Dr. Kim joined Korea University in the spring semester of 2006 after 18 years of professional life in the United States of America. He is a microbial geneticist by training and a graduate with Master's and Ph.D. degrees from the Department of Microbiology of the University of lllinois at Urbana-Champaign (https://illinois.edu). He augmented and broadened his academic background during postdoctoral years at Stanford University (https://www.stanford.edu) studying anaerobic microbiology and genomics using the newly-born microarray technology of the time. In 2001, he joined a research group at TIGR (The Institute for Genomic Research), which is now called the J. Craig Venter Institute (http://www.jcvi.org). He obtained hands-on experiences on cutting edge bioinformatics and genomics while conducting various functional genomic projects, including those with plant (i.e. Arabidopsis thaliana), bacteria (i.e. Burkholderia spp. and Myxococcus), and fungi (i.e. Aspergillus fumigatus and Aspergillus flavus), as a staff scientist until the time he left the institute to join the Korea University faculty.

In his lab at Korea University, Dr. Kim continued to work on human pathogens that belong to Burkholderia species. He is interested in dissecting the mechanisms of virulence functions in these pathogens and of the development of resistance and tolerance to antimicrobials. The knowledge accumulated through his studies will be used to develop accurate diagnostic tools for the pathogen infections and, ultimately, therapeutic means and vaccines.

Another area of interest that is actively being developed in his lab is regarding human commensal bacteria (the human microbiota) residing in the gut. These bacteria generally weigh about 0.2 kg in a human body, and they are deeply associated with human physiology and development. Consequently, various modern diseases, including atopic diseases, metabolic diseases, inflammatory bowel diseases, and abnormal mental conditions are implicated with malfunction of these gut bacteria. The research with the gut bacteria as a major functional entity affecting human health and disease is very young, but it is considered of tremendous importance with a potential to impact the future of medicine.

Education

• Ph.D. (1993-1998): Department of Microbiology, University of Illinois at Urbana-Champaign
• MS (1991-1993): Department of Microbiology, University of Illinois at Urbana-Champaign
• BS (1984-1988): Korea University

Professional activities

• 2022-present: Editor, Microbiology Spectrum (https://journals.asm.org/journal/spectrum) published by the American Society for Microbiology
• 2016-present: Member of the scientific committee of the International Society of Microbiota (https://www.microbiota-site.com/)
• 2019-present : Professor, Division of Biosystems & Biomedical Sciences, College of Health Sciences, Korea University
• 2006-2018 : Professor, Department of Biomedical Sciences, College of Medicine, Korea University
• 2000-2006: Staff Scientist, The Institute for Genomic Research (now called J. Craig Venter Institute)
• 1998-2000: Postdoctoral fellow, Stanford University

수상 경력

• BRIC (생물학연구정보센터) 선정 2015 국내 바이오 성과 Top 5 "아토피 유발하는 장 세균 메커니즘 규명"
• https://www.ibric.org/myboard/read.php?Board=interview&id=1626
•  

Ph.D. Thesis:

Kim, H. 1998. Characterization of the acc (agrocinopine catabolism) locus on the nopaline-type Ti plasmid from Agrobacterium tumefaciens strain C58. Ph.D. dissertation. Department of Microbiology, University of Illinois at Urbana-Champaign.

Selected recent publications:

Heenam Stanley Kim. 2021. Do an Altered Gut Microbiota and an Associated Leaky Gut Affect COVID-19 Severity? mBio. 12:e03022-20.

•    ·  https://asm.org/Press-Releases/2021/January/Poor-Gut-Health-Connected-to-Severe-COVID-19,-New
•    ·  https://www.eurekalert.org/news-releases/563161
•    ·  https://www.sciencedaily.com/releases/2021/01/210112085347.htm
•    ·  https://www.verywellhealth.com/gut-health-covid-19-severity-5096565
•    ·  https://www.nationalgeographic.com/science/article/microbes-in-your-gut-may-be-new-recruits-in-the-fight-against-viruses
•    ·  https://www.spiegel.de/wissenschaft/mensch/corona-und-die-wunderwaffe-darm-gesunde-ernaehrung-kann-vor-schweren-covid-19-verlaeufen-schuetzen-a-b202c68f-b8b1-4881-8dd1-87a45ff6bc66
•    ·  https://www.chosun.com/economy/science/2021/01/13/MVJ2BYAUCFGSPIVFGJTFHNVT5U/

•  

  Hyojeong Yi, Jongwook Park, Kwang-Hwi Cho, and Heenam Stanley Kim. 2020. Mutations in ArgS Arginine-tRNA Synthetase Confer Additional Antibiotic Tolerance Protection to Extended- Spectrum-β-Lactamase-Producing Burkholderia thailandensis. Antimicrobial Agents and Chemotherapy. 64(6): e02252.
•  
• Hyojeong Yi and Heenam Stanley Kim. 2018. Scars left on the gut microbiota from the stringent response. Trends in Microbiology. 26(9): 735-737.
•  
• Hyojeong Yi, Hyeri Lee, Kwang-Hwi Cho, and Heenam Stanley Kim. 2018. Mutations in MetG (methionyl-tRNA synthetase) and TrmD (tRNA (guanine-N1)-methyltransferase) conferring the meropenem tolerance in Burkholderia thailandensis. Journal of Antimicrobial Chemotherapy. 73: 332-338.
•  
• Hyojeong Yi, Jin Myung Choi, Junghyun Hwang, Fabio Prati, Thinh-Phat Cao, Sung Haeng Lee, and Heenam Stanley Kim. 2016. High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A β-lactamase, PenL. Scientific Reports. 6:36527.
•  
• Han Song, Young Yoo, Junghyun Hwang, Yun-Cheol Na, and Heenam Stanley Kim. 2016. Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis. Journal of Allergy and Clinical Immunology. 137(3): 852–860.
•  
• Junghyun Hwang and Heenam Stanley Kim. 2015. Cell wall recycling-linked co-regulation of AmpC and PenB β-lactamases through ampD mutations in Burkholderia cenocepacia. Antimicrobial Agents and Chemotherapy. 59(12): 7602-10.
•  
• Hyojeong Yi, Song Han, Junghyun Hwang, Karan Kim, William C. Nierman, and Heenam Stanley Kim. 2014. The tandem repeats enabling reversible switching between the two phases of β-lactamase substrate spectrum. PLoS Genetics 10(9): e1004640.
•  
• Junghyun Hwang, Kwang-Hwi Cho, Han Song, Jae Hwan Chun, and Heenam Stanley Kim. 2014. Deletion mutations conferring substrate spectrum extension in the class A β-lactamase. Antimicrobial Agents and Chemotherapy. 58(10): 6265-6269.
•  
• Hyojeong Yi, Kwang-Hwi Cho, Yun Sung Cho, Karan Kim, William C. Nierman, and Heenam Stanley Kim. 2012. Twelve positions in a β-lactamase that can expand its substrate spectrum with a single amino acid substitution. PLoS ONE. 7(5): e37585.
•  
• Hyojeong Yi, Karan Kim, Kwang-Hwi Cho, Oksung Jung, and Heenam Stanley Kim. 2012. Substrate spectrum extension of PenA in Burkholderia thailandensis with a single amino acid deletion, Glu168del. Antimicrob. Agents Chemother. 56(7): 4005-4008.
•  
• Han Song, Junghyun Hwang, Hyojeong Yi, Ricky L. Ulrich, Yan Yu, William C. Nierman, and Heenam Stanley Kim. 2010. The early stage of bacterial genome-reductive evolution in the host. PLoS Pathogens. 6(5): e1000922.

Research Topic

• Gut microbiota-host interactions underlying modern chronic conditions
• Microbial genome evolution
• Microbial physiology, genetics, and genomics of antibiotic resistance, persistence, and tolerance

본 연구실은 인간의 건강과 질환을 결정하는 미생물 연구를 수행하고 있습니다.

크게 두가지 분야의 연구에 집중하고 있습니다.

1. 휴먼 장내 마이크로바이오타와 현대 질환(Human gut microbiota and modern diseases)

최근 생명과학과 의학에서의 두드러진 발전중 하나는 인간이 미생물과의 공생체라는 것을 발견한 것입니다. 이들 미생물들이 인간의 발생과 생리활동에 절대적으로 중요한 역할을 한다는 것이 밝혀지며 인간생물학과 의학의 근간이 바뀌고 있습니다. 우리 실험실에서는 장내 마이크로바이오타(미생물군집)의 기능에 문제가 발생했을 때 촉진되는 인간 질병에 대한 연구를 첨단 유전체학과 유전학을 주요 도구로 사용하며 수행하고 있습니다. 최근에는 아토피 피부염의 발생과 깊이 관련된 장내 세균을 세계 최초로 발견하여 발표하였고, 항생제가 장내 미이크로바이오타에 어떻게 수년간 치료되지 않는 깊은 상처를 입히는가를 연구하여 발표하기도 했습니다. 이런 연구는 현재 근본적 치료가 어려운 이들 질환의 진단과 치료를 가능하게 할 것으로 기대합니다.

2. 세균 유전체 진화와 항생제 내성 (Bacterial genome evolution for the antibiotic resistance and tolerance)

글로벌 스케일의 항생제내성세균 발생은 인류의 건강을 심각하게 위협하고 있습니다. 위기의 극복을 위해서는 항생제내성 진화, 항생제의 살균경로, 그리고 세균내의 대항경로를 잘 이해해야 합니다. 우리 실험실에서는 베타락탐항생제의 내성에 제일 중요한 베타락탐분해효소의 진화경로를 연구해 왔습니다. 최근에는 베타락탐분해효소의 진화를 일으키는 다양한 돌연변이를 분석하여 발표해 왔고, 항생제의 살균 메커니즘에 대한 연구를 집중적으로 진행하고 있습니다. 우리 연구는 현재 사용되는 항생제의 효능을 증진시키거나 세균의 항생제 감수성을 증가시키는 기능을 가진 신약 개발에 크게 기여할 것입니다.

* 실험실을 취재한 최근 YTN science 방송분

https://science.ytn.co.kr/program/program_view.php?s_mcd=0082&s_hcd=&key=201810041221145692&page=6

https://science.ytn.co.kr/program/program_view.php?s_mcd=1213&s_hcd=&key=201911010956232233&page=1

Topics related to: 

• General microbiology
• Gut microbiome
• Human-microbe interactions
• Bacterial pathogens
• Antibiotic resistance, persistence, and tolerance

미생물과 건강_마이크로바이옴(microbiome)

Research Professor

• Hyojeong Yi

Ph.D. course

• Dongju Lee
• Jongwook Park
• Jieun Nam

M.S-Ph.D course

• Seohee Jeong
• Yumin Han
• Juwon Han