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. Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ. Simvastatin induces human gut bacterial cell surface genes. Mol Microbiol. 2023 Sep 15.  View on PubMed
  2. Piawah S, Kyaw TS, Trepka K, Stewart AL, Mora RV, Stanfield D, Levine K, Van Blarigan EL, Venook A, Turnbaugh PJ, Nguyen T, Atreya CE. Associations between the Gut Microbiota, Race, and Ethnicity of Patients with Colorectal Cancer: A Pilot and Feasibility Study. Cancers (Basel). 2023 Sep 13; 15(18).  View on PubMed
  3. Pieper LM, Spanogiannopoulos P, Volk RF, Miller CJ, Wright AT, Turnbaugh PJ. The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli. mBio. 2023 Aug 29; e0157323.  View on PubMed
  4. Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR. Microbiome single cell atlases generated with a commercial instrument. bioRxiv. 2023 Aug 10.  View on PubMed
  5. 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. Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors. Am J Clin Nutr. 2023 09; 118(3):518-529.  View on PubMed
  6. Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS. SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations. Elife. 2023 Jun 12; 12.  View on PubMed
  7. 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. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio. 2023 08 31; 14(4):e0088923.  View on PubMed
  8. Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. PLoS Biol. 2023 05; 21(5):e3002125.  View on PubMed
  9. Rock RR, Turnbaugh PJ. Forging the microbiome to help us live long and prosper. PLoS Biol. 2023 04; 21(4):e3002087.  View on PubMed
  10. Dong X, Guthrie BGH, Alexander M, Noecker C, Ramirez L, Glasser NR, Turnbaugh PJ, Balskus EP. Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators. Nat Commun. 2022 Dec 09; 13(1):7624.  View on PubMed
  11. 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. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv. 2022 Dec 08.  View on PubMed
  12. Upadhyay V, Turnbaugh PJ. nicX-ing bad habits with your microbial friends. Nat Metab. 2022 Nov; 4(11):1442-1443.  View on PubMed
  13. Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, Goga A, Pollard KS, Turnbaugh PJ. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat Microbiol. 2022 10; 7(10):1605-1620.  View on PubMed
  14. Kyaw TS, Turnbaugh PJ. Tiny Gatekeepers: Microbial Control of Host Drug Transporters. Clin Pharmacol Ther. 2022 09; 112(3):443-445.  View on PubMed
  15. Olson CA, Turnbaugh PJ. Designed secretion deters microbiome depletion. Nat Microbiol. 2022 06; 7(6):745-746.  View on PubMed
  16. Benjamin G. H. Guthrie, Peter J. Turnbaugh. Fluoropyrimidine Bioactivation and Metabolism by the Gut Microbiome. The FASEB Journal. 2022 May 13; 36(S1).  View on PubMed
  17. Peter J. Turnbaugh. The tiny pharmacists within: How the microbiome impacts the treatment of human disease. The FASEB Journal. 2022 May 13; 36(S1).  View on PubMed
  18. Iulia Rusu, Elvira Mennillo, Jared L. Bain, Zhongmei Li, Xiaofei Sun, Kimberly Ly, Yenny Y. Rosli, Mohammad Naser, Zunqiu Wang, Rommel Advincula, Philip Achacoso, Ling Shao, Bahram Razani, Ophir D. Klein, Alexander Marson, Jessie A. Turnbaugh, Peter J. Turnbaugh, Barbara Malynn, Averil Ma, Michael Kattah. Tu1517: MICROBIAL SIGNALS, MYD88, AND LYMPHOTOXIN DRIVE TNFINDEPENDENT DEATH OF A20 AND ABIN-1 DEFICIENT EPITHELIUM. Gastroenterology. 2022 May 1; 162(7):s-995.  View on PubMed
  19. Sbierski-Kind J, Grenkowitz S, Schlickeiser S, Sandforth A, Friedrich M, Kunkel D, Glauben R, Brachs S, Mai K, Thürmer A, Radonic A, Drechsel O, Turnbaugh PJ, Bisanz JE, Volk HD, Spranger J, von Schwartzenberg RJ. Effects of caloric restriction on the gut microbiome are linked with immune senescence. Microbiome. 2022 04 04; 10(1):57.  View on PubMed
  20. Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS. Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. Nature. 2022 03; 603(7903):907-912.  View on PubMed

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