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

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. Rock RR, Turnbaugh PJ. Forging the microbiome to help us live long and prosper. PLoS Biol. 2023 Apr; 21(4):e3002087.  View on PubMed
  2. 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
  3. 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
  4. Upadhyay V, Turnbaugh PJ. nicX-ing bad habits with your microbial friends. Nat Metab. 2022 Nov; 4(11):1442-1443.  View on PubMed
  5. 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
  6. Kyaw TS, Turnbaugh PJ. Tiny Gatekeepers: Microbial Control of Host Drug Transporters. Clin Pharmacol Ther. 2022 09; 112(3):443-445.  View on PubMed
  7. Olson CA, Turnbaugh PJ. Designed secretion deters microbiome depletion. Nat Microbiol. 2022 06; 7(6):745-746.  View on PubMed
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. Tolonen AC, Beauchemin N, Bayne C, Li L, Tan J, Lee J, Meehan BM, Meisner J, Millet Y, LeBlanc G, Kottler R, Rapp E, Murphy C, Turnbaugh PJ, von Maltzahn G, Liu CM, van Hylckama Vlieg JET. Synthetic glycans control gut microbiome structure and mitigate colitis in mice. Nat Commun. 2022 03 10; 13(1):1244.  View on PubMed
  14. Rusu I, Mennillo E, Bain JL, Li Z, Sun X, Ly KM, Rosli YY, Naser M, Wang Z, Advincula R, Achacoso P, Shao L, Razani B, Klein OD, Marson A, Turnbaugh JA, Turnbaugh PJ, Malynn BA, Ma A, Kattah MG. Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage. J Clin Invest. 2022 03 01; 132(5).  View on PubMed
  15. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe. 2022 01 12; 30(1):17-30.e9.  View on PubMed
  16. 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 FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med. 2021 11; 27(11):1885-1892.  View on PubMed
  17. Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, Nayak RR, Weakley AM, Yu FB, Turnbaugh PJ. Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome. Cell Rep. 2021 11 02; 37(5):109930.  View on PubMed
  18. Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK, Turnbaugh PJ. The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health. Elife. 2021 10 07; 10.  View on PubMed
  19. von Schwartzenberg RJ, Bisanz JE, Lyalina S, Spanogiannopoulos P, Ang QY, Cai J, Dickmann S, Friedrich M, Liu SY, Collins SL, Ingebrigtsen D, Miller S, Turnbaugh JA, Patterson AD, Pollard KS, Mai K, Spranger J, Turnbaugh PJ. Caloric restriction disrupts the microbiota and colonization resistance. Nature. 2021 07; 595(7866):272-277.  View on PubMed
  20. Artacho A, Isaac S, Nayak R, Flor-Duro A, Alexander M, Koo I, Manasson J, Smith PB, Rosenthal P, Homsi Y, Gulko P, Pons J, Puchades-Carrasco L, Izmirly P, Patterson A, Abramson SB, Pineda-Lucena A, Turnbaugh PJ, Ubeda C, Scher JU. The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis. Arthritis Rheumatol. 2021 06; 73(6):931-942.  View on PubMed

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