Peter Turnbaugh, PhD

Professor
Microbiology and Immunology
[email protected]
+1 415 502-3237

The research in our laboratory focuses on obtaining mechanistic insights into the role of the trillions of bacteria and viruses within the gastrointestinal tract in nutrition and pharmacology. To achieve these goals, we take a multi-disciplinary team approach, using diverse techniques from biochemistry, genetics, genomics, microbial ecology, and pharmacology coupled to studies in the lab, in gnotobiotic mice, and in human cohorts. These projects have involved collaborations within UCSF and with investigators around the world. Members of our group benefit from the strong training environment at UCSF, with world-class programs in microbiome research, microbiology, immunology, and pharmacology coupled to a unique spirit of collaboration and support for trainees.

Research Summary: 
The research in our laboratory focuses on obtaining mechanistic insights into the role of the trillions of bacteria and viruses within the gastrointestinal tract in nutrition and pharmacology.
Publications: 

Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity.

mBio

Hillege LE, Trepka KR, Guthrie BGH, Fu X, Aarnoutse R, Paymar MR, Olson C, Zhang C, Ortega E, Ramirez L, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Baars A, Vestjens JHMJ, Penders J, Deutschbauer A, Atreya CE, Kidder WA, Smidt ML, Ziemons J, Turnbaugh PJ

Gut Bacterial Lactic Acid Stimulates Lung Epithelial Mitochondria and Exacerbates Acute Lung Injury.

American journal of respiratory and critical care medicine

V. Upadhyay, G. Kaur, E.F. Ortega, K. Trepka, R.R. Rock, L. Ramirez Hernandez, W.C. Cheshire, N. Alipanah-Lechner, C.S. Calfee, M.A. Matthay, S. Blume, I. Jain, P.J. Turnbaugh

Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.

Science translational medicine

Trepka KR, Kidder WA, Kyaw TS, Halsey T, Olson CA, Ortega EF, Noecker C, Upadhyay V, Stanfield D, Steiding P, Guthrie BGH, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ

Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury.

bioRxiv : the preprint server for biology

Upadhyay V, Ortega EF, Ramirez Hernandez LA, Alexander M, Kaur G, Trepka K, Rock RR, Shima RT, Cheshire WC, Alipanah-Lechner N, Calfee CS, Matthay MA, Lee JV, Goga A, Jain IH, Turnbaugh PJ

Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response.

Annual review of pharmacology and toxicology

Trepka KR, Olson CA, Upadhyay V, Zhang C, Turnbaugh PJ

Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states.

bioRxiv : the preprint server for biology

Babdor J, Patel RK, Davidson B, Noecker C, Rahim M, Bisanz JE, Tenvooren I, Marquez D, Calvo M, Johri V, McCarthy E, Shaheed A, Ekstrand C, Weakley AM, Yu FB, Fiehn O, Turnbaugh PJ, Combes AJ, Fragiadakis GK, Spitzer MH

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.

bioRxiv : the preprint server for biology

Rendina M, Turnbaugh PJ, Bradley PH

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

Cell reports

Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ

Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme.

Cell host & microbe

Bae M, Le C, Mehta RS, Dong X, Pieper LM, Ramirez L, Alexander M, Kiamehr S, Turnbaugh PJ, Huttenhower C, Chan AT, Balskus EP

Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity.

bioRxiv : the preprint server for biology

Trepka KR, Kidder WA, Kyaw TS, Halsey T, Olson CA, Ortega EF, Noecker C, Upadhyay V, Stanfield D, Steiding P, Guthrie BGH, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ

Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients.

medRxiv : the preprint server for health sciences

Hillege LE, Trepka KR, Ziemons J, Aarnoutse R, Guthrie BGH, de Vos-Geelen J, Valkenburg-van Iersel L, van Hellemond IEG, Baars A, Vestjens JHMJ, Penders J, Deutschbauer A, Atreya CE, Kidder WA, Turnbaugh PJ, Smidt ML

Rationale and protocol for a safety, tolerability and feasibility randomized, parallel arm, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms.

PloS one

Stubbs BJ, Alvarez Azañedo G, Peralta S, Diaz SR, Gray W, Alexander L, Silverman-Martin W, Garcia TY, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC

Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.

Environmental health perspectives

Tian Y, Rimal B, Bisanz JE, Gui W, Wolfe TM, Koo I, Murray IA, Nettleford SK, Yokoyama S, Dong F, Koshkin S, Prabhu KS, Turnbaugh PJ, Walk ST, Perdew GH, Patterson AD

Short-Term Caloric Restriction Alters the Microbiome Modulating Resistance to Clostridioides difficile Infection.

Current Developments in Nutrition

Jingcheng Zhao, Arvid Sandforth, Shuchang Tian, Peter J Turnbaugh, Reiner Jumpertz Von Schwartzenberg, Jordan E Bisanz

Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice.

JBMR plus

Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Brito IL, Booth SL, Hernandez CJ

Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors.

iScience

Kyaw TS, Zhang C, Sandy M, Trepka K, Zhang S, Ramirez Hernandez LA, Ramirez L, Goh JJN, Yu K, Dimassa V, Bess EN, Brockert JG, Dumlao DS, Bisanz JE, Turnbaugh PJ

Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas.

Cell

McCurry MD, D'Agostino GD, Walsh JT, Bisanz JE, Zalosnik I, Dong X, Morris DJ, Korzenik JR, Edlow AG, Balskus EP, Turnbaugh PJ, Huh JR, Devlin AS

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity.

bioRxiv : the preprint server for biology

Alexander M, Upadhyay V, Rock R, Ramirez L, Trepka K, Puchalska P, Orellana D, Ang QY, Whitty C, Turnbaugh JA, Tian Y, Dumlao D, Nayak R, Patterson A, Newman JC, Crawford PA, Turnbaugh PJ

Microbiome single cell atlases generated with a commercial instrument.

bioRxiv : the preprint server for biology

Li X, Xu L, Demaree B, Noecker C, Bisanz JE, Weisgerber DW, Modavi C, Turnbaugh PJ, Abate AR

High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion from the gut microbiota.

Cell

Lee JY, Tiffany CR, Mahan SP, Kellom M, Rogers AWL, Nguyen H, Stevens ET, Masson HLP, Yamazaki K, Marco ML, Eloe-Fadrosh EA, Turnbaugh PJ, Bäumler AJ

Effects of long-term high dose aspartame on body mass, bone strength, femoral geometry, and microbiota composition in a young and aged cohort of male and female mice.

bioRxiv : the preprint server for biology

Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Brito IL, Booth SL, Hernandez CJ

Rationale and protocol for a safety, tolerability and feasibility randomized, parallel group, double-blind, placebo-controlled, pilot study of a novel ketone ester targeting frailty via immunometabolic geroscience mechanisms.

medRxiv : the preprint server for health sciences

Stubbs BJ, Alvarez-Azanedo G, Peralta S, Roa-Diaz S, Gray W, Alexander L, Silverman-Martin W, Garcia T, Blonquist TM, Upadhyay V, Turnbaugh PJ, Johnson JB, Newman JC

Simvastatin induces human gut bacterial cell surface genes.

Molecular microbiology

Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ

Microbiome single cell atlases generated with a commercial instrument.

Research square

Abate A, Li X, Xu L, Demaree B, Noecker C, Bisanz J, Weisgerber D, Modavi C, Turnbaugh P

Associations between the Gut Microbiota, Race, and Ethnicity of Patients with Colorectal Cancer: A Pilot and Feasibility Study.

Cancers

Piawah S, Kyaw TS, Trepka K, Stewart AL, Mora RV, Stanfield D, Levine K, Van Blarigan EL, Venook A, Turnbaugh PJ, Nguyen T, Atreya CE

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli.

mBio

Pieper LM, Spanogiannopoulos P, Volk RF, Miller CJ, Wright AT, Turnbaugh PJ

Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors.

The American journal of clinical nutrition

Kyaw TS, Upadhyay V, Tolstykh I, Van Loon K, Laffan A, Stanfield D, Gempis D, Kenfield SA, Chan JM, Piawah S, Atreya CE, Ng K, Venook A, Kidder W, Turnbaugh PJ, Van Blarigan EL

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

mBio

Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ

Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta.

PLoS biology

Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ

Early-life exposure to a potent Aryl hydrocarbon receptor ligand results in persistent changes to the microbiota and host glucose homeostasis.

Yuan Tian, Bipin Rimal, Jordan E Bisanz, Wei Gui, Trenton M Wolfe, Imhoi Koo, Iain M Murray, Shaneice K Nettleford, Shigetoshi Yokoyama, Fangcong Dong, K Sandeep Prabhu, Peter J Turnbaugh, Seth T Walk, Gary H Perdew, Andrew D Patterson

Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators.

Nature communications

Dong X, Guthrie BGH, Alexander M, Noecker C, Ramirez L, Glasser NR, Turnbaugh PJ, Balskus EP

Mild SARS-CoV-2 infection results in long-lasting microbiota instability.

bioRxiv : the preprint server for biology

Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ

nicX-ing bad habits with your microbial friends.

Nature metabolism

Upadhyay V, Turnbaugh PJ

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism.

Nature microbiology

Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, Goga A, Pollard KS, Turnbaugh PJ

Tiny Gatekeepers: Microbial Control of Host Drug Transporters.

Clinical pharmacology and therapeutics

Kyaw TS, Turnbaugh PJ

Designed secretion deters microbiome depletion.

Nature microbiology

Olson CA, Turnbaugh PJ

Fluoropyrimidine Bioactivation and Metabolism by the Gut Microbiome.

The FASEB Journal

Benjamin G. H. Guthrie, Peter J. Turnbaugh

Tu1517: MICROBIAL SIGNALS, MYD88, AND LYMPHOTOXIN DRIVE TNFINDEPENDENT DEATH OF A20 AND ABIN-1 DEFICIENT EPITHELIUM.

Gastroenterology

Iulia Rusu, Elvira Mennillo, Jared L. Bain, Zhongmei Li, Xiaofei Sun, Kimberly Ly, Yenny Y. Rosli, Mohammad Naser, Zunqiu Wang, Rommel Advincula, Philip Achacoso, Ling Shao, Bahram Razani, Ophir D. Klein, Alexander Marson, Jessie A. Turnbaugh, Peter J. Turnbaugh, Barbara Malynn, Averil Ma, Michael Kattah

Effects of caloric restriction on the gut microbiome are linked with immune senescence.

Microbiome

Sbierski-Kind J, Grenkowitz S, Schlickeiser S, Sandforth A, Friedrich M, Kunkel D, Glauben R, Brachs S, Mai K, Thürmer A, Radonic A, Drechsel O, Turnbaugh PJ, Bisanz JE, Volk HD, Spranger J, von Schwartzenberg RJ

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites.

Nature

Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS

Synthetic glycans control gut microbiome structure and mitigate colitis in mice.

Nature communications

Tolonen AC, Beauchemin N, Bayne C, Li L, Tan J, Lee J, Meehan BM, Meisner J, Millet Y, LeBlanc G, Kottler R, Rapp E, Murphy C, Turnbaugh PJ, von Maltzahn G, Liu CM, van Hylckama Vlieg JET

Microbial signals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage.

The Journal of clinical investigation

Rusu I, Mennillo E, Bain JL, Li Z, Sun X, Ly KM, Rosli YY, Naser M, Wang Z, Advincula R, Achacoso P, Shao L, Razani B, Klein OD, Marson A, Turnbaugh JA, Turnbaugh PJ, Malynn BA, Ma A, Kattah MG

Human gut bacterial metabolism drives Th17 activation and colitis.

Cell host & microbe

Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ

Reporting guidelines for human microbiome research: the STORMS checklist.

Nature medicine

Mirzayi C, Renson A, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L

Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome.

Cell reports

Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, Nayak RR, Weakley AM, Yu FB, Turnbaugh PJ

The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health.

eLife

Ang QY, Alba DL, Upadhyay V, Bisanz JE, Cai J, Lee HL, Barajas E, Wei G, Noecker C, Patterson AD, Koliwad SK, Turnbaugh PJ

Caloric restriction disrupts the microbiota and colonization resistance.

Nature

von Schwartzenberg RJ, Bisanz JE, Lyalina S, Spanogiannopoulos P, Ang QY, Cai J, Dickmann S, Friedrich M, Liu SY, Collins SL, Ingebrigtsen D, Miller S, Turnbaugh JA, Patterson AD, Pollard KS, Mai K, Spranger J, Turnbaugh PJ

The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis.

Arthritis & rheumatology (Hoboken, N.J.)

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

Dissecting the contribution of host genetics and the microbiome in complex behaviors.

Cell

Buffington SA, Dooling SW, Sgritta M, Noecker C, Murillo OD, Felice DF, Turnbaugh PJ, Costa-Mattioli M

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments.

Cell reports

Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM

Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.

Cell host & microbe

Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ

A thermogenic fat-epithelium cell axis regulates intestinal disease tolerance.

Proceedings of the National Academy of Sciences of the United States of America

Man K, Bowman C, Braverman KN, Escalante V, Tian Y, Bisanz JE, Ganeshan K, Wang B, Patterson A, Bayrer JR, Turnbaugh PJ, Chawla A

Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis.

Science immunology

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

Stressed-out gut bacteria are pterin up gut inflammation.

Nature microbiology

Alexander M, Turnbaugh PJ

Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections.

Med (New York, N.Y.)

Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC

Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives.

Proceedings of the National Academy of Sciences of the United States of America

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

Probing the tumor micro(b)environment.

Science (New York, N.Y.)

Atreya CE, Turnbaugh PJ

Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.

Cell

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

A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.

Cell host & microbe

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

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans.

Nature medicine

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

Non-catalytic ubiquitin binding by A20 prevents psoriatic arthritis-like disease and inflammation.

Nature immunology

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

Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response.

Nature reviews. Rheumatology

Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB

A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols.

eLife

Maini Rekdal V, Nol Bernadino P, Luescher MU, Kiamehr S, Le C, Bisanz JE, Turnbaugh PJ, Bess EN, Balskus EP

Sensing Living Bacteria in Vivo Using d-Alanine-Derived 11C Radiotracers.

ACS central science

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

S4.3 - Impact of the human gut microbiome on drug disposition.

Drug Metabolism and Pharmacokinetics

Peter Turnbaugh

Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.

Nature microbiology

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

Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept.

mSystems

Reese AT, Kartzinel TR, Petrone BL, Turnbaugh PJ, Pringle RM, David LA

Cooking shapes the structure and function of the gut microbiome.

Nature microbiology

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

CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.

Cell host & microbe

Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Nature biotechnology

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, 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

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Nature biotechnology

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, 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

Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet.

Cell host & microbe

Bisanz JE, Upadhyay V, Turnbaugh JA, Ly K, Turnbaugh PJ

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism.

Science (New York, N.Y.)

Maini Rekdal V, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP

OP0119 THE PRE-TREATMENT GUT MICROBIOME PREDICTS EARLY RESPONSE TO RHEUMATOID ARTHRITIS THERAPY.

Oral Presentations

Sandrine Isaac, Alejandro Artacho, Renuka Nayak, Alejandra Flor, Steven Abramson, Pamela Rosenthal, Leonor Puchades, Andrew Patterson, Antonio Pineda-Lucena, Peter Turnbaugh, Carles Ubeda, Jose Scher

Nutrient Sensing in CD11c Cells Alters the Gut Microbiota to Regulate Food Intake and Body Mass.

Cell metabolism

Chagwedera DN, Ang QY, Bisanz JE, Leong YA, Ganeshan K, Cai J, Patterson AD, Turnbaugh PJ, Chawla A

Megaphages infect Prevotella and variants are widespread in gut microbiomes.

Nature microbiology

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

Predicting and preventing the inactivation of drugs by human gut bacteria.

Drug Metabolism and Pharmacokinetics

Peter Turnbaugh

How to Determine the Role of the Microbiome in Drug Disposition.

Drug metabolism and disposition: the biological fate of chemicals

Bisanz JE, Spanogiannopoulos P, Pieper LM, Bustion AE, Turnbaugh PJ

Broad collateral damage of drugs against the gut microbiome.

Nature reviews. Gastroenterology & hepatology

Spanogiannopoulos P, Turnbaugh PJ

A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling.

Cell

Schneider C, O'Leary CE, von Moltke J, Liang HE, Ang QY, Turnbaugh PJ, Radhakrishnan S, Pellizzon M, Ma A, Locksley RM

Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories.

Obesity reviews : an official journal of the International Association for the Study of Obesity

Stanhope KL, Goran MI, Bosy-Westphal A, King JC, Schmidt LA, Schwarz JM, 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

The Metabolism of Fluoropyrimidine Anticancer Drugs by the Human Gut Microbiome.

The FASEB Journal

Peter Spanogiannopoulos, Andrew D. Patteron, Peter J. Turnbaugh

Grape proanthocyanidin-induced intestinal bloom of Akkermansia muciniphila is dependent on its baseline abundance and precedes activation of host genes related to metabolic health.

The Journal of nutritional biochemistry

Zhang L, Carmody RN, Kalariya HM, Duran RM, Moskal K, Poulev A, Kuhn P, Tveter KM, Turnbaugh PJ, Raskin I, Roopchand DE

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.

Microbiome

Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, Shental N

Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Mallory EK, Acharya A, Rensi SE, Turnbaugh PJ, Bright RA, Altman RB

Characterization of a cardiac drug-inactivating enzyme from the prominent human gut microbe, Eggerthella lenta.

The FASEB Journal

Nitzan Koppel, Jordan Bisanz, Peter Turnbaugh, Emily P Balskus

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 pharmaceutica Sinica. B

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

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

mSystems

Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG

Metabolism of anticancer drugs by the human gut microbiome.

Toxicology Letters

P. Spanogiannopoulos, P.J. Turnbaugh

The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism.

Nature reviews. Microbiology

Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ

Siri, What Should I Eat?

Cell

Jumpertz von Schwartzenberg R, Turnbaugh PJ

Marked seasonal variation in the wild mouse gut microbiota.

The ISME journal

Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ

Gut microbial succession follows acute secretory diarrhea in humans.

mBio

David LA, Weil A, Ryan ET, Calderwood SB, Harris JB, Chowdhury F, Begum Y, Qadri F, LaRocque RC, Turnbaugh PJ

Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria.

mBio

Martínez-del Campo A, Bodea S, Hamer HA, Marks JA, Haiser HJ, Turnbaugh PJ, Balskus EP

Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome.

Diabetes

Roopchand DE, Carmody RN, Kuhn P, Moskal K, Rojas-Silva P, Turnbaugh PJ, Raskin I

Diet dominates host genotype in shaping the murine gut microbiota.

Cell host & microbe

Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, Turnbaugh PJ

Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013.

Microbiome

Jacques Ravel, Martin J Blaser, Jonathan Braun, Eric Brown, Frederic D Bushman, Eugene B Chang, Julian Davies, Kathryn G Dewey, Timothy Dinan, Maria Dominguez-Bello, Susan E Erdman, B Brett Finlay, Wendy S Garrett, Gary B Huffnagle, Curtis Huttenhower, Janet Jansson, Ian B Jeffery, Christian Jobin, Alexander Khoruts, Heidi H Kong, Johanna W Lampe, Ruth E Ley, Dan R Littman, Sarkis K Mazmanian, David A Mills, Andrew S Neish, Elaine Petrof, David A Relman, Rosamond Rhodes, Peter J Turnbaugh, Vincent B Young, Rob Knight, Owen White

Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness.

Nature

Pickard JM, Maurice CF, Kinnebrew MA, Abt MC, Schenten D, Golovkina TV, Bogatyrev SR, Ismagilov RF, Pamer EG, Turnbaugh PJ, Chervonsky AV

Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics.

The Journal of clinical investigation

Carmody RN, Turnbaugh PJ

The intestinal metabolome: an intersection between microbiota and host.

Gastroenterology

Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J, Dorrestein PC, Turnbaugh PJ, Knight R

Diet rapidly and reproducibly alters the human gut microbiome.

Nature

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

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

Nucleic acids research

Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N

Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta.

Science (New York, N.Y.)

Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ

Cancer: An acidic link.

Nature

Devkota S, Turnbaugh PJ

Translating the human microbiome.

Nature biotechnology

Brown J, de Vos WM, DiStefano PS, Doré J, Huttenhower C, Knight R, Lawley TD, Raes J, Turnbaugh P

Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity.

Science translational medicine

Liou AP, Paziuk M, Luevano JM, Machineni S, Turnbaugh PJ, Kaplan LM

Antibiotic exposure promotes fat gain.

Cell metabolism

Liou AP, Turnbaugh PJ

Gut microbes make for fattier fish.

Cell host & microbe

Carmody RN, Turnbaugh PJ

Taking a metagenomic view of human nutrition.

Current opinion in clinical nutrition and metabolic care

Dutton RJ, Turnbaugh PJ

Developing a metagenomic view of xenobiotic metabolism.

Pharmacological research

Haiser HJ, Turnbaugh PJ

Is it time for a metagenomic basis of therapeutics?

Science (New York, N.Y.)

Haiser HJ, Turnbaugh PJ

515 Weight-Independent Changes in Gut Microbial Ecology Regulate Adiposity Following Roux-en-Y Gastric Bypass Surgery in Mice.

Gastroenterology

Alice P. Liou, Jesus M. Luevano, Peter J. Turnbaugh, Lee M. Kaplan

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.

Proceedings of the National Academy of Sciences of the United States of America

Greenblum S, Turnbaugh PJ, Borenstein E

Detecting novel associations in large data sets.

Science (New York, N.Y.)

Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC

Wild immunology: converging on the real world.

Annals of the New York Academy of Sciences

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

Human health and disease in a microbial world.

Frontiers in microbiology

Turnbaugh PJ, Stintzi A

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans.

The American journal of clinical nutrition

Jumpertz R, Le DS, Turnbaugh PJ, Trinidad C, Bogardus C, Gordon JI, Krakoff J

Companion animals symposium: microbes and health.

Journal of animal science

Swanson KS, Suchodolski JS, Turnbaugh PJ

Taxonomic metagenome sequence assignment with structured output models.

Nature methods

Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC

Removing noise from pyrosequenced amplicons.

BMC bioinformatics

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ

The mind-body-microbial continuum.

Dialogues in clinical neuroscience

Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R

Companion animals symposium: humanized animal models of the microbiome.

Journal of animal science

Gootenberg DB, Turnbaugh PJ

A microbe-dependent viral key to Crohn's box.

Science translational medicine

Peterson DA, Turnbaugh PJ

Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes.

Acta crystallographica. Section F, Structural biology and crystallization communications

Turnbaugh PJ, Henrissat B, Gordon JI

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Proceedings of the National Academy of Sciences of the United States of America

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R

QIIME allows analysis of high-throughput community sequencing data.

Nature methods

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

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins.

Proceedings of the National Academy of Sciences of the United States of America

Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

Science translational medicine

Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI

The core gut microbiome, energy balance and obesity.

The Journal of physiology

Turnbaugh PJ, Gordon JI

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.

Proceedings of the National Academy of Sciences of the United States of America

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

A core gut microbiome in obese and lean twins.

Nature

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

Evolution of mammals and their gut microbes.

Science (New York, N.Y.)

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI

Host-bacterial coevolution and the search for new drug targets.

Current opinion in chemical biology

Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, Knight R

The human microbiome project.

Nature

Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI

An obesity-associated gut microbiome with increased capacity for energy harvest.

Nature

Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI

Microbial ecology: human gut microbes associated with obesity.

Nature

Ley RE, Turnbaugh PJ, Klein S, Gordon JI

Metagenomic analysis of the human distal gut microbiome.

Science (New York, N.Y.)

Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE

Obesity alters gut microbial ecology.

Proceedings of the National Academy of Sciences of the United States of America

Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI