Advertisement
No access
Special Issue Review

Interactions Between the Microbiota and the Immune System

Science
8 Jun 2012
Vol 336, Issue 6086
pp. 1268-1273

Abstract

The large numbers of microorganisms that inhabit mammalian body surfaces have a highly coevolved relationship with the immune system. Although many of these microbes carry out functions that are critical for host physiology, they nevertheless pose the threat of breach with ensuing pathologies. The mammalian immune system plays an essential role in maintaining homeostasis with resident microbial communities, thus ensuring that the mutualistic nature of the host-microbial relationship is maintained. At the same time, resident bacteria profoundly shape mammalian immunity. Here, we review advances in our understanding of the interactions between resident microbes and the immune system and the implications of these findings for human health.

Get full access to this article

View all available purchase options and get full access to this article.

References and Notes

1
Ley R. E., Lozupone C. A., Hamady M., Knight R., Gordon J. I., Worlds within worlds: Evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6, 776 (2008). 10.1038/nrmicro1978
2
McFall-Ngai M., Adaptive immunity: Care for the community. Nature 445, 153 (2007). 10.1038/445153a
3
A. J. Macpherson, M. B. Geuking, J. Kirundi, S. Collins, K. D. McCoy, in Encyclopedia of Microbiology (Elsevier, London, 2009), vol. 156, pp. 237–246.
4
Geuking M. B., et al., Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity 34, 794 (2011). 10.1016/j.immuni.2011.03.021
5
Vaishnava S., et al., The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255 (2011). 10.1126/science.1209791
6
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 (1999).10085047
7
Blumberg R. S., Powrie F., Microbiota, disease, and back to health: A metastable journey. Sci. Transl. Med. 4, 137rv7 (2012).
8
Goodman A. L., et al., Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl. Acad. Sci. U.S.A. 108, 6252 (2011). 10.1073/pnas.1102938108
9
Legrand N., et al., Humanized mice for modeling human infectious disease: Challenges, progress, and outlook. Cell Host Microbe 6, 5 (2009). 10.1016/j.chom.2009.06.006
10
Hapfelmeier S., et al., Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science 328, 1705 (2010). 10.1126/science.1188454
11
Hooper L. V., et al., Molecular analysis of commensal host-microbial relationships in the intestine. Science 291, 881 (2001). 10.1126/science.291.5505.881
12
Holmes E., Li J. V., Athanasiou T., Ashrafian H., Nicholson J. K., Understanding the role of gut microbiome-host metabolic signal disruption in health and disease. Trends Microbiol. 19, 349 (2011).21684749
13
Hooper L. V., Stappenbeck T. S., Hong C. V., Gordon J. I., Angiogenins: A new class of microbicidal proteins involved in innate immunity. Nat. Immunol. 4, 269 (2003). 10.1038/ni888
14
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 2, 328 (2007). 10.1016/j.chom.2007.09.013
15
Stappenbeck T. S., Hooper L. V., Gordon J. I., Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc. Natl. Acad. Sci. U.S.A. 99, 15451 (2002). 10.1073/pnas.202604299
16
Johansson M. E. V., et al., The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc. Natl. Acad. Sci. U.S.A. 105, 15064 (2008). 10.1073/pnas.0803124105
17
Johansson M. E. V., Larsson J. M. H., Hansson G. C., The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc. Natl. Acad. Sci. U.S.A. 108 (suppl. 1), 4659 (2011). 10.1073/pnas.1006451107
18
Cash H. L., Whitham C. V., Behrendt C. L., Hooper L. V., Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313, 1126 (2006). 10.1126/science.1127119
19
Brandl K., Plitas G., Schnabl B., DeMatteo R. P., Pamer E. G., MyD88-mediated signals induce the bactericidal lectin RegIII gamma and protect mice against intestinal Listeria monocytogenes infection. J. Exp. Med. 204, 1891 (2007). 10.1084/jem.20070563
20
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. U.S.A. 105, 20858 (2008). 10.1073/pnas.0808723105
21
Macpherson A. J., Uhr T., Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303, 1662 (2004). 10.1126/science.1091334
22
Macpherson A. J., et al., A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science 288, 2222 (2000). 10.1126/science.288.5474.2222
23
Kelsall B., Recent progress in understanding the phenotype and function of intestinal dendritic cells and macrophages. Mucosal Immunol. 1, 460 (2008). 10.1038/mi.2008.61
24
Spits H., Di Santo J. P., The expanding family of innate lymphoid cells: regulators and effectors of immunity and tissue remodeling. Nat. Immunol. 12, 21 (2011). 10.1038/ni.1962
25
Sonnenberg G. F., et al., Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science 336, 1321 (2012).
26
Slack E., et al., Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism. Science 325, 617 (2009). 10.1126/science.1172747
27
Sonnenburg E. D., et al., Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241 (2010). 10.1016/j.cell.2010.05.005
28
Sonnenburg J. L., et al., Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955 (2005). 10.1126/science.1109051
29
Salzman N. H., Ghosh D., Huttner K. M., Paterson Y., Bevins C. L., Protection against enteric salmonellosis in transgenic mice expressing a human intestinal defensin. Nature 422, 522 (2003). 10.1038/nature01520
30
Garrett W. S., et al., Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131, 33 (2007). 10.1016/j.cell.2007.08.017
31
Vijay-Kumar M., et al., Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228 (2010). 10.1126/science.1179721
32
Elinav E., et al., NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145, 745 (2011). 10.1016/j.cell.2011.04.022
33
Costello E. K., Relman D. A., The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255 (2012).
34
Rakoff-Nahoum S., Medzhitov R., Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88. Science 317, 124 (2007). 10.1126/science.1140488
35
Pull S. L., Doherty J. M., Mills J. C., Gordon J. I., Stappenbeck T. S., Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc. Natl. Acad. Sci. U.S.A. 102, 99 (2005). 10.1073/pnas.0405979102
36
Kinnebrew M. A., et al., Bacterial flagellin stimulates Toll-like receptor 5-dependent defense against vancomycin-resistant Enterococcus infection. J. Infect. Dis. 201, 534 (2010). 10.1086/650203
37
Kinnebrew M. A., et al., Interleukin 23 production by intestinal CD103(+)CD11b(+) dendritic cells in response to bacterial flagellin enhances mucosal innate immune defense. Immunity 36, 276 (2012). 10.1016/j.immuni.2011.12.011
38
Gaboriau-Routhiau V., et al., The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31, 677 (2009). 10.1016/j.immuni.2009.08.020
39
Ivanov I. I., et al., Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485 (2009). 10.1016/j.cell.2009.09.033
40
Atarashi K., et al., Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337 (2011). 10.1126/science.1198469
41
Round J. L., et al., The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 332, 974 (2011). 10.1126/science.1206095
42
Abraham C., Cho J. H., IL-23 and autoimmunity: New insights into the pathogenesis of inflammatory bowel disease. Annu. Rev. Med. 60, 97 (2009). 10.1146/annurev.med.60.051407.123757
43
Glocker E.-O., et al., Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. N. Engl. J. Med. 361, 2033 (2009). 10.1056/NEJMoa0907206
44
Kieper W. C., et al., Recent immune status determines the source of antigens that drive homeostatic T cell expansion. J. Immunol. 174, 3158 (2005).15749843
45
Lee Y. K., Menezes J. S., Umesaki Y., Mazmanian S. K., Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc. Natl. Acad. Sci. U.S.A. 108, (suppl. 1), 4615 (2011). 10.1073/pnas.1000082107
46
Wu H.-J., et al., Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 32, 815 (2010). 10.1016/j.immuni.2010.06.001
47
Lathrop S. K., et al., Peripheral education of the immune system by colonic commensal microbiota. Nature 478, 250 (2011). 10.1038/nature10434
48
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 122, 107 (2005). 10.1016/j.cell.2005.05.007
49
Olszak T., et al., Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336, 489 (2012). 10.1126/science.1219328
50
Buonocore S., et al., Innate lymphoid cells drive interleukin-23-dependent innate intestinal pathology. Nature 464, 1371 (2010). 10.1038/nature08949
51
Sonnenberg G. F., Monticelli L. A., Elloso M. M., Fouser L. A., Artis D., CD4(+) lymphoid tissue-inducer cells promote innate immunity in the gut. Immunity 34, 122 (2011). 10.1016/j.immuni.2010.12.009
52
Vonarbourg C., et al., Regulated expression of nuclear receptor RORI3t confers distinct functional fates to NK cell receptor-expressing RORI3t(+) innate lymphocytes. Immunity 33, 736 (2010). 10.1016/j.immuni.2010.10.017
53
Satoh-Takayama N., et al., Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense. Immunity 29, 958 (2008). 10.1016/j.immuni.2008.11.001
54
Sawa S., et al., Lineage relationship analysis of RORgammat+ innate lymphoid cells. Science 330, 665 (2010). 10.1126/science.1194597
55
Lorenz R. G., Chaplin D. D., McDonald K. G., McDonough J. S., Newberry R. D., Isolated lymphoid follicle formation is inducible and dependent upon lymphotoxin-sufficient B lymphocytes, lymphotoxin beta receptor, and TNF receptor I function. J. Immunol. 170, _5475 (2003).12759424
56
Croker B. A., et al., Inflammation and autoimmunity caused by a SHP1 mutation depend on IL-1, MyD88, and a microbial trigger. Proc. Natl. Acad. Sci. U.S.A. 105, 15028 (2008). 10.1073/pnas.0806619105
57
Yu C. C., et al., B and T cells are not required for the viable motheaten phenotype. J. Exp. Med. 183, 371 (1996). 10.1084/jem.183.2.371
58
Inohara N., Nuñez G., NODs: Intracellular proteins involved in inflammation and apoptosis. Nat. Rev. Immunol. 3, 371 (2003). 10.1038/nri1086
59
Brydges S. D., et al., Inflammasome-mediated disease animal models reveal roles for innate but not adaptive immunity. Immunity 30, 875 (2009). 10.1016/j.immuni.2009.05.005
60
Henderson C., Goldbach-Mansky R., Monogenic autoinflammatory diseases: New insights into clinical aspects and pathogenesis. Curr. Opin. Rheumatol. 22, 567 (2010).20671522
61
Henao-Mejia J., et al., Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482, 179 (2012).22297845
62
Tschopp J., Schroder K., NLRP3 inflammasome activation: The convergence of multiple signalling pathways on ROS production? Nat. Rev. Immunol. 10, 210 (2010). 10.1038/nri2725
63
Meng G., Zhang F., Fuss I., Kitani A., Strober W., A mutation in the Nlrp3 gene causing inflammasome hyperactivation potentiates Th17 cell-dominant immune responses. Immunity 30, 860 (2009). 10.1016/j.immuni.2009.04.012
64
Ogura Y., et al., A frameshift mutation in NOD2 associated with susceptibility to Crohn?(tm)s disease. Nature 411, 603 (2001). 10.1038/35079114
65
Hugot J. P., et al., Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn?(tm)s disease. Nature 411, 599 (2001). 10.1038/35079107
66
Rutgeerts P., et al., Effect of faecal stream diversion on recurrence of Crohn?(tm)s disease in the neoterminal ileum. Lancet 338, 771 (1991). 10.1016/0140-6736(91)90663-A
67
Cummings J. H., Kong S. C., Probiotics, prebiotics and antibiotics in inflammatory bowel disease. Novartis Found. Symp. 263, 99–, discussion 111, 211 (2004). 10.1002/0470090480.ch8
68
Franke A., et al., Genome-wide meta-analysis increases to 71 the number of confirmed Crohn?(tm)s disease susceptibility loci. Nat. Genet. 42, 1118 (2010). 10.1038/ng.717
69
McGovern D. P. B., et al.NIDDK IBD Genetics Consortium, Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat. Genet. 42, 332 (2010). 10.1038/ng.549
70
Kühn R., LAhler J., Rennick D., Rajewsky K., Müller W., Interleukin-10-deficient mice develop chronic enterocolitis. Cell 75, 263 (1993). 10.1016/0092-8674(93)80068-P
71
Verdaguer J., et al., Spontaneous autoimmune diabetes in monoclonal T cell nonobese diabetic mice. J. Exp. Med. 186, 1663 (1997). 10.1084/jem.186.10.1663
72
Schmidt D., Amrani A., Verdaguer J., Bou S., Santamaria P., Autoantigen-independent deletion of diabetogenic CD4+ thymocytes by protective MHC class II molecules. J. Immunol. 162, 4627 (1999).10202002
73
Ohsugi T., Kurosawa T., Increased incidence of diabetes mellitus in specific pathogen-eliminated offspring produced by embryo transfer in NOD mice with low incidence of the disease. Lab. Anim. Sci. 44, 386 _(1994).7983856
74
E. Leiter, in The Role of Microorganisms in Non-Infectious Disease, R. R. P. de Vries, I. R. Cohen, J. J. van Rood, Eds. (Springer Verlag, Berlin, 1990), pp. 39–55.
75
Wen L., et al., Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455, 1109 (2008). 10.1038/nature07336
76
Carvalho F. A., Aitken J. D., Vijay-Kumar M., Gewirtz A. T., Toll-like receptor-gut microbiota interactions: perturb at your own risk! Annu. Rev. Physiol. 74, 177 (2012). 10.1146/annurev-physiol-020911-153330
77
Zhang Y., et al., TLR9 blockade inhibits activation of diabetogenic CD8+ T cells and delays autoimmune diabetes. J. Immunol. 184, 5645 (2010). 10.4049/jimmunol.0901814
78
Bach J.-F., The effect of infections on susceptibility to autoimmune and allergic diseases. N. Engl. J. Med. 347, 911 (2002). 10.1056/NEJMra020100
79
Nicholson J. K., et al., Host-gut microbiota metabolic interactions. Science 336, 1262 (2012).
80
Moller D. E., Kaufman K. D., Metabolic syndrome: A clinical and molecular perspective. Annu. Rev. Med. 56, 45 (2005). 10.1146/annurev.med.56.082103.104751
81
Ivanov I. I., et al., Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4, 337 (2008). 10.1016/j.chom.2008.09.009
82
Reyes A., et al., Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334 (2010). 10.1038/nature09199

(0)eLetters

eLetters is a forum for ongoing peer review. eLetters are not edited, proofread, or indexed, but they are screened. eLetters should provide substantive and scholarly commentary on the article. Embedded figures cannot be submitted, and we discourage the use of figures within eLetters in general. If a figure is essential, please include a link to the figure within the text of the eLetter. Please read our Terms of Service before submitting an eLetter.

Log In to Submit a Response

No eLetters have been published for this article yet.

Information & Authors

Information

Published In

Science
Volume 336 | Issue 6086
8 June 2012

Article versions

You are viewing the most recent version of this article.

Submission history

Published in print: 8 June 2012

Permissions

Request permissions for this article.

Acknowledgments

L.V.H. is supported by NIH grant DK070855, a Burroughs Wellcome Foundation Investigators in the Pathogenesis of Infectious Diseases Award, and the Howard Hughes Medical Institute. D.R.L. is supported by NIH grant AI080885 and the Howard Hughes Medical Institute. A.J.M. is supported by Swiss National Science Foundation grants 310030-1247324 and CRSII3_136286.

Authors

Affiliations

Lora V. Hooper* [email protected]
The Howard Hughes Medical Institute and Department of Immunology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.
Dan R. Littman
Howard Hughes Medical Institute and Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
Andrew J. Macpherson
Maurice Müller Laboratories, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland.

Notes

*
To whom correspondence should be addressed. E-mail: [email protected]

Metrics & Citations

Metrics

Article Usage

Altmetrics

Citations

Cite as

Export citation

Select the format you want to export the citation of this publication.

Cited by

  1. Stochastic dynamic analysis of a chemostat model of intestinal microbes with migratory effect, AIMS Mathematics, 8, 3, (6356-6374), (2023).https://doi.org/10.3934/math.2023321
    Crossref
  2. Probiotic-educated Tregs are more potent than naïve Tregs for immune tolerance in stressed new-born mice, Beneficial Microbes, 14, 1, (73-84), (2023).https://doi.org/10.3920/BM2022.0095
    Crossref
  3. Microbiome-liver crosstalk: A multihit therapeutic target for liver disease, World Journal of Gastroenterology, 29, 11, (1651-1668), (2023).https://doi.org/10.3748/wjg.v29.i11.1651
    Crossref
  4. A Review Focusing on Microbial Vertical Transmission during Sow Pregnancy, Veterinary Sciences, 10, 2, (123), (2023).https://doi.org/10.3390/vetsci10020123
    Crossref
  5. Nanoparticles: Taking a Unique Position in Medicine, Nanomaterials, 13, 3, (574), (2023).https://doi.org/10.3390/nano13030574
    Crossref
  6. How Do Diet Patterns, Single Foods, Prebiotics and Probiotics Impact Gut Microbiota?, Microbiology Research, 14, 1, (390-408), (2023).https://doi.org/10.3390/microbiolres14010030
    Crossref
  7. Correlations between Gut Microbial Composition, Pathophysiological and Surgical Aspects in Endometriosis: A Review of the Literature, Medicina, 59, 2, (347), (2023).https://doi.org/10.3390/medicina59020347
    Crossref
  8. Inflammatory Bowel Diseases and Gut Microbiota, International Journal of Molecular Sciences, 24, 4, (3817), (2023).https://doi.org/10.3390/ijms24043817
    Crossref
  9. Endometrial Microbiota and Immune Tolerance in Pregnancy, International Journal of Molecular Sciences, 24, 3, (2995), (2023).https://doi.org/10.3390/ijms24032995
    Crossref
  10. Clostridium butyricum Can Promote Bone Development by Regulating Lymphocyte Function in Layer Pullets, International Journal of Molecular Sciences, 24, 2, (1457), (2023).https://doi.org/10.3390/ijms24021457
    Crossref
  11. See more
Loading...

View Options

Check Access

Log in to view the full text

AAAS ID LOGIN

AAAS login provides access to Science for AAAS Members, and access to other journals in the Science family to users who have purchased individual subscriptions.

Log in via OpenAthens.
Log in via Shibboleth.

More options

Register for free to read this article

As a service to the community, this article is available for free. Login or register for free to read this article.

Purchase this issue in print

Buy a single issue of Science for just $15 USD.

View options

PDF format

Download this article as a PDF file

Download PDF

Full Text

FULL TEXT

Media

Figures

Multimedia

Tables

Share

Share

Share article link

Share on social media