Papers

2020

Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives.
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.
Proc Natl Acad Sci U S A. 2020 Jun 22:201920483. doi: 10.1073/pnas.1920483117. Online ahead of print.

Probing the tumor micro(b)environment.
Atreya CE, Turnbaugh PJ.
Science. 2020 May 29;368(6494):938-939. doi: 10.1126/science.abc1464.PMID: 32467376 

Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.
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. 
Cell. 2020 May 14:S0092-8674(20)30490-6. doi: 10.1016/j.cell.2020.04.027. Online ahead of print.PMID: 32437658

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.
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. 
Cell Host Microbe. 2020 Apr 22:S1931-3128(20)30233-X. doi: 10.1016/j.chom.2020.04.006. Online ahead of print.PMID: 32348781

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans.
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.
Nat Med. 2020 Mar 23. doi: 10.1038/s41591-020-0801-z. Online ahead of print.

Non-catalytic ubiquitin binding by A20 prevents psoriatic arthritis-like disease and inflammation.
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.
Nat Immunol. 2020 Apr;21(4):422-433. doi: 10.1038/s41590-020-0634-4. Epub 2020 Mar 16.

Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response.
Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB.
Nat Rev Rheumatol. 2020 Mar 10. doi: 10.1038/s41584-020-0395-3. [Epub ahead of print] Review.

Sensing Living Bacteria in Vivo Using d-Alanine-Derived 11C Radiotracers.
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.
ACS Cent Sci. 2020 Feb 26;6(2):155-165. doi: 10.1021/acscentsci.9b00743. Epub 2020 Feb 4.

A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols.
Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP.
Elife. 2020 Feb 18;9. pii: e50845. doi: 10.7554/eLife.50845.

Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.
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.
Nat Microbiol. 2020 Jan;5(1):56-66. doi: 10.1038/s41564-019-0596-1. Epub 2019 Nov 4.

Diet should be a tool for researchers, not a treatment.
Turnbaugh PJ.
Nature. 2020 Jan;577(7792):S23. doi: 10.1038/d41586-020-00202-5. No abstract available.

2019

Cooking shapes the structure and function of the gut microbiome 
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.
Nat Microbiol. 2019 Dec;4(12):2052-2063. doi: 10.1038/s41564-019-0569-4. Epub 2019 Sep 30.

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept.
Reese AT, Kartzinel TR, Petrone BL, Turnbaugh PJ, Pringle RM, David LA.
mSystems. 2019 Oct 8;4(5). pii: e00458-19. doi: 10.1128/mSystems.00458-19.  

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog 
Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ.
Cell Host Microbe. 2019 Sep 11;26(3):325-335.e5. doi: 10.1016/j.chom.2019.08.008. 

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.
Nat Biotechnol. 2019 Jul 24. doi: 10.1038/s41587-019-0209-9. [Epub ahead of print]

Meta-analysis reveals reproducible gut microbiome alterations in response to a high-fat diet
Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ.
Cell Host Microbe. 2019 Jul 12. pii: S1931-3128(19)30302-6. doi: 10.1016/j.chom.2019.06.013. [Epub ahead of print]

Precision medicine goes microscopic: engineering the microbiome to improve drug outcomes
Lam KN, Alexander M, Turnbaugh PJ.
Cell Host Microbe. 2019 Jul 10;26(1):22-34. doi: 10.1016/j.chom.2019.06.011.

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism
Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP.
Science. 2019 Jun 14;364(6445). pii: eaau6323. doi: 10.1126/science.aau6323.

Nutrient sensing in CD11c cells alters the gut microbiota to regulate food intake and body mass
Chagwedera DN, Ang QY, Bisanz JE, Leong YA, Ganeshan K, Cai J, Patterson AD, Turnbaugh PJ, Chawla A.
Cell Metab. 2019 May 21. pii: S1550-4131(19)30242-6. doi: 10.1016/j.cmet.2019.05.002.

Megaphages infect Prevotella and variants are widespread in gut microbiomes
Devoto, AE, Santini, JM, Olm, MR, Anantharaman, K, Munk, P, Tung, J, Archie, EA, Turnbaugh, PJ, Seed, KD, Blekhman, R, Aarestrup, FM, Thomas, BC, Banfield, JF
Nat Microbiol. 2019 Apr;4(4):693-700. doi: 10.1038/s41564-018-0338-9. Epub 2019 Jan 28.

2018

Announcement of 2019 Keystone Symposia Conference: "Microbiome: Chemical Mechanisms and Biological Consequences"
Balskus, EP, Turnbaugh, PJ, Wolan, DW
mSystems. 2018 Jul 24;3(4). pii: e00115-18. doi: 10.1128/mSystems.00115-18. eCollection 2018 Jul-Aug.

Broad collateral damage of drugs against the gut microbiome
Spanogiannopoulos, P, Turnbaugh, PJ
Nat Rev Gastroenterol Hepatol. 2018 Aug;15(8):457-458. doi: 10.1038/s41575-018-0028-3.

Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome
Mallory, EK, Acharya, A, Rensi, SE, Turnbaugh, PJ, Bright, RA, Altman, RB
Pac Symp Biocomput. 2018;23:56-67.

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling
Fuks, G, Elgart, M, Amir, A, Zeisel, A, Turnbaugh, PJ, Soen, Y, Shental, N
Microbiome. 2018 Jan 26;6(1):17. doi: 10.1186/s40168-017-0396-x.

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins
Koppel, N, Bisanz, JE, Pandelia, M-E, Turnbaugh, PJ, Balskus, EP
Elife. 2018 May 15;7. pii: e33953. doi: 10.7554/eLife.33953.

Grape proanthocyanidin-induced intestinal bloom of Akkermansia muciniphila is dependent on its baseline abundance and precedes activation of host genes related to metabolic health
Zhang, L, Carmody, RN, Kalariya, HM, Duran, RM, Moskal, K, Poulev, A, Kuhn, P, Tveter, KM, Turnbaugh, PJ, Raskin, I, Roopchand, DE
J Nutr Biochem. 2018 Jun;56:142-151. doi: 10.1016/j.jnutbio.2018.02.009. Epub 2018 Feb 15.

How to determine the role of the microbiome in drug disposition
Bisanz, JE, Spanogiannopoulos, P, Pieper, LM, Bustion, AE, Turnbaugh, PJ
Drug Metab Dispos. 2018 Nov;46(11):1588-1595. doi: 10.1124/dmd.118.083402. Epub 2018 Aug 15.

Making millennial medicine more meta
Turnbaugh, PJ
mSystems. 2018 Mar 6;3(2). pii: e00154-17. doi: 10.1128/mSystems.00154-17. eCollection 2018 Mar-Apr.

A metabolite-triggered tuft cell-ILC2 circuit drives small intestinal remodeling
Schneider, C, O'Leary, CE, von Moltke, J, Liang, H-E, Ang, QYan, Turnbaugh, PJ, Radhakrishnan, S, Pellizzon, M, Ma, A, Locksley, RM
Cell. 2018 Jul 12;174(2):271-284.e14. doi: 10.1016/j.cell.2018.05.014. Epub 2018 Jun 7.

Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories
Stanhope, KL, Goran, MI, Bosy-Westphal, A, King, JC, Schmidt, LA, Schwarz, J-M, Stice, E, Sylvetsky, AC, Turnbaugh, PJ, Bray, GA, Gardner, CD, Havel, PJ, Malik, V, Mason, AE, Ravussin, E, Rosenbaum, M, Welsh, JA, Allister-Price, C, Sigala, DM, Greenwood, MRC, Astrup, A, Krauss, RM
Obes Rev. 2018 Sep;19(9):1205-1235. doi: 10.1111/obr.12699. Epub 2018 May 14.

2017

Microbes and diet-induced obesity: fast, cheap, and out of control
Turnbaugh, PJ
Cell Host Microbe. 2017 Mar 8;21(3):278-281. doi: 10.1016/j.chom.2017.02.021.

Regulation of drug metabolism and toxicity by multiple factors of genetics, epigenetics, lncRNAs, gut microbiota, and diseases: a meeting report of the 21(st) International Symposium on Microsomes and Drug Oxidations (MDO)
Yu, A-M, Ingelman-Sundberg, M, Cherrington, NJ, Aleksunes, LM, Zanger, UM, Xie, W, Jeong, H, Morgan, EM, Turnbaugh, PJ, Klaassen, CD, Bhatt, AP, Redinbo, MR, Hao, P, Waxman, DJ, Wang, L, Zhong, X-B
Acta Pharm Sin B. 2017 Mar;7(2):241-248. doi: 10.1016/j.apsb.2016.12.006. Epub 2017 Feb 1.

2016

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism
Spanogiannopoulos, P, Bess, EN, Carmody, RN, Turnbaugh, PJ
Nat Rev Microbiol. 2016 Apr;14(5):273-87. doi: 10.1038/nrmicro.2016.17. Epub 2016 Mar 14.

Mirror, mirror on the wall: which microbiomes will help heal them all?
Nayak, RR, Turnbaugh, PJ
BMC Med. 2016 May 4;14:72. doi: 10.1186/s12916-016-0622-6.

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
Bokulich, NA, Rideout, JRam, Mercurio, WG, Shiffer, A, Wolfe, B, Maurice, CF, Dutton, RJ, Turnbaugh, PJ, Knight, R, J Caporaso, G
mSystems. 2016 Oct 18;1(5). pii: e00062-16. eCollection 2016 Sep-Oct.

2015

Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria
del Campo, AMartínez-, Bodea, S, Hamer, HA, Marks, JA, Haiser, HJ, Turnbaugh, PJ, Balskus, EP
MBio. 2015 Apr 14;6(2). pii: e00042-15. doi: 10.1128/mBio.00042-15.

Diet dominates host genotype in shaping the murine gut microbiota.
Carmody, RN, Gerber, GK, Luevano, JM, Gatti, DM, Somes, L, Svenson, KL, Turnbaugh, PJ
Cell Host Microbe. 2015 Jan 14;17(1):72-84. doi: 10.1016/j.chom.2014.11.010. Epub 2014 Dec 18.

Dietary polyphenols promote growth of the gut bacterium Akkermansia muciniphila and attenuate high-fat diet-induced metabolic syndrome
Roopchand, DE, Carmody, RN, Kuhn, P, Moskal, K, Rojas-Silva, P, Turnbaugh, PJ, Raskin, I
Diabetes. 2015 Aug;64(8):2847-58. doi: 10.2337/db14-1916. Epub 2015 Apr 6.

Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics
Perron, GG, Whyte, L, Turnbaugh, PJ, Goordial, J, Hanage, WP, Dantas, G, Desai, MM
PLoS One. 2015 Mar 25;10(3):e0069533. doi: 10.1371/journal.pone.0069533. eCollection 2015.

Gut microbial succession follows acute secretory diarrhea in humans
David, LA, Weil, A, Ryan, ET, Calderwood, SB, Harris, JB, Chowdhury, F, Begum, Y, Qadri, F, LaRocque, RC, Turnbaugh, PJ
MBio. 2015 May 19;6(3):e00381-15. doi: 10.1128/mBio.00381-15.

Marked seasonal variation in the wild mouse gut microbiota
Maurice, CF, Knowles, SCL, Ladau, J, Pollard, KS, Fenton, A, Pedersen, AB, Turnbaugh, PJ
ISME J. 2015 Nov;9(11):2423-34. doi: 10.1038/ismej.2015.53. Epub 2015 May 29.

Siri, What Should I Eat?​
von Schwartzenberg, RJumpertz, Turnbaugh, PJ
Cell. 2015 Nov 19;163(5):1051-1052. doi: 10.1016/j.cell.2015.11.012.

2014

Diet rapidly and reproducibly alters the human gut microbiome
David, LA, Maurice, CF, Carmody, RN, Gootenberg, DB, Button, JE, Wolfe, BE, Ling, AV, A Devlin, S, Varma, Y, Fischbach, MA, Biddinger, SB, Dutton, RJ, Turnbaugh, PJ
Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11.

Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics.
Carmody, RN, Turnbaugh, PJ
J Clin Invest. 2014 Oct;124(10):4173-81. doi: 10.1172/JCI72335. Epub 2014 Aug 8.

The intestinal metabolome: an intersection between microbiota and host
Ursell, LK, Haiser, HJ, Van Treuren, W, Garg, N, Reddivari, L, Vanamala, J, Dorrestein, PC, Turnbaugh, PJ, Knight, R
Gastroenterology. 2014 May;146(6):1470-6. doi: 10.1053/j.gastro.2014.03.001. Epub 2014 Mar 11.

Mechanistic insight into digoxin inactivation by Eggerthella lenta augments our understanding of its pharmacokinetics
Haiser, HJ, Seim, KL, Balskus, EP, Turnbaugh, PJ
Gut Microbes. 2014 Mar-Apr;5(2):233-8. doi: 10.4161/gmic.27915. Epub 2014 Jan 23.

Microbial determinants of biochemical individuality and their impact on toxicology and pharmacology
Patterson, AD, Turnbaugh, PJ
Cell Metab. 2014 Nov 4;20(5):761-768. doi: 10.1016/j.cmet.2014.07.002. Epub 2014 Aug 21.

Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness
Pickard, JM, Maurice, CF, Kinnebrew, MA, Abt, MC, Schenten, D, Golovkina, TV, Bogatyrev, SR, Ismagilov, RF, Pamer, EG, Turnbaugh, PJ, Chervonsky, AV
Nature. 2014 Oct 30;514(7524):638-41. doi: 10.1038/nature13823. Epub 2014 Oct 1.

2013

Cancer: An acidic link
Devkota, S, Turnbaugh, PJ
Nature. 2013 Jul 4;499(7456):37-8. doi: 10.1038/nature12404. Epub 2013 Jun 26.

Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity
Liou, AP, Paziuk, M, Luevano, J-M, Machineni, S, Turnbaugh, PJ, Kaplan, LM
Sci Transl Med. 2013 Mar 27;5(178):178ra41. doi: 10.1126/scitranslmed.3005687.

Developing a metagenomic view of xenobiotic metabolism
Haiser, HJ, Turnbaugh, PJ
Pharmacol Res. 2013 Mar;69(1):21-31. doi: 10.1016/j.phrs.2012.07.009. Epub 2012 Aug 9.

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions
Amir, A, Zeisel, A, Zuk, O, Elgart, M, Stern, S, Shamir, O, Turnbaugh, PJ, Soen, Y, Shental, N
Nucleic Acids Res. 2013 Dec;41(22):e205. doi: 10.1093/nar/gkt1070. Epub 2013 Nov 7.

Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta
Haiser, HJ, Gootenberg, DB, Chatman, K, Sirasani, G, Balskus, EP, Turnbaugh, PJ
Science. 2013 Jul 19;341(6143):295-8. doi: 10.1126/science.1235872.

Quantifying and identifying the active and damaged subsets of indigenous microbial communities
Maurice, CFerrier, Turnbaugh, PJames
Methods Enzymol. 2013;531:91-107. doi: 10.1016/B978-0-12-407863-5.00005-8.

Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales
Maurice, CF, Turnbaugh, PJ
FEMS Microbiol Rev. 2013 Sep;37(5):830-48. doi: 10.1111/1574-6976.12022. Epub 2013 Apr 22.

Translating the human microbiome
Brown, J, de Vos, WM, DiStefano, PS, Doré, J, Huttenhower, C, Knight, R, Lawley, TD, Raes, J, Turnbaugh, P
Nat Biotechnol. 2013 Apr;31(4):304-8. doi: 10.1038/nbt.2543.

Xenobiotics shape the physiology and gene expression of the active human gut microbiome
Maurice, CFerrier, Haiser, HJoseph, Turnbaugh, PJames
Cell. 2013 Jan 17;152(1-2):39-50. doi: 10.1016/j.cell.2012.10.052.

2012

Antibiotic exposure promotes fat gain
Liou, AP, Turnbaugh, PJ
Cell Metab. 2012 Oct 3;16(4):408-10. doi: 10.1016/j.cmet.2012.09.009.

Gut microbes make for fattier fish
Carmody, RN, Turnbaugh, PJ
Cell Host Microbe. 2012 Sep 13;12(3):259-61. doi: 10.1016/j.chom.2012.08.006.

Is it time for a metagenomic basis of therapeutics?
Haiser, HJ, Turnbaugh, PJ
Science. 2012 Jun 8;336(6086):1253-5. doi: 10.1126/science.1224396. Epub 2012 Jun 6.

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
Greenblum, S, Turnbaugh, PJ, Borenstein, E
Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):594-9. doi: 10.1073/pnas.1116053109. Epub 2011 Dec 19.

Microbiology: fat, bile and gut microbes
Turnbaugh, PJ
Nature. 2012 Jul 4;487(7405):47-8. doi: 10.1038/487047a.

Taking a metagenomic view of human nutrition
Dutton, RJ, Turnbaugh, PJ
Curr Opin Clin Nutr Metab Care. 2012 Sep;15(5):448-54. doi: 10.1097/MCO.0b013e3283561133.

2011

Companion animals symposium: humanized animal models of the microbiome
Gootenberg, DB, Turnbaugh, PJ
J Anim Sci. 2011 May;89(5):1531-7. doi: 10.2527/jas.2010-3371. Epub 2010 Sep 10.

Companion animals symposium: microbes and health
Swanson, KS, Suchodolski, JS, Turnbaugh, PJ
J Anim Sci. 2011 May;89(5):1496-7. doi: 10.2527/jas.2011-3873.

Detecting novel associations in large data sets
Reshef, DN, Reshef, YA, Finucane, HK, Grossman, SR, McVean, G, Turnbaugh, PJ, Lander, ES, Mitzenmacher, M, Sabeti, PC
Science. 2011 Dec 16;334(6062):1518-24. doi: 10.1126/science.1205438.

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans
Jumpertz, R, Le, DSon, Turnbaugh, PJ, Trinidad, C, Bogardus, C, Gordon, JI, Krakoff, J
Am J Clin Nutr. 2011 Jul;94(1):58-65. doi: 10.3945/ajcn.110.010132. Epub 2011 May 4.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J Caporaso, G, Lauber, CL, Walters, WA, Berg-Lyons, D, Lozupone, CA, Turnbaugh, PJ, Fierer, N, Knight, R
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22. doi: 10.1073/pnas.1000080107. Epub 2010 Jun 3.

Human health and disease in a microbial world
Turnbaugh, PJ, Stintzi, A
Front Microbiol. 2011 Sep 16;2:190. doi: 10.3389/fmicb.2011.00190. eCollection 2011.

The mind-body-microbial continuum
Gonzalez, A, Stombaugh, J, Lozupone, C, Turnbaugh, PJ, Gordon, JI, Knight, R
Dialogues Clin Neurosci. 2011;13(1):55-62.

Removing noise from pyrosequenced amplicons.​
Quince, C, Lanzen, A, Davenport, RJ, Turnbaugh, PJ
BMC Bioinformatics. 2011 Jan 28;12:38. doi: 10.1186/1471-2105-12-38.

Taxonomic metagenome sequence assignment with structured output models
Patil, KR, Haider, P, Pope, PB, Turnbaugh, PJ, Morrison, M, Scheffer, T, McHardy, AC
Nat Methods. 2011 Mar;8(3):191-2. doi: 10.1038/nmeth0311-191.

Wild immunology: converging on the real world
Babayan, SA, Allen, JE, Bradley, JE, Geuking, MB, Graham, AL, Grencis, RK, Kaufman, J, McCoy, KD, Paterson, S, Smith, KGC, Turnbaugh, PJ, Viney, ME, Maizels, RM, Pedersen, AB
Ann N Y Acad Sci. 2011 Oct;1236:17-29. doi: 10.1111/j.1749-6632.2011.06251.x.

2010

A microbe-dependent viral key to Crohn's box
Peterson, DA, Turnbaugh, PJ
Sci Transl Med. 2010 Aug 4;2(43):43ps39. doi: 10.1126/scitranslmed.3001422.

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
Turnbaugh, PJ, Quince, C, Faith, JJ, McHardy, AC, Yatsunenko, T, Niazi, F, Affourtit, J, Egholm, M, Henrissat, B, Knight, R, Gordon, JI
Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8. doi: 10.1073/pnas.1002355107. Epub 2010 Apr 2.

QIIME allows analysis of high-throughput community sequencing data
J Caporaso, G, Kuczynski, J, Stombaugh, J, Bittinger, K, Bushman, FD, Costello, EK, Fierer, N, Peña, AGonzalez, 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
Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11.

Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes
Turnbaugh, PJ, Henrissat, B, Gordon, JI
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1261-4. doi: 10.1107/S1744309110029088. Epub 2010 Jul 31.

2009

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
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
Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5859-64. doi: 10.1073/pnas.0901529106. Epub 2009 Mar 24.

The core gut microbiome, energy balance and obesity
Turnbaugh, PJ, Gordon, JI
J Physiol. 2009 Sep 1;587(Pt 17):4153-8. doi: 10.1113/jphysiol.2009.174136. Epub 2009 Jun 2.

A core gut microbiome in obese and lean twins
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
Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540. Epub 2008 Nov 30.

2008

Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
Turnbaugh, PJ, Bäckhed, F, Fulton, L, Gordon, JI
Cell Host Microbe. 2008 Apr 17;3(4):213-23. doi: 10.1016/j.chom.2008.02.015.

Evolution of mammals and their gut microbes
Ley, RE, Hamady, M, Lozupone, C, Turnbaugh, PJ, Ramey, RRoy, J Bircher, S, Schlegel, ML, Tucker, TA, Schrenzel, MD, Knight, R, Gordon, JI
Science. 2008 Jun 20;320(5883):1647-51. doi: 10.1126/science.1155725. Epub 2008 May 22.

Host-bacterial coevolution and the search for new drug targets
Zaneveld, J, Turnbaugh, PJ, Lozupone, C, Ley, RE, Hamady, M, Gordon, JI, Knight, R
Curr Opin Chem Biol. 2008 Feb;12(1):109-14. doi: 10.1016/j.cbpa.2008.01.015. Epub 2008 Mar 5.

An invitation to the marriage of metagenomics and metabolomics
Turnbaugh, PJ, Gordon, JI
Cell. 2008 Sep 5;134(5):708-13. doi: 10.1016/j.cell.2008.08.025.

2007

The human microbiome project
Turnbaugh, PJ, Ley, RE, Hamady, M, Fraser-Liggett, CM, Knight, R, Gordon, JI
Nature. 2007 Oct 18;449(7164):804-10.

2006

Metagenomic analysis of the human distal gut microbiome
Gill, SR, Pop, M, Deboy, RT, Eckburg, PB, Turnbaugh, PJ, Samuel, BS, Gordon, JI, Relman, DA, Fraser-Liggett, CM, Nelson, KE
Science. 2006 Jun 2;312(5778):1355-9.

Microbial ecology: human gut microbes associated with obesity
Ley, RE, Turnbaugh, PJ, Klein, S, Gordon, JI
Nature. 2006 Dec 21;444(7122):1022-3.

An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, PJ, Ley, RE, Mahowald, MA, Magrini, V, Mardis, ER, Gordon, JI
Nature. 2006 Dec 21;444(7122):1027-31.

2005

Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics
Gertz, J, Riles, L, Turnbaugh, P, Ho, S-W, Cohen, BA
Genome Res. 2005 Aug;15(8):1145-52.

Obesity alters gut microbial ecology
Ley, RE, Bäckhed, F, Turnbaugh, P, Lozupone, CA, Knight, RD, Gordon, JI
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):11070-5. Epub 2005 Jul 20.