Jonathan Wei Jie LEE

Affiliations

Senior Consultant, Division of Gastroenterology and Hepatology, Department of Medicine, National University Hospital
Principal Investigator, NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)
Principal Investigator, iHealthtech, NUS
Visiting Scientist, MIT-Harvard Broad Institute, Boston, USA
Chief Scientific Officer, AMILI Pte Ltd, Singapore

Biography

Dr Jonathan Lee is a clinician-scientist at NUS Medicine specializing in translational microbiome research in gastrointestinal diseases. He is a Senior Consultant Gastroenterologist at the National University Hospital, where he leads the Inflammatory Bowel Disease (IBD) Unit and the clinical fecal microbiota transplantation program. His research integrates multi-omics analytics, microbiome–host interactions, and biomarker discovery to enable precision medicine.

Dr Lee completed his PhD at NUS Medicine and a two-year overseas research fellowship at the Broad Institute of MIT and Harvard, supported by the NMRC Research Training Fellowship, where he developed expertise in metagenomics, metabolomics, and microbial culturomics. His work spans gastric cancer, colorectal cancer, IBD, and MASLD, with key contributions to microbiome-based diagnostics, therapeutic response prediction, and mechanistic disease modeling.

He leads microbiome analytics for large multi-center cohorts, including COLONT2, and directs experimental programs encompassing ex vivo microbiome systems, microbial strain isolation, and microbiome-modifiable animal models. Dr Lee currently serves as the microbiome platform lead for the NUHS Digestive Centre of Excellence and chairs the NUS Microbiome Work-in-Progress series. His research aims to translate microbiome discoveries into clinically actionable diagnostics and therapeutics.

Professional Appointments

Research Director, Division of Gastroenterology and Hepatology, Department of Medicine, National University Hospital

Education

Ph.D. (Medicine) National University of Singapore Singapore 2024
Masters of Clinical Investigation National University of Singapore 2017
MRCP (UK) Royal College of Physicians, 2014
BSc (Hons), MBBS (Hons) University of New South Wales Australia 2010

Research Interest

• Microbiome biomarkers for gastrointestinal diseases
• Microbiome-based precision therapy in IBD
• Diet–drug–microbiome interactions
• Ex vivo and in vivo microbiome models
• Translational microbiome therapeutics

Current Research Projects

• Treating Non-Alcoholic Fatty Liver Disease through Modification of Microbiome-modulated Metabolites
• Reduction in Steatohepatitis Through Bacterial Bile Acid Modification in the Gut
• Characterizing Pathogen Associated Molecular Patterns (PAMPs) propogating Non-Alcoholic Steatohepatitis (NASH)
• Metabolic Associated Steatotic Liver Disease: Endotyping Asian Disease Trajectory for Personalised Risk
• Investigating the role of bile acids in non- alcoholic fatty liver disease and insulin resistance
• Singapore Gastric Cancer Consortium – Therapeutic Interception of Gastric
• Engineering in Medicine: One stop H. pylori testing kit
• Early detection and prevention of colorectal cancer –development of miRNA biomarker panel and discovery of microbiome signatures
• Harnessing Microbial SCFAs to Accelerate Mucosal Healing in Ulcerative Colitis
• Ileal Microbiota Transplantation: Enhancing Mucosal Healing in Crohn’s Disease through Arginine Metabolism
• Molecular Mechanisms and Therapeutic Potential of miR-187-Expressing Lactococcus lactis in the Treatment of Inflammatory Bowel
• Microbiome-Immune Interactions as Predictive Biomarkers for Personalized Therapy in IBD
• Rapid detection of Indole-3-propionic acid and Development of Raman spectral library for Gut health monitoring using a portable Spectrometer
• Ingestible Gas Sensing Capsule for Real-Time In Situ Monitoring and Study
• of Gastrointestinal Disorder
• Revealing the role of paternal microbiota – the neglected partner in shaping offspring health

Selected Publications

1.  *Lee JWJ, Plichta DR, Asher S, Delsignore M, Jeong T, McGoldrick J, Staller K, Khalili H, Xavier RJ, Chung DC. Association of distinct microbial signatures with premalignant colorectal adenomas. Cell Host Microbe. 2023 May 10;31(5):827-838.e3.
2. *Png CW, Lee WJJ, Chua SJ, Zhu F, Yeoh KG, Zhang Y. Mucosal microbiome associates with progression to gastric cancer. Theranostics. 2022;12(1):48-58.
3. *Lee JWJ, Zhu F, Srivastava S, Tsao SKK, Khor C, Ho KY, Fock KM, Lim WC, Ang TL, Chow WC, So JBY, Koh CJ, Chua SJ, Wong ASY, Rao J, Lim LG, Ling KL, Chia CK, Ooi CJ, Rajnakova A, Yap WM, Salto-Tellez M, Ho B, Soong R, Chia KS, Teo YY, Teh M, Yeoh KG. Severity of gastric intestinal metaplasia predicts the risk of gastric cancer: a
   a. prospective multicentre cohort study (GCEP). Gut. 2022;71(5):854-63.
4. *Koh E, Hwang IY, Lee HL, De Sotto R, Lee JWJ, Lee YS, March JC, Chang MW. Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism. Nature Communications. 2022;13(1).
5. *Walker RL, Vlamakis H, Lee JWJ, Besse LA, Xanthakis V, Vasan RS, Shaw SY, Xavier RJ. Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease. Genome Medicine. 2021;13(1).
6. So JBY, Kapoor R, Zhu F, Koh C, Zhou L, Zou R, Tang YC, Goo PCK, Rha SY, Chung HC, Yoong J, Yap CT, Rao J, Chia CK, Tsao S, Shabbir A, Lee JWJ, Lam KP, Hartman M, Yong WP, Too HP, Yeoh KG. Development and validation of a serum microRNA biomarker panel for detecting gastric cancer in a high-risk population. Gut. 2021;70(5):829-37.
7. *Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host and Microbe. 2021;29(8):1294-304.e4.
8. Huang KK, Ramnarayanan K, Zhu F, Srivastava S, Xu C, Tan ALK, Lee M, Tay S, Das K, Xing M, Fatehullah A, Alkaff SMF, Lim TKH, Lee JWJ, Ho KY, Rozen SG, Teh BT, Barker N, Chia CK, Khor C, Ooi CJ, Fock KM, So J, Lim WC, Ling KL, Ang TL, Wong A, Rao J, Rajnakova A, Lim LG, Yap WM, Teh M, Yeoh KG, Tan P. Genomic and Epigenomic Profiling of High-Risk Intestinal Metaplasia Reveals Molecular Determinants of Progression to Gastric Cancer. Cancer Cell. 2018;33(1):137-50.e5.
9. Huang KK, Ma H, Chong RHH, Uchihara T, Lian BSX, Zhu F, Sheng T, Srivastava S, Tay ST, Sundar R, Tan ALK, Ong X, Lee M, Ho SWT, Lesluyes T, Ashktorab H, Smoot D, Van Loo P, Chua JS, Ramnarayanan K, Lau LHS, Gotoda T, Kim HS, Ang TL, Khor C, Lee JWJ, Tsao SKK, Yang WL, Teh M, Chung H, So JBY, Yeoh KG, Tan P; Singapore Gastric Cancer Consortium. Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression. Cancer Cell. 2023 Dec 11;41(12):2019- 2037.e8.
10. Shijia Hu, John Mok, Michelle Gowans, David E H Ong, Juanda Leo Hartono, Lee JWJ, Oral Microbiome of Crohn’s Disease Patients With and Without Oral Manifestations, Journal of Crohn’s and Colitis, Volume 16, Issue 10, October 2022, Pages1628–1636