela Ibáñez-Cervantes
Antibiotics.2026; 15(8): 804. CrossRef
Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting
Abdullateef Abdullah Alshehri
Frontiers in Microbiology.2026;[Epub] CrossRef
Evolution of pathogenic Escherichia coli harboring the transmissible locus of stress tolerance: from food sources to clinical environments
Maxsueli Machado, Pedro Panzenhagen, Flávia Figueira Aburjaile, Bertram Brenig, Mateus Matiuzzi da Costa, Vasco Ariston de Carvalho Azevedo, Eduardo Eustáquio de Souza Figueiredo, Carlos Adam Conte-Junior
Scientific Reports.2025;[Epub] CrossRef
Integrating whole-genome sequencing into antimicrobial resistance surveillance: methodologies, challenges, and perspectives
Yasufumi Matsumura, Masaki Yamamoto, Ryota Gomi, Yasuhiro Tsuchido, Koh Shinohara, Taro Noguchi, Miki Nagao, Jose M. Munita, Alexander Sundermann
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Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions
Nami Morales-Durán, Angel León-Buitimea, José R. Morones-Ramírez
Heliyon.2024; 10(6): e27984. CrossRef
Resistome Mapping in Foodborne Pathogens: Understanding Role in the Transmission Dynamics of Resistance Genes
Muneer Oladipupo Yaqub, Chinedu Eucharia Joseph, Aashika Jain, Lekshmi K. Edison
Applied Microbiology.2024; 4(4): 1476. CrossRef
Metagenomic assemblies tend to break around antibiotic resistance genes
Anna Abramova, Antti Karkman, Johan Bengtsson-Palme
BMC Genomics.2024;[Epub] CrossRef
Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis
Do-Hoon Lee, Kihyun Lee, Yong-Seok Kim, Chang-Jun Cha, Jack A. Gilbert
mSystems.2024;[Epub] CrossRef
Web-Based Tools Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis
Sweta Padma Routray, Swayamprabha Sahoo, Debasish Swapnesh Kumar Nayak, Sejal Shah, Tripti Swarnkar
SN Computer Science.2024;[Epub] CrossRef
Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater
Nafi’u Abdulkadir, Joao Pedro Saraiva, Junya Zhang, Stefan Stolte, Osnat Gillor, Hauke Harms, Ulisses Rocha, Adriana E. Rosato
Microbiology Spectrum.2024;[Epub] CrossRef
Identification of Antibiotic Resistance in ESKAPE Pathogens through Plasmonic Nanosensors and Machine Learning
Ting Yu, Ying Fu, Jintao He, Jun Zhang, Yunlei Xianyu
ACS Nano.2023; 17(5): 4551. CrossRef
The challenges of defining the human nasopharyngeal resistome
Lucy O’Connor, Robert Heyderman
Trends in Microbiology.2023; 31(8): 816. CrossRef
Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant
Animesh Tripathi, Dinesh Kumar, Priyank Chavda, Dalip Singh Rathore, Ramesh Pandit, Damer Blake, Fiona Tomley, Madhvi Joshi, Chaitanya G. Joshi, Suresh Kumar Dubey
Environmental Pollution.2023; 327: 121517. CrossRef
Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review
Jung Hun Lee, Nam-Hoon Kim, Kyung-Min Jang, Hyeonku Jin, Kyoungmin Shin, Byeong Chul Jeong, Dae-Wi Kim, Sang Hee Lee
International Journal of Molecular Sciences.2023; 24(20): 15209. CrossRef
Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil
Yong-Seok Kim, Eun-Mi Hwang, Chang-Myeong Jeong, Chang-Jun Cha
Journal of Microbiology.2023; 61(10): 891. CrossRef
Antimicrobial Resistance Genes (ARGs), the Gut Microbiome, and Infant Nutrition
Rufus J. Theophilus, Diana Hazard Taft
Nutrients.2023; 15(14): 3177. CrossRef
Metagenomic Insight into Sulfonamide-Induced Variation in Antibiotic Resistome of Soil Associated with Taxonomy, Mobile Genetic Elements (MGEs), and Function
Mi Li, Xiaoyu Xiao, Zhangsong Jiang, Haihui Tang, Lingling Rong, Tiao Zhang, Taijia Li, Cui Hu, Ligui Wu, Xiaoming Zou
ACS Agricultural Science & Technology.2022; 2(1): 123. CrossRef
Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
Jaeyeong Park, Eunkyoung Shin, Ji-Hyun Yeom, Younkyung Choi, Minju Joo, Minho Lee, Je Hyeong Kim, Jeehyeon Bae, Kangseok Lee
Journal of Microbiology.2022; 60(1): 128. CrossRef
Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years
Yong Chiang Tan, Chandrajit Lahiri
Frontiers in Immunology.2022;[Epub] CrossRef
Recent Advances in Rapid Antimicrobial Susceptibility Testing
Rucha Datar, Sylvain Orenga, Romain Pogorelcnik, Olivier Rochas, Patricia J Simner, Alex van Belkum
Clinical Chemistry.2021; 68(1): 91. CrossRef
Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE)
Francesco Santoro, Valeria Fox, Alessandra Romeo, Elisa Lazzeri, Gianni Pozzi, Francesco Iannelli
Mobile DNA.2021;[Epub] CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef

Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation: Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha; J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8372-0

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Abstract PDF

The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.

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