News & Issues

Prof. Kim elected the 52nd President of the Microbiological Society of Korea

Prof. Jihyun F. Kim has been elected the 52nd President of the Microbiological Society of Korea (MSK) (announced Oct. 27, 2026). The one-year term will begin in January 2028.

Prof. Kim studies microbial genomes and the microbiome, focusing on microbe-host interactions and the discovery of biomarkers and therapeutic technologies related to disease and aging. Prof. Kim is Director of the Yonsei Microbiome Research Institute and a member of the Korean Academy of Science and Technology, and previously served MSK as executive committee chair, board member, and vice president. Prof. Kim has received the National Academy of Sciences Award, a Presidential Citation, and academic awards from several societies.

As president-elect, Prof. Kim plans to strengthen the society's international exchange and research collaboration while supporting exchange among members and the activities of regional branches and divisions.

Novel Antarctic chemolithotroph drives iron biomineralization (Microbiome, Oct. 2026)

Snowball Earth's iron deposits may have formed through microbes living without sunlight.

A study led by Prof. Jihyun F. Kim (Yonsei University) together with Prof. Hwan Su Yoon (Sungkyunkwan University) was published in Microbiome. Analyzing sedimentary ancient DNA from beneath Antarctica's Larsen C Ice Shelf, an environment without light or oxygen, the team discovered novel iron-oxidizing chemolithotrophic bacteria. Laboratory experiments showed that the bacterial Cyc2 protein converts Fe(II) to Fe(III), which precipitates as iron minerals. These findings suggest a non-photosynthetic route for the formation of iron deposits, including banded iron formations of the Snowball Earth period.

The study was featured by Phys.org (Oct. 7, 2026).

Yoon J, Lee B, Yoo KC, Kwak MJ, Song HJ, Hwang CY, Chung Y, Kim K, et al. Novel Antarctic chemolithotroph drives iron biomineralization. Microbiome 14:225 (2026).
doi: 10.1186/s40168-026-02536-0

Mouth-to-gut microbial transmission signatures enable non-invasive diagnosis of gastrointestinal cancers (Cell Host & Microbe, Aug. 2026)

Our study on mouth-to-gut microbial transmission in gastrointestinal cancers was published online in Cell Host & Microbe on August 20, 2026.

Using paired oral and fecal samples from 507 adults (healthy individuals, people with metabolic disorders, and patients with gastric or colorectal cancer), the team developed a "mouth-to-feces (MF) index" that measures how many identical microbial sequence variants are shared between the mouth and the gut of the same person. Patients with gastric or colorectal cancer showed about 2.6–3 times greater oral-gut overlap than healthy participants, a pattern not seen in metabolic disorders. Classifiers based on oral samples distinguished cancer patients from healthy individuals across independent cohorts, suggesting a path toward non-invasive cancer screening.

The work was featured by Newsweek, ScienceAlert, Inside Precision Medicine, The Microbiologist, and other media.

Jang LG, Huh JW, Kim S, et al., Kim JF. Mouth-to-gut microbial transmission signatures enable robust, non-invasive diagnosis of gastrointestinal cancers. Cell Host & Microbe (2026).
doi: 10.1016/j.chom.2026.07.007

metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches (Gut Microbes, 2026)

Our lab has published metaFun, an analysis pipeline for metagenomic big data, in Gut Microbes.

metaFun provides an integrated workflow for large-scale metagenomic data, with fast and unified functional searches.

Lee HG, Song JY, Yoon J, Chung Y, Kwon SK, Kim JF. metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches. Gut Microbes 18(1):2611544 (2026).
doi: 10.1080/19490976.2025.2611544

Research on “the microbiome structure of tomato rhizosphere and its involvement in disease resistance” selected in National Research and Development Achievements 100 and won Ministry of Science and ICT Citation

Research on “the microbiome structure of tomato rhizosphere and its involvement in disease resistance” selected in National Research and Development Achievements 100 and won Ministry of Science and ICT Citation

The research output produced by our laboratory has been selected as one of the top 100 achievements in 2019 among the research and development projects financially supported from the Korean government. Our research team discovered a ‘bodyguard bacterium’ from the tomato rhizosphere, and proved that the bacterium suppresses the progress of bacterial wilt disease. The study revealed the structure and function of plant microbiome associated with disease resistance by analyzing the metagenome and verified the contribution of plant microbiome to disease resistance for the first time. It has been published in the journal Nature Biotechnology in November 2018 as a cover-entitled Article paper, and domestic and international patents have been filed, too. The work was featured several times in Nature journals, and was highlighted as the discovery of ‘new potential plant probiotics’ in The Economist. The project was supported from Ministry of Agriculture, Food and Rural Affairs, Rural development Administration, and Ministry of Science and ICT, and has been awarded as National Research and Development Achievements 100 in October 2019 and Ministry of Science and ICT Citation on Dec. 20, 2019.

Prof. Kim wins the NAS Award

Prof. Kim wins the NAS Award

The National Academy of Sciences of the Republic of Korea (President Dongki Kim) nominated prof. Jihyun F. Kim at Yonsei University as a winner of the NAS Awards in Natural Sciences – Basic, and held the 64th awards ceremony on Sep. 17, 2019 at the auditorium of the Academy. Deputy Prime Minister & Minister of Education Eunhye Yu, academy members, and friends and families of the winners participated in the ceremony. The NAS awards, the most prestigious prizes with the oldest history and the highest authority in Korea, have been granted to scholars who contributed to the advancement of the humanity by accomplishing outstanding academic achievements in a specific subject of research.

With his dedication to microbial genome research, prof. Kim analyzed the genomes of Escherichia coli, which has evolved in the laboratory for a long time, to reveal that the relationship between genetic variation and environmental adaptation is not proportional and occurs much more complex and dynamically than is known. He contributed greatly to the identification of the evolutionary principles of life. The findings, published as an Article in the journal Nature in 2009 (Genome evolution and adaptation in a long-term experiment with Escherichia coli), have been cited more than 1,000 times over the past decade. In addition to being rated as "Exceptional (FFa 19)" by F1000 Prime, it has been featured as an excellent paper in Nature sister journals and others. He has published a number of excellent papers on microbial genomics and evolutionary research, and was given the On-BIT Award from the Korean Society for Bioinformatics and Biology in 2009, KRIBB Award – Grand Prize from Korea Research Institute of Bioscience and Biotechnology in 2010, and Grand Prize for Academic Achievement from the Microbiological Society of Korea in 2018 among others.

Furthermore, prof. Kim has contributed to systems/synthetic biology and microbiome research and development. His efforts have been focused on understanding the interactions among biomolecules, among microbes, and/or between microbes and plant/human hosts at the systems level using genomics and multi-omics technologies. Also, he made efforts to establish the foundation for bioeconomy by utilizing synthetic biology and other biotechnological platforms aimed at modulating microbes and microbiomes to maintain health and prevent, diagnose, and/or treat disease, and has reported results to Genome Biology and Nature Biotechnology.

Toward unrestricted use of public genomic data

Please click the link for the full article.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280

POLICY FORUM/DATA ACCESS

Rudolf I. Amann, Shakuntala Baichoo, Benjamin J. Blencowe, Peer Bork, Mark Borodovsky, Cath Brooksbank, Patrick S. G. Chain, Rita R. Colwell, Daniele G. Daffonchio, Antoine Danchin, Victor de Lorenzo, Pieter C. Dorrestein, Robert D. Finn, Claire M. Fraser, Jack A. Gilbert, Steven J. Hallam, Philip Hugenholtz, John P. A. Ioannidis, Janet K. Jansson, Jihyun F. Kim, Hans-Peter Klenk, Martin G. Klotz, Rob Knight, Konstantinos T. Konstantinidis, Nikos C. Kyrpides, Christopher E. Mason, Alice C. McHardy, Folker Meyer, Christos A. Ouzounis, Aristides A. N. Patrinos, Mircea Podar, Katherine S. Pollard, Jacques Ravel, Alejandro Reyes Muñoz, Richard J. Roberts, Ramon Rosselló-Móra, Susanna-Assunta Sansone, Patrick D. Schloss, Lynn M. Schriml, João C. Setubal, Rotem Sorek, Rick L. Stevens, James M. Tiedje, Adrian Turjanski, Gene W. Tyson, David W. Ussery, George M. Weinstock, Owen White, William B. Whitman, Ioannis Xenarios

Microbial mercenaries for plant disease resistance ungrounded

Certain microbes thriving in soil near the roots of the tomato plant that can resist bacterial wilt were found to inhibit the disease development and progression.
The work led by professors Jihyun F. Kim, Department of Systems Biology, Yonsei University, and Seon-Woo Lee, Department of Applied Biology, Dong-A University, appeared online in Nature Biotechnology as a research article (https://www.nature.com/articles/nbt.4232). Domestic and international patents have been filed for the bacterium, too.
Pathogens, pests and weeds are big problems when cultivating crops. Plant diseases can cause serious economic losses to major crops, such as rice blast and bacterial blight, and can lead to a great socio-cultural aftermath, such as a potato blight that has brought massive overseas migration to Ireland.
Understanding plant disease resistance is essential to preventing and treating plant diseases. In plant pathology, plant defense has been known to occur when a protein made from a resistance gene detects the invasion of a pathogen and various inhibitory substances are formed to attack the pathogen.
To investigate the possibility that plant microbiome may be involved in plant disease resistance, they set out in 2011 to collaborate on a tomato variety that is resistant to bacterial wilt. The disease causes enormous damage to hundreds of crops such as tomatoes, potatoes, and peppers.
The pathogen Ralstonia solanacearum enters the plant through the root and, even if the diseased plant is removed, it remains in soil for long. It is a very important pathogen in quarantine, along with the fire blight pathogen, and is classified as a biologically active microorganism that is likely to be abused as a biological weapon in crop bioterrorism.
The researchers cultivated tomato varieties Hawaii 7996 (resistant to bacterial wilt) and Moneymaker (susceptible) in a soil mesocosm experiment to analyze the microbiota differences in the soil near the root called the rhizosphere. Drs. Min-Jung Kwak and Ju Yeon Song along with members of Prof. Lee’s lab examined the types, frequencies, and networks of microorganisms in 16S rDNA of the rhizosphere microbial communities and analyzed the types and frequencies of microbes and their genes in the metagenome, the entire DNA sequences.
As a result, they found that certain bacteria including Flavobacteriaceae were inhabited more in the rhizosphere of Hawaii 7996 than Moneymaker, and noticed the possibility that microbiota in the resistant plant-grown soil could prevent occurrence and progress of the disease in a microbiota transplant (or microbiota transplantation) experiment.
Dr. Kwak then analyzed the metagenomic sequences to investigate which microorganisms have an effect on the disease occurrence in the tomato rhizosphere. A genomic draft of a bacterium, which has not been isolated and cultivated so far in the rhizosphere of resistant tomato varieties, was found to be much more numerous in Hawaii 7996 than Moneymaker.
Based on this, Jidam Lee succeeded in isolating a specific microorganism of a novel taxon that grows very slowly using various genomic information collected from the metagenomic data, and named it TRM1. According to Drs. Kwak, Song, and Soon-Kyeong Kwon, it has a wealth of genes that may make the bacterium competitive in the rhizosphere.
In addition to the inoculation experiment of tomato pathogens in various conditions including concentration of TRM1, soil type, soil sterilization, etc., Dr. Kwon and Hyein Park as well as Prof. Lee’s people finally proved that TRM1 reduces the incidence and progress of bacterial wilt by monitoring the population changes of TRM1 and R. solanacearum in the tomato rhizosphere.
The research was highlighted by the Senior Editor Susan Jones (https://naturemicrobiologycommunity.nature.com/users/5449-susan-jones/posts/39685-charting-a-pathway-to-plant-probiotics), covered by The Economist (https://www.economist.com/science-and-technology/2018/10/09/some-plants-nurture-soil-bacteria-that-keep-them-healthy), and briefed in Nature Reviews Microbiology (https://www.nature.com/articles/s41579-018-0104-2).
This study is the first to reveal the structure and function of the plant microbiome related to disease resistance, and it opens up a new era of phytobiome research as well as development of a new generation of eco-friendly microbials dubbed ‘plant probiotics’.

Prof. Kim wins the Grand Prize of the MSK Awards!

Professor Jihyun F. Kim has won the Grand Prize of the 2018 MSK Awards for his lifetime achievements in microbial research and contributions to microbiology. He published more than a hundred research/review papers on microbial genomics, genome evolution, microbe-host interactions, and systems/synthetic biology including those published in Nature, Nature Communications, Genome Biology, Trends in Genetics, Nucleic Acids Research, Bioinformatics, Genome Biology and Evolution, Molecular Plant-Microbe Interactions, Journal of Molecular Biology, and Journal of Bacteriology, and filed over thirty patents and software programs.

http://www.msk.or.kr/msk/award/award_1.asp

http://www.msk.or.kr/msk/board/notice_view.asp?NBIDX=510

Yusook Chung won the Best Poster Presentation Award at the KMB 2018 Winter Symposium.

Yusook Chung wins the Best Poster Presentation Award at the KMB 2018 Winter Symposium.
Congrats to our graduate student, Yusook Chung. She won the Best Poster Presentation Award at the KMB 2018 Winter Symposium for her work on the comparative analysis of Lactobacillus genomes.

Dr. Kwon wins the Grand Prize of the MSK Young Investigator Awards

Dr. Soon-Kyeong Kwon, a research professor in the JFK lab at Yonsei University, has won the Grand Prize of the MSK Young Investigator Awards for 2017. Among other contributions, she found a new class of microbial rhodopsins that pumps out sodium ions from her work on microbial genomics.

http://www.msk.or.kr/msk/board/notice_view.asp?NBIDX=455

https://www.kofst.or.kr/general.bit?sys_type=0000&menu_code=600600&ctype_id=notice&ctype_depth=01&bbSeq=213184

http://www.yonhapnews.co.kr/bulletin/2017/04/17/0200000000AKR20170417038700017.HTML

http://news.khan.co.kr/kh_news/khan_art_view.html?artid=201704172104025&code=100303

http://www.sedaily.com/NewsView/1OEOKOFYLX

Prof. Kim became a member of the Korean Academy of Science and Technology.

한림원은 과학기술분야에서 국내외적으로 학문적 수월성을 인정받은 석학들을 회원으로 선별해 이들의 부문별 전문성을 효율적으로 활용함으로써 국가 과학기술의 진흥과 창달에 이바지하고 있는 순수 민간 과학기술 아카데미다. 현재 500여 명의 정회원을 보유한 한림원은 매년 엄격한 심사를 통해 신입회원을 영입하고 있으며 김지현 교수는 지난 11월 27일 개최된 한립원 정기총회에서 인준받아 2016년 1월 8일에 신입 준회원 수여를 받았다.
http://systemsbiology.yonsei.ac.kr/sub/catalog.php?operation=view&no=46&CatNo=32