Immune-microbiota interactions in health and disease

Clinical Immunology

Volumn 159, Issue 2, 2015, Pages 122-127

  Palm, Noah W ^a   de Zoete, Marcel R ^a   Flavell, Richard A ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Adaptive immunity; Commensals; Immunoglobulin A; Inflammation; Microbiota; T cells

Indexed keywords

IMMUNOGLOBULIN A;

ADAPTIVE IMMUNITY; B LYMPHOCYTE; COMMENSAL; HOST PATHOGEN INTERACTION; HUMAN; IMMUNE SYSTEM; IMMUNOREGULATION; INNATE IMMUNITY; INTESTINE FLORA; NONHUMAN; PRIORITY JOURNAL; REVIEW; T LYMPHOCYTE; IMMUNOLOGY; INFLAMMATION; INTESTINE; MICROBIOLOGY; SYMBIOSIS;

ADAPTIVE IMMUNITY; B-LYMPHOCYTES; GASTROINTESTINAL MICROBIOME; HUMANS; IMMUNE SYSTEM; IMMUNITY, INNATE; IMMUNOGLOBULIN A; INFLAMMATION; INTESTINES; SYMBIOSIS; T-LYMPHOCYTES;

EID: 84952324827     PISSN: 15216616     EISSN: 15217035     Source Type: Journal    
DOI: 10.1016/j.clim.2015.05.014     Document Type: Review

References (79)

1. Faith J.J., et al. The long-term stability of the human gut microbiota. Science 2013, 341:1237439.
2. Qin J., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
3. Littman D.R., Pamer E.G. Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host Microbe 2011, 10:311-323.
4. Blumberg R., Powrie F. Microbiota, disease, and back to health: a metastable journey. Sci. Transl. Med. 2012, 4. (137rv137).
5. Hooper L.V., Littman D.R., Macpherson A.J. Interactions between the microbiota and the immune system. Science 2012, 336:1268-1273.
6. Backhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., Gordon J.I. Host-bacterial mutualism in the human intestine. Science 2005, 307:1915-1920.
7. Deplancke B., Gaskins H.R. Microbial modulation of innate defense: goblet cells and the intestinal mucus layer. Am. J. Clin. Nutr. 2001, 73:1131s-1141s.
8. Smith K., McCoy K.D., Macpherson A.J. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin. Immunol. 2007, 19:59-69.
9. Macpherson A.J., McCoy K.D. Standardised animal models of host microbial mutualism. Mucosal Immunol. 2014.
10. Kernbauer E., Ding Y., Cadwell K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 2014, 516:94-98.
11. Bouskra D., et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 2008, 456:507-510.
12. Chow J., Tang H.Q., Mazmanian S.K. Pathobionts of the gastrointestinal microbiota and inflammatory disease. Curr. Opin. Immunol. 2011, 23:473-480.
13. Ivanov I.I., Honda K. Intestinal commensal microbes as immune modulators. Cell Host Microbe 2012, 12:496-508.
14. Gaboriau-Routhiau V., et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 2009, 31:677-689.
15. Ivanov I.I., et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009, 139:485-498.
16. Yang Y., et al. Focused specificity of intestinal TH17 cells towards commensal bacterial antigens. Nature 2014, 510:152-156.
17. Goto Y., et al. Segmented filamentous bacteria antigens presented by intestinal dendritic cells drive mucosal Th17 cell differentiation. Immunity 2014, 40:594-607.
18. Lecuyer E., et al. Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses. Immunity 2014, 40:608-620.
19. Qiu J., et al. Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora. Immunity 2013, 39:386-399.
20. Stepankova R., et al. Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RB high CD4+ T cells. Inflamm. Bowel Dis. 2007, 13:1202-1211.
21. Wu H.J., et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 2010, 32:815-827.
22. Song-Zhao G.X., Maloy K.J. Experimental mouse models of T cell-dependent inflammatory bowel disease. Methods Mol. Biol. 2014, 1193:199-211.
23. Coccia M., et al. IL-1beta mediates chronic intestinal inflammation by promoting the accumulation of IL-17A secreting innate lymphoid cells and CD4(+) Th17 cells. J. Exp. Med. 2012, 209:1595-1609.
24. Elinav E., et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 2011, 145:745-757.
25. Garrett W.S., et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 2010, 8:292-300.
26. Garrett W.S., et al. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 2007, 131:33-45.
27. Powell N., et al. The transcription factor T-bet regulates intestinal inflammation mediated by interleukin-7 receptor+ innate lymphoid cells. Immunity 2012, 37:674-684.
28. Devkota S., et al. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 2012, 487:104-108.
29. 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. Cell 2005, 122:107-118.
30. Round J.L., Mazmanian S.K. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:12204-12209.
31. An D., et al. Sphingolipids from a symbiotic microbe regulate homeostasis of host intestinal natural killer T cells. Cell 2014, 156:123-133.
32. Wieland Brown L.C., et al. Production of alpha-galactosylceramide by a prominent member of the human gut microbiota. PLoS Biol. 2013, 11:e1001610.
33. Huang J.Y., Lee S.M., Mazmanian S.K. The human commensal Bacteroides fragilis binds intestinal mucin. Anaerobe 2011, 17:137-141.
34. Geuking M.B., et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity 2011, 34:794-806.
35. Atarashi K., et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011, 331:337-341.
36. Atarashi K., et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 2013, 500:232-236.
37. Smith P.M., et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 2013, 341:569-573.
38. Furusawa Y., et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013, 504:446-450.
39. Arpaia N., et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013, 504:451-455.
40. Mazmanian S.K., Round J.L., Kasper D.L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008, 453:620-625.
41. Round J.L., et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011, 332:974-977.
42. Rakoff-Nahoum S., Paglino J., Eslami-Varzaneh F., Edberg S., Medzhitov R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 2004, 118:229-241.
43. Larsson E., et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut 2012, 61:1124-1131.
44. Wen L., et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008, 455:1109-1113.
45. Vijay-Kumar M., et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010, 328:228-231.
46. Carvalho F.A., et al. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 2012, 12:139-152.
47. Chassaing B., Koren O., Carvalho F.A., Ley R.E., Gewirtz A.T. AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut 2014, 63:1069-1080.
48. Chassaing B., Ley R.E., Gewirtz A.T. Intestinal epithelial cell toll-like receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice. Gastroenterology 2014, 147. (1363-1377 e1317).
49. Ubeda C., et al. Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J. Exp. Med. 2012, 209:1445-1456.
50. Couturier-Maillard A., et al. NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer. J. Clin. Invest. 2013, 123:700-711.
51. Petnicki-Ocwieja T., et al. Nod2 is required for the regulation of commensal microbiota in the intestine. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:15813-15818.
52. Robertson S.J., et al. Nod1 and Nod2 signaling does not alter the composition of intestinal bacterial communities at homeostasis. Gut Microbes 2013, 4:222-231.
53. Henao-Mejia J., et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 2012, 482:179-185.
54. Hu B., et al. Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:9862-9867.
55. Wlodarska M., et al. NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion. Cell 2014, 156:1045-1059.
56. Salzman N.H., et al. Enteric defensins are essential regulators of intestinal microbial ecology. Nat. Immunol. 2010, 11:76-83.
57. Salzman N.H., Bevins C.L. Dysbiosis-a consequence of Paneth cell dysfunction. Semin. Immunol. 2013, 25:334-341.
58. Vaishnava S., et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 2011, 334:255-258.
59. Jakobsson H.E., et al. The composition of the gut microbiota shapes the colon mucus barrier. EMBO Rep. 2015, 16:164-177.
60. Sommer F., et al. Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture. PLoS One 2014, 9:e85254.
61. Lee Y.K., Mazmanian S.K. Has the microbiota played a critical role in the evolution of the adaptive immune system?. Science 2010, 330:1768-1773.
62. Zhang H., Sparks J.B., Karyala S.V., Settlage R., Luo X.M. Host adaptive immunity alters gut microbiota. ISME J. 2015, 9:770-781.
63. Kato L.M., Kawamoto S., Maruya M., Fagarasan S. The role of the adaptive immune system in regulation of gut microbiota. Immunol. Rev. 2014, 260:67-75.
64. Kawamoto S., et al. Foxp3(+) T cells regulate immunoglobulin a selection and facilitate diversification of bacterial species responsible for immune homeostasis. Immunity 2014, 41:152-165.
65. Tsuji M., et al. Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer's patches. Science 2009, 323:1488-1492.
66. Cong Y., Feng T., Fujihashi K., Schoeb T.R., Elson C.O. A dominant, coordinated T regulatory cell-IgA response to the intestinal microbiota. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:19256-19261.
67. Hirota K., et al. Plasticity of Th17 cells in Peyer's patches is responsible for the induction of T cell-dependent IgA responses. Nat. Immunol. 2013, 14:372-379.
68. Klaasen H.L., et al. Apathogenic, intestinal, segmented, filamentous bacteria stimulate the mucosal immune system of mice. Infect. Immun. 1993, 61:303-306.
69. 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. 1999, 67:1992-2000.
70. Fagarasan S., et al. Critical roles of activation-induced cytidine deaminase in the homeostasis of gut flora. Science 2002, 298:1424-1427.
71. Suzuki K., et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:1981-1986.
72. Maruya M., Kawamoto S., Kato L.M., Fagarasan S. Impaired selection of IgA and intestinal dysbiosis associated with PD-1-deficiency. Gut Microbes 2013, 4:165-171.
73. Kawamoto S., et al. The inhibitory receptor PD-1 regulates IgA selection and bacterial composition in the gut. Science 2012, 336:485-489.
74. Kubinak J.L., et al. MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health. Cell Host Microbe 2015, 17:153-163.
75. Mirpuri J., et al. Proteobacteria-specific IgA regulates maturation of the intestinal microbiota. Gut Microbes 2014, 5:28-39.
76. 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 Microbe 2007, 2:328-339.
77. Corthesy B. Multi-faceted functions of secretory IgA at mucosal surfaces. Front. Immunol. 2013, 4:185.
78. Cullender T.C., et al. Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. Cell Host Microbe 2013, 14:571-581.
79. Palm N.W., et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 2014, 158:1000-1010.