Role of the gut microbiota in immunity and inflammatory disease

Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease

Hugot, J.-P., Chamaillard, M., Zouali, H., Lesage, S., Cézard, J.-P., Belaiche, J., Almer, S., Tysk, C., O'Morain, C. A., Gassull, M., et al. (2001) · Nature · doi:10.1038/35079107 · Cited by 5,591

A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease

Ogura, Y., Bonen, D. K., Inohara, N., Nicolae, D. L., Chen, F. F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R. H., et al. (2001) · Nature · doi:10.1038/35079114 · Cited by 5,030

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermúdez-Humarán, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804812105 · Cited by 4,413

Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis

Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004) · Cell · doi:10.1016/j.cell.2004.07.002 · Cited by 4,251

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) · Science · doi:10.1126/science.1198469 · Cited by 3,752

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

An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System

Mazmanian, S. K., Liu, C. H., Tzianabos, A. O., & Kasper, D. L. (2005) · Cell · doi:10.1016/j.cell.2005.05.007 · Cited by 2,910

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

A microbial symbiosis factor prevents intestinal inflammatory disease

Mazmanian, S. K., Round, J. L., & Kasper, D. L. (2008) · Nature · doi:10.1038/nature07008 · Cited by 2,340

Intestinal inflammation targets cancer-inducing activity of the microbiota

Arthur, J. C., Perez-Chanona, E., Mühlbauer, M., Tomkovich, S., Uronis, J. M., Fan, T.-J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., et al. (2012) · Science · doi:10.1126/science.1224820 · Cited by 2,263

Inducible Foxp3 + regulatory T-cell development by a commensal bacterium of the intestinal microbiota

Round, J. L., & Mazmanian, S. K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909122107 · Cited by 2,233

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200

Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity

Markle, J. G. M., Frank, D. N., Mortin-Toth, S., Robertson, C. E., Feazel, L. M., Rolle-Kampczyk, U., von Bergen, M., McCoy, K. D., Macpherson, A. J., & Danska, J. S. (2013) · Science · doi:10.1126/science.1233521 · Cited by 2,025

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

Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens

Zheng, Y., Valdez, P. A., Danilenko, D. M., Hu, Y., Susan, M. L., Gong, Q., Abbas, A. R., Modrusan, Z. D., Ghilardi, N., de Sauvage, F. J., et al. (2008) · Nature Medicine · doi:10.1038/nm1720 · Cited by 1,972

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A. J., Tabernero, J., et al. (2012) · Genome Research · doi:10.1101/gr.126573.111 · Cited by 1,960

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1

Hampe, J., Franke, A., Rosenstiel, P. C., Till, A., Teuber, M., Huse, K., Albrecht, M., Mayr, G., Vega, F. M. D. L., Briggs, J. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1954 · Cited by 1,948

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

Wen, L., Ley, R. E., Volchkov, P. Y., Stranges, P. B., Avanesyan, L., Stonebraker, A. C., Hu, C., Wong, F. S., Szot, G. L., Bluestone, J. A., et al. (2008) · Nature · doi:10.1038/nature07336 · Cited by 1,921

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

A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses

Wu, S., Rhee, K.-J., Albesiano, E., Rabizadeh, S., Wu, X., Yen, H.-R., Huso, D. L., Brancati, F. L., Wick, E., McAllister, F., et al. (2009) · Nature Medicine · doi:10.1038/nm.2015 · Cited by 1,812

The keystone-pathogen hypothesis

Hajishengallis, G., Darveau, R. P., & Curtis, M. A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2873 · Cited by 1,790

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770

Host Recognition of Bacterial Muramyl Dipeptide Mediated through NOD2

Inohara, N., Ogura, Y., Fontalba, A., Gutierrez, O., Pons, F., Crespo, J., Fukase, K., Inamura, S., Kusumoto, S., Hashimoto, M., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.c200673200 · Cited by 1,694

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

Olszak, T., An, D., Zeissig, S., Vera, M. P., Richter, J., Franke, A., Glickman, J. N., Siebert, R., Baron, R. M., Kasper, D. L., et al. (2012) · Science · doi:10.1126/science.1219328 · Cited by 1,661

The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota

Round, J. L., Lee, S. M., Li, J., Tran, G., Jabri, B., Chatila, T. A., & Mazmanian, S. K. (2011) · Science · doi:10.1126/science.1206095 · Cited by 1,604

Gut-Residing Segmented Filamentous Bacteria Drive Autoimmune Arthritis via T Helper 17 Cells

Wu, H.-J., Ivanov, I. I., Darce, J., Hattori, K., Shima, T., Umesaki, Y., Littman, D. R., Benoist, C., & Mathis, D. (2010) · Immunity · doi:10.1016/j.immuni.2010.06.001 · Cited by 1,577

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

Cadwell, K., Liu, J. Y., Brown, S. L., Miyoshi, H., Loh, J., Lennerz, J. K., Kishi, C., Kc, W., Carrero, J. A., Hunt, S., et al. (2008) · Nature · doi:10.1038/nature07416 · Cited by 1,542

Immune adaptations that maintain homeostasis with the intestinal microbiota

Hooper, L. V., & Macpherson, A. J. (2010) · Nature reviews. Immunology · doi:10.1038/nri2710 · Cited by 1,530

Microbiota regulates immune defense against respiratory tract influenza A virus infection

Ichinohe, T., Pang, I. K., Kumamoto, Y., Peaper, D. R., Ho, J. H., Murray, T. S., & Iwasaki, A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019378108 · Cited by 1,502

Resident Enteric Bacteria Are Necessary for Development of Spontaneous Colitis and Immune System Activation in Interleukin-10-Deficient Mice

Sellon, R. K., Tonkonogy, S., Schultz, M., Dieleman, L. A., Grenther, W., Balish, E., Rennick, D. M., & Sartor, R. B. (1998) · Infection and Immunity · doi:10.1128/iai.66.11.5224-5231.1998 · Cited by 1,483

The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

Gaboriau-Routhiau, V., Rakotobe, S., Lécuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., et al. (2009) · Immunity · doi:10.1016/j.immuni.2009.08.020 · Cited by 1,452

Symbiotic bacteria direct expression of an intestinal bactericidal lectin

Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006) · Science · doi:10.1126/science.1127119 · Cited by 1,432

The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine

Vaishnava, S., Yamamoto, M., Severson, K. M., Ruhn, K. A., Yu, X., Koren, O., Ley, R., Wakeland, E. K., & Hooper, L. V. (2011) · Science · doi:10.1126/science.1209791 · Cited by 1,412

Clostridium difficile infection: new developments in epidemiology and pathogenesis

Rupnik, M., Wilcox, M. H., & Gerding, D. N. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2164 · Cited by 1,380

Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis

Lee, Y. K., Menezes, J. S., Umesaki, Y., & Mazmanian, S. K. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000082107 · Cited by 1,323

Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry

Travassos, L. H., Carneiro, L. A. M., Ramjeet, M., Hussey, S., Kim, Y.-G., Magalhães, J. G., Yuan, L., Soares, F., Chea, E., Le Bourhis, L., et al. (2010) · Nature Immunology · doi:10.1038/ni.1823 · Cited by 1,306

A human natural killer cell subset provides an innate source of IL-22 for mucosal immunity

Cella, M., Fuchs, A. G., Vermi, W., Facchetti, F., Otero, K., Lennerz, J. K., Doherty, J. M., Mills, J. C., & Colonna, M. (2008) · Nature · doi:10.1038/nature07537 · Cited by 1,298

Gut inflammation provides a respiratory electron acceptor for Salmonella

Winter, S., Thiennimitr, P., Winter, M. G., Butler, B. P., Huseby, D. L., Crawford, R. W., Russell, J. M., Bevins, C. L., Adams, L. G., Tsolis, R. M., et al. (2010) · Nature · doi:10.1038/nature09415 · Cited by 1,271

Commensal microbiota and myelin autoantigen cooperate to trigger autoimmune demyelination

Berer, K., Mues, M., Koutrolos, M., Rasbi, Z. A., Boziki, M., Johner, C., Wekerle, H., & Krishnamoorthy, G. (2011) · Nature · doi:10.1038/nature10554 · Cited by 1,251

Gut immune maturation depends on colonization with a host-specific microbiota

Chung, H., Pamp, S. J., Hill, J. A., Surana, N. K., Edelman, S. M., Troy, E. B., Reading, N. C., Villablanca, E. J., Wang, S., Mora, J. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.037 · Cited by 1,241

Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis

Bevins, C. L., & Salzman, N. H. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2546 · Cited by 1,238

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility

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The germfree state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats.

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Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity

Clarke, T. B., Davis, K. M., Lysenko, E. S., Zhou, A. Y., Yu, Y., & Weiser, J. N. (2010) · Nature Medicine · doi:10.1038/nm.2087 · Cited by 1,154

Microbial Flora Drives Interleukin 22 Production in Intestinal NKp46+ Cells that Provide Innate Mucosal Immune Defense

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A Primitive T Cell-Independent Mechanism of Intestinal Mucosal IgA Responses to Commensal Bacteria

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Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis

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Compartmentalized Control of Skin Immunity by Resident Commensals

Naik, S., Bouladoux, N., Wilhelm, C., Molloy, M. J., Salcedo, R., Kastenmuller, W., Deming, C., Quinones, M., Koo, L., Conlan, S., et al. (2012) · Science · doi:10.1126/science.1225152 · Cited by 1,092

ATP drives lamina propria TH17 cell differentiation

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NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation

Cooney, R. M., BAKER, J. T., Brain, O., Danis, B., Pichulik, T., Allan, P., Ferguson, D. J. P., Campbell, B. J., Jewell, D. P., & Simmons, A. (2009) · Nature Medicine · doi:10.1038/nm.2069 · Cited by 1,088

Phenotypically distinct subsets of CD4 + T cells induce or protect from chronic intestinal inflammation in C. B-17 scid mice

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Epithelial NEMO links innate immunity to chronic intestinal inflammation

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Th17 and regulatory T cells in mediating and restraining inflammation

Littman, D. R., & Rudensky, A. Y. (2010) · Cell · doi:10.1016/j.cell.2010.02.021 · Cited by 1,039

Peripheral education of the immune system by colonic commensal microbiota

Lathrop, S. K., Bloom, S. M., Rao, S. M., Nutsch, K., Lio, C.-W., Santacruz, N., Peterson, D. A., Stappenbeck, T. S., & Hsieh, C.-S. (2011) · Nature · doi:10.1038/nature10434 · Cited by 1,034

Generation of Gut-Homing IgA-Secreting B Cells by Intestinal Dendritic Cells

Mora, J. R., Iwata, M., Eksteen, B., Song, S., Junt, T., Senman, B. C., Otipoby, K. L., Yokota, A., Takeuchi, H., Ricciardi‐Castagnoli, P., et al. (2006) · Science · doi:10.1126/science.1132742 · Cited by 1,014

Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17–producing T cell responses

Denning, T. L., Wang, Y., Patel, S. R., Williams, I. R., & Pulendran, B. (2007) · Nature Immunology · doi:10.1038/ni1511 · Cited by 995

Commensal bacteria calibrate the activation threshold of innate antiviral immunity

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Human intestinal macrophages display profound inflammatory anergy despite avid phagocytic and bacteriocidal activity

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The genetics and immunopathogenesis of inflammatory bowel disease

Cho, J. H. (2008) · Nature Reviews Immunology · doi:10.1038/nri2340 · Cited by 940

Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine

Cadwell, K., Patel, K., Maloney, N. S., Liu, T., Ng, A., Storer, C. E., Head, R. D., Xavier, R. J., Stappenbeck, T. S., & Virgin, H. W. (2010) · Cell · doi:10.1016/j.cell.2010.05.009 · Cited by 927

Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System

Garrett, W. S., Lord, G. M., Punit, S., Lugo‐Villarino, G., Mazmanian, S. K., Ito, S., Glickman, J. N., & Glimcher, L. H. (2007) · Cell · doi:10.1016/j.cell.2007.08.017 · Cited by 915

The Aryl Hydrocarbon Receptor Regulates Gut Immunity through Modulation of Innate Lymphoid Cells

Qiu, J., Heller, J. J., Guo, X., Chen, Z. E., Fish, K., Fu, Y., & Zhou, L. (2011) · Immunity · doi:10.1016/j.immuni.2011.11.011 · Cited by 889

RORγt and commensal microflora are required for the differentiation of mucosal interleukin 22–producing NKp46+ cells

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NOD2 (CARD15) mutations in Crohn’s disease are associated with diminished mucosal α-defensin expression

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Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

Geuking, M. B., Cahenzli, J., Lawson, M. A. E., Ng, D. C. K., Slack, E., Hapfelmeier, S., McCoy, K. D., & Macpherson, A. J. (2011) · Immunity · doi:10.1016/j.immuni.2011.03.021 · Cited by 840

The expanding family of innate lymphoid cells: regulators and effectors of immunity and tissue remodeling

Spits, H., & Santo, J. P. D. (2010) · Nature Immunology · doi:10.1038/ni.1962 · Cited by 840

IgA Response to Symbiotic Bacteria as a Mediator of Gut Homeostasis

Peterson, D. A., McNulty, N. P., Guruge, J. L., & Gordon, J. I. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.09.013 · Cited by 828

Natural aryl hydrocarbon receptor ligands control organogenesis of intestinal lymphoid follicles

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The microbiome in infectious disease and inflammation

Honda, K., & Littman, D. R. (2012) · Annual Review of Immunology · doi:10.1146/annurev-immunol-020711-074937 · Cited by 791

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

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Regulation of humoral and cellular gut immunity by lamina propria dendritic cells expressing Toll-like receptor 5

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Innate Lymphoid Cells Promote Anatomical Containment of Lymphoid-Resident Commensal Bacteria

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Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection

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Regulated virulence controls the ability of a pathogen to compete with the gut microbiota

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Fecal microbiota transplantation and emerging applications

Borody, T. J., & Khoruts, A. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2011.244 · Cited by 677

Innate lymphoid cells — how did we miss them?

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Unique CD14+ intestinal macrophages contribute to the pathogenesis of Crohn disease via IL-23/IFN-γ axis

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Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis

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Muc2 Protects against Lethal Infectious Colitis by Disassociating Pathogenic and Commensal Bacteria from the Colonic Mucosa

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Acute pancreatitis

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Maintenance of colonic homeostasis by distinctive apical TLR9 signalling in intestinal epithelial cells

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