Research Summary

I lead an interdisciplinary group of microbiome researchers committed to understanding host-associated microbes, reducing these complex microbial ecologies to molecular mechanism, and applying these lessons to improve the practice of medicine. Our three major topics of interest right now are pharmacology, nutrition, and phage biology. While we love sequencing and gnotobiotic mice, our work is question-driven not limited to a specific approach. Prior studies have ranged from the molecular (e.g., biochemistry, bacterial genetics, structural biology) to the organismal (e.g., gnotobiotic mice, conventional animals, and clinical trials) to the ecological (e.g., synthetic microbial communities and metagenomic sequencing). We embrace high-risk, high-reward projects and thrive on collaboration.

Research Funding

  • March 1, 2016 - July 31, 2025 - Predicting and preventing drug metabolism by the human gut microbiome , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01HL122593
  • July 1, 2020 - March 31, 2025 - Host-microbiome interactions shape the metabolic effects of ketogenic diets , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK114034
  • September 1, 2019 - August 31, 2024 - Employing the gut microbiome to accelerate effective initiation of rheumatoid arthritis therapy , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AR074500
  • August 1, 2020 - July 31, 2024 - Establishing the feasibility of editing the human gut microbiome , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AT011117
  • June 21, 2018 - May 31, 2021 - (PQ10) Harnessing the human gut microbiome to predict chemotherapy outcomes , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R21CA227232

Education

Whitman College, B.A., 05/2003, Biochemistry, Biophysics, and Molecular Biology
Washington University in Saint Louis, Ph.D., 05/2009, Molecular Genetics and Genomics
Harvard University, Postdoctoral, 08/2014, Systems Biology

Honors & Awards

  • 2007
    Kauffman Fellowship for Life Sciences Entrepreneurship, Washington University in Saint Louis
  • 2007
    Bridging GAPS Interschool Award (BioEntrepreneurship Core), Washington University in Saint Louis
  • 2009
    David M. Kipnis Award in Biomedical Sciences, Washington University in Saint Louis
  • 2010
    Philip Needleman Pharmacology Prize, Washington University in Saint Louis
  • 2015
    Young Investigator Grant for Probiotics Research, Global Probiotics Council
  • 2016
    Damon Runyon-Rachleff Innovation Award, Damon Runyon Cancer Research Foundation
  • 2016
    UCSF Program for Breakthrough Biomedical Research, UCSF
  • 2016
    UCSF Breakthrough Program for Rheumatoid Arthritis-related Research, UCSF
  • 2016
    UCSF School of Medicine Faculty Travel Award, UCSF
  • 2016
    GENEWIZ Week Lab Startup Award, Genewiz
  • 2016
    Searle Scholar, Kinship Foundation
  • 2017
    UCSF Facilities Services First Impressions Contest, UCSF
  • 2018
    CZ Biohub Investigator, Microbiome Initiative, Chan Zuckerberg Biohub
  • 2018
    ASM Young Investigator Award
  • 2018
    Agilent Early Career Professor Award Finalist
  • 2018
    Burroughs Wellcome Fund Investigators in the Pathogenesis of Disease Award

Selected Publications

  1. Hillege LE, Trepka KR, Guthrie BGH, Fu X, Aarnoutse R, Paymar MR, Olson C, Zhang C, Ortega E, Ramirez L, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Baars A, Vestjens JHMJ, Penders J, Deutschbauer A, Atreya CE, Kidder WA, Smidt ML, Ziemons J, Turnbaugh PJ. Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity. mBio. 2025 May 20; e0093025.  View on PubMed
  2. V. Upadhyay, G. Kaur, E.F. Ortega, K. Trepka, R.R. Rock, L. Ramirez Hernandez, W.C. Cheshire, N. Alipanah-Lechner, C.S. Calfee, M.A. Matthay, S. Blume, I. Jain, P.J. Turnbaugh. Gut Bacterial Lactic Acid Stimulates Lung Epithelial Mitochondria and Exacerbates Acute Lung Injury. American Journal of Respiratory and Critical Care Medicine. 2025 May 1; 211(Abstracts):a5186-a5186.  View on PubMed
  3. 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, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity. Sci Transl Med. 2025 Apr 16; 17(794):eadq8870.  View on PubMed
  4. Upadhyay V, Ortega EF, Ramirez Hernandez LA, Alexander M, Kaur G, Trepka K, Rock RR, Shima RT, Cheshire WC, Alipanah-Lechner N, Calfee CS, Matthay MA, Lee JV, Goga A, Jain IH, Turnbaugh PJ. Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury. bioRxiv. 2025 Mar 25.  View on PubMed
  5. Trepka KR, Olson CA, Upadhyay V, Zhang C, Turnbaugh PJ. Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response. Annu Rev Pharmacol Toxicol. 2025 Jan; 65(1):355-373.  View on PubMed
  6. Babdor J, Patel RK, Davidson B, Noecker C, Rahim M, Bisanz JE, Tenvooren I, Marquez D, Calvo M, Johri V, McCarthy E, Shaheed A, Ekstrand C, Weakley AM, Yu FB, Fiehn O, Turnbaugh PJ, Combes AJ, Fragiadakis GK, Spitzer MH. Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states. bioRxiv. 2024 Dec 03.  View on PubMed
  7. Rendina M, Turnbaugh PJ, Bradley PH. Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome. bioRxiv. 2024 Nov 08.  View on PubMed
  8. 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. A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. Cell Rep. 2024 11 26; 43(11):114891.  View on PubMed
  9. Bae M, Le C, Mehta RS, Dong X, Pieper LM, Ramirez L, Alexander M, Kiamehr S, Turnbaugh PJ, Huttenhower C, Chan AT, Balskus EP. Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme. Cell Host Microbe. 2024 Nov 13; 32(11):1887-1896.e8.  View on PubMed
  10. 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, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. bioRxiv. 2024 Oct 15.  View on PubMed
  11. Hillege LE, Trepka KR, Ziemons J, Aarnoutse R, Guthrie BGH, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Baars A, Vestjens JHMJ, Penders J, Deutschbauer A, Atreya CE, Kidder WA, Turnbaugh PJ, Smidt ML. Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients. medRxiv. 2024 Oct 15.  View on PubMed
  12. 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. 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; 19(9):e0307951.  View on PubMed
  13. Tian Y, Rimal B, Bisanz JE, Gui W, Wolfe TM, Koo I, Murray IA, Nettleford SK, Yokoyama S, Dong F, Koshkin S, Prabhu KS, Turnbaugh PJ, Walk ST, Perdew GH, Patterson AD. Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice. Environ Health Perspect. 2024 Aug; 132(8):87005.  View on PubMed
  14. Carmody RN, Varady K, Turnbaugh PJ. Digesting the complex metabolic effects of diet on the host and microbiome. Cell. 2024 Jul 25; 187(15):3857-3876.  View on PubMed
  15. Noecker C, Turnbaugh PJ. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab. 2024 Jul; 6(7):1225-1236.  View on PubMed
  16. Jingcheng Zhao, Arvid Sandforth, Shuchang Tian, Peter J Turnbaugh, Reiner Jumpertz Von Schwartzenberg, Jordan E Bisanz. Short-Term Caloric Restriction Alters the Microbiome Modulating Resistance to Clostridioides difficile Infection. Current Developments in Nutrition. 2024 Jul 1; 8:103447.  View on PubMed
  17. Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Brito IL, Booth SL, Hernandez CJ. Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice. JBMR Plus. 2024 Aug; 8(8):ziae082.  View on PubMed
  18. Kyaw TS, Zhang C, Sandy M, Trepka K, Zhang S, Ramirez Hernandez LA, Ramirez L, Goh JJN, Yu K, Dimassa V, Bess EN, Brockert JG, Dumlao DS, Bisanz JE, Turnbaugh PJ. Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors. iScience. 2024 Jun 21; 27(6):110122.  View on PubMed
  19. McCurry MD, D'Agostino GD, Walsh JT, Bisanz JE, Zalosnik I, Dong X, Morris DJ, Korzenik JR, Edlow AG, Balskus EP, Turnbaugh PJ, Huh JR, Devlin AS. Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas. Cell. 2024 Jun 06; 187(12):2952-2968.e13.  View on PubMed
  20. 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. A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. bioRxiv. 2024 May 13.  View on PubMed

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