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Peter Turnbaugh, PhD

TitleAssociate Professor
InstitutionUniversity of California San Francisco
DepartmentMicrobiology and Immunology
Address513 Parnassus Ave
San Francisco CA 94143
Phone415-502-3237
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    Collapse Biography 
    Collapse Education and Training
    Whitman College, Walla Walla, WAB.A.05/2003Biochemistry, Biophysics, and Molecular Biology
    Washington University in Saint Louis, St. Louis, MOPh.D.05/2009Molecular Genetics and Genomics
    Collapse Awards and Honors
    1999National Merit Scholar
    2006  - 2009NSF Graduate Fellowship
    2009David Kipnis Award in Biomedical Sciences
    2010Philip Needleman Pharmacology Prize
    2015Young Investigator Grant for Probiotics Research
    2016Damon Runyon-Rachleff Cancer Innovator
    2016Searle Scholar
    2017CZ Biohub Investigator
    2018ASM Young Investigator Award
    Burroughs Wellcome Fund2018Investigators in the Pathogenesis of Infectious Disease

    Collapse Overview 
    Collapse Overview
    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).


    Collapse Research 
    Collapse Research Activities and Funding
    (PQ10) Harnessing the human gut microbiome to predict chemotherapy outcomes
    NIH/NCI R21CA227232Jun 21, 2018 - May 31, 2020
    Role: Principal Investigator
    Predicting and preventing drug metabolism by the human gut microbiome
    NIH/NHLBI R01HL122593Mar 1, 2016 - Feb 28, 2021
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Global Health
    Collapse In The News
    Collapse Featured Videos

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. 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 Aug 15. PMID: 30111623.
      View in: PubMed
    2. Balskus EP, Turnbaugh PJ, Wolan DW. Announcement of 2019 Keystone Symposia Conference: "Microbiome: Chemical Mechanisms and Biological Consequences". mSystems. 2018 Jul-Aug; 3(4). PMID: 30057942.
      View in: PubMed
    3. Schneider C, O'Leary CE, von Moltke J, Liang HE, Ang QY, Turnbaugh PJ, Radhakrishnan S, Pellizzon M, Ma A, Locksley RM. A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling. Cell. 2018 May 23. PMID: 29887373.
      View in: PubMed
    4. Koppel N, Bisanz JE, Pandelia ME, Turnbaugh PJ, Balskus EP. Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins. Elife. 2018 May 15; 7. PMID: 29761785.
      View in: PubMed
    5. Spanogiannopoulos P, Turnbaugh PJ. Broad collateral damage of drugs against the gut microbiome. Nat Rev Gastroenterol Hepatol. 2018 May 11. PMID: 29752457.
      View in: PubMed
    6. Turnbaugh PJ. Making Millennial Medicine More Meta. mSystems. 2018 Mar-Apr; 3(2). PMID: 29556544.
      View in: PubMed
    7. Zhang L, Carmody RN, Kalariya HM, Duran RM, Moskal K, Poulev A, Kuhn P, Tveter KM, Turnbaugh PJ, Raskin I, Roopchand DE. Grape proanthocyanidin-induced intestinal bloom of Akkermansia muciniphila is dependent on its baseline abundance and precedes activation of host genes related to metabolic health. J Nutr Biochem. 2018 Feb 15; 56:142-151. PMID: 29571008.
      View in: PubMed
    8. Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, Shental N. Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. Microbiome. 2018 Jan 26; 6(1):17. PMID: 29373999.
      View in: PubMed
    9. Mallory EK, Acharya A, Rensi SE, Turnbaugh PJ, Bright RA, Altman RB. Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. Pac Symp Biocomput. 2018; 23:56-67. PMID: 29218869.
      View in: PubMed
    10. Turnbaugh PJ. Microbes and Diet-Induced Obesity: Fast, Cheap, and Out of Control. Cell Host Microbe. 2017 Mar 08; 21(3):278-281. PMID: 28279330.
      View in: PubMed
    11. Yu AM, Ingelman-Sundberg M, Cherrington NJ, Aleksunes LM, Zanger UM, Xie W, Jeong H, Morgan ET, Turnbaugh PJ, Klaassen CD, Bhatt AP, Redinbo MR, Hao P, Waxman DJ, Wang L, Zhong XB. Regulation of drug metabolism and toxicity by multiple factors of genetics, epigenetics, lncRNAs, gut microbiota, and diseases: a meeting report of the 21st International Symposium on Microsomes and Drug Oxidations (MDO). Acta Pharm Sin B. 2017 03; 7(2):241-248. PMID: 28388695.
      View in: PubMed
    12. Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. mSystems. 2016 Sep-Oct; 1(5). PMID: 27822553.
      View in: PubMed
    13. Nayak RR, Turnbaugh PJ. Mirror, mirror on the wall: which microbiomes will help heal them all? BMC Med. 2016 May 04; 14:72. PMID: 27146150; PMCID: PMC4857263.
    14. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Microbiol. 2016 Apr; 14(5):273-87. PMID: 26972811.
      View in: PubMed
    15. Jumpertz von Schwartzenberg R, Turnbaugh PJ. Siri, What Should I Eat? Cell. 2015 Nov 19; 163(5):1051-1052. PMID: 26590412.
      View in: PubMed
    16. Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015 Nov; 9(11):2423-34. PMID: 26023870; PMCID: PMC4611506.
    17. David LA, Weil A, Ryan ET, Calderwood SB, Harris JB, Chowdhury F, Begum Y, Qadri F, LaRocque RC, Turnbaugh PJ. Gut microbial succession follows acute secretory diarrhea in humans. MBio. 2015 May 19; 6(3):e00381-15. PMID: 25991682; PMCID: PMC4442136.
    18. Martínez-del Campo A, Bodea S, Hamer HA, Marks JA, Haiser HJ, Turnbaugh PJ, Balskus EP. Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria. MBio. 2015 Apr 14; 6(2). PMID: 25873372; PMCID: PMC4453576.
    19. Roopchand DE, Carmody RN, Kuhn P, Moskal K, Rojas-Silva P, Turnbaugh PJ, Raskin I. Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome. Diabetes. 2015 Aug; 64(8):2847-58. PMID: 25845659; PMCID: PMC4512228.
    20. Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, Desai MM. Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS One. 2015; 10(3):e0069533. PMID: 25807523.
      View in: PubMed
    21. Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015 Jan 14; 17(1):72-84. PMID: 25532804; PMCID: PMC4297240.
    22. Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh PJ, Chervonsky AV. Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature. 2014 Oct 30; 514(7524):638-41. PMID: 25274297; PMCID: PMC4214913.
    23. Patterson AD, Turnbaugh PJ. Microbial determinants of biochemical individuality and their impact on toxicology and pharmacology. Cell Metab. 2014 Nov 04; 20(5):761-768. PMID: 25156450.
      View in: PubMed
    24. Carmody RN, Turnbaugh PJ. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J Clin Invest. 2014 Oct; 124(10):4173-81. PMID: 25105361; PMCID: PMC4191041.
    25. Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology. 2014 May; 146(6):1470-6. PMID: 24631493; PMCID: PMC4102302.
    26. Haiser HJ, Seim KL, Balskus EP, Turnbaugh PJ. Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics. Gut Microbes. 2014 Mar-Apr; 5(2):233-8. PMID: 24637603; PMCID: PMC4063850.
    27. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23; 505(7484):559-63. PMID: 24336217; PMCID: PMC3957428.
    28. Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N. High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions. Nucleic Acids Res. 2013 Dec; 41(22):e205. PMID: 24214960; PMCID: PMC3905898.
    29. Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science. 2013 Jul 19; 341(6143):295-8. PMID: 23869020; PMCID: PMC3736355.
    30. Devkota S, Turnbaugh PJ. Cancer: An acidic link. Nature. 2013 Jul 04; 499(7456):37-8. PMID: 23803768.
      View in: PubMed
    31. Maurice CF, Turnbaugh PJ. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. FEMS Microbiol Rev. 2013 Sep; 37(5):830-48. PMID: 23550823; PMCID: PMC3729610.
    32. Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P. Translating the human microbiome. Nat Biotechnol. 2013 Apr; 31(4):304-8. PMID: 23563424.
      View in: PubMed
    33. Liou AP, Paziuk M, Luevano JM, Machineni S, Turnbaugh PJ, Kaplan LM. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med. 2013 Mar 27; 5(178):178ra41. PMID: 23536013; PMCID: PMC3652229.
    34. Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell. 2013 Jan 17; 152(1-2):39-50. PMID: 23332745; PMCID: PMC3552296.
    35. Maurice CF, Turnbaugh PJ. Quantifying and identifying the active and damaged subsets of indigenous microbial communities. Methods Enzymol. 2013; 531:91-107. PMID: 24060117.
      View in: PubMed
    36. Liou AP, Turnbaugh PJ. Antibiotic exposure promotes fat gain. Cell Metab. 2012 Oct 03; 16(4):408-10. PMID: 23040064; PMCID: PMC3494989.
    37. Carmody RN, Turnbaugh PJ. Gut microbes make for fattier fish. Cell Host Microbe. 2012 Sep 13; 12(3):259-61. PMID: 22980321; PMCID: PMC3888188.
    38. Dutton RJ, Turnbaugh PJ. Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care. 2012 Sep; 15(5):448-54. PMID: 22878238.
      View in: PubMed
    39. Haiser HJ, Turnbaugh PJ. Developing a metagenomic view of xenobiotic metabolism. Pharmacol Res. 2013 Mar; 69(1):21-31. PMID: 22902524; PMCID: PMC3526672.
    40. Turnbaugh PJ. Microbiology: fat, bile and gut microbes. Nature. 2012 Jul 04; 487(7405):47-8. PMID: 22763552.
      View in: PubMed
    41. Haiser HJ, Turnbaugh PJ. Is it time for a metagenomic basis of therapeutics? Science. 2012 Jun 08; 336(6086):1253-5. PMID: 22674325.
      View in: PubMed
    42. Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci U S A. 2012 Jan 10; 109(2):594-9. PMID: 22184244; PMCID: PMC3258644.
    43. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC. Detecting novel associations in large data sets. Science. 2011 Dec 16; 334(6062):1518-24. PMID: 22174245.
      View in: PubMed
    44. Babayan SA, Allen JE, Bradley JE, Geuking MB, Graham AL, Grencis RK, Kaufman J, McCoy KD, Paterson S, Smith KG, Turnbaugh PJ, Viney ME, Maizels RM, Pedersen AB. Wild immunology: converging on the real world. Ann N Y Acad Sci. 2011 Oct; 1236:17-29. PMID: 22032399.
      View in: PubMed
    45. Turnbaugh PJ, Stintzi A. Human health and disease in a microbial world. Front Microbiol. 2011; 2:190. PMID: 21954396; PMCID: PMC3174398.
    46. Jumpertz R, Le DS, Turnbaugh PJ, Trinidad C, Bogardus C, Gordon JI, Krakoff J. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr. 2011 Jul; 94(1):58-65. PMID: 21543530; PMCID: PMC3127503.
    47. Swanson KS, Suchodolski JS, Turnbaugh PJ. Companion animals symposium: microbes and health. J Anim Sci. 2011 May; 89(5):1496-7. PMID: 21521817.
      View in: PubMed
    48. Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC. Taxonomic metagenome sequence assignment with structured output models. Nat Methods. 2011 Mar; 8(3):191-2. PMID: 21358620; PMCID: PMC3131843.
    49. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011 Jan 28; 12:38. PMID: 21276213; PMCID: PMC3045300.
    50. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R. The mind-body-microbial continuum. Dialogues Clin Neurosci. 2011; 13(1):55-62. PMID: 21485746; PMCID: PMC3139398.
    51. Gootenberg DB, Turnbaugh PJ. Companion animals symposium: humanized animal models of the microbiome. J Anim Sci. 2011 May; 89(5):1531-7. PMID: 20833767.
      View in: PubMed
    52. Peterson DA, Turnbaugh PJ. A microbe-dependent viral key to Crohn's box. Sci Transl Med. 2010 Aug 04; 2(43):43ps39. PMID: 20686177.
      View in: PubMed
    53. Turnbaugh PJ, Henrissat B, Gordon JI. Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 01; 66(Pt 10):1261-4. PMID: 20944220; PMCID: PMC2954214.
    54. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011 Mar 15; 108 Suppl 1:4516-22. PMID: 20534432; PMCID: PMC3063599.
    55. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May; 7(5):335-6. PMID: 20383131; PMCID: PMC3156573.
    56. Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A. 2010 Apr 20; 107(16):7503-8. PMID: 20363958; PMCID: PMC2867707.
    57. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009 Nov 11; 1(6):6ra14. PMID: 20368178; PMCID: PMC2894525.
    58. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol. 2009 Sep 01; 587(Pt 17):4153-8. PMID: 19491241; PMCID: PMC2754355.
    59. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A. 2009 Apr 07; 106(14):5859-64. PMID: 19321416; PMCID: PMC2660063.
    60. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature. 2009 Jan 22; 457(7228):480-4. PMID: 19043404; PMCID: PMC2677729.
    61. Turnbaugh PJ, Gordon JI. An invitation to the marriage of metagenomics and metabolomics. Cell. 2008 Sep 05; 134(5):708-13. PMID: 18775300.
      View in: PubMed
    62. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. Evolution of mammals and their gut microbes. Science. 2008 Jun 20; 320(5883):1647-51. PMID: 18497261; PMCID: PMC2649005.
    63. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008 Apr 17; 3(4):213-23. PMID: 18407065; PMCID: PMC3687783.
    64. Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, Knight R. Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol. 2008 Feb; 12(1):109-14. PMID: 18280814; PMCID: PMC2348432.
    65. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007 Oct 18; 449(7164):804-10. PMID: 17943116; PMCID: PMC3709439.
    66. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006 Dec 21; 444(7122):1022-3. PMID: 17183309.
      View in: PubMed
    67. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006 Dec 21; 444(7122):1027-31. PMID: 17183312.
      View in: PubMed
    68. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science. 2006 Jun 02; 312(5778):1355-9. PMID: 16741115; PMCID: PMC3027896.
    69. Gertz J, Riles L, Turnbaugh P, Ho SW, Cohen BA. Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics. Genome Res. 2005 Aug; 15(8):1145-52. PMID: 16077013; PMCID: PMC1182227.
    70. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A. 2005 Aug 02; 102(31):11070-5. PMID: 16033867; PMCID: PMC1176910.