Shanghai Institute of Material Medical Chinese Academy of Sciences

Biography

Dr. Yan Yan is a Principal Investigator and Doctoral Supervisor at the Shanghai Institute of Materia Medica, Chinese Academy of Sciences, where she leads the Gut Microbiota and Computational Metagenomics research group. She serves as the Chief Young Scientist under the "Youth Ascent Program for Seizing Scientific High Ground" initiative of the Chinese Academy of Sciences Shanghai Branch.

During her postdoctoral fellowship at the Harvard T.H. Chan School of Public Health, she worked under the mentorship of Prof. Curtis Huttenhower, a leading expert in computational microbiology and a key architect of the Human Microbiome Project. As a core team member, she contributed significantly to the Human Microbiome Project and the OPTIMISTICC Grand Challenge funded by Cancer Research UK.

Dr. Yan has published over 20 high-impact SCI papers as first or corresponding author in prestigious international journals such as Cell Host & Microbe (2020/2023), Genome Medicine, and The ISME Journal, with more than 2,000 citations. She has been selected for several prestigious programs, including the "Youth Talent Cultivation Program" of the Chinese Academy of Sciences Shanghai Branch, the Charles A. King Research Fellowship (USA), and the Keystone Symposia Trainee Fellowship (USA).

She currently serves as an Associate Editor for Nutrition & Metabolism and a Youth Editorial Board Member of iMeta.

Education

2017.02-2022.06 Postdoctoral fellow in Harvard T.H. Chan School of Public Health, Boston

2011.12-2016.06 Ph.D. in Microbial Ecology, Leiden University, Netherlands

Research Directions

1.Epidemiological risk factors correlate of the cancer microbiome

We are integrating metagenome profiling with machine learning approaches to unveil the influence of lifestyle and environmental factors on the microbiome in large scale investigations of human populations. We expect to have far-reaching implications in the field of hypothesis-driven microbiome discovery, forward from the correlative studies based on large-scale population cohorts.

2.Dynamics of gut microbiome in tumor microenvironment

Several cancer risk-associated microbes have been identified, however, the influence of these microorganisms on the tumor microenvironment is poorly understood. We will combine approaches for direct visualization of host-microbe interactions in the tumor microenvironment and functional validation in vivo model systems.

3.The role of microbiome in cancer therapeutic response

We are developing computational algorithm and statistical modeling to investigate how the tumor microbiome influences the impact of or shaped in cancer patients receiving novel cancer therapy. These will provide multiple opportunities for potential translation into the clinic through the development of novel diagnostics and therapeutics that target microbes to improve cancer treatment efficacy, and ultimately facilitate the personalized medicine in public health.

Grants & Research Projects

Two General Programs of the NSFC (2024–2029, 2025–2028),

National Key Laboratory Cultivation Project (2024–2029),

Shanghai Branch of the CAS Young Talent Program (2023–2025),

First Batch of the "Pioneering Peak Youth Climbing Plan" of the Shanghai Branch, CAS (2023–2027),

Shanghai High-Level Overseas Talent Program (2022–2024),

Charles A. King Trust Research Project (USA) (2020–2022)

Achievements

1. Epidemiological risk factors correlate of the cancer microbiome（Cell Host & Microbe, 2020；Genome Medicine，2020）

2. The role of microbiome in cancer therapeutic response（Cell Host & Microbe, 2023；Genome Medicine，2020）

3. Assembly and dynamics of gut microbiome in host ecological microenvironment (Soil Biology and Biochemistry, 2019；ISME Journal, 2017)

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Social Titles

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Awards & Honors

1.2024: Chief Scientist, "Youth Ascent Program for Seizing the High Ground" (Chinese Academy of Sciences Shanghai Branch)

2.2024: "Woman Pace-setter" (Chinese Academy of Sciences Shanghai Institute of Immunity and Infection)

3.2023: "May 4th Youth Shock Team" (Chinese Academy of Sciences Shanghai Branch)

4.2020: Keystone Symposia Young Investigator Award (International)

5.2020: Harvard University Award for Outstanding Academic Funding (USA)

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Pubilcations

Selected Publications

1. Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the mucosal and stool microbiome in Lynch syndrome. Cell Host Microbe . 2020 Apr 8;27(4):585-600.e4. doi: 10.1016/j.chom.2020.03.005.

2. Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of the human microbiome. Genome Medicine.2020 Aug 13;12(1):71. doi: 10.1186/s13073-020-00765-y.

3. Yan Y, Klinkhamer PGL, Van Veen JA, Kuramae EE. Environmental filtering: A case of bacterial community assembly in soil. Soil Biology and Biochemistry. 2019. Volume 136, 107531. doi.org/10.1016/j.soilbio.2019.107531.

4. Yan Y, Kuramae EE, de Hollander M, Klinkhamer PGL, Van Veen JA. Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME J. 2017. ISME J . 2017 Jan;11(1):56-66. doi: 10.1038/ismej.2016.108.

5. Yan Y, Kuramae EE, de Hollander M, Klinkhamer PGL, Van Veen JA. Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems. Applied Environmental Microbiology. 2015. Appl Environ Microbiol . 2015 Jul;81(13):4246-52. doi: 10.1128/AEM.00958-15.

6. Wang Y, Yan Y, Thompson K, Bae S, Shen JX, Vlamakis H, Hartman EM, Huttenhower C. Characterizing microbial community viability from built environment using propidium monoazide. Microbiome . 2021 Jan 21;9(1):17. doi: 10.1186/s40168-020-00961-3.

7. Wang DD, Nguyen LH, Li YP, Yan Y, Ma WJ, Rinott E, Ivey K, Shai I, Willett WC, Hu FB, Eric B. Rimm EB, Stampfer MJ, Chan AT, Huttenhower C. The gut microbiome modifies the protective effects of a Mediterranean diet against cardiometabolic disease risk. Nature Medicine. 2021 Feb;27(2):333-343. doi: 10.1038/s41591-020-01223-3.

8. Spencer C. et.al. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science. 2021. 2021 Dec 24;374(6575):1632-1640. doi: 10.1126/science.aaz7015.

9. Young C, Wood HM, Seshadri RA, Nang PV, Vaccaro C, Melendez LC, Bose M, Doi MV, Pi？ero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer (CRC)-associated faecal microbiome of developing countries resembles that of developed countries. Genome Medicine. 2021 Feb 16;13(1):27. doi: 10.1186/s13073-021-00844-8.

10. Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P. Microbiome analysis of over 2000 NHS Bowel Cancer Screening Programme (NHSBCSP) samples shows the potential to improve screening accuracy. Clinical Cancer Research. 2021 Apr 15;27(8):2246-2254. doi: 10.1158/1078-0432.CCR-20-3807.

11. Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma WJ, Wang DD, Thompson K, Yan Y, Branck T, Wilkinson J, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song MY, Huttenhower C, Ogino SJ, Chan AT. The sulfur microbial diet and risk of colorectal cancer by molecular subtypes and intratumoral microbial species in adult men. Clinical and Translational Gastroenterology. 2021 Aug 1;12(8):e00338. doi: 10.14309/ctg.0000000000000338.

12. Zhang YC, Thompson K, Branck T, Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the human microbiome and microbial community functional profiling. Annual Review of Biomedical Data Science. 2021 Jul 20:4:279-311. doi: 10.1146/annurev-biodatasci-031121-103035.

13. Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT. Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. 2020 Apr;158(5):1313-1325. doi: 10.1053/j.gastro.2019.12.029.

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