CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands


Complex interactions between the host and the gut microbiota govern intestinal homeostasis but remain poorly understood. Here we reveal a relationship between gut microbiota and caspase recruitment domain family member 9 (CARD9), a susceptibility gene for inflammatory bowel disease (IBD) that functions in the immune response against microorganisms. CARD9 promotes recovery from colitis by promoting interleukin (IL)-22 production, and Card9−/− mice are more susceptible to colitis. The microbiota is altered in Card9−/− mice, and transfer of the microbiota from Card9−/− to wild-type, germ-free recipients increases their susceptibility to colitis. The microbiota from Card9−/− mice fails to metabolize tryptophan into metabolites that act as aryl hydrocarbon receptor (AHR) ligands. Intestinal inflammation is attenuated after inoculation of mice with three Lactobacillus strains capable of metabolizing tryptophan or by treatment with an AHR agonist. Reduced production of AHR ligands is also observed in the microbiota from individuals with IBD, particularly in those with CARD9 risk alleles associated with IBD. Our findings reveal that host genes affect the composition and function of the gut microbiota, altering the production of microbial metabolites and intestinal inflammation.

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Figure 1: CARD9 is involved in recovery from colitis.
Figure 2: The fungal and bacterial microbiota are altered in Card9−/− mice.
Figure 3: Transfer of the microbiota from Card9−/− mice is sufficient to increase susceptibility to colitis and reduce IL-22 production.
Figure 4: Tryptophan metabolism is impaired in the gut microbiota of Card9−/− mice, leading to defective AHR activation and colitis recovery.
Figure 5: Inoculation with lactobacilli that metabolize tryptophan and produce AHR ligands reduces colitis in an AHR-dependent manner.
Figure 6: Reduced tryptophan metabolism and AHR activation in the gut microbiota of individuals with IBD, and its association with the CARD9 genotype.

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Gene Expression Omnibus


  1. 1

    Silva, M.J. et al. The multifaceted role of commensal microbiota in homeostasis and gastrointestinal diseases. J. Immunol. Res. 2015, 321241 (2015).

    PubMed  PubMed Central  Google Scholar 

  2. 2

    Molodecky, N.A. et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 142, 46–54.e42; quiz e30 (2012).

    PubMed  Google Scholar 

  3. 3

    Ananthakrishnan, A.N. Epidemiology and risk factors for IBD. Nat. Rev. Gastroenterol. Hepatol. 12, 205–217 (2015).

    PubMed  PubMed Central  Google Scholar 

  4. 4

    Lanternier, F. et al. Inherited CARD9 deficiency in otherwise healthy children and adults with Candida species–induced meningoencephalitis, colitis, or both. J. Allergy Clin. Immunol. 135, 1558–1568.e2 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Hsu, Y.-M.S.M. et al. The adaptor protein CARD9 is required for innate immune responses to intracellular pathogens. Nat. Immunol. 8, 198–205 (2007).

    CAS  PubMed  Google Scholar 

  6. 6

    Goodridge, H.S. et al. Differential use of CARD9 by dectin-1 in macrophages and dendritic cells. J. Immunol. 182, 1146–1154 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Hara, H. et al. Cell-type-specific regulation of ITAM-mediated NF-κB activation by the adaptors CARMA1 and CARD9. J. Immunol. 181, 918–930 (2008).

    CAS  PubMed  Google Scholar 

  8. 8

    Sokol, H. et al. CARD9 mediates intestinal epithelial cell restitution, T helper 17 responses, and control of bacterial infection in mice. Gastroenterology 145, 591–601 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9

    Darfeuille-Michaud, A. et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127, 412–421 (2004).

    PubMed  Google Scholar 

  10. 10

    Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn's disease patients. Proc. Natl. Acad. Sci. USA 105, 16731–16736 (2008).

    CAS  PubMed  Google Scholar 

  11. 11

    Atarashi, K. et al. Treg induction by a rationally selected mixture of clostridia strains from the human microbiota. Nature 500, 232–236 (2013).

    CAS  PubMed  Google Scholar 

  12. 12

    Zelante, T. et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39, 372–385 (2013).

    CAS  PubMed  Google Scholar 

  13. 13

    Rutz, S., Eidenschenk, C. & Ouyang, W. IL-22, not simply a TH17 cytokine. Immunol. Rev. 252, 116–132 (2013).

    PubMed  Google Scholar 

  14. 14

    Sonnenberg, G.F., Fouser, L.A. & Artis, D. Border patrol: regulation of immunity, inflammation, and tissue homeostasis at barrier surfaces by IL-22. Nat. Immunol. 12, 383–390 (2011).

    CAS  PubMed  Google Scholar 

  15. 15

    Stelter, C. et al. Salmonella-induced mucosal lectin RegIII-β kills competing gut microbiota. PLoS One 6, e20749 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    De Luca, A. et al. IL-22 defines a novel immune pathway of antifungal resistance. Mucosal Immunol. 3, 361–373 (2010).

    CAS  PubMed  Google Scholar 

  17. 17

    Ishigame, H. et al. Differential roles of interleukin (IL)-17A and IL-17F in host defense against mucoepithelial bacterial infection and allergic responses. Immunity 30, 108–119 (2009).

    CAS  PubMed  Google Scholar 

  18. 18

    Wu, W., Hsu, Y.-M.S.M., Bi, L., Songyang, Z. & Lin, X. CARD9 facilitates microbe-elicited production of reactive oxygen species by regulating the LyGDI–Rac1 complex. Nat. Immunol. 10, 1208–1214 (2009).

    CAS  PubMed  Google Scholar 

  19. 19

    Iliev, I.D. et al. Interactions between commensal fungi and the C-type lectin receptor dectin-1 influence colitis. Science 336, 1314–1317 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Richard, M.L., Lamas, B., Liguori, G., Hoffmann, T.W. & Sokol, H. Gut fungal microbiota: the yin and yang of inflammatory bowel disease. Inflamm. Bowel Dis. 21, 656–665 (2015).

    PubMed  Google Scholar 

  21. 21

    Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    PubMed  PubMed Central  Google Scholar 

  22. 22

    Kim, K. et al. Interleukin-22 promotes epithelial cell transformation and breast tumorigenesis via MAP3K8 activation. Carcinogenesis 35, 1352–1361 (2014).

    CAS  PubMed  Google Scholar 

  23. 23

    Andoh, A. et al. Interleukin-22, a member of the IL-10 subfamily, induces inflammatory responses in colonic subepithelial myofibroblasts. Gastroenterology 129, 969–984 (2005).

    CAS  PubMed  Google Scholar 

  24. 24

    Sabat, R., Ouyang, W. & Wolk, K. Therapeutic opportunities of the IL-22–IL-22R1 system. Nat. Rev. Drug Discov. 13, 21–38 (2014).

    CAS  PubMed  Google Scholar 

  25. 25

    Pickert, G. et al. STAT3 links IL-22 signaling in intestinal epithelial cells to mucosal wound healing. J. Exp. Med. 206, 1465–1472 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26

    Spits, H. et al. Innate lymphoid cells—a proposal for uniform nomenclature. Nat. Rev. Immunol. 13, 145–149 (2013).

    CAS  PubMed  Google Scholar 

  27. 27

    Chung, K.-T.T. & Gadupudi, G.S. Possible roles of excess tryptophan metabolites in cancer. Environ. Mol. Mutagen. 52, 81–104 (2011).

    CAS  PubMed  Google Scholar 

  28. 28

    Jin, U.-H.H. et al. Microbiome-derived tryptophan metabolites and their aryl-hydrocarbon-receptor-dependent agonist and antagonist activities. Mol. Pharmacol. 85, 777–788 (2014).

    PubMed  PubMed Central  Google Scholar 

  29. 29

    Lee, J.S. et al. AHR drives the development of gut ILC22 cells and postnatal lymphoid tissues via pathways dependent on, and independent of, Notch. Nat. Immunol. 13, 144–151 (2012).

    CAS  Google Scholar 

  30. 30

    Zenewicz, L.A. et al. IL-22 deficiency alters colonic microbiota to be transmissible and colitogenic. J. Immunol. 190, 5306–5312 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31

    Jostins, L. et al. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119–124 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    Wikoff, W.R. et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. USA 106, 3698–3703 (2009).

    CAS  PubMed  Google Scholar 

  33. 33

    Behnsen, J. et al. The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria. Immunity 40, 262–273 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Lin, L. & Xu, X. Indole-3-acetic acid production by endophytic Streptomyces sp. En-1 isolated from medicinal plants. Curr. Microbiol. 67, 209–217 (2013).

    CAS  PubMed  Google Scholar 

  35. 35

    Hara, H. et al. The adaptor protein CARD9 is essential for the activation of myeloid cells through ITAM-associated and Toll-like receptors. Nat. Immunol. 8, 619–629 (2007).

    CAS  PubMed  Google Scholar 

  36. 36

    Suau, A. et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65, 4799–4807 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37

    Tomas, J. et al. Primocolonization is associated with colonic epithelial maturation during conventionalization. FASEB J. 27, 645–655 (2013).

    CAS  PubMed  Google Scholar 

  38. 38

    Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Magocč, T. & Salzberg, S.L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

    Google Scholar 

  40. 40

    Caporaso, J.G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Edgar, R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42

    McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archea. ISME J. 6, 610–618 (2012).

    CAS  PubMed  Google Scholar 

  43. 43

    Kõljalg, U. et al. Toward a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22, 5271–5277 (2013).

    PubMed  Google Scholar 

  44. 44

    Thioulouse, J., Chessel, D., Dolédec, S. & Olivier, J. ADE-4: a multivariate analysis and graphical display software. Stat. Comput. 7, 75–83 (1997).

    Google Scholar 

  45. 45

    Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003).

    CAS  PubMed  Google Scholar 

  46. 46

    Smyth, G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, e3 (2004).

    Google Scholar 

  47. 47

    Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).

    CAS  Google Scholar 

  48. 48

    Huang, W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009).

    Google Scholar 

  49. 49

    Zhao, B. et al. Common commercial and consumer products contain activators of the aryl hydrocarbon (dioxin) receptor. PLoS One 8, e56860 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50

    He, G., Zhao, B. & Denison, M.S. Identification of benzothiazole derivatives and polycyclic aromatic hydrocarbons as aryl hydrocarbon receptor agonists present in tire extracts. Environ. Toxicol. Chem. 30, 1915–1925 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51

    Gao, X. et al. Metabolite analysis of human fecal water by gas chromatography–mass spectrometry with ethyl chloroformate derivatization. Anal. Biochem. 393, 163–175 (2009).

    CAS  PubMed  Google Scholar 

  52. 52

    Maneglier, B. et al. Simultaneous measurement of kynurenine and tryptophan in human plasma and supernatants of cultured human cells by HPLC with coulometric detection. Clin. Chem. 50, 2166–2168 (2004).

    CAS  PubMed  Google Scholar 

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We thank the members of the ANAXEM germ-free platform, the members of the animal facilities of INRA, and T. Ledent of the animal facilities of Saint-Antoine Hospital for their assistance in mouse care; M. Moroldo and J. Lecardonnel from the CRB GADIE core facility for technical assistance in performing the microarray analyses; S. Dumont for technical help in histology and immunochemistry; and C. Aubry, N.M. Breyner, F. Chain, S. Le Guin, C. Cherbuy, N. Lapaque, and D. Skurnik for fruitful discussions and technical help. We also thank E. Drouet and the Clinical Research Assistant team of Unité de Recherche Clinique de l'Est Parisien for their help in obtaining samples from patients with IBD. Ido1−/− and Il22−/− mice were provided by S. Taleb (INSERM Unit 970) and B. Ryffel (CNRS, UMR7355), respectively. The H1L1.1c2 cell line was provided by M.S. Denison (University of California, Davis). Funding was provided by Equipe ATIP–Avenir 2012 (H.S.), INSERM–ITMO SP 2013 (H.S.) and ECCO grant 2012 (H.S.).

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B.L., M.L.R., and H.S. conceived and designed the study, performed data analysis, and wrote the manuscript; B.L. designed and conducted all experiments, unless otherwise indicated; V.L. designed and performed the AHR activity experiments; G.D.C., C.B., S.J., T.W.H., J.M.N., L. Brot, F.M., and M.-L.M. provided technical help for the in vitro and in vivo experiments; H.-P.P. conducted the bioinformatics studies and analyzed the microarray experiments; J.-M.L. performed and analyzed HPLC experiments; S.T. provided material from the Ido1−/− mice and discussed the results; A.C.-M. and B.R. provided material from the Il22−/− mice and discussed the results; H.S., J.C., I.N.-L., A.B., L. Beaugerie, and P.S. provided data and samples for the patients with IBD; B.L., M.L.R., R.J.X., P.L., and H.S. discussed the experiments and results.

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Correspondence to Harry Sokol.

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Lamas, B., Richard, M., Leducq, V. et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med 22, 598–605 (2016).

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