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Peter Turnbaugh, PhD

TitleAssistant 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. Schneider C, O'Leary CE, von Moltke J, Liang HE, Ang QY, Turnbaugh P, 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
    2. Koppel N, Bisanz JE, Pandelia ME, Turnbaugh P, 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
    3. Spanogiannopoulos P, Turnbaugh P. Broad collateral damage of drugs against the gut microbiome. Nat Rev Gastroenterol Hepatol. 2018 May 11. PMID: 29752457.
      View in: PubMed
    4. Turnbaugh P. Making Millennial Medicine More Meta. mSystems. 2018 Mar-Apr; 3(2). PMID: 29556544.
      View in: PubMed
    5. Zhang L, Carmody RN, Kalariya HM, Duran RM, Moskal K, Poulev A, Kuhn P, Tveter KM, Turnbaugh P, 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
    6. Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh P, 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
    7. Mallory EK, Acharya A, Rensi SE, Turnbaugh P, 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
    8. Turnbaugh P. 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
    9. Yu AM, Ingelman-Sundberg M, Cherrington NJ, Aleksunes LM, Zanger UM, Xie W, Jeong H, Morgan ET, Turnbaugh P, 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
    10. Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh P, Knight R, Caporaso JG. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. mSystems. 2016 Sep-Oct; 1(5). PMID: 27822553.
      View in: PubMed
    11. Nayak RR, Turnbaugh P. Mirror, mirror on the wall: which microbiomes will help heal them all? BMC Med. 2016 May 04; 14:72. PMID: 27146150; PMCID: PMC4857263.
      View in: PubMed, PubMed Central
    12. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh P. 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
    13. Jumpertz von Schwartzenberg R, Turnbaugh P. Siri, What Should I Eat? Cell. 2015 Nov 19; 163(5):1051-1052. PMID: 26590412.
      View in: PubMed
    14. Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh P. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015 Nov; 9(11):2423-34. PMID: 26023870; PMCID: PMC4611506.
      View in: PubMed, PubMed Central
    15. David LA, Weil A, Ryan ET, Calderwood SB, Harris JB, Chowdhury F, Begum Y, Qadri F, LaRocque RC, Turnbaugh P. Gut microbial succession follows acute secretory diarrhea in humans. MBio. 2015 May 19; 6(3):e00381-15. PMID: 25991682; PMCID: PMC4442136.
      View in: PubMed, PubMed Central
    16. Martínez-del Campo A, Bodea S, Hamer HA, Marks JA, Haiser HJ, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    17. Roopchand DE, Carmody RN, Kuhn P, Moskal K, Rojas-Silva P, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    18. Perron GG, Whyte L, Turnbaugh P, 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
    19. Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh P. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe. 2015 Jan 14; 17(1):72-84. PMID: 25532804; PMCID: PMC4297240.
      View in: PubMed, PubMed Central
    20. Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    21. Patterson AD, Turnbaugh P. 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
    22. Carmody RN, Turnbaugh P. 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.
      View in: PubMed, PubMed Central
    23. Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh P, Knight R. The intestinal metabolome: an intersection between microbiota and host. Gastroenterology. 2014 May; 146(6):1470-6. PMID: 24631493; PMCID: PMC4102302.
      View in: PubMed, PubMed Central
    24. Haiser HJ, Seim KL, Balskus EP, Turnbaugh P. 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.
      View in: PubMed, PubMed Central
    25. 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 P. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23; 505(7484):559-63. PMID: 24336217; PMCID: PMC3957428.
      View in: PubMed, PubMed Central
    26. Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    27. Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh P. 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.
      View in: PubMed, PubMed Central
    28. Devkota S, Turnbaugh P. Cancer: An acidic link. Nature. 2013 Jul 04; 499(7456):37-8. PMID: 23803768.
      View in: PubMed
    29. Maurice CF, Turnbaugh P. 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.
      View in: PubMed, PubMed Central
    30. 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
    31. Liou AP, Paziuk M, Luevano JM, Machineni S, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    32. Maurice CF, Haiser HJ, Turnbaugh P. 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.
      View in: PubMed, PubMed Central
    33. Maurice CF, Turnbaugh P. Quantifying and identifying the active and damaged subsets of indigenous microbial communities. Methods Enzymol. 2013; 531:91-107. PMID: 24060117.
      View in: PubMed
    34. Liou AP, Turnbaugh P. Antibiotic exposure promotes fat gain. Cell Metab. 2012 Oct 03; 16(4):408-10. PMID: 23040064; PMCID: PMC3494989.
      View in: PubMed, PubMed Central
    35. Carmody RN, Turnbaugh P. Gut microbes make for fattier fish. Cell Host Microbe. 2012 Sep 13; 12(3):259-61. PMID: 22980321; PMCID: PMC3888188.
      View in: PubMed, PubMed Central
    36. Dutton RJ, Turnbaugh P. Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care. 2012 Sep; 15(5):448-54. PMID: 22878238.
      View in: PubMed
    37. Haiser HJ, Turnbaugh P. Developing a metagenomic view of xenobiotic metabolism. Pharmacol Res. 2013 Mar; 69(1):21-31. PMID: 22902524; PMCID: PMC3526672.
      View in: PubMed, PubMed Central
    38. Turnbaugh P. Microbiology: fat, bile and gut microbes. Nature. 2012 Jul 04; 487(7405):47-8. PMID: 22763552.
      View in: PubMed
    39. Haiser HJ, Turnbaugh P. Is it time for a metagenomic basis of therapeutics? Science. 2012 Jun 08; 336(6086):1253-5. PMID: 22674325.
      View in: PubMed
    40. Greenblum S, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    41. Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh P, 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
    42. Babayan SA, Allen JE, Bradley JE, Geuking MB, Graham AL, Grencis RK, Kaufman J, McCoy KD, Paterson S, Smith KG, Turnbaugh P, 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
    43. Turnbaugh P, Stintzi A. Human health and disease in a microbial world. Front Microbiol. 2011; 2:190. PMID: 21954396; PMCID: PMC3174398.
      View in: PubMed, PubMed Central
    44. Jumpertz R, Le DS, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    45. Swanson KS, Suchodolski JS, Turnbaugh P. Companion animals symposium: microbes and health. J Anim Sci. 2011 May; 89(5):1496-7. PMID: 21521817.
      View in: PubMed
    46. Patil KR, Haider P, Pope PB, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    47. Quince C, Lanzen A, Davenport RJ, Turnbaugh P. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011 Jan 28; 12:38. PMID: 21276213; PMCID: PMC3045300.
      View in: PubMed, PubMed Central
    48. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh P, Gordon JI, Knight R. The mind-body-microbial continuum. Dialogues Clin Neurosci. 2011; 13(1):55-62. PMID: 21485746; PMCID: PMC3139398.
      View in: PubMed, PubMed Central
    49. Gootenberg DB, Turnbaugh P. Companion animals symposium: humanized animal models of the microbiome. J Anim Sci. 2011 May; 89(5):1531-7. PMID: 20833767.
      View in: PubMed
    50. Peterson DA, Turnbaugh P. A microbe-dependent viral key to Crohn's box. Sci Transl Med. 2010 Aug 04; 2(43):43ps39. PMID: 20686177.
      View in: PubMed
    51. Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    52. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    53. 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 P, 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.
      View in: PubMed, PubMed Central
    54. Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    55. Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    56. Turnbaugh P, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol. 2009 Sep 01; 587(Pt 17):4153-8. PMID: 19491241; PMCID: PMC2754355.
      View in: PubMed, PubMed Central
    57. Mahowald MA, Rey FE, Seedorf H, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    58. Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    59. Turnbaugh P, Gordon JI. An invitation to the marriage of metagenomics and metabolomics. Cell. 2008 Sep 05; 134(5):708-13. PMID: 18775300.
      View in: PubMed
    60. Ley RE, Hamady M, Lozupone C, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    61. Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    62. Zaneveld J, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    63. Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    64. Ley RE, Turnbaugh P, 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
    65. Turnbaugh P, 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
    66. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh P, 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.
      View in: PubMed, PubMed Central
    67. 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.
      View in: PubMed, PubMed Central
    68. 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.
      View in: PubMed, PubMed Central
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