Author Correction: Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy (Nature Medicine, (2019), 25, 7, (1164-1174), 10.1038/s41591-019-0461-z);Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy

Nature Medicine

Volumn 25, Issue 7, 2019, Pages 1164-1174

  Abdel Gadir, Azza ^a,b   Stephen Victor, Emmanuel ^a,b   Gerber, Georg K ^b   Noval Rivas, Magali ^c   Wang, Sen ^a,b   Harb, Hani ^a,b   Wang, Leighanne ^a   Li, Ning ^b   Crestani, Elena ^a,b   Spielman, Sara ^a   Secor, William ^a   Biehl, Heather ^a   Dibendetto, Nicholas ^b   Dong, Xiaoxi ^b   Umetsu, Dale T ^d   Bry, Lynn ^b   Rachid, Rima ^a,b   Chatila, Talal A ^a,b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c CEDARS SINAI MEDICAL CENTER   (United States)

^d GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD3 ANTIGEN; CD4 ANTIGEN; DNA 16S; IMMUNOGLOBULIN A; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G1; IMMUNOGLOBULIN G2A; INTERLEUKIN 4; INTERLEUKIN 7 RECEPTOR; MESSENGER RNA; MYELOID DIFFERENTIATION FACTOR 88; NEUROPILIN 1; RETINOID RELATED ORPHAN RECEPTOR GAMMA; SECRETORY IMMUNOGLOBULIN; TRANSCRIPTION FACTOR FOXP3; TRANSCRIPTION FACTOR GATA 3; OVALBUMIN;

ADULT; ANIMAL EXPERIMENT; ANIMAL MODEL; ANTIGEN EXPRESSION; ARTICLE; BACTEROIDALES; BACTEROIDES FRAGILIS; BACTEROIDES OVATUS; BACTEROIDES VULGATUS; BINDING AFFINITY; CLINICAL ASSESSMENT; CLOSTRIDIALES; CLOSTRIDIUM BIFERMENTANS; CLOSTRIDIUM HIRANONIS; CLOSTRIDIUM LEPTUM; CLOSTRIDIUM SARDINIENSE; CLOSTRIDIUM SCINDENS; COMMENSALISM; CONTROLLED STUDY; DYSBIOSIS; ERYSIPELATOCLOSTRIDIUM RAMOSUM; FECAL MICROBIOTA TRANSPLANTATION; FECES MICROFLORA; GENE DELETION; HUMAN; IMMUNE RESPONSE; IMMUNOMODULATION; INFANT; INTESTINE FLORA; MAJOR CLINICAL STUDY; MILK ALLERGY; MONOTHERAPY; MOUSE; NONHUMAN; PARABACTEROIDES DISTASONIS; PREVOTELLA MELANINOGENICA; PRIORITY JOURNAL; REGULATORY MECHANISM; REGULATORY T LYMPHOCYTE; SIGNAL TRANSDUCTION; SUBDOLIGRANULUMV ARIABILE; ANIMAL; BACTEROIDES; BAGG ALBINO MOUSE; C57BL MOUSE; FECES; FOOD ALLERGY; IMMUNOLOGY; MICROBIOLOGY; PHYSIOLOGY;

ANIMALS; BACTEROIDES; CLOSTRIDIALES; DYSBIOSIS; FECES; FOOD HYPERSENSITIVITY; GASTROINTESTINAL MICROBIOME; MICE; MICE, INBRED BALB C; MICE, INBRED C57BL; MYELOID DIFFERENTIATION FACTOR 88; NUCLEAR RECEPTOR SUBFAMILY 1, GROUP F, MEMBER 3; OVALBUMIN; SIGNAL TRANSDUCTION; T-LYMPHOCYTES, REGULATORY;

EID: 85068081172     PISSN: 10788956     EISSN: 1546170X     Source Type: Journal    
DOI: 10.1038/s41591-019-0572-6     Document Type: Erratum

References (69)

1. Branum, A. M. & Lukacs, S. L. Food allergy among children in the United States. Pediatrics 124, 1549–1555 (2009).
2. Wills-Karp, M., Santeliz, J. & Karp, C. L. The germless theory of allergic disease: revisiting the hygiene hypothesis. Nat. Rev. Immunol. 1, 69–75 (2001).
3. Ly, N. P., Litonjua, A., Gold, D. R. & Celedon, J. C. Gut microbiota, probiotics, and vitamin D: interrelated exposures influencing allergy, asthma, and obesity? J. Allergy Clin. Immunol. 127, 1087–1094 (2011).
4. Koplin, J. et al. Is caesarean delivery associated with sensitization to food allergens and IgE-mediated food allergy? A systematic review. Pediatr. Allergy Immunol. 19, 682–687 (2008).
5. Bjorksten, B. Disease outcomes as a consequence of environmental influences on the development of the immune system. Curr. Opin. Allergy Clin. Immunol. 9, 185–189 (2009).
6. Rachid, R. & Chatila, T. A. The role of the gut microbiota in food allergy. Curr. Opin. Pediatr. 28, 748–753 (2016).
7. Azad, M. B. et al. Infant gut microbiota and food sensitization: associations in the first year of life. Clin. Exp. Allergy 45, 632–643 (2015).
8. Sudo, N. et al. The requirement of intestinal bacterial flora for the development of an IgE production system fully susceptible to oral tolerance induction. J. Immunol. 159, 1739–1745 (1997).
9. Fritz, J. H. et al. Acquisition of a multifunctional IgA+plasma cell phenotype in the gut. Nature 481, 199–203 (2012).
10. Geuking, M. B. et al. Intestinal bacterial colonization induces mutualistic regulatory T cell responses. Immunity 34, 794–806 (2011).
11. Stefka, A. T. et al. Commensal bacteria protect against food allergen sensitization. Proc. Natl Acad. Sci. USA 111, 13145–13150 (2014).
12. Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337–341 (2011).
13. Noval Rivas, M. et al. A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis. J. Allergy Clin. Immunol. 131, 201–212 (2013).
14. Wesemann, D. R. & Nagler, C. R. The microbiome, timing, and barrier function in the context of allergic disease. Immunity 44, 728–738 (2016).
15. Noval Rivas, M. & Chatila, T. A. Regulatory T cells in allergic diseases. J. Allergy Clin. Immunol. 138, 639–652 (2016).
16. Abdel-Gadir, A., Massoud, A. H. & Chatila, T. A. Antigen-specific Treg cells in immunological tolerance: implications for allergic diseases. F1000Res. 7, 38 (2018).
17. Furusawa, Y. et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504, 446–450 (2013).
18. Smith, P. M. et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341, 569–573 (2013).
19. Arpaia, N. et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504, 451–455 (2013).
20. Tan, J. et al. Dietary fiber and bacterial SCFA enhance oral tolerance and protect against food allergy through diverse cellular pathways. Cell Rep. 15, 2809–2824 (2016).
21. +T cells. Science 349, 989–993 (2015).
22. + regulatory T cells. Science 349, 993–997 (2015).
23. Burton, O. T. et al. Immunoglobulin E signal inhibition during allergen ingestion leads to reversal of established food allergy and induction of regulatory T cells. Immunity 41, 141–151 (2014).
24. Noval Rivas, M., Burton, O. T., Oettgen, H. C. & Chatila, T. IL-4 production by group 2 innate lymphoid cells promotes food allergy by blocking regulatory T-cell function. J. Allergy Clin. Immunol. 138, 801–811.e9 (2016).
25. Noval Rivas, M. et al. Regulatory T cell reprogramming toward a Th2-cell-like lineage impairs oral tolerance and promotes food allergy. Immunity 42, 512–523 (2015).
26. Fagarasan, S. et al. Critical roles of activation-induced cytidine deaminase in the homeostasis of gut flora. Science 298, 1424–1427 (2002).
27. Kubinak, J. L. et al. MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health. Cell Host Microbe 17, 153–163 (2015).
28. Wang, S. et al. MyD88 adaptor-dependent microbial sensing by regulatory T cells promotes mucosal tolerance and enforces commensalism. Immunity 43, 289–303 (2015).
29. Donaldson, G. P. et al. Gut microbiota utilize immunoglobulin A for mucosal colonization. Science 360, 795–800 (2018).
30. Macpherson, A. J., Yilmaz, B., Limenitakis, J. P. & Ganal-Vonarburg, S. C. IgA function in relation to the intestinal microbiota. Annu. Rev. Immunol. 36, 359–381 (2018).
31. Mathias, C. B. et al. IgE-mediated systemic anaphylaxis and impaired tolerance to food antigens in mice with enhanced IL-4 receptor signaling. J. Allergy Clin. Immunol. 127, e791–e796 (2011).
32. Kalia, V. C. et al. Analysis of the unexplored features of rrs (16S rDNA) of the genus Clostridium. BMC Genom. 12, 18 (2011).
33. Rajilic-Stojanovic, M. & de Vos, W. M. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol. Rev. 38, 996–1047 (2014).
34. Blander, J. M., Longman, R. S., Iliev, I. D., Sonnenberg, G. F. & Artis, D. Regulation of inflammation by microbiota interactions with the host. Nat. Immunol. 18, 851–860 (2017).
35. Narushima, S. et al. Characterization of the 17 strains of regulatory T cell-inducing human-derived Clostridia. Gut Microbes 5, 333–339 (2014).
36. Walker, A. W. & Lawley, T. D. Therapeutic modulation of intestinal dysbiosis. Pharm. Res. 69, 75–86 (2013).
37. Kim, K. S. et al. Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine. Science 351, 858–863 (2016).
38. Lathrop, S. K. et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 478, 250–254 (2011).
39. Russler-Germain, E. V., Rengarajan, S. & Hsieh, C. S. Antigen-specific regulatory T-cell responses to intestinal microbiota. Mucosal Immunol. 10, 1375–1386 (2017).
40. +T regulatory cells. J. Immunol. 184, 3433–3441 (2010).
41. +T reg cells. J. Exp. Med. 209, S1721 (2012).
42. Yadav, M. et al. Neuropilin-1 distinguishes natural and inducible regulatory T cells among regulatory T cell subsets in vivo. J. Exp. Med. 209, S1711–S1719 (2012).
43. + regulatory T cells in immune tolerance. Annu Rev. Immunol. 30, 733–758 (2012).
44. Xu, M. et al. c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont. Nature 554, 373–377 (2018).
45. Abdel-Gadir, A. et al. Oral immunotherapy with omalizumab reverses the Th2 cell-like programme of regulatory T cells and restores their function. Clin. Exp. Allergy 48, 825–836 (2018).
46. Bartnikas, L. M. et al. Epicutaneous sensitization results in IgE-dependent intestinal mast cell expansion and food-induced anaphylaxis. J. Allergy Clin. Immunol. 131, e451–e456 (2013).
47. Round, J. L. et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 332, 974–977 (2011).
48. Kverka, M. et al. Oral administration of Parabacteroides distasonis antigens attenuates experimental murine colitis through modulation of immunity and microbiota composition. Clin. Exp. Immunol. 163, 250–259 (2011).
49. Geva-Zatorsky, N. et al. Mining the human gut microbiota for immunomodulatory organisms. Cell 168, 928–943 e911 (2017).
50. Mangalam, A. et al. Human gut-derived commensal bacteria suppress CNS inflammatory and demyelinating disease. Cell Rep. 20, 1269–1277 (2017).
51. Haribhai, D. et al. A requisite role for induced regulatory T cells in tolerance based on expanding antigen receptor diversity. Immunity 35, 109–122 (2011).
52. Rios-Covian, D., Salazar, N., Gueimonde, M. & de Los Reyes-Gavilan, C. G. Shaping the metabolism of intestinal Bacteroides population through diet to improve human health. Front. Microbiol. 8, 376 (2017).
53. Atarashi, K. et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500, 232–236 (2013).
54. +regulatory T cells and exacerbate colitis in mice. Immunity 50, 212–224 e214 (2019).
55. Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108 (Suppl. 1), 4554–4561 (2011).
56. Gerber, G. K., Onderdonk, A. B. & Bry, L. Inferring dynamic signatures of microbes in complex host ecosystems. PLoS Comput. Biol. 8, e1002624 (2012).
57. Bucci, V. et al. MDSINE: microbial dynamical systems inference engine for microbiome time-series analyses. Genome Biol. 17, 121 (2016).
58. Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
59. Excoffier, L., Smouse, P. E. & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479–491 (1992).
60. Lozupone, C., Hamady, M. & Knight, R. UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma. 7, 371 (2006).
61. Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228–8235 (2005).
62. McMurdie, P. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).
63. McMurdie, P. & Holmes, S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10, e1003531 (2014).
64. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).
65. Matsen, F., Kodner, R. B. & Armbrust, E. V. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinforma. 11, 538 (2010).
66. Cole, J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic acids Res. 42, D633–642 (2014).
67. Massoud, A. H. et al. An asthma-associated IL4R variant exacerbates airway inflammation by promoting conversion of regulatory T cells to TH17-like cells. Nat. Med. 22, 1013–1022 (2016).
68. Rubtsov, Y. P. et al. Regulatory T cell-derived interleukin-10 limits inflammation at environmental interfaces. Immunity 28, 546–558 (2008).
69. Pinciroli, R. et al. Endotracheal Tubes cleaned with a novel mechanism for secretion removal: a randomized controlled clinical study. Respir. Care 61, 1431–1439 (2016).