Eberl, G. A new vision of immunity: homeostasis of the superorganism. Mucosal Immunol. 5 May 2010 (doi:10.1038/mi.2010.20). ArticleCASPubMed Google Scholar
Moran, N. A., McCutcheon, J. P. & Nakabachi, A. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet.42, 165–190 (2008). ArticleCASPubMed Google Scholar
Hooper, L. V. & Macpherson, A. J. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nature Rev. Immunol.10, 159–169 (2010). ArticleCAS Google Scholar
Eberl, G. & Lochner, M. The development of intestinal lymphoid tissues at the interface of self and microbiota. Mucosal Immunol.2, 478–485 (2009). ArticleCASPubMed Google Scholar
Gaboriau-Routhiau, V. et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity31, 677–689 (2009). ArticleCASPubMed Google Scholar
Vaishnava, S., Behrendt, C. L., Ismail, A. S., Eckmann, L. & Hooper, L. V. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proc. Natl Acad. Sci. USA105, 20858–20863 (2008). ArticleCASPubMedPubMed Central Google Scholar
Peterson, D. A., McNulty, N. P., Guruge, J. L. & Gordon, J. I. IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe2, 328–339 (2007). ArticleCASPubMed Google Scholar
Macpherson, A. J. & Uhr, T. Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science303, 1662–1665 (2004). ArticleCASPubMed Google Scholar
Mazmanian, S. K., Round, J. L. & Kasper, D. L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature453, 620–625 (2008). ArticleCASPubMed Google Scholar
Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl Acad. Sci. USA105, 16731–16736 (2008). ArticleCASPubMedPubMed Central Google Scholar
Round, J. L. & Mazmanian, S. K. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc. Natl Acad. Sci. USA107, 12204–12209 (2010). ArticleCASPubMedPubMed Central Google Scholar
Fagarasan, S. et al. Critical roles of activation-induced cytidine deaminase in the homeostasis of gut flora. Science298, 1424–1427 (2002). ArticleCASPubMed Google Scholar
Malamut, G. et al. The enteropathy associated with common variable immunodeficiency: the delineated frontiers with celiac disease. Am. J. Gastroenterol. 15 Jun 2010 (doi:10.1038/ajg.2010.214). ArticleCASPubMed Google Scholar
Bouma, G. & Strober, W. The immunological and genetic basis of inflammatory bowel disease. Nature Rev. Immunol.3, 521–533 (2003). ArticleCAS Google Scholar
Glocker, E. O. et al. Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. N. Engl. J. Med.361, 2033–2045 (2009). CASPubMedPubMed Central Google Scholar
Talham, G. L., Jiang, H. Q., Bos, N. A. & Cebra, J. J. Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system. Infect. Immun.67, 1992–2000 (1999). CASPubMedPubMed Central Google Scholar
Klaasen, H. L. et al. Intestinal, segmented, filamentous bacteria in a wide range of vertebrate species. Lab. Anim.27, 141–150 (1993). ArticleCASPubMed Google Scholar
Lupp, C. et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe2, 119–129 (2007). ArticleCASPubMed Google Scholar
Stecher, B. et al. Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol.5, 2177–2189 (2007). ArticleCASPubMed Google Scholar
Snel, J. et al. Comparison of 16S rRNA sequences of segmented filamentous bacteria isolated from mice, rats, and chickens and proposal of “Candidatus Arthromitus”. Int. J. Syst. Bacteriol.45, 780–782 (1995). ArticleCASPubMed Google Scholar
Stepankova, R. et al. Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells. Inflamm. Bowel Dis.13, 1202–1211 (2007). ArticlePubMed Google Scholar
Wu, H.-S. et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity32, 815–827 (2010). ArticleCASPubMedPubMed Central Google Scholar
Lee, Y. K., Menezes, J. S., Umesaki, Y. & Mazmanian, S. K. Microbes and health sackler colloquium: proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc. Natl Acad. Sci. USA 28 Jul 2010 (doi:10.1073/pnas.10000.82107).
Chow, J. & Mazmanian, S. K. A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe7, 265–276 (2010). ArticleCASPubMedPubMed Central Google Scholar
Polk, D. B. & Peek, R. M. Jr. Helicobacter pylori: gastric cancer and beyond. Nature Rev. Cancer10, 403–414 (2010). ArticleCAS Google Scholar
Wu, S. et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nature Med.15, 1016–1022 (2009). ArticleCASPubMed Google Scholar
Carvalho, F. A. et al. Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM. J. Exp. Med.206, 2179–2189 (2009). ArticleCASPubMedPubMed Central Google Scholar
Darfeuille-Michaud, A. et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology127, 412–421 (2004). ArticlePubMed Google Scholar
Barnich, N. et al. CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease. J. Clin. Invest.117, 1566–1574 (2007). ArticleCASPubMedPubMed Central Google Scholar
Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA104, 13780–13785 (2007). ArticleCASPubMedPubMed Central Google Scholar
Sokol, H. et al. Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm. Bowel Dis.12, 106–111 (2006). ArticlePubMed Google Scholar
Swidsinski, A., Weber, J., Loening-Baucke, V., Hale, L. P. & Lochs, H. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J. Clin. Microbiol.43, 3380–3389 (2005). ArticlePubMedPubMed Central Google Scholar
Garrett, W. S. et al. Colitis-associated colorectal cancer driven by T-bet deficiency in dendritic cells. Cancer Cell16, 208–219 (2009). ArticleCASPubMedPubMed Central Google Scholar
Garrett, W. et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally-transmitted colitis. Cell Host Microbe (in the press).
Konrad, A., Cong, Y., Duck, W., Borlaza, R. & Elson, C. O. Tight mucosal compartmentation of the murine immune response to antigens of the enteric microbiota. Gastroenterology130, 2050–2059 (2006). ArticleCASPubMed Google Scholar
Bauer, H., Horowitz, R. E., Levenson, S. M. & Popper, H. The response of the lymphatic tissue to the microbial flora. Studies on germfree mice. Am. J. Pathol.42, 471–483 (1963). CASPubMedPubMed Central Google Scholar
Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell122, 107–118 (2005). ArticleCASPubMed Google Scholar
Clarke, T. B. et al. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nature Med.16, 228–231 (2010). ArticleCASPubMed Google Scholar
Noverr, M. C. & Huffnagle, G. B. The 'microflora hypothesis' of allergic diseases. Clin. Exp. Allergy35, 1511–1520 (2005). ArticleCASPubMed Google Scholar
Sjogren, Y. M., Jenmalm, M. C., Bottcher, M. F., Bjorksten, B. & Sverremark-Ekstrom, E. Altered early infant gut microbiota in children developing allergy up to 5 years of age. Clin. Exp. Allergy39, 518–526 (2009). ArticleCASPubMed Google Scholar
Kuitunen, M. et al. Probiotics prevent IgE-associated allergy until age 5 years in cesarean-delivered children but not in the total cohort. J. Allergy Clin. Immunol.123, 335–341 (2009). ArticlePubMed Google Scholar
Penders, J., Stobberingh, E. E., van den Brandt, P. A. & Thijs, C. The role of the intestinal microbiota in the development of atopic disorders. Allergy62, 1223–1236 (2007). ArticleCASPubMed Google Scholar
Noverr, M. C., Falkowski, N. R., McDonald, R. A., McKenzie, A. N. & Huffnagle, G. B. Development of allergic airway disease in mice following antibiotic therapy and fungal microbiota increase: role of host genetics, antigen, and interleukin-13. Infect. Immun.73, 30–38 (2005). ArticleCASPubMedPubMed Central Google Scholar
Bashir, M. E., Louie, S., Shi, H. N. & Nagler-Anderson, C. Toll-like receptor 4 signaling by intestinal microbes influences susceptibility to food allergy. J. Immunol.172, 6978–6987 (2004). ArticleCASPubMed Google Scholar
Vaahtovuo, J., Munukka, E., Korkeamaki, M., Luukkainen, R. & Toivanen, P. Fecal microbiota in early rheumatoid arthritis. J. Rheumatol.35, 1500–1505 (2008). CASPubMed Google Scholar
Gray, D. H., Gavanescu, I., Benoist, C. & Mathis, D. Danger-free autoimmune disease in Aire-deficient mice. Proc. Natl Acad. Sci. USA104, 18193–18198 (2007). ArticleCASPubMedPubMed Central Google Scholar
Hase, K. et al. Activation-induced cytidine deaminase deficiency causes organ-specific autoimmune disease. PLoS ONE3, e3033 (2008). ArticlePubMedPubMed Central Google Scholar
Maldonado, M. A. et al. The role of environmental antigens in the spontaneous development of autoimmunity in MRL-lpr mice. J. Immunol.162, 6322–6330 (1999). CASPubMed Google Scholar
Sinkorova, Z., Capkova, J., Niederlova, J., Stepankova, R. & Sinkora, J. Commensal intestinal bacterial strains trigger ankylosing enthesopathy of the ankle in inbred B10.BR (H-2k) male mice. Hum. Immunol.69, 845–850 (2008). ArticleCASPubMed Google Scholar
Abdollahi-Roodsaz, S. et al. Stimulation of TLR2 and TLR4 differentially skews the balance of T cells in a mouse model of arthritis. J. Clin. Invest.118, 205–216 (2008). ArticleCASPubMed Google Scholar
Breban, M. A., Moreau, M. C., Fournier, C., Ducluzeau, R. & Kahn, M. F. Influence of the bacterial flora on collagen-induced arthritis in susceptible and resistant strains of rats. Clin. Exp. Rheumatol.11, 61–64 (1993). CASPubMed Google Scholar
Giraud, A. et al. Dissecting the genetic components of adaptation of Escherichia coli to the mouse gut. PLoS Genet.4, e2 (2008). ArticlePubMedPubMed Central Google Scholar
Turnbaugh, P. J., Backhed, F., Fulton, L. & Gordon, J. I. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe3, 213–223 (2008). ArticleCASPubMedPubMed Central Google Scholar
Backhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl Acad. Sci. USA101, 15718–15723 (2004). ArticlePubMedPubMed Central Google Scholar
Samuel, B. S. et al. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc. Natl Acad. Sci. USA105, 16767–16772 (2008). ArticleCASPubMedPubMed Central Google Scholar
Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science328, 228–231 (2010). ArticleCASPubMedPubMed Central Google Scholar
Peyrin-Biroulet, L. et al. Peroxisome proliferator-activated receptor γ activation is required for maintenance of innate antimicrobial immunity in the colon. Proc. Natl Acad. Sci. USA107, 8772–8777 (2010). ArticleCASPubMedPubMed Central Google Scholar
Kumar, A. et al. Commensal bacteria modulate cullin-dependent signaling via generation of reactive oxygen species. EMBO J.26, 4457–4466 (2007). ArticleCASPubMedPubMed Central Google Scholar
Dubuquoy, L. et al. Impaired expression of peroxisome proliferator-activated receptor γ in ulcerative colitis. Gastroenterology124, 1265–1276 (2003). ArticleCASPubMed Google Scholar
Kelly, D. et al. Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-γ and RelA. Nature Immunol.5, 104–112 (2004). ArticleCAS Google Scholar
Chieppa, M., Rescigno, M., Huang, A. Y. & Germain, R. N. Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement. J. Exp. Med.203, 2841–2852 (2006). ArticleCASPubMedPubMed Central Google Scholar
Schulz, O. et al. Intestinal CD103+, but not CX3CR1+, antigen sampling cells migrate in lymph and serve classical dendritic cell functions. J. Exp. Med.206, 3101–3114 (2009). ArticleCASPubMedPubMed Central Google Scholar
Tsuji, M. et al. Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer's patches. Science323, 1488–1492 (2009). ArticleCASPubMed Google Scholar
Coombes, J. L. & Powrie, F. Dendritic cells in intestinal immune regulation. Nature Rev. Immunol.8, 435–446 (2008). ArticleCAS Google Scholar
Atarashi, K. et al. ATP drives lamina propria TH17 cell differentiation. Nature455, 808–812 (2008). ArticleCASPubMed Google Scholar
Zhou, L., Chong, M. M. & Littman, D. R. Plasticity of CD4+ T cell lineage differentiation. Immunity30, 646–655 (2009). ArticleCASPubMed Google Scholar
Keilbaugh, S. A. et al. Activation of RegIIIβ/γ and interferon γ expression in the intestinal tract of SCID mice: an innate response to bacterial colonisation of the gut. Gut54, 623–629 (2005). ArticleCASPubMedPubMed Central Google Scholar
Umesaki, Y., Okada, Y., Matsumoto, S., Imaoka, A. & Setoyama, H. Segmented filamentous bacteria are indigenous intestinal bacteria that activate intraepithelial lymphocytes and induce MHC class II molecules and fucosyl asialo GM1 glycolipids on the small intestinal epithelial cells in the ex-germ-free mouse. Microbiol. Immunol.39, 555–562 (1995). ArticleCASPubMed Google Scholar