Vaibhav Upadhyay, MD, PhD
Assistant Professor
Medicine
School of Medicine

I'm a K08 funded physician scientist studying impact of gut microorganisms on human health and applying multi-omic technologies to the study of chronic diseases with clinical focus in pulmonary medicine.

Awards

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• ATS RCMB Abstract Scholarship, ATS, 2022
• Jeffrey Golden Outstanding Clinical Fellow Award, UCSF Pulmonary and Critical Care Division, 2021
• Pulmonary Division Clinical Fellow Award, UCSF Department of Medicine, 2020
• UCSF Fellows Leadership Cohort, UCSF Department of Medicine, 2020
• Pulmonary Division Clinical Fellow Award, UCSF Department of Medicine, 2019
• Nominated for Clinical Fellow of the Year (one of a group of finalists), ZSFG Department of Medicine, 2019
• Abstract selected for oral presentation, UCSF Resident Research Symposium, 2018
• Jeffrey Weingarten Award, UCSF, Internal Medicine Residency, 2018
• Graduation with Honors, University of Chicago, Pritzker School of Medicine, 2015
• John Van Prohaska Award, University of Chicago, Pritzker School of Medicine, 2015
• Best poster describing basic science investgiation, University of Chicago, Prtizker School of Medicine, 2015
• Alpha omega alpha, University of Chicago, 2014
• Travel scholarship, Keystone Symposia, 2013
• Best Dissertation, University of Chicago, Committee on Immunology, 2013
• Best Poster, ASCI/APSA Conference, 2012
• Travel award, American Association of Immunologists, 2012
• Summa cum laude, Duke University, 2007
• American Chemistry Society Analytical Division Undergraduate Award, Duke University, 2006
• Phi Beta Kappa, Duke University, 2006

Education & Training

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• Pulmonary and Critical Care UCSF 2021
• Chief Fellow Pulmonary and Critical Care UCSF 2021
• Internal Medicine UCSF 2018
• MD Medicine University of Chicago 2015
• PhD Immunology University of Chicago 2013
• BS Biochemistry Duke University 2007

Interests

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• Gut microbiome
• acute lung injury
• pulmonary medicine

Websites

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• Linked In Home Page (linkedin.com)

Grants and Projects

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• Impact of gut bacterial metabolites on lung function and disease, NIH/NHLBI, 2023-2028
• The Gut Microbiome in Predisposition to and as a Marker of Sars-CoV-2 Infection, Benioff Center for Microbiome Medicine, 2020-2021
• Exploration of Novel Autoantigens in Patients with Idiopathic Pneumonia with Autoimmune Features, UCSF CTSI, 2017-2018

Publications (28)

Top publication keywords:
Immunity, MucosalHabitsGastrointestinal MicrobiomeMicrobiotaLymphotoxin beta ReceptorGastrointestinal TractTh17 CellsDiet, KetogenicMetabolic DiseasesFriendsLymphotoxin-betaLymphotoxin-alphaEstersImmunity, InnateLymphotoxin alpha1, beta2 Heterotrimer

• Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response.
  Annual review of pharmacology and toxicology 2024 Trepka KR, Olson CA, Upadhyay V, Zhang C, Turnbaugh PJ
• A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.
  Cell reports 2024 Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ
• Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity.
  bioRxiv : the preprint server for biology 2024 Trepka KR, Kidder WA, Kyaw TS, Halsey T, Olson CA, Ortega EF, Noecker C, Upadhyay V, Stanfield D, Steiding P, Guthrie BGH, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, …
• Rationale and protocol for a safety, tolerability and feasibility randomized, parallel arm, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms.
  PloS one 2024 Stubbs BJ, Alvarez Azañedo G, Peralta S, Diaz SR, Gray W, Alexander L, Silverman-Martin W, Garcia TY, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC
• Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease.
  ACR open rheumatology 2024 Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson MS, DeRisi JL, Sperling AI, Shum AK

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• A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.
  bioRxiv : the preprint server for biology 2024 Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ
• Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy.
  Neurology. Genetics 2024 Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V
• Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy.
  bioRxiv : the preprint server for biology 2024 Leng K, Cadwell CR, Patrick Devine W, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V
• Rationale and protocol for a safety, tolerability and feasibility randomized, parallel group, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms.
  medRxiv : the preprint server for health sciences 2023 Stubbs BJ, Alvarez-Azanedo G, Peralta S, Roa-Diaz S, Gray W, Alexander L, Silverman-Martin W, Garcia T, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC
• Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors.
  The American journal of clinical nutrition 2023 Kyaw TS, Upadhyay V, Tolstykh I, Van Loon K, Laffan A, Stanfield D, Gempis D, Kenfield SA, Chan JM, Piawah S, Atreya CE, Ng K, Venook A, Kidder W, Turnbaugh PJ, Van Blarigan EL
• Mild SARS-CoV-2 infection results in long-lasting microbiota instability.
  mBio 2023 Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ
• PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease.
  bioRxiv : the preprint server for biology 2023 Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson M, DeRisi J, Sperling AI, Shum AK
• Mild SARS-CoV-2 infection results in long-lasting microbiota instability.
  bioRxiv : the preprint server for biology 2022 Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ
• nicX-ing bad habits with your microbial friends.
  Nature metabolism 2022 Upadhyay V, Turnbaugh PJ
• Human gut bacterial metabolism drives Th17 activation and colitis.
  Cell host & microbe 2021 Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ
• Reporting guidelines for human microbiome research: the STORMS checklist.
  Nature medicine 2021 Mirzayi C, Renson A, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques …
• The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health.
  eLife 2021 Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK, Turnbaugh PJ
• Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections.
  Med (New York, N.Y.) 2020 Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC
• Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.
  Cell 2020 Ang QY, Alexander M, Newman JC, Tian Y, Cai J, Upadhyay V, Turnbaugh JA, Verdin E, Hall KD, Leibel RL, Ravussin E, Rosenbaum M, Patterson AD, Turnbaugh PJ
• Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet.
  Cell host & microbe 2019 Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ
• Interprofessional primary care electronic intervention to reduce hypoglycaemic agent use in high-risk veterans with diabetes.
  BMJ open quality 2018 Upadhyay V, Walker E, Govea A, Rife T, Jimenez I, Dulay M, Beaman J
• Type 3 innate lymphoid cell-derived lymphotoxin prevents microbiota-dependent inflammation.
  Cellular & molecular immunology 2017 Zhang Y, Kim TJ, Wroblewska JA, Tesic V, Upadhyay V, Weichselbaum RR, Tumanov AV, Tang H, Guo X, Tang H, Fu YX
• Innate lymphoid cells facilitate NK cell development through a lymphotoxin-mediated stromal microenvironment.
  The Journal of experimental medicine 2014 Kim TJ, Upadhyay V, Kumar V, Lee KM, Fu YX
• Lymphotoxin organizes contributions to host defense and metabolic illness from innate lymphoid cells.
  Cytokine & growth factor reviews 2013 Upadhyay V, Fu YX
• Linking the microbiota and metabolic disease with lymphotoxin.
  International immunology 2013 Upadhyay V, Fu YX
• From infection to colonization: the role of microbiota in transplantation.
  American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2013 Upadhyay V, Fu YX, Bromberg JS
• Lymphotoxin signalling in immune homeostasis and the control of microorganisms.
  Nature reviews. Immunology 2013 Upadhyay V, Fu YX
• Lymphotoxin regulates commensal responses to enable diet-induced obesity.
  Nature immunology 2012 Upadhyay V, Poroyko V, Kim TJ, Devkota S, Fu S, Liu D, Tumanov AV, Koroleva EP, Deng L, Nagler C, Chang EB, Tang H, Fu YX