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

  • July 1, 2020 - March 31, 2025 - Host-microbiome interactions shape the metabolic effects of ketogenic diets, Principal Investigator. Sponsor: NIH/NIDDK, 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/NIAMS, Sponsor Award ID: R01AR074500
  • August 1, 2020 - July 31, 2024 - Establishing the feasibility of editing the human gut microbiome, Principal Investigator. Sponsor: NIH/NCCIH, Sponsor Award ID: R01AT011117
  • March 1, 2016 - February 28, 2021 - Predicting and preventing drug metabolism by the human gut microbiome, Principal Investigator. Sponsor: NIH/NHLBI, Sponsor Award ID: R01HL122593

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. Buffington SA, Dooling SW, Sgritta M, Noecker C, Murillo OD, Felice DF, Turnbaugh PJ, Costa-Mattioli M Dissecting the contribution of host genetics and the microbiome in complex behaviors.  View on PubMed
  2. Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments.  View on PubMed
  3. Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.  View on PubMed
  4. 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 Pre-treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis.  View on PubMed
  5. Man K, Bowman C, Braverman KN, Escalante V, Tian Y, Bisanz JE, Ganeshan K, Wang B, Patterson A, Bayrer JR, Turnbaugh PJ, Chawla A A thermogenic fat-epithelium cell axis regulates intestinal disease tolerance.  View on PubMed
  6. Pröbstel AK, Zhou X, Baumann R, Wischnewski S, Kutza M, Rojas OL, Sellrie K, Bischof A, Kim K, Ramesh A, Dandekar R, Greenfield AL, Schubert RD, Bisanz JE, Vistnes S, Khaleghi K, Landefeld J, Kirkish G, Liesche-Starnecker F, Ramaglia V, Singh S, Tran EB, Barba P, Zorn K, Oechtering J, Forsberg K, Shiow LR, Henry RG, Graves J, Cree BAC, Hauser SL, Kuhle J, Gelfand JM, Andersen PM, Schlegel J, Turnbaugh PJ, Seeberger PH, Gommerman JL, Wilson MR, Schirmer L, Baranzini SE Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis.  View on PubMed
  7. Alexander M, Turnbaugh PJ Stressed-out gut bacteria are pterin up gut inflammation.  View on PubMed
  8. Alexander M, Turnbaugh PJ Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions.  View on PubMed
  9. Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections.  View on PubMed
  10. Zou L, Spanogiannopoulos P, Pieper LM, Chien HC, Cai W, Khuri N, Pottel J, Vora B, Ni Z, Tsakalozou E, Zhang W, Shoichet BK, Giacomini KM, Turnbaugh PJ Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives.  View on PubMed
  11. Atreya CE, Turnbaugh PJ Probing the tumor micro(b)environment.  View on PubMed
  12. 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 Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.  View on PubMed
  13. 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.  View on PubMed
  14. 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.  View on PubMed
  15. 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.  View on PubMed
  16. Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response.  View on PubMed
  17. 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.  View on PubMed
  18. 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.  View on PubMed
  19. Turnbaugh PJ Diet should be a tool for researchers, not a treatment.  View on PubMed
  20. 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.  View on PubMed

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