Role of the Commensal Microbiota in Normal and Pathogenic Host Immune Responses

Antonopoulos, 2009, Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation, Infect. Immun., 77, 2367, 10.1128/IAI.01520-08 Antunes, 2011, A comparative analysis of the effect of antibiotic treatment and enteric infection on intestinal homeostasis, Gut Microbes, 2, 105, 10.4161/gmic.2.2.15610 Antunes, 2011, Effect of antibiotic treatment on the intestinal metabolome, Antimicrob. Agents Chemother., 55, 1494, 10.1128/AAC.01664-10 Arumugam, 2011, Enterotypes of the human gut microbiome, Nature, 473, 174, 10.1038/nature09944 Atarashi, 2011, Induction of colonic regulatory T cells by indigenous Clostridium species, Science, 331, 337, 10.1126/science.1198469 Bartlett, 2008, Clinical recognition and diagnosis of Clostridium difficile infection, Clin. Infect. Dis., 46, S12, 10.1086/521863 Bhan, 1999, Colitis in transgenic and knockout animals as models of human inflammatory bowel disease, Immunol. Rev., 169, 195, 10.1111/j.1600-065X.1999.tb01316.x Bloom, 2011, Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease, Cell Host Microbe, 9, 390, 10.1016/j.chom.2011.04.009 Bohnhoff, 1962, Enhanced susceptibility to Salmonella infection in streptomycin-treated mice, J. Infect. Dis., 111, 117, 10.1093/infdis/111.2.117 Bohnhoff, 1964, Resistance of the Mouse's Intestinal Tract to Experimental Salmonella Infection. I. Factors Which Interfere with the Initiation of Infection by Oral Inoculation, J. Exp. Med., 120, 805, 10.1084/jem.120.5.805 Bohnhoff, 1964, Resistance of the Mouse's Intestinal Tract to Experimental Salmonella Infection. Ii. Factors Responsible for Its Loss Following Streptomycin Treatment, J. Exp. Med., 120, 817, 10.1084/jem.120.5.817 Bouskra, 2008, Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis, Nature, 456, 507, 10.1038/nature07450 Brandl, 2007, MyD88-mediated signals induce the bactericidal lectin RegIII gamma and protect mice against intestinal Listeria monocytogenes infection, J. Exp. Med., 204, 1891, 10.1084/jem.20070563 Brandl, 2008, Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits, Nature, 455, 804, 10.1038/nature07250 Buonocore, 2010, Innate lymphoid cells drive interleukin-23-dependent innate intestinal pathology, Nature, 464, 1371, 10.1038/nature08949 Cadwell, 2010, Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine, Cell, 141, 1135, 10.1016/j.cell.2010.05.009 Cash, 1974, Response of man to infection with Vibrio cholerae. I. Clinical, serologic, and bacteriologic responses to a known inoculum, J. Infect. Dis., 129, 45, 10.1093/infdis/129.1.45 Cash, 2006, Symbiotic bacteria direct expression of an intestinal bactericidal lectin, Science, 313, 1126, 10.1126/science.1127119 Chang, 2008, Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea, J. Infect. Dis., 197, 435, 10.1086/525047 Chen, 2008, A mouse model of Clostridium difficile-associated disease, Gastroenterology, 135, 1984, 10.1053/j.gastro.2008.09.002 Chieppa, 2006, Dynamic imaging of dendritic cell extension into the small bowel lumen in response to epithelial cell TLR engagement, J. Exp. Med., 203, 2841, 10.1084/jem.20061884 Conti, 2009, Th17 cells and IL-17 receptor signaling are essential for mucosal host defense against oral candidiasis, J. Exp. Med., 206, 299, 10.1084/jem.20081463 Curotto de Lafaille, 2009, Natural and adaptive foxp3+ regulatory T cells: more of the same or a division of labor?, Immunity, 30, 626, 10.1016/j.immuni.2009.05.002 Dethlefsen, 2008, The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing, PLoS Biol., 6, e280, 10.1371/journal.pbio.0060280 Donskey, 2000, Effect of antibiotic therapy on the density of vancomycin-resistant enterococci in the stool of colonized patients, N. Engl. J. Med., 343, 1925, 10.1056/NEJM200012283432604 DuPont, 1989, Inoculum size in shigellosis and implications for expected mode of transmission, J. Infect. Dis., 159, 1126, 10.1093/infdis/159.6.1126 Eckburg, 2005, Diversity of the human intestinal microbial flora, Science, 308, 1635, 10.1126/science.1110591 Elinav, 2011, NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis, Cell, 145, 745, 10.1016/j.cell.2011.04.022 Endt, 2010, The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea, PLoS Pathog., 6, e1001097, 10.1371/journal.ppat.1001097 Ferreira, 2011, The intestinal microbiota plays a role in Salmonella-induced colitis independent of pathogen colonization, PLoS ONE, 6, e20338, 10.1371/journal.pone.0020338 Freter, 1955, The fatal enteric cholera infection in the guinea pig, achieved by inhibition of normal enteric flora, J. Infect. Dis., 97, 57, 10.1093/infdis/97.1.57 Fukuda, 2011, Bifidobacteria can protect from enteropathogenic infection through production of acetate, Nature, 469, 543, 10.1038/nature09646 Gaboriau-Routhiau, 2009, The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses, Immunity, 31, 677, 10.1016/j.immuni.2009.08.020 Garrett, 2007, Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system, Cell, 131, 33, 10.1016/j.cell.2007.08.017 Garrett, 2010, Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis, Cell Host Microbe, 8, 292, 10.1016/j.chom.2010.08.004 Glynn, 1995, Infecting dose and severity of typhoid: analysis of volunteer data and examination of the influence of the definition of illness used, Epidemiol. Infect., 115, 23, 10.1017/S0950268800058088 Godinez, 2008, T cells help to amplify inflammatory responses induced by Salmonella enterica serotype Typhimurium in the intestinal mucosa, Infect. Immun., 76, 2008, 10.1128/IAI.01691-07 Godinez, 2009, Interleukin-23 orchestrates mucosal responses to Salmonella enterica serotype Typhimurium in the intestine, Infect. Immun., 77, 387, 10.1128/IAI.00933-08 Hadis, 2011, Intestinal tolerance requires gut homing and expansion of FoxP3+ regulatory T cells in the lamina propria, Immunity, 34, 237, 10.1016/j.immuni.2011.01.016 Happel, 2005, Divergent roles of IL-23 and IL-12 in host defense against Klebsiella pneumoniae, J. Exp. Med., 202, 761, 10.1084/jem.20050193 Hasegawa, 2011, Nucleotide-binding oligomerization domain 1 mediates recognition of Clostridium difficile and induces neutrophil recruitment and protection against the pathogen, J. Immunol., 186, 4872, 10.4049/jimmunol.1003761 Hill, 2010, Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis, Mucosal Immunol., 3, 148, 10.1038/mi.2009.132 Hirota, 2011, Fate mapping of IL-17-producing T cells in inflammatory responses, Nat. Immunol., 12, 255, 10.1038/ni.1993 Ismail, 2011, Gammadelta intraepithelial lymphocytes are essential mediators of host-microbial homeostasis at the intestinal mucosal surface, Proc. Natl. Acad. Sci. USA, 108, 8743, 10.1073/pnas.1019574108 Ivanov, 2008, Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine, Cell Host Microbe, 4, 337, 10.1016/j.chom.2008.09.009 Ivanov, 2009, Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell, 139, 485, 10.1016/j.cell.2009.09.033 Jarchum, 2011, Toll-like receptor 5 stimulation protects mice from acute Clostridium difficile colitis, Infect. Immun., 79, 1498, 10.1128/IAI.01196-10 Jensen, 2008, Thymic selection determines gammadelta T cell effector fate: antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon gamma, Immunity, 29, 90, 10.1016/j.immuni.2008.04.022 Jernberg, 2007, Long-term ecological impacts of antibiotic administration on the human intestinal microbiota, ISME J., 1, 56, 10.1038/ismej.2007.3 Kamboj, 2010, The changing epidemiology of vancomycin-resistant Enterococcus (VRE) bacteremia in allogeneic hematopoietic stem cell transplant (HSCT) recipients, Biol. Blood Marrow Transplant., 16, 1576, 10.1016/j.bbmt.2010.05.008 Kelly, 2008, Clostridium difficile—more difficult than ever, N. Engl. J. Med., 359, 1932, 10.1056/NEJMra0707500 Kinnebrew, 2010, Bacterial flagellin stimulates Toll-like receptor 5-dependent defense against vancomycin-resistant Enterococcus infection, J. Infect. Dis., 201, 534, 10.1086/650203 Kobayashi, 2005, Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract, Science, 307, 731, 10.1126/science.1104911 Kuwahara, 2011, The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing, DNA Res., 18, 291, 10.1093/dnares/dsr022 Lathrop, 2011, Peripheral education of the immune system by colonic commensal microbiota, Nature, 10.1038/nature10434 Lawley, 2009, Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts, Infect. Immun., 77, 3661, 10.1128/IAI.00558-09 Lee, 2011, Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis, Proc. Natl. Acad. Sci. USA, 108, 4615, 10.1073/pnas.1000082107 Lochner, 2011, Restricted microbiota and absence of cognate TCR antigen leads to an unbalanced generation of Th17 cells, J. Immunol., 186, 1531, 10.4049/jimmunol.1001723 Lupp, 2007, Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae, Cell Host Microbe, 2, 204, 10.1016/j.chom.2007.08.002 Macpherson, 2008, The immune geography of IgA induction and function, Mucosal Immunol., 1, 11, 10.1038/mi.2007.6 Maloy, 2011, Intestinal homeostasis and its breakdown in inflammatory bowel disease, Nature, 474, 298, 10.1038/nature10208 Maslowski, 2009, Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43, Nature, 461, 1282, 10.1038/nature08530 Mathis, 2011, Microbiota and autoimmune disease: the hosted self, Cell Host Microbe, 10, 297, 10.1016/j.chom.2011.09.007 Mazmanian, 2008, A microbial symbiosis factor prevents intestinal inflammatory disease, Nature, 453, 620, 10.1038/nature07008 Niess, 2005, CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance, Science, 307, 254, 10.1126/science.1102901 O'Connor, 2009, Clostridium difficile infection caused by the epidemic BI/NAP1/027 strain, Gastroenterology, 136, 1913, 10.1053/j.gastro.2009.02.073 Petnicki-Ocwieja, 2009, Nod2 is required for the regulation of commensal microbiota in the intestine, Proc. Natl. Acad. Sci. USA, 106, 15813, 10.1073/pnas.0907722106 Prakash, 2011, Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation, Cell Host Microbe, 10, 273, 10.1016/j.chom.2011.08.007 Raffatellu, 2009, Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine, Cell Host Microbe, 5, 476, 10.1016/j.chom.2009.03.011 Rakoff-Nahoum, 2004, Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis, Cell, 118, 229, 10.1016/j.cell.2004.07.002 Reid, 2009, Pattern recognition: recent insights from Dectin-1, Curr. Opin. Immunol., 21, 30, 10.1016/j.coi.2009.01.003 Round, 2009, The gut microbiota shapes intestinal immune responses during health and disease, Nat. Rev. Immunol., 9, 313, 10.1038/nri2515 Round, 2011, The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota, Science, 332, 974, 10.1126/science.1206095 Rupnik, 2009, Clostridium difficile infection: new developments in epidemiology and pathogenesis, Nat. Rev. Microbiol., 7, 526, 10.1038/nrmicro2164 Sadlack, 1993, Ulcerative colitis-like disease in mice with a disrupted interleukin-2 gene, Cell, 75, 253, 10.1016/0092-8674(93)80067-O Schneider, 2008, Two ways to survive infection: what resistance and tolerance can teach us about treating infectious diseases, Nat. Rev. Immunol., 8, 889, 10.1038/nri2432 Schulz, 2008, IL-17A is produced by Th17, gammadelta T cells and other CD4- lymphocytes during infection with Salmonella enterica serovar Enteritidis and has a mild effect in bacterial clearance, Int. Immunol., 20, 1129, 10.1093/intimm/dxn069 Sczesnak, 2011, The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment, Cell Host Microbe, 10, 260, 10.1016/j.chom.2011.08.005 Sekirov, 2008, Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection, Infect. Immun., 76, 4726, 10.1128/IAI.00319-08 Sekirov, 2010, Salmonella SPI-1-mediated neutrophil recruitment during enteric colitis is associated with reduction and alteration in intestinal microbiota, Gut Microbes, 1, 30, 10.4161/gmic.1.1.10950 Simor, 2002, Clostridium difficile in long-term-care facilities for the elderly, Infect. Control Hosp. Epidemiol., 23, 696, 10.1086/501997 Sonnenberg, 2011, CD4(+) lymphoid tissue-inducer cells promote innate immunity in the gut, Immunity, 34, 122, 10.1016/j.immuni.2010.12.009 Spits, 2011, The expanding family of innate lymphoid cells: regulators and effectors of immunity and tissue remodeling, Nat. Immunol., 12, 21, 10.1038/ni.1962 Stecher, 2007, Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota, PLoS Biol., 5, 2177, 10.1371/journal.pbio.0050244 Stecher, 2010, Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria, PLoS Pathog., 6, e1000711, 10.1371/journal.ppat.1000711 Suau, 1999, Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut, Appl. Environ. Microbiol., 65, 4799, 10.1128/AEM.65.11.4799-4807.1999 Sutton, 2009, Interleukin-1 and IL-23 induce innate IL-17 production from gammadelta T cells, amplifying Th17 responses and autoimmunity, Immunity, 31, 331, 10.1016/j.immuni.2009.08.001 Tsuji, 2008, Requirement for lymphoid tissue-inducer cells in isolated follicle formation and T cell-independent immunoglobulin A generation in the gut, Immunity, 29, 261, 10.1016/j.immuni.2008.05.014 Ubeda, 2010, Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans, J. Clin. Invest., 120, 4332, 10.1172/JCI43918 Umesaki, 1995, 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, 10.1111/j.1348-0421.1995.tb02242.x Vaishnava, 2008, Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface, Proc. Natl. Acad. Sci. USA, 105, 20858, 10.1073/pnas.0808723105 van de Pavert, 2010, New insights into the development of lymphoid tissues, Nat. Rev. Immunol., 10, 664, 10.1038/nri2832 van der Waaij, 1971, Colonization resistance of the digestive tract in conventional and antibiotic-treated mice, J. Hyg. (Lond.), 69, 405, 10.1017/S0022172400021653 Vollaard, 1994, Colonization resistance, Antimicrob. Agents Chemother., 38, 409, 10.1128/AAC.38.3.409 Winter, 2010, Gut inflammation provides a respiratory electron acceptor for Salmonella, Nature, 467, 426, 10.1038/nature09415 Wlodarska, 2011, Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis, Infect. Immun., 79, 1536, 10.1128/IAI.01104-10 Wu, 2010, Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells, Immunity, 32, 815, 10.1016/j.immuni.2010.06.001 Zheng, 2008, Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens, Nat. Med., 14, 282, 10.1038/nm1720