Food, Immunity, and the Microbiome

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

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100

Diversity of the Human Intestinal Microbial Flora

Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913

A core gut microbiome in obese and lean twins

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823

Human gut microbiome viewed across age and geography

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815

Enterotypes of the human gut microbiome

MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548

Linking long-term dietary patterns with gut microbial enterotypes

Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., DuGar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., et al. (2011) · Nature · doi:10.1038/nature09922 · Cited by 5,597

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

Furusawa, Y., Obata, Y., Fukuda, S., Endo, T. A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., et al. (2013) · Nature · doi:10.1038/nature12721 · Cited by 5,549

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis

Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., deRoos, P., Liu, H., Cross, J. R., Pfeffer, K., Coffer, P. J., et al. (2013) · Nature · doi:10.1038/nature12726 · Cited by 4,838

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774

Functional interactions between the gut microbiota and host metabolism

Tremaroli, V., & Bäckhed, F. (2012) · Nature · doi:10.1038/nature11552 · Cited by 4,387

Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis

Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., et al. (2013) · Nature Medicine · doi:10.1038/nm.3145 · Cited by 4,386

Succinate is an inflammatory signal that induces IL-1β through HIF-1α

Tannahill, G. M., Curtis, A. M., Adamik, J., Palsson-McDermott, E. M., McGettrick, A. F., Goel, G., Frezza, C., Bernard, N. J., Kelly, B., Foley, N. H., et al. (2013) · Nature · doi:10.1038/nature11986 · Cited by 4,176

Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk

Tang, W. H. W., Wang, Z., Levison, B. S., Koeth, R. A., Britt, E. B., Fu, X., Wu, Y., & Hazen, S. L. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1109400 · Cited by 3,400

Gut microbiota composition correlates with diet and health in the elderly

Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O’Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O’Sullivan, O., et al. (2012) · Nature · doi:10.1038/nature11319 · Cited by 3,314

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43

Maslowski, K. M., Vieira, A. T., Ng, A., Kranich, J., Sierro, F., Yu, D., Schilter, H. C., Rolph, M. S., Mackay, F., Artis, D., et al. (2009) · Nature · doi:10.1038/nature08530 · Cited by 3,241

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058

Gut Microbiota Metabolism of Dietary Fiber Influences Allergic Airway Disease and Hematopoiesis

Trompette, A., Gollwitzer, E. S., Yadava, K., Sichelstiel, A. K., Sprenger, N., Ngom-Bru, C., Blanchard, C., Junt, T., Nicod, L. P., Harris, N. L., et al. (2014) · Nature Medicine · doi:10.1038/nm.3444 · Cited by 2,862

Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22

Zelante, T., Iannitti, R. G., Cunha, C., De Luca, A., Giovannini, G., Pieraccini, G., Zecchi, R., D’Angelo, C., Massi-Benedetti, C., Fallarino, F., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.08.003 · Cited by 2,614

Human nutrition, the gut microbiome and the immune system

Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011) · Nature · doi:10.1038/nature10213 · Cited by 2,588

Immunol. Cell Biol.

Fitzgerald, M., Hayward, I. P., Thomas, A. C., Campbell, J. H., & CAMPBELL, G. R. (1995) · Cited by 2,552

Succession of microbial consortia in the developing infant gut microbiome

Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540

GPR120 is an omega-3 fatty acid receptor mediating potent anti-inflammatory and insulin-sensitizing effects

Oh, D. Y., Talukdar, S., Bae, E. J., Imamura, T., Morinaga, H., Fan, W., Li, P., Lu, W. J., Watkins, S. M., & Olefsky, J. M. (2010) · Cell · doi:10.1016/j.cell.2010.07.041 · Cited by 2,428

The role of short chain fatty acids in health and disease

Tan, J., McKenzie, C., Potamitis, M., Thorburn, A. N., Mackay, C. R., & Macia, L. (2014) · Advances in immunology · doi:10.1016/b978-0-12-800100-4.00003-9 · Cited by 2,425

The Orphan G Protein-coupled Receptors GPR41 and GPR43 Are Activated by Propionate and Other Short Chain Carboxylic Acids

Brown, A. J., Goldsworthy, S. M., Barnes, A. A., Eilert, M. M., Tcheang, L., Daniels, D., Muir, A. I., Wigglesworth, M. J., Kinghorn, I., Fraser, N. J., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211609200 · Cited by 2,409

Bifidobacteria can protect from enteropathogenic infection through production of acetate

Fukuda, S., Toh, H., Hase, K., Oshima, K., Nakanishi, Y., Yoshimura, K., Tobe, T., Clarke, J. M., Topping, D. L., Suzuki, T., et al. (2011) · Nature · doi:10.1038/nature09646 · Cited by 2,387

Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis

Singh, N., Gurav, A., Sivaprakasam, S., Brady, E., Padia, R., Shi, H., Thangaraju, M., Prasad, P. D., Manicassamy, S., Munn, D. H., et al. (2014) · Immunity · doi:10.1016/j.immuni.2013.12.007 · Cited by 2,368

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition.

Chang, P. V., Hao, L., Offermanns, S., & Medzhitov, R. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322269111 · Cited by 2,175

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

Elinav, E., Strowig, T., Kau, A. L., Henao-Mejia, J., Thaiss, C. A., Booth, C. J., Peaper, D. R., Bertin, J., Eisenbarth, S. C., Gordon, J. I., et al. (2011) · Cell · doi:10.1016/j.cell.2011.04.022 · Cited by 2,024

Microbial Influences in Inflammatory Bowel Diseases

Sartor, R. B. (2008) · Gastroenterology · doi:10.1053/j.gastro.2007.11.059 · Cited by 1,927

The Effect of Dietary Supplementation with n—3 Polyunsaturated Fatty Acids on the Synthesis of Interleukin-1 and Tumor Necrosis Factor by Mononuclear Cells

Endres, S., Ghorbani, R., Kelley, V. E., Georgilis, K., Lonnemann, G., van der Meer, J. W. M., Cannon, J. G., Rogers, T. S., Klempner, M. S., Weber, P. C., et al. (1989) · New England Journal of Medicine · doi:10.1056/nejm198902023200501 · Cited by 1,911

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice

Devkota, S., Wang, Y., Musch, M. W., Leone, V., Fehlner-Peach, H., Nadimpalli, A., Antonopoulos, D. A., Jabri, B., & Chang, E. B. (2012) · Nature · doi:10.1038/nature11225 · Cited by 1,904

An endogenous tumour-promoting ligand of the human aryl hydrocarbon receptor

Opitz, C. A., Litzenburger, U. M., Sahm, F., Ott, M., Tritschler, I., Trump, S., Schumacher, T., Jestaedt, L., Schrenk, D., Weller, M., et al. (2011) · Nature · doi:10.1038/nature10491 · Cited by 1,898

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences

Cox, L. M., Yamanishi, S., Sohn, J., Alekseyenko, A. V., Leung, J. M., Cho, I., Kim, S. G., Li, H., Gao, Z., Mahana, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.052 · Cited by 1,859

Dietary intervention impact on gut microbial gene richness

Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., et al. (2013) · Nature · doi:10.1038/nature12480 · Cited by 1,832

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

Claesson, M. J., Cusack, S., O'Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., Marchesi, J. R., Falush, D., Dinan, T., Fitzgerald, G., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000097107 · Cited by 1,754

Functional Characterization of Human Receptors for Short Chain Fatty Acids and Their Role in Polymorphonuclear Cell Activation

Le Poul, E., Loison, C., Struyf, S., Springael, J.-Y., Lannoy, V., Decobecq, M.-E., Brezillon, S., Dupriez, V., Vassart, G., Van Damme, J., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m301403200 · Cited by 1,651

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2010.118 · Cited by 1,632

High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity

Hildebrandt, M. A., Hoffmann, C., Sherrill–Mix, S. A., Keilbaugh, S. A., Hamady, M., Chen, Y., Knight, R., Ahima, R. S., Bushman, F., & Wu, G. D. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.08.042 · Cited by 1,576

Exercise and associated dietary extremes impact on gut microbial diversity

Clarke, S. F., Murphy, E. F., O'Sullivan, O., Lucey, A. J., Humphreys, M., Hogan, A., Hayes, P., O'Reilly, M., Jeffery, I. B., Wood-Martin, R., et al. (2014) · Gut · doi:10.1136/gutjnl-2013-306541 · Cited by 1,439

Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells

Kleinewietfeld, M., Manzel, A., Titze, J., Kvakan, H., Yosef, N., Linker, R. A., Muller, D. N., & Hafler, D. A. (2013) · Nature · doi:10.1038/nature11868 · Cited by 1,394

Saturated Fatty Acids, but Not Unsaturated Fatty Acids, Induce the Expression of Cyclooxygenase-2 Mediated through Toll-like Receptor 4

Lee, J. Y., Sohn, K. H., Rhee, S. H., & Hwang, D. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m011695200 · Cited by 1,299

ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation

Hashimoto, T., Perlot, T., Rehman, A., Trichereau, J., Ishiguro, H., Paolino, M., Sigl, V., Hanada, T., Hanada, R., Lipinski, S., et al. (2012) · Nature · doi:10.1038/nature11228 · Cited by 1,271

Persistent gut microbiota immaturity in malnourished Bangladeshi children

Subramanian, S., Huq, S., Yatsunenko, T., Haque, R., Mahfuz, M., Alam, M. A., Benezra, A., DeStefano, J., Meier, M. F., Muegge, B. D., et al. (2014) · Nature · doi:10.1038/nature13421 · Cited by 1,270

Global Sodium Consumption and Death from Cardiovascular Causes

Mozaffarian, D., Fahimi, S., Singh, G. M., Micha, R., Khatibzadeh, S., Engell, R. E., Lim, S., Danaei, G., Ezzati, M., & Powles, J. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1304127 · Cited by 1,218

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173

Trimethylamine-N-Oxide, a Metabolite Associated with Atherosclerosis, Exhibits Complex Genetic and Dietary Regulation

Bennett, B. J., Vallim, T. Q. D. A., Wang, Z., Shih, D. M., Meng, Y., Gregory, J., Allayee, H., Lee, R., Graham, M., Crooke, R., et al. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2012.12.011 · Cited by 1,070

Indoleamine 2,3 dioxygenase and metabolic control of immune responses

Munn, D. H., & Mellor, A. L. (2013) · Trends in Immunology · doi:10.1016/j.it.2012.10.001 · Cited by 1,037

Diet, metabolites, and “western-lifestyle” inflammatory diseases

Thorburn, A. N., Macia, L., & Mackay, C. R. (2014) · Immunity · doi:10.1016/j.immuni.2014.05.014 · Cited by 879

Bacteroides thetaiotaomicron and Faecalibacterium prausnitziiinfluence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent

Wrzosek, L., Miquel, S., Noordine, M.-L., Bouet, S., Curt, M. J.-C., Robert, V., Philippe, C., Bridonneau, C., Cherbuy, C., Masselot, C. R., et al. (2013) · BMC Biology · doi:10.1186/1741-7007-11-61 · Cited by 863

Gut microbiome, obesity, and metabolic dysfunction

Tilg, H., & Kaser, A. (2011) · Journal of Clinical Investigation · doi:10.1172/jci58109 · Cited by 860

Exogenous Stimuli Maintain Intraepithelial Lymphocytes via Aryl Hydrocarbon Receptor Activation

Li, Y., Innocentin, S., Withers, D. R., Roberts, N. A., Gallagher, A., Grigorieva, E. F., Wilhelm, C., & Veldhoen, M. (2011) · Cell · doi:10.1016/j.cell.2011.09.025 · Cited by 837

Commensal bacteria protect against food allergen sensitization

Stefka, A. T., Feehley, T., Tripathi, P., Qiu, J., McCoy, K. D., Mazmanian, S. K., Tjota, M. Y., Seo, G., Cao, S. Z., Theriault, B. R., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412008111 · Cited by 812

Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles

Kiss, E. A., Vonarbourg, C., Kopfmann, S., Hobeika, E., Finke, D., Esser, C., & Diefenbach, A. (2011) · Science · doi:10.1126/science.1214914 · Cited by 801

High-Fat Diet: Bacteria Interactions Promote Intestinal Inflammation Which Precedes and Correlates with Obesity and Insulin Resistance in Mouse

Ding, S., Chi, M. M., Scull, B. P., Rigby, R., Schwerbrock, N. M. J., Magness, S., Jobin, C., & Lund, P. K. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012191 · Cited by 713

Aryl hydrocarbon receptor-induced signals up-regulate IL-22 production and inhibit inflammation in the gastrointestinal tract

Monteleone, I., Rizzo, A., Sarra, M., Sica, G., Sileri, P., Biancone, L., MacDonald, T. T., Pallone, F., & Monteleone, G. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.04.007 · Cited by 656

Saturated fatty acids activate TLR-mediated proinflammatory signaling pathways

Huang, S., Rutkowsky, J. M., Snodgrass, R. G., Ono‐Moore, K. D., Schneider, D. A., Newman, J. W. I., Adams, S. H., & Hwang, D. H. (2012) · Journal of Lipid Research · doi:10.1194/jlr.d029546 · Cited by 615

Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease

Albenberg, L. G., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.058 · Cited by 606

Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide

Wang, Z., Tang, W. H. W., Buffa, J. A., Fu, X., Britt, E. B., Koeth, R. A., Levison, B. S., Fan, Y., Wu, Y., & Hazen, S. L. (2014) · European Heart Journal · doi:10.1093/eurheartj/ehu002 · Cited by 559

A high-fat diet is associated with endotoxemia that originates from the gut

Pendyala, S., Walker, J. M., & Holt, P. R. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.01.034 · Cited by 546

Western diet induces dysbiosis with increased E coli in CEABAC10 mice , alters host barrier function favouring AIEC colonisation

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Fatty acids and inflammation: The cutting edge between food and pharma

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Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants

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Interleukin-22 alleviates metabolic disorders and restores mucosal immunity in diabetes

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The luminal short-chain fatty acid butyrate modulates NF-κB activity in a human colonic epithelial cell line

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A vegan or vegetarian diet substantially alters the human colonic faecal microbiota

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Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

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Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity

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AhR sensing of bacterial pigments regulates antibacterial defence

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Antibiotics as Part of the Management of Severe Acute Malnutrition

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Dietary Fiber Intake and Mortality in the NIH-AARP Diet and Health Study

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Dietary fructose in nonalcoholic fatty liver disease

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Isoform specificity of trimethylamine N-oxygenation by human flavin-containing monooxygenase (FMO) and P450 enzymes

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Effects of Fat and Fatty Acid Intake on Inflammatory and Immune Responses: A Critical Review

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Pathways in Microbe-Induced Obesity

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Nicotinic acid inhibits progression of atherosclerosis in mice through its receptor GPR109A expressed by immune cells

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Archaebiotics: Proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease

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Effect of diet on asthma and allergic sensitisation in the International Study on Allergies and Asthma in Childhood (ISAAC) Phase Two

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