Shanlin Ke (柯善林), PhD

Shanlin Ke (柯善林), PhD

About me

I am a biologist with expertise in bioinformatics, microbiology, machine learning, and animal experiments. My long-term goal is to establish an independent research group to explore the biosynthetic potential within microbial communities and develop novel microbiome-based strategies to manage multi-drug resistant infections (C. difficile infection, COVID-19, and Urinary Tract Infection) and chronic diseases (Posttraumatic Stress Disorder, aging, and Inflammatory Bowel Disease).

Education

State Key Lab of Animal Genetics, Jiangxi Agricultural University, Jiangxi, CHINA, Ph.D., 09/2015-12/2020, Microbiology and Bioinformatics

Channing Division of Network Medicine, Harvard Medical School, MA, USA, Visiting student, 09/2018-02/2021, Microbiology and Bioinformatics

Jiangxi Agricultural University, Jiangxi, CHINA, B.S., 09/2011-07/2015, Veterinary Medicine

Publications

  1. Ke S, Gálvez JAV, Sun Z, Cao Y, Pollock NR, Chen X, Kelly CP, Liu Y.Y. Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. 2024, Doi: 10.1093/infdis/jiae470, The Journal of Infectious Diseases.

  2. Guimond A.J, Ke S, Tworoger S.S., Huang T., Chan A.T, Kubzansky L.D., and Liu Y.Y. Fulfilled mind, healthy gut? Relationships of eudaimonic psychological well-being with the gut microbiome in postmenopausal women, Psychosomatic Medicine, 2024, PMID: 38345311, doi: 10.1097/PSY.0000000000001278 (* indicates co-first authors).

  3. Ke S., Liu Y, Koenen KC. Role of the Gut Microbiome in Posttraumatic Stress Disorder. 2023, Brain Behavior and Immunity, doi: 10.1016/j.bbi.2023.09.005.

  4. Ke S., Wang X, Ratanatharathorn A, Huang T, Roberts A, Grodstein F, Kubzansky L, Koenen KC, Liu Y. Association of Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women. 2023, Nature Mental Health, doi: 10.1038/s44220-023-00145-6.

  5. Ke S, Xiao Y, Weiss ST, Chen X, Kelly CP, Liu Y.Y. A Computational Method to Dissect Colonization Resistance of the Gut Microbiota against Pathogens. 2023, doi: 10.1016/j.crmeth.2023.100576. Cell Reports Methods (* indicates co-first authors).

  6. Ke, S, Guimond A.J, Tworoger, S.S., Huang, T., Chan, A.T., Liu, Y.Y., Kubzansky, L.D. Gut feelings: Associations of emotions and emotion regulation with the gut microbiome in women. Psychological Medicine (2023), doi: 10.1017/S0033291723000612 (* indicates co-first authors).

  7. Wang X., Wang T., Schaub D.P., Chen C., Sun Z., Ke S., Hecker., Maaser-Hecker A., Zeleznik O.A., Zeleznik R., Litonjua A.A., DeMeo D.L., Lasky-Su J., Silverman E.K., Liu Y.Y., Weiss S.T. Benchmarking omics-based prediction of asthma development in children. Respiratory Research (2023), doi: 10.1186/s12931-023-02368-8. PMID: 36842969.

  8. Liu Q., He M., Zeng Z., Huang X., Fang S., Zhao Y., Ke S., Wu J., Zhou Y., Xiong X., Li Z., Fu H., Huang L., Chen C. Extensive identification of serum metabolites related to microbes in different gut locations and evaluating their associations with porcine fatness. Microbial Biotechnology (2023), doi: 10.1111/1751-7915.14245.

  9. Zhao C., Wang L., Ke .S., Chen X., Kenéz Á., Xu W., Wang D., Zhang F., Li Y., Cui Z., Qiao Y., Wang J., Sun W., Zhao J., Yao J., Yu Z., Cao Y. Yak rumen microbiome elevates fiber degradation ability and alters rumen fermentation pattern to increase feed efficiency. Animal Nutrition (2022), doi: 10.1016/j.aninu.2022.07.014.

  10. Ke S., Weiss S.T., Liu Y.Y. Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes. Nature Communications, doi: 10.1038/s41467-022-32991-w. PMID: 36068270.

  11. Cao Y , Wang L *, Ke S , Kelly P, Pollock R, Gálvez J, Daugherty K, Xu H, Yao J, Chen Y, Liu Y.Y, Chen X. Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort. Microbiology Spectrum (2022), doi: 10.1128/spectrum.01362-22. PMID: 35867408 ( indicates co-first authors).

  12. Ke S., Weiss S.T., Liu Y.Y. (2022). Rejuvenating the Human Gut Microbiome. Trends in Molecular Medicine (2022), doi.10.1016/j.molmed.2022.05.005, PMID: 35781423. (Highlighted by more than 90 news, including NBC News, The Economists, Yahoo, Science daily, etc.)

  13. Yang H., Wu J., Huang X., Zhou Y., Zhang Y., Liu M., Liu Q., Ke S., He M., Fu H., Fang S., Xiong X., Jiang H., Chen Z., Wu Z., Gong H., Tong X., Huang Y., Ma J., Gao J., Charlier C., Coppieters W., Shagam L., Zhang Z., Ai H., Yang B., Georges M., Chen C., Huang L. ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature (2022), doi: 10.1038/s41586-022-04769-z. PMID: 35477154.

  14. Ke S., Mitchell S.J., MacArthur M.R., Kane A.E., Sinclair D.A., Venable E.M., Chadaideh K.S., Carmody R.N., Grodstein F., Mitchell J.R., Liu Y.Y. Gut Microbiota Predicts Healthy Late-Life Aging in Male Mice. Nutrients (2021), doi: 10.3390/nu13093290. PMID: 34579167.

  15. Fu H., He M., Wu J., Zhou Y., Ke S., Chen Z., Liu Q., Liu M., Jiang H., Huang L., Chen C. Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows. Frontiers in Microbiology (2021), doi: 10.3389/fmicb.2021.729039. PMID: 34603257.

  16. Zhang J., Liu M., Ke S., Huang X., Fang S., He M., Fu H., Chen C., Huang L. Gut and Vagina Microbiota Associated With Estrus Return of Weaning Sows and Its Correlation With the Changes in Serum Metabolites. Frontiers in Microbiology (2021), doi: 10.3389/fmicb.2021.690091. PMID: 34489885.

  17. Cao Y, Wang L, Ke S*, Villafuerte Gálvez JA., Pollock N.R., Barrett C., Sprague R., Daugherty K., Xu H., Lin Q., Yao J., Chen Y., Kelly C.P., Liu Y.Y., Chen X. Fecal Mycobiota Combined With Host Immune Factors Distinguish Clostridioides difficile Infection From Asymptomatic Carriage. Gastroenterology (2021), doi: 10.1053/j.gastro.2021.02.069. PMID: 33684427 ( indicates co-first authors).

  18. Ke S., Pollock N.R., Wang XW., Chen X., Daugherty K., Lin Q., Xu H., Garey KW., Gonzales-Luna AJ., Kelly C.P., Liu Y.Y. Integrating gut microbiome and host immune markers to understand the pathogenesis of Clostridioides difficile infection. Gut Microbes (2021), doi: 10.1080/19490976.2021.1935186. PMID: 34132169.

  19. Huang X., Gao J., Zhao Y, He M, Ke S., Wu J, Zhou Y, Fu H, Yang H, Chen C, Huang L. Dramatic Remodeling of the Gut Microbiome Around Parturition and Its Relationship With Host Serum Metabolic Changes in Sows. Frontiers in Microbiology (2019), doi: 10.3389/fmicb.2019.02123. PMID: 31572329.

  20. He M., Gao J., Wu J., Zhou Y., Fu H., Ke S., Yang H., Chen C., Huang L. Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles. Frontiers in Microbiology (2019), doi: 10.3389/fmicb.2019.01359. PMID: 31275280.

  21. Ke S., Fang S., He M., Huang X, Yang H, Yang B, Chen C, Huang L. Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition. BMC Veterinary Research (2019), doi: 10.1186/s12917-019-1918-5. PMID: 31126262.

  22. Yang H, Yang M, Fang S, Huang X, He M, Ke S., Gao J, Wu J, Zhou Y, Fu H, Chen C, Huang L. Evaluating the profound effect of gut microbiome on host appetite in pigs. BMC Microbiology (2018), doi: 10.1186/s12866-018-1364-8. PMID: 30547751.

  23. Huang X, Fang S, Yang H, Gao J, He M, Ke S., Zhao Y, Chen C, Huang L. Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration. Scientific Report (2017), doi: 10.1038/s41598-017-15044-x. PMID: 29097803.

  24. Hu G., Song Y., Ke S., Cao H, Zhang C, Deng G, Yang F, Zhou S, Liu P, Guo X, Liu P. Tanshinone IIA protects against pulmonary arterial hypertension in broilers. Poultry Science (2017), doi: 10.3382/ps/pew322. PMID: 27702914. ( indicates co-first authors).

  25. Huang X., Huang T., Deng W., Yan G, Qiu H, Huang Y, Ke S., Hou Y, Zhang Y, Zhang Z, Fang S, Zhou L, Yang B, Ren J, Ai H, Huang L. Genome-wide association studies identify susceptibility loci affecting respiratory disease in Chinese Erhualian pigs under natural conditions. Animal Genetics (2017), doi: 10.1111/age.12504. PMID: 27615547.

  26. He M., Fang S., Huang X., Zhao Y., Ke S., Yang H., Li Z., Gao J, Chen C., Huang L. Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples. Frontiers in Microbiology (2016), doi: 10.3389/fmicb.2016.02108. PMID: 28066405.

Scientific papers (submitted)

  1. Zhang Y, Ke S., Wang X, Liu Y.Y. Association rule mining of the human gut microbiome. 2022, doi: 10.1101/2022.11.27.518104. Bioinformatics Advances, under revision.
  2. Yin X, Sasson G, Sun Z, Ke S, Babazadeh D, Mahmood SD, Andrews M, Hurwitz S, Chikowore T, Paul M, Javier N, Dave M, Austin A, Gray L, Steinberg F, Souza E, Bowlus S, Liu Y, Korzenik J. Demonstrating the beneficial effect of low protein diet in primary sclerosing cholangitis through a randomized clinical trial and multi-omics data analysis. 2024, Cell Reports Medicine, under review.

Awards

Women’s Health Interdisciplinary Stress Program of Research (WHISPR) award, 06/2023~05/2025.

Talks

  1. Harnessing the microbiota for therapeutic purposes, Ohio State University, 09/2024
  2. Towards the rational design of microbiome-based therapeutics, Ohio State University, 04/2024
  3. Decipher the role of human microbiome in Posttraumatic stress disorders, UCLA, 04/2024
  4. Biosynthetic potential of the human microbiome, Michigan State University, 03/2024
  5. Revealing the interaction between Posttraumatic Stress Disorder and the gut microbiome in older women, The 6th annual WHISPR symposium, BWH, 05/2023
  6. Rejuvenating the Human Gut Microbiome, HMS-CSSA lighting talk, 02/2023
  7. Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes, New York Genome Center, 09/2022
  8. Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes, Microbiome meeting in Shandong University, 10/2022

Publicity

S. Ke, X-W. Wang, A. Ratanatharathorn, T. Huang, A. Roberts, F. Grodstein, L. Kubzansky, K. Koenen, Y-Y. Liu. Association of probable post-traumatic stress disorder with dietary pattern and gut microbiome in a cohort of women

https://www.miragenews.com/ptsd-diet-and-gut-microbiome-link-found-study-1107130/

https://www.nbcnews.com/health/health-news/mediterranean-diet-may-reduce-prevent-ptsd-symptoms-new-research-shows-rcna121223

https://www.hngn.com/articles/253212/20231022/diet-impact-ptsd-research-suggests-mediterranean-key.htm

https://www.usnews.com/news/health-news/articles/2023-10-23/mediterranean-diet-may-ease-ptsd-symptoms

https://vegnews.com/vegan-news/plant-based-diet-ptsd-study

https://www.the-microbiologist.com/news/researchers-discover-associations-among-ptsd-diet-and-the-gut-microbiome/1781.article

S. Ke, Guimond A.J., S.S. Tworoger, T. Huang, A.T. Chan, Y.Y. Liu, L.D. Kubzansky (2023). Gut feelings: Associations of emotions and emotion regulation with the gut microbiome in women.

NutritionInsight: Gut feelings: Emotions, diets and microbiome link investigated in studies, https://www.nutritioninsight.com/news/gut-feelings-emotions-diets-and-microbiome-link-investigated-in-studies.html

Neuroscience News: Is Your Emotional Wellbeing Related to Your Gut Health? New Study Reveals Possible Link in Women? https://neurosciencenews.com/emotion-gut-microbiome-23129/

BWH News: Emotional Wellbeing May be Directly Linked to Women’s Gut Health, https://www.brighamandwomens.org/about-bwh/newsroom/press-releases-detail?id=4417

Boston 25 News: You really do ‘feel’ it in your gut: Study links GI bacteria levels to emotions, https://www.boston25news.com/news/local/you-really-do-feel-it-your-gut-study-links-gi-bacteria-levels emotions/6IBKNBOZCZBN5HSG7ACH3QCOHY/

The Harvard Gazette: Expanding our understanding of gut feelings, https://news.harvard.edu/gazette/story/2023/04/expanding-our-understanding-of-the-gut-feeling/

Ke S, Weiss ST, Liu Y.Y. (2022). Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes.

Nature portfolio: The role of the human microbiome in COVID-19; https://microbiologycommunity.nature.com/posts/the-role-of-the-human-microbiome-in-covid-19

Brigham and Women’s Hospital-On a mission: Brigham researchers create COVID-19 genome catalog of the human microbiome; https://www.brighamhealthonamission.org/2022/10/17/brigham-researchers-create-covid-19-genome-catalog-of-the-human-microbiome/

Ke S, Weiss ST, Liu Y.Y. (2022). Rejuvenating the Human Gut Microbiome (covered by 90+ news)

Best of 2022: Trends in Molecular Medicine: https://www.cell.com/trends/molecular-medicine/collections/best-of-2022

NBC News: The secret to good health later in life? Researchers think it could be banking your poop now; https://www.nbcnews.com/science/science-news/secret-good-health-later-life-researchers-think-banking-poop-now-rcna36184

The Economist: People bank blood. Why not faeces? https://www.economist.com/science-and-technology/2022/06/29/people-bank-blood-why-not-faeces

WIRED: Could Your Old Poop Cure You of Future Diseases?https://www.wired.com/story/could-old-poop-cure-future-diseases/

Science Daily: Researchers propose widespread banking of stool samples for fecal transplants later in life; https://www.sciencedaily.com/releases/2022/06/220630114518.htm

Yahoo: Building a poop bank for human fecal transplants; https://www.yahoo.com/entertainment/building-poop-bank-human-fecal-183005666.html

The Daily Beast: You Need to Make a Personal Poop Bank, Scientists Say; https://www.thedailybeast.com/you-need-to-make-a-personal-poop-bank-for-fecal-transplants-scientists-say?source=articles&via=rs

Cosmos Magazine: Would you store your poo to help future you?https://cosmosmagazine.com/science/biology/autologous-fmt-store-your-poo/

WebMd: Your Poop May Hold the Secret to Long Life; https://www.webmd.com/digestive-disorders/news/20220913/poop-may-hold-secret-long-life

Healthy Day: Will You Be Depositing at the ‘Stool Bank’ Someday? https://consumer.healthday.com/6-30-will-you-be-depositing-at-the-stool-bank-someday-2657551064.html

New York Post: LefroyPreserving your poop could help save your life: Harvard scientists, https://nypost.com/2022/07/19/preserving-your-poop-could-help-save-your-life-harvard-scientists/