University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Peter Turnbaugh, PhD

Peter Turnbaugh, PhD

Associate Professor, Microbiology & Immunology, UCSF

Cancer Center Program Memberships

Experimental Therapeutics

Research Summary

The Turnbaugh lab is 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. We are currently focused on two major areas: pharmacology and nutrition. We use a variety of inter-disciplinary approaches ranging from the molecular (biochemistry, bacterial genetics, structural biology) to the organismal (gnotobiotic mice, conventional animals, and human cohorts) to the ecological (synthetic microbial communities and metagenomic sequencing).

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


Professional Experience

  • 2014-2018
    Assistant Professor, Microbiology & Immunology, University of California, San Francisco
  • 2018-present
    Associate Professor, Microbiology & Immunology, University of California, San Francisco
  • 2018-present
    Chan Zuckerberg Biohub Investigator, San Francisco, CA

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. Bisanz JE, Soto-Perez P, Noecker C, Aksenov AA, Lam KN, Kenney GE, Bess EN, Haiser HJ, Kyaw TS, Yu FB, Rekdal VM, Ha CWY, Devkota S, Balskus EP, Dorrestein PC, Allen-Vercoe E, Turnbaugh PJ. A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. Cell Host Microbe. 2020 Apr 22.
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  2. Basolo A, Hohenadel M, Ang QY, Piaggi P, Heinitz S, Walter M, Walter P, Parrington S, Trinidad DD, von Schwartzenberg RJ, Turnbaugh PJ, Krakoff J. Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans. Nat Med. 2020 Mar 23.
    View on PubMed
  3. Razani B, Whang MI, Kim FS, Nakamura MC, Sun X, Advincula R, Turnbaugh JA, Pendse M, Tanbun P, Achacoso P, Turnbaugh PJ, Malynn BA, Ma A. Non-catalytic ubiquitin binding by A20 prevents psoriatic arthritis-like disease and inflammation. Nat Immunol. 2020 Apr; 21(4):422-433.
    View on PubMed
  4. Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB. Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response. Nat Rev Rheumatol. 2020 Mar 10.
    View on PubMed
  5. Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP. A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols. Elife. 2020 Feb 18; 9.
    View on PubMed
  6. Parker MFL, Luu JM, Schulte B, Huynh TL, Stewart MN, Sriram R, Yu MA, Jivan S, Turnbaugh PJ, Flavell RR, Rosenberg OS, Ohliger MA, Wilson DM. Sensing Living Bacteria in Vivo Using d-Alanine-Derived 11C Radiotracers. ACS Cent Sci. 2020 Feb 26; 6(2):155-165.
    View on PubMed
  7. Turnbaugh PJ. Diet should be a tool for researchers, not a treatment. Nature. 2020 01; 577(7792):S23.
    View on PubMed
  8. Bess EN, Bisanz JE, Yarza F, Bustion A, Rich BE, Li X, Kitamura S, Waligurski E, Ang QY, Alba DL, Spanogiannopoulos P, Nayfach S, Koliwad SK, Wolan DW, Franke AA, Turnbaugh PJ. Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria. Nat Microbiol. 2020 01; 5(1):56-66.
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  9. Reese AT, Kartzinel TR, Petrone BL, Turnbaugh PJ, Pringle RM, David LA. Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept. mSystems. 2019 Oct 08; 4(5).
    View on PubMed
  10. Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ. Cooking shapes the structure and function of the gut microbiome. Nat Microbiol. 2019 12; 4(12):2052-2063.
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  11. Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. Cell Host Microbe. 2019 Sep 11; 26(3):325-335.e5.
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  12. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 Sep; 37(9):1091.
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  13. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857.
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  14. Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ. Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet. Cell Host Microbe. 2019 08 14; 26(2):265-272.e4.
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  15. Lam KN, Alexander M, Turnbaugh PJ. Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes. Cell Host Microbe. 2019 Jul 10; 26(1):22-34.
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  16. Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP. Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Science. 2019 06 14; 364(6445).
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  17. Chagwedera DN, Ang QY, Bisanz JE, Leong YA, Ganeshan K, Cai J, Patterson AD, Turnbaugh PJ, Chawla A. Nutrient Sensing in CD11c Cells Alters the Gut Microbiota to Regulate Food Intake and Body Mass. Cell Metab. 2019 08 06; 30(2):364-373.e7.
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  18. Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol. 2019 04; 4(4):693-700.
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  19. Peter Turnbaugh. Predicting and preventing the inactivation of drugs by human gut bacteria. Drug Metabolism and Pharmacokinetics. 2019 Jan 1; 34(1):s10.
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  20. Bisanz JE, Spanogiannopoulos P, Pieper LM, Bustion AE, Turnbaugh PJ. How to Determine the Role of the Microbiome in Drug Disposition. Drug Metab Dispos. 2018 11; 46(11):1588-1595.
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