Sign in to see private stats on your profile page — or add photo, interests, videos, mentoring, etc.

    Peter Turnbaugh, PhD

    TitleAssistant Professor
    SchoolUCSF School of Medicine
    DepartmentMicrobiology and Immunology
    Address513 Parnassus Ave
    San Francisco CA 94143
    Phone415-502-3237
    vCardDownload vCard

      Collapse Biography 
      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

      Collapse Overview 
      Collapse Overview
      You are not alone - humans are each home to trillions of microbes that have a widespread impact on our physiology and predisposition to disease. Our lab studies the role of these microbes in two major areas, pharmacology and nutrition, with a current focus on the role of gut microbial metabolism in influencing the predisposition to and treatment of heart disease, cancer, and autoimmune disease. Our main two experimental approaches are gnotobiotics (germ-free and colonized mice) and metagenomics (culture-independent methods for studying microbial communities). We collaborate closely with other members of the rich UCSF microbiome community, including Michael Fischbach, Susan Lynch, and Katie Pollard.

      Collapse Interests
      human gut microbiome, gnotobiotics, metagenomics, nutrition, pharmacology, pharmacogenetics, cancer

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

      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. 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
      2. Nayak RR, Turnbaugh PJ. Mirror, mirror on the wall: which microbiomes will help heal them all? BMC Med. 2016; 14(1):72. PMID: 27146150.
        View in: PubMed
      3. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat Rev Microbiol. 2016 May; 14(5):273-87. PMID: 26972811.
        View in: PubMed
      4. Jumpertz von Schwartzenberg R, Turnbaugh PJ. Siri, What Should I Eat? Cell. 2015 Nov 19; 163(5):1051-2. PMID: 26590412.
        View in: PubMed
      5. Maurice CF, Cl Knowles S, 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.
      6. 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; 6(3):e00381-15. PMID: 25991682; PMCID: PMC4442136.
      7. 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; 6(2). PMID: 25873372; PMCID: PMC4453576.
      8. 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 [Available on 08/01/16].
      9. 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; PMCID: PMC4373940.
      10. 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 [Available on 01/14/16].
      11. 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.
      12. Patterson AD, Turnbaugh PJ. Microbial determinants of biochemical individuality and their impact on toxicology and pharmacology. Cell Metab. 2014 Nov 4; 20(5):761-8. PMID: 25156450; PMCID: PMC4252706.
      13. 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.
      14. 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.
      15. 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.
      16. 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.
      17. 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.
      18. 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.
      19. Devkota S, Turnbaugh PJ. Cancer: An acidic link. Nature. 2013 Jul 4; 499(7456):37-8. PMID: 23803768.
        View in: PubMed
      20. 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.
      21. 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
      22. 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.
      23. 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.
      24. 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
      25. Liou AP, Turnbaugh PJ. Antibiotic exposure promotes fat gain. Cell Metab. 2012 Oct 3; 16(4):408-10. PMID: 23040064; PMCID: PMC3494989.
      26. Carmody RN, Turnbaugh PJ. Gut microbes make for fattier fish. Cell Host Microbe. 2012 Sep 13; 12(3):259-61. PMID: 22980321; PMCID: PMC3888188.
      27. 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
      28. Haiser HJ, Turnbaugh PJ. Developing a metagenomic view of xenobiotic metabolism. Pharmacol Res. 2013 Mar; 69(1):21-31. PMID: 22902524; PMCID: PMC3526672.
      29. Turnbaugh PJ. Microbiology: fat, bile and gut microbes. Nature. 2012 Jul 5; 487(7405):47-8. PMID: 22763552.
        View in: PubMed
      30. Haiser HJ, Turnbaugh PJ. Is it time for a metagenomic basis of therapeutics? Science. 2012 Jun 8; 336(6086):1253-5. PMID: 22674325.
        View in: PubMed
      31. 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.
      32. 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; PMCID: PMC3325791.
      33. 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
      34. Turnbaugh PJ, Stintzi A. Human health and disease in a microbial world. Front Microbiol. 2011; 2:190. PMID: 21954396; PMCID: PMC3174398.
      35. 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.
      36. 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
      37. 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.
      38. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011; 12:38. PMID: 21276213; PMCID: PMC3045300.
      39. 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.
      40. 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
      41. Peterson DA, Turnbaugh PJ. A microbe-dependent viral key to Crohn's box. Sci Transl Med. 2010 Aug 4; 2(43):43ps39. PMID: 20686177.
        View in: PubMed
      42. 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 1; 66(Pt 10):1261-4. PMID: 20944220; PMCID: PMC2954214.
      43. 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.
      44. 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.
      45. 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.
      46. 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.
      47. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol. 2009 Sep 1; 587(Pt 17):4153-8. PMID: 19491241; PMCID: PMC2754355.
      48. 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 7; 106(14):5859-64. PMID: 19321416; PMCID: PMC2660063.
      49. 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.
      50. Turnbaugh PJ, Gordon JI. An invitation to the marriage of metagenomics and metabolomics. Cell. 2008 Sep 5; 134(5):708-13. PMID: 18775300.
        View in: PubMed
      51. 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.
      52. 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.
      53. 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.
      54. 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.
      55. 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
      56. 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
      57. 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 2; 312(5778):1355-9. PMID: 16741115; PMCID: PMC3027896.
      58. 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.
      59. 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 2; 102(31):11070-5. PMID: 16033867; PMCID: PMC1176910.
      Peter's Networks
      Related Concepts
      Derived automatically from this person's publications.
      _
      Co-Authors
      People in Profiles who have published with this person.
      _
      Related Authors
      People who share related concepts with this person.
      _
      Back to TOP