Specializing In
- 24-hour pH monitoring
- 48-hour bravo pH monitoring
- Anorectal Manometry
- Colonoscopy
- Esophagogastroduodenoscopy (EGD)
- Gastrointestinal Nutrition
Biography
Sean Spencer, MD,PhD is a Gastroenterologist and Physician Scientist at Stanford University working with Justin Sonennburg,PhD to uncover the role of dietary intake on the gut microbiome and mucosal immune system. Sean obtained his medical degree University of Pennsylvania, earning his PhD studying nutritional immunology with Yasmine Belkaid,PhD at the National Institutes of Health (NIH), after which he moved to Boston for residency training at Massachusetts General Hospital and completed his Gastroenterology training at Stanford University. Sean’s career goal is to study mechanisms by which dietary intake influences our microbiome and immune system to better understand and treat gastrointestinal disease.
View Full Biography
Professional Summary
Education & Certifications
- Fellowship: Stanford University Division of Gastroenterology and Hepatology (2021) CA
- Fellowship: Stanford University Division of Gastroenterology and Hepatology (2020) CA
- Board Certification: American Board of Gastroenterology, Gastroenterology (2022)
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- MD/PhD, University of Pennsylvania, Immunology (2015)
- Residency: Massachusetts General Hospital Internal Medicine Residency (2017) MA
- Board Certification: American Board of Internal Medicine, Internal Medicine (2018)
- Board Certification, American Board of Internal Medicine, Gastroenterology (2022)
Honors & Awards
- A.P. Giannini Postdoctoral Fellow, AP Giannini Foundation (2021-2023)
- K08 Clinical Scientist Research Career Development Award, NIH/NIDDK (2023-2028)
- Medical Scientist Training Program (T32), National Institute of General Medical Sciences (2007-2009)
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- Ruth L. Kirschstein NRSA Individual Predoctoral MD/PhD fellowship (F30), National Institute of Diabetes and Digestive and Kidney Disease (2011-2014)
- Training Grant in Academic Gastroenterology (T32), National Institute of Diabetes and Digestive and Kidney Diseases (2019-2021)
Publications
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The long noncoding RNA Morrbid regulates CD8 T cells in response to viral infection
Kotzin, J. J., Iseka, F., Wright, J., Basavappa, M. G., Clark, M. L., Ali, M.-A., … Henao-Mejia, J. (2019). The long noncoding RNA Morrbid regulates CD8 T cells in response to viral infection. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(24), 11916–25. -
Pursuing Human-Relevant Gut Microbiota-Immune Interactions.
Spencer, S. P., Fragiadakis, G. K., & Sonnenburg, J. L. (2019). Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity, 51(2), 225–39. -
High Prevalence of Concurrent Gastrointestinal Manifestations in Patients with SARS-CoV-2: Early Experience from California.
Cholankeril, G., Podboy, A., Aivaliotis, V. I., Tarlow, B., Pham, E. A., Spencer, S., … Ahmed, A. (2020). High Prevalence of Concurrent Gastrointestinal Manifestations in Patients with SARS-CoV-2: Early Experience from California. Gastroenterology. -
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Colons or semi-colons: punctuating the regional variation of intestinal microbial-immune interactions.
Culver, R. N., Spencer, S. P., & Huang, K. C. (2020). Colons or semi-colons: punctuating the regional variation of intestinal microbial-immune interactions. Nature Reviews. Gastroenterology & Hepatology. -
Association of Digestive Symptoms and Hospitalization in Patients With SARS-CoV-2 Infection.
Cholankeril, G., Podboy, A., Aivaliotis, V. I., Pham, E. A., Spencer, S. P., Kim, D., & Ahmed, A. (2020). Association of Digestive Symptoms and Hospitalization in Patients With SARS-CoV-2 Infection. The American Journal of Gastroenterology, 115(7), 1129–32. -
When Gut Microbiota Creep into Fat, the Fat Creeps Back.
Spencer, S. P., & Sonnenburg, J. L. (2020). When Gut Microbiota Creep into Fat, the Fat Creeps Back. Cell, 183(3), 589–91. -
Environmental enteric dysfunction induces regulatory T cells that inhibit local CD4+T cell responses and impair oral vaccine efficacy
Bhattacharjee, A., Burr, A. H. P., Overacre-Delgoffe, A. E., Tometich, J. T., Yang, D., Huckestein, B. R., … Hand, T. W. (2021). Environmental enteric dysfunction induces regulatory T cells that inhibit local CD4+T cell responses and impair oral vaccine efficacy. IMMUNITY, 54(8), 1745-+. -
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.
Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., … Wyss-Coray, T. (2022). The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science (New York, N.Y.), 376(6594), eabl4896. -
Dietary and commensal derived nutrients: shaping mucosal and systemic immunity.
Spencer, S. P., & Belkaid, Y. (2012). Dietary and commensal derived nutrients: shaping mucosal and systemic immunity. Current Opinion in Immunology, 24(4), 379–84. -
Adaptation of innate lymphoid cells to a micronutrient deficiency promotes type 2 barrier immunity.
Spencer, S. P., Wilhelm, C., Yang, Q., Hall, J. A., Bouladoux, N., Boyd, A., … Belkaid, Y. (2014). Adaptation of innate lymphoid cells to a micronutrient deficiency promotes type 2 barrier immunity. Science (New York, N.Y.), 343(6169), 432–7. -
The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan.
Kotzin, J. J., Spencer, S. P., McCright, S. J., Kumar, D. B., Collet, M. A., Mowel, W. K., … Henao-Mejia, J. (2016). The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature, 537(7619), 239–243. -
Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes.
Guthrie, L., Spencer, S. P., Perelman, D., Van Treuren, W., Han, S., Yu, F. B., … Sonnenburg, J. L. (2022). Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes. Cell Host & Microbe. -
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes.
Merrill, B. D., Carter, M. M., Olm, M. R., Dahan, D., Tripathi, S., Spencer, S. P., … Sonnenburg, J. L. (2022). Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes. BioRxiv : the Preprint Server for Biology. -
Profiling the human intestinal environment under physiological conditions.
Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., … Huang, K. C. (2023). Profiling the human intestinal environment under physiological conditions. Nature. -
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.
Carter, M. M., Olm, M. R., Merrill, B. D., Dahan, D., Tripathi, S., Spencer, S. P., … Sonnenburg, J. L. (2023). Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell. -
CH4, H2S, and H2O: How Do They Relate to Microbiome-Driven IBS Pathogenesis?
Spencer, S. (2023). CH4, H2S, and H2O: How Do They Relate to Microbiome-Driven IBS Pathogenesis? Digestive Diseases and Sciences. -
Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome.
Olm, M. R., Spencer, S. P., Silva, E. L., & Sonnenburg, J. L. (2023). Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome. BioRxiv : the Preprint Server for Biology. -
Cromolyn Reduces Symptoms in Patients With Irritable Bowel Syndrome, Functional Dyspepsia, or Gastroparesis
Karhu, E., Linda Anh Nguyen, Sonu, I., Neshatian, L., Gottfried-Blackmore, A., Fernandez-Becker, N., & Spencer, S. (2023). Cromolyn Reduces Symptoms in Patients With Irritable Bowel Syndrome, Functional Dyspepsia, or Gastroparesis. AMERICAN JOURNAL OF GASTROENTEROLOGY. LIPPINCOTT WILLIAMS & WILKINS. -
Resisting weight gain with prebiotic fibre.
Carter, M. M., & Spencer, S. P. (2024). Resisting weight gain with prebiotic fibre. Nature Metabolism. -
Improved mouse models of the small intestine microbiota using region-specific sampling from humans.
Culver, R. N., Spencer, S. P., Violette, A., Lemus Silva, E. G., Takeuchi, T., Nafarzadegan, C., … Huang, K. C. (2024). Improved mouse models of the small intestine microbiota using region-specific sampling from humans. BioRxiv : the Preprint Server for Biology. -
Intestinal Methanogen Overgrowth (IMO) Is Associated with Delayed Small Bowel and Colonic Transit Time (TT) on the Wireless Motility Capsule (WMC).
Talamantes, S., Steiner, F., Spencer, S., Neshatian, L., & Sonu, I. (2024). Intestinal Methanogen Overgrowth (IMO) Is Associated with Delayed Small Bowel and Colonic Transit Time (TT) on the Wireless Motility Capsule (WMC). Digestive Diseases and Sciences. -
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.
Olm, M. R., Spencer, S. P., Takeuchi, T., Silva, E. L., & Sonnenburg, J. L. (2025). Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut. Nature Microbiology.
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Colons or semi-colons: punctuating the regional variation of intestinal microbial-immune interactions.
Clinical Trials
Clinical trials are research studies that evaluate a new medical approach, device, drug, or other treatment. As a Stanford Health Care patient, you may have access to the latest, advanced clinical trials.
Open trials refer to studies currently accepting participants. Closed trials are not currently enrolling, but may open in the future.
Practice Locations
Digestive Health Center in Redwood City Redwood City, CA
Redwood City, CA
Digestive Health Center in Redwood City
420 Broadway Street, Pavilion D 2nd Floor
Redwood City , CA 94063
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Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners are each independent nonprofit organizations that are affiliated with but separate from each other and from Stanford University. The physicians who provide care at facilities operated by Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners are faculty, foundation, or community physicians who are not employees, representatives, or agents of Stanford Health Care, Stanford Health Care Tri- Valley, or Stanford Medicine Partners. Stanford Health Care, Stanford Health Care Tri-Valley, and Stanford Medicine Partners do not exercise control over the care provided by such faculty, foundation, and community physicians and are not responsible for their actions.
Patient Reviews
(60 reviews)
He is AMAZING!!!
THE BEST OF THE BEST!
Intersted, good suggestions, very personable, good, knowledable advice, friendly and curteous. 0
Very knowledgeable
Good listener, could have been a bit more responsive to my questions.
Thank you for establishing a diagnosis, and treatment help.
Knowledgeable doctor and easy to speak with.. did not achieve ant breakthroughs but verified the efficacy of what my local doctors were achieving to help my condition.
Dr. Spencer is a very caring and knowledgeable doctor. He is doing all he can to help me and makes me feel like I am not alone.
Dr Spencer is excellent answers my questions so that I understand the terminology. Dr always asks me if he has answered all my questions.
Sean Spencer is perhaps one of the best doctors I have seen. He understands the problems in medicine and with clinicians and actively does the opposite. Sean is amazing. I have had hundreds of medical appointments, and Sean is one of the best.
Dr. Spencer was very professional and made it okay to talk about the issues I’m having that I feel embarrassed about. He was comfortable to speak to and I felt like he heard what I had to say.
Dr Spencer listened well; knew my history; asked specific questions; answered my concerns. Followup tests & meds. I'm in good hands with Dr Sean Spencer.
Sean Spenser listens, was timely on his visit and followed through on his recommendations by having a member of his team contact me within the hour after our visit. He is patient and thorough and is a credit to Stanford!
Dr. Spencer was great. He communicated clearly and took my concerns seriously. He was very thorough in reviewing my health history and came up with new suggestions about what might be causing my SIBO and EPI. He ordered a list of tests that check all the boxes of potential issues.
I have been in treatment with another doctor for 2 years who refused to explore the root causes of my condition in spite of me asking repeatedly for exactly the type of testing that Dr. Spencer offered without me even having to ask. I'm impressed and grateful.
The doctor, staff, facility are very professional
He was great, very patient, gave me time to understand and speak explaining my situation
intelligent doctors and carried on meaningful discussion of the issues which brought me here
He is thorough, thoughtful and fully present.
He does an awesome job making me feel important and I believe he will help me!
Very knowledgeable and thorough doctor.
Sean Spencer was very knowledgeable and helpful. He listened to my questions and answered them in a way I could understand. He was very thorough and kind and gave me hope.
Superb care!!
Very Happy with the Doctor
The absolute best! Honest, helpful, patient and knowledgeable!
Dr Spencer is very knowledgeable & easy to talk with… especially with the sensitive subject of my health issues. I feel very comfortable being under his care & I feel confident that he is going to get to the root of my health issues & get me back to better health!
Dr. Spencer is a stellar provider. He approaches unusual, complex medical problems with the open mind of a scientist, instead of solely attributing them to what is known at present. He welcomes patients that advocate for their health, and he encourages patients with stigmatized conditions to keep seeking care (by treating them the same as anyone else). This kind of medicine is healing in and of itself.
Dr. Spencer was very professional and answered all my questions. I felt very comfortable. At the end of our visit.
He was very thorough and I know I have had a lot of history on my GI issues and he was able to pin point majority of my problems
He is excellent and extremely knowledgeable about my condition, SEIBO.
he is fine
Listened to all my concerns.
I am hoping that he can solve my very difficult problem.
He is a phenomenal and caring doctor. Very knowledgable and thoughtful.
Thank you, Dr. Spencer, for not giving up on me!
Best in class service and facilities
He listens well, responded to my questions and concerns, is informative and caring, and has a good and gentle sense of humor.
He was great to talk to.
Dr. Spencer was knowledgeable, efficient and caring. He had a new way to look at my condition. He recommended a course of action that no other doctor has before him. I am grateful and optimistic about my recovery.
Excellent knowledge, excellent communication
very concern about patients care.I appreciate everyone.Thank you so very much.
Dr. Spencer was a very good listener. I felt I was heard !
he was very thorough in understanding my health challenges. I look forward to moving forward with Dr. Spencer. We were able to cover a lot of territory during this video visit.
Dr. Spencer was clear, responsive, helpful and kind. What more can you ask! Thank you.
Dr. Spencer was very helpful and answered my questions. He was very good at explaining the next steps with me.
Dr Spencer was amazing. Very empathetic, explained everything thoroughly and took his time answering my questions
He is the most understanding, kind, thoughtful specialist I have ever talked to. He was honest and helpful and empathetic.
He listened, was friendly, full of resources, clear, supportive, direct, helpful. Outstanding care.
Very professional and informative
He listens to my concerns as a physician,
tells me his as my specialist, and so is collaborative, which I very much appreciate. He is also very clear in educating me in areas that I am not expert. I also appreciate this very much as well.
It really care to find the solution what's going on with you
Exceptional Dr. Takes his time to explain everything so I can understand the issues.
Dr Sean Spencer is excellent.
Good visit. Thank you very much.
I believe that he is doing all he can to help me.
Very courteous & helpful
Great service from beginning to the end !
Very friendly, very comfortable speaking with him
Excellent physician
He was the first doctor to actually listen to me in a long time.
You need more doctors like Sean. Caring, knowledgeable.
I"m very impressed with the doctor, very friendly and knowledgeable
Generally a good listener and certainly a better listener than most physicians. I found Sean Spencer personable and interested in helping me as a patient. He was also very knowledgeable, seemed to be on top of his game, and he was appeared to be aware of the latest science in nutrition and issues associated with IBS.
Extremely easy to exchange information with. Very comfortable atmosphere and easy to feel at ease. Really appreciate his research knowledge and how he integrates the information with patient care.
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