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).

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. 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
  2. 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
  3. 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
  4. 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
  5. Alexander M, Turnbaugh PJ Stressed-out gut bacteria are pterin up gut inflammation.  View on PubMed
  6. Alexander M, Turnbaugh PJ Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions.  View on PubMed
  7. 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
  8. 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
  9. Atreya CE, Turnbaugh PJ Probing the tumor micro(b)environment.  View on PubMed
  10. 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
  11. 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
  12. 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
  13. 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
  14. Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response.  View on PubMed
  15. 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
  16. 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
  17. Turnbaugh PJ Diet should be a tool for researchers, not a treatment.  View on PubMed
  18. 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
  19. 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.  View on PubMed
  20. 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.  View on PubMed

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