Mining the human gut microbiota for effector strains that shape the immune system

Immunity

Volumn 40, Issue 6, 2014, Pages 815-823

  Ahern, Philip P ^a   Faith, Jeremiah J ^a,b   Gordon, Jeffrey I ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL STRAIN; BACTERIUM CULTURE; FECES MICROFLORA; GERMFREE ANIMAL; GNOTOBIOTICS; HUMAN; IMMUNE SYSTEM; INTESTINE FLORA; MICROBIAL COMMUNITY; MICROBIAL CONSORTIUM; MICROBIAL DIVERSITY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REGULATORY T LYMPHOCYTE; REVIEW;

EID: 84902649784     PISSN: 10747613     EISSN: 10974180     Source Type: Journal    
DOI: 10.1016/j.immuni.2014.05.012     Document Type: Review

References (37)

1. Arpaia N., Campbell C., Fan X., Dikiy S., van der Veeken J., deRoos P., Liu H., Cross J.R., Pfeffer K., Coffer P.J., Rudensky A.Y. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013, 504:451-455.
2. Arthur J.C., Perez-Chanona E., Mühlbauer M., Tomkovich S., Uronis J.M., Fan T.J., Campbell B.J., Abujamel T., Dogan B., Rogers A.B., et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 2012, 338:120-123.
3. Atarashi K., Tanoue T., Shima T., Imaoka A., Kuwahara T., Momose Y., Cheng G., Yamasaki S., Saito T., Ohba Y., et al. Induction of colonic regulatory Tcells by indigenous Clostridium species. Science 2011, 331:337-341.
4. Atarashi K., Tanoue T., Oshima K., Suda W., Nagano Y., Nishikawa H., Fukuda S., Saito T., Narushima S., Hase K., et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 2013, 500:232-236.
5. Bilate A.B., Lafaille J.J. It takes two to tango. Immunity 2011, 35:6-8.
6. Bloom S.M., Bijanki V.N., Nava G.M., Sun L., Malvin N.P., Donermeyer D.L., Dunne W.M., Allen P.M., Stappenbeck T.S. Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host Microbe 2011, 9:390-403.
7. Box G.E.P., Hunter J.S., Hunter W.G. Statistics for experimenters: design, innovation, and discovery. Wiley series in probability and statistics 2005, Wiley-Interscience, Hoboken, N.J., pp. xvii-633. Second Edition.
8. Breiman L. Random Forests. Mach. Learn. 2001, 45:5-32.
9. Cebula A., Seweryn M., Rempala G.A., Pabla S.S., McIndoe R.A., Denning T.L., Bry L., Kraj P., Kisielow P., Ignatowicz L. Thymus-derived regulatory Tcells contribute to tolerance to commensal microbiota. Nature 2013, 497:258-262.
10. Chang P.V., Hao L., Offermanns S., Medzhitov R. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc. Natl. Acad. Sci. USA 2014, 111:2247-2252.
11. Curotto de Lafaille M.A., Lafaille J.J. Natural and adaptive foxp3+ regulatory Tcells: more of the same or a division of labor?. Immunity 2009, 30:626-635.
12. Efron B., Hastie T., Johnstone I., Tibshirani R. Lease angle regression. Ann. Stat. 2004, 32:407-499.
13. Faith J.J., Ahern P.P., Ridaura V.K., Cheng J., Gordon J.I. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Science Translational Med. 2014, 6:220ra211.
14. Faith J.J., Guruge J.L., Charbonneau M., Subramanian S., Seedorf H., Goodman A.L., Clemente J.C., Knight R., Heath A.C., Leibel R.L., et al. The long-term stability of the human gut microbiota. Science 2013, 341:1237439.
15. Faith J.J., McNulty N.P., Rey F.E., Gordon J.I. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 2011, 333:101-104.
16. Faith J.J., Rey F.E., O'Donnell D., Karlsson M., McNulty N.P., Kallstrom G., Goodman A.L., Gordon J.I. Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J. 2010, 4:1094-1098.
17. Furusawa Y., Obata Y., Fukuda S., Endo T.A., Nakato G., Takahashi D., Nakanishi Y., Uetake C., Kato K., Kato T., et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory Tcells. Nature 2013, 504:446-450.
18. Gaboriau-Routhiau V., Rakotobe S., Lécuyer E., Mulder I., Lan A., Bridonneau C., Rochet V., Pisi A., De Paepe M., Brandi G., et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper Tcell responses. Immunity 2009, 31:677-689.
19. Garrett W.S., Gallini C.A., Yatsunenko T., Michaud M., DuBois A., Delaney M.L., Punit S., Karlsson M., Bry L., Glickman J.N., et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 2010, 8:292-300.
20. Geuking M.B., Cahenzli J., Lawson M.A., Ng D.C., Slack E., Hapfelmeier S., McCoy K.D., Macpherson A.J. Intestinal bacterial colonization induces mutualistic regulatory Tcell responses. Immunity 2011, 34:794-806.
21. Goodman A.L., Kallstrom G., Faith J.J., Reyes A., Moore A., Dantas G., Gordon J.I. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl. Acad. Sci. USA 2011, 108:6252-6257.
22. Haribhai D., Lin W., Edwards B., Ziegelbauer J., Salzman N.H., Carlson M.R., Li S.H., Simpson P.M., Chatila T.A., Williams C.B. A central role for induced regulatory Tcells in tolerance induction in experimental colitis. J.Immunol. 2009, 182:3461-3468.
23. Haribhai D., Williams J.B., Jia S., Nickerson D., Schmitt E.G., Edwards B., Ziegelbauer J., Yassai M., Li S.H., Relland L.M., et al. A requisite role for induced regulatory Tcells in tolerance based on expanding antigen receptor diversity. Immunity 2011, 35:109-122.
24. Hastie T., Tibshirani R., Friedman J.H. The elements of statistical learning: data mining, inference, and prediction. Springer series in statistics 2009, Springer, New York, NY, pp. xxii-745. Second Edition.
25. Ivanov I.I., Frutos Rde.L., Manel N., Yoshinaga K., Rifkin D.B., Sartor R.B., Finlay B.B., Littman D.R. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 2008, 4:337-349.
26. Ivanov I.I., Atarashi K., Manel N., Brodie E.L., Shima T., Karaoz U., Wei D., Goldfarb K.C., Santee C.A., Lynch S.V., et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009, 139:485-498.
27. Lagier J.C., Armougom F., Million M., Hugon P., Pagnier I., Robert C., Bittar F., Fournous G., Gimenez G., Maraninchi M., et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin. Microbiol. Infect. 2012, 18:1185-1193.
28. Lathrop S.K., Bloom S.M., Rao S.M., Nutsch K., Lio C.W., Santacruz N., Peterson D.A., Stappenbeck T.S., Hsieh C.S. Peripheral education of the immune system by colonic commensal microbiota. Nature 2011, 478:250-254.
29. Mucida D., Kutchukhidze N., Erazo A., Russo M., Lafaille J.J., Curotto de Lafaille M.A. Oral tolerance in the absence of naturally occurring Tregs. J.Clin. Invest. 2005, 115:1923-1933.
30. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. MetaHIT Consortium.
31. Ridaura V.K., Faith J.J., Rey F.E., Cheng J., Duncan A.E., Kau A.L., Griffin N.W., Lombard V., Henrissat B., Bain J.R., et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013, 341:1241214.
32. Round J.L., Mazmanian S.K. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc. Natl. Acad. Sci. USA 2010, 107:12204-12209.
33. Smith P.M., Howitt M.R., Panikov N., Michaud M., Gallini C.A., Bohlooly-Y M., Glickman J.N., Garrett W.S. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 2013, 341:569-573.
34. Weiss J.M., Bilate A.M., Gobert M., Ding Y., Curotto de Lafaille M.A., Parkhurst C.N., Xiong H., Dolpady J., Frey A.B., Ruocco M.G., et al. Neuropilin 1 is expressed on thymus-derived natural regulatory Tcells, but not mucosa-generated induced Foxp3+ T reg cells. J.Exp. Med. 2012, 209:1723-1742. S1721.
35. Wieland Brown L.C., Penaranda C., Kashyap P.C., Williams B.B., Clardy J., Kronenberg M., Sonnenburg J.L., Comstock L.E., Bluestone J.A., Fischbach M.A. Production of α-galactosylceramide by a prominent member of the human gut microbiota. PLoS Biol. 2013, 11:e1001610.
36. Wu S., Rhee K.J., Albesiano E., Rabizadeh S., Wu X., Yen H.R., Huso D.L., Brancati F.L., Wick E., McAllister F., et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 Tcell responses. Nat. Med. 2009, 15:1016-1022.
37. Zelante T., Iannitti R.G., Cunha C., De Luca A., Giovannini G., Pieraccini G., Zecchi R., D'Angelo C., Massi-Benedetti C., Fallarino F., et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 2013, 39:372-385.