Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease

Cell

Volumn 158, Issue 5, 2014, Pages 1000-1010

  Palm, Noah W ^a   De Zoete, Marcel R ^a,c   Cullen, Thomas W ^a   Barry, Natasha A ^a   Stefanowski, Jonathan ^a   Hao, Liming ^a   Degnan, Patrick H ^a   Hu, Jianzhong ^b   Peter, Inga ^b   Zhang, Wei ^a   Ruggiero, Elizabeth ^a   Cho, Judy H ^a   Goodman, Andrew L ^a   Flavell, Richard A ^a,c  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN A; INFLAMMASOME; RNA 16S; BACTERIAL DNA;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ANTIGEN SPECIFICITY; ARTICLE; BACTERIAL CELL; BACTERIUM IDENTIFICATION; BACTEROIDALES; BACTEROIDES FRAGILIS; CELL SELECTION; CONTROLLED STUDY; DEXTRAN SODIUM SULFATE-INDUCED COLITIS; DISEASE PREDISPOSITION; DYSBIOSIS; ERYSIPELOTRICHACEAE; FECES MICROFLORA; FLOW CYTOMETRY; GENE SEQUENCE; HELICOBACTER; HUMAN; HUMAN TISSUE; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; LACTOBACILLUS; MOUSE; NONHUMAN; PREVOTELLACEAE; PRIORITY JOURNAL; TAXONOMY; ANIMAL; C57BL MOUSE; CROHN DISEASE; GERMFREE ANIMAL; IMMUNOLOGY; INFLAMMATION; INTESTINE; MICROBIOLOGY; MICROFLORA; PATHOLOGY; ULCERATIVE COLITIS;

ANIMALS; COLITIS, ULCERATIVE; CROHN DISEASE; DNA, BACTERIAL; DYSBIOSIS; HUMANS; IMMUNOGLOBULIN A; INFLAMMASOMES; INFLAMMATION; INTESTINES; MICE; MICE, INBRED C57BL; MICROBIOTA; RNA, RIBOSOMAL, 16S; SPECIFIC PATHOGEN-FREE ORGANISMS;

EID: 84907300008     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.08.006     Document Type: Article

References (53)

1. C. Abraham, and J.H. Cho Inflammatory bowel disease N. Engl. J. Med. 361 2009 2066 2078
2. A. Bankevich, S. Nurk, D. Antipov, A.A. Gurevich, M. Dvorkin, A.S. Kulikov, V.M. Lesin, S.I. Nikolenko, S. Pham, and A.D. Prjibelski et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing J. Comput. Biol. 19 2012 455 477
3. Y. Belkaid, and T.W. Hand Role of the microbiota in immunity and inflammation Cell 157 2014 121 141
4. M. Bemark, P. Boysen, and N.Y. Lycke Induction of gut IgA production through T cell-dependent and T cell-independent pathways Ann. N Y Acad. Sci. 1247 2012 97 116
5. K. Ben-Amor, H. Heilig, H. Smidt, E.E. Vaughan, T. Abee, and W.M. de Vos Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis Appl. Environ. Microbiol. 71 2005 4679 4689
6. R. Blumberg, and F. Powrie Microbiota, disease, and back to health: a metastable journey Sci. Transl. Med. 4 2012 137rv137
7. G. Canny, A. Swidsinski, and B.A. McCormick Interactions of intestinal epithelial cells with bacteria and immune cells: methods to characterize microflora and functional consequences Methods Mol. Biol. 341 2006 17 35
8. J.G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A.G. Peña, J.K. Goodrich, and J.I. Gordon et al. QIIME allows analysis of high-throughput community sequencing data Nat. Methods 7 2010 335 336
9. J.G. Caporaso, C.L. Lauber, W.A. Walters, D. Berg-Lyons, C.A. Lozupone, P.J. Turnbaugh, N. Fierer, and R. Knight Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample Proc. Natl. Acad. Sci. USA 108 Suppl 1 2011 4516 4522
10. J.G. Caporaso, C.L. Lauber, W.A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S.M. Owens, J. Betley, L. Fraser, and M. Bauer et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms ISME J. 6 2012 1621 1624
11. J. Chow, H. Tang, and S.K. Mazmanian Pathobionts of the gastrointestinal microbiota and inflammatory disease Curr. Opin. Immunol. 23 2011 473 480
12. Y. Cong, T. Feng, K. Fujihashi, T.R. Schoeb, and C.O. Elson A dominant, coordinated T regulatory cell-IgA response to the intestinal microbiota Proc. Natl. Acad. Sci. USA 106 2009 19256 19261
13. T.C. Cullender, B. Chassaing, A. Janzon, K. Kumar, C.E. Muller, J.J. Werner, L.T. Angenent, M.E. Bell, A.G. Hay, and D.A. Peterson et al. Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut Cell Host Microbe 14 2013 571 581
14. G. D'Auria, F. Peris-Bondia, M. Dzunkova, A. Mira, M.C. Collado, A. Latorre, and A. Moya Active and secreted IgA-coated bacterial fractions from the human gut reveal an under-represented microbiota core Sci. Rep. 3 2013 3515
15. G. Dantas, M.O. Sommer, P.H. Degnan, and A.L. Goodman Experimental approaches for defining functional roles of microbes in the human gut Annu. Rev. Microbiol. 67 2013 459 475
16. A.C. Darling, B. Mau, F.R. Blattner, and N.T. Perna Mauve: multiple alignment of conserved genomic sequence with rearrangements Genome Res. 14 2004 1394 1403
17. E. Elinav, T. Strowig, A.L. Kau, J. Henao-Mejia, C.A. Thaiss, C.J. Booth, D.R. Peaper, J. Bertin, S.C. Eisenbarth, J.I. Gordon, and R.A. Flavell NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis Cell 145 2011 745 757
18. K. Fujihashi, J.R. McGhee, M.N. Kweon, M.D. Cooper, S. Tonegawa, I. Takahashi, T. Hiroi, J. Mestecky, and H. Kiyono gamma/delta T cell-deficient mice have impaired mucosal immunoglobulin A responses J. Exp. Med. 183 1996 1929 1935
19. D. Gevers, S. Kugathasan, L.A. Denson, Y. Vázquez-Baeza, W. Van Treuren, B. Ren, E. Schwager, D. Knights, S.J. Song, and M. Yassour et al. The treatment-naive microbiome in new-onset Crohn's disease Cell Host Microbe 15 2014 382 392
20. A.L. Goodman, G. Kallstrom, J.J. Faith, A. Reyes, A. Moore, G. Dantas, and J.I. Gordon Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice Proc. Natl. Acad. Sci. USA 108 2011 6252 6257
21. K. Hirota, J.E. Turner, M. Villa, J.H. Duarte, J. Demengeot, O.M. Steinmetz, and B. Stockinger Plasticity of Th17 cells in Peyer's patches is responsible for the induction of T cell-dependent IgA responses Nat. Immunol. 14 2013 372 379
22. L.V. Hooper, D.R. Littman, and A.J. Macpherson Interactions between the microbiota and the immune system Science 336 2012 1268 1273
23. Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome Nature 486 2012 207 214
24. I.I. Ivanov, K. Atarashi, N. Manel, E.L. Brodie, T. Shima, U. Karaoz, D. Wei, K.C. Goldfarb, C.A. Santee, and S.V. Lynch et al. Induction of intestinal Th17 cells by segmented filamentous bacteria Cell 139 2009 485 498
25. L.M. Kato, S. Kawamoto, M. Maruya, and S. Fagarasan Gut TFH and IgA: key players for regulation of bacterial communities and immune homeostasis Immunol. Cell Biol. 92 2014 49 56
26. S. Kawamoto, T.H. Tran, M. Maruya, K. Suzuki, Y. Doi, Y. Tsutsui, L.M. Kato, and S. Fagarasan The inhibitory receptor PD-1 regulates IgA selection and bacterial composition in the gut Science 336 2012 485 489
27. D. Knights, K.G. Lassen, and R.J. Xavier Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome Gut 62 2013 1505 1510
28. M.C. Kullberg, J.M. Ward, P.L. Gorelick, P. Caspar, S. Hieny, A. Cheever, D. Jankovic, and A. Sher Helicobacter hepaticus triggers colitis in specific-pathogen-free interleukin-10 (IL-10)-deficient mice through an IL-12- and gamma interferon-dependent mechanism Infect. Immun. 66 1998 5157 5166
29. D.R. Littman, and E.G. Pamer Role of the commensal microbiota in normal and pathogenic host immune responses Cell Host Microbe 10 2011 311 323
30. C.A. Lozupone, J.I. Stombaugh, J.I. Gordon, J.K. Jansson, and R. Knight Diversity, stability and resilience of the human gut microbiota Nature 489 2012 220 230
31. A. Mathias, and B. Corthésy N-Glycans on secretory component: mediators of the interaction between secretory IgA and gram-positive commensals sustaining intestinal homeostasis Gut Microbes 2 2011 287 293
32. C.F. Maurice, H.J. Haiser, and P.J. Turnbaugh Xenobiotics shape the physiology and gene expression of the active human gut microbiome Cell 152 2013 39 50
33. O. Pabst New concepts in the generation and functions of IgA Nat. Rev. Immunol. 12 2012 821 832
34. C.D. Packey, and R.B. Sartor Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases Curr. Opin. Infect. Dis. 22 2009 292 301
35. F. Peris-Bondia, A. Latorre, A. Artacho, A. Moya, and G. D'Auria The active human gut microbiota differs from the total microbiota PLoS ONE 6 2011 e22448
36. D.A. Peterson, N.P. McNulty, J.L. Guruge, and J.I. Gordon IgA response to symbiotic bacteria as a mediator of gut homeostasis Cell Host Microbe 2 2007 328 339
37. J.L. Round, and S.K. Mazmanian The gut microbiota shapes intestinal immune responses during health and disease Nat. Rev. Immunol. 9 2009 313 323
38. M. Saleh, and C.O. Elson Experimental inflammatory bowel disease: insights into the host-microbiota dialog Immunity 34 2011 293 302
39. P.J. Sansonetti To be or not to be a pathogen: that is the mucosally relevant question Mucosal Immunol. 4 2011 8 14
40. J.U. Scher, A. Sczesnak, R.S. Longman, N. Segata, C. Ubeda, C. Bielski, T. Rostron, V. Cerundolo, E.G. Pamer, and S.B. Abramson et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis Elife 2 2013 e01202
41. N. Segata, J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W.S. Garrett, and C. Huttenhower Metagenomic biomarker discovery and explanation Genome Biol. 12 2011 R60
42. R. Shinkura, S. Ito, N.A. Begum, H. Nagaoka, M. Muramatsu, K. Kinoshita, Y. Sakakibara, H. Hijikata, and T. Honjo Separate domains of AID are required for somatic hypermutation and class-switch recombination Nat. Immunol. 5 2004 707 712
43. E. Slack, M.L. Balmer, J.H. Fritz, and S. Hapfelmeier Functional flexibility of intestinal IgA - broadening the fine line Front. Immunol. 3 2012 100
44. R. Stepankova, F. Powrie, O. Kofronova, H. Kozakova, T. Hudcovic, T. Hrncir, H. Uhlig, S. Read, Z. Rehakova, and O. Benada 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 2007 1202 1211
45. W. Strober Impact of the gut microbiome on mucosal inflammation Trends Immunol. 34 2013 423 430
46. H. Tezuka, Y. Abe, M. Iwata, H. Takeuchi, H. Ishikawa, M. Matsushita, T. Shiohara, S. Akira, and T. Ohteki Regulation of IgA production by naturally occurring TNF/iNOS-producing dendritic cells Nature 448 2007 929 933
47. T. Tsuruta, R. Inoue, I. Nojima, T. Tsukahara, H. Hara, and T. Yajima The amount of secreted IgA may not determine the secretory IgA coating ratio of gastrointestinal bacteria FEMS Immunol. Med. Microbiol. 56 2009 185 189
48. L.A. van der Waaij, G. Mesander, P.C. Limburg, and D. van der Waaij Direct flow cytometry of anaerobic bacteria in human feces Cytometry 16 1994 270 279
49. L.A. van der Waaij, F.G. Kroese, A. Visser, G.F. Nelis, B.D. Westerveld, P.L. Jansen, and J.O. Hunter Immunoglobulin coating of faecal bacteria in inflammatory bowel disease Eur. J. Gastroenterol. Hepatol. 16 2004 669 674
50. H.J. Wu, I.I. Ivanov, J. Darce, K. Hattori, T. Shima, Y. Umesaki, D.R. Littman, C. Benoist, and D. Mathis Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells Immunity 32 2010 815 827
51. C. Lozupone, and R. Knight UniFrac: a new phylogenetic method for comparing microbial communities Appl. Environ. Microbiol. 71 2005 8228 8235
52. A.P. Masella, A.K. Bartram, J.M. Truszkowski, D.G. Brown, and J.D. Neufeld PANDAseq: paired-end assembler for illumina sequences BMC Bioinformatics 13 2012 31
53. Q. Wang, G.M. Garrity, J.M. Tiedje, and J.R. Cole Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Appl. Environ. Microbiol. 73 2007 5261 5267