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Bindloss et al 8. Alex S, et al. Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor gamma. Mol Cell Biol.2013;33:1303-1316.[ PubMed:2339868 9. Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio 2014; 5: e00889 [PubMe 10. Atarashi K, et al. Treg induction by a rationally selected mixture of Clostridia strains from the aman microbiota Nature. 2013: 500: 232-236[PubMed 23842501] 11. Kelly C, et al. Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function. Cell Host Microbe. 2015; 17: 662-671 [ PubMed:25865369 12. Furuta GT, et al. Hypoxia-inducible factor 1-dependent induction of intestinal trefoil factor protects barrier function during hypoxia. J Exp Med. 2001; 193: 1027-1034[PubMed: 1 1342587 13. Xavier MN, et al. 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Wang B, Morinobu A, Horiuchi M, Liu J, Kumagai S. Butyrate inhibits functional differentiation of human monocyte-derived dendritic cells. Cell Immunol. 2008: 253: 54-58. [PubMed: 18522857] 19.Chang PV, Hao L, Offermanns S, Medzhitov R. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad SciUSA 2014;111247-2252.[ PubMed:24390544 20. Atarashi K, et al. Induction of colonic regulatory t cells by indigenous Clostridium species. Science.2011;331:337-341.[ PubMed:21205640 21. Arpaia N, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013: 504: 451-455.(PubMed: 24226773 22. Furusawa Y, et al. Commensal microbe-derived butyrate induces the differentiation of colonic egulatory T cells. Nature. 2013: 504: 446-450[PubMed: 24226770 23. Smith PM, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science. 2013: 341: 569-573. [PubMed: 238288911 24. Singh N, et al. Activation of Gpr109a, receptor for I niacin a suppresses colonic inflammation and carcinogenesis. Immunity. 2014; 40: 128-139[ PubMed 4412617 25. Peyrin-Biroulet L, et al. Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon. Proc Natl Acad SciU SA. 2010, 107:8772-877 PubMed:20421464] 26. Narushima S, et al. Characterization of the 17 strains of regulatory T cell-inducing human-derived Clostridia. Gut microbes. 2014: 5: 333-339.[PubMed: 24642476 27. Behnsen J, et al. The cytokine IL-22 promotes pathogen colonization by suppressing related commensal bacteria. Immunity. 2014: 40: 262-273. PubMed: 24508234 28. Setiady YY, Coccia JA, Park PU In vivo depletion of CD4+FOXP3+ Treg cells by the PC61 anti- CD25 monoclonal antibody is mediated by FcgammaRIll+ phagocytes. Eur J Immunol. 2010; 40:780-786.[ PubMed:20039297] 29. Barrientos A. In vivo and in organello assessment of oXPHOS activities. Methods. 2002 26: 307- 316.[ PubMed:12054921] Science Author manuscript; available in PMC 2017 October 18. Alex S, et al. Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor gamma. Mol Cell Biol. 2013; 33:1303–1316. [PubMed: 23339868] 9. Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. MBio. 2014; 5:e00889. [PubMed: 24757212] 10. Atarashi K, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013; 500:232–236. [PubMed: 23842501] 11. Kelly CJ, et al. Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function. Cell Host Microbe. 2015; 17:662–671. [PubMed: 25865369] 12. Furuta GT, et al. Hypoxia-inducible factor 1-dependent induction of intestinal trefoil factor protects barrier function during hypoxia. J Exp Med. 2001; 193:1027–1034. [PubMed: 11342587] 13. Xavier MN, et al. PPARgamma-mediated increase in glucose availability sustains chronic Brucella abortus infection in alternatively activated macrophages. Cell Host Microbe. 2013; 14:159–170. [PubMed: 23954155] 14. Terada N, Ohno N, Saitoh S, Ohno S. Immunohistochemical detection of hypoxia in mouse liver tissues treated with pimonidazole using “in vivo cryotechnique”. Histochem Cell Biol. 2007; 128:253–261. [PubMed: 17680263] 15. Kizaka-Kondoh S, Konse-Nagasawa H. Significance of nitroimidazole compounds and hypoxia￾inducible factor-1 for imaging tumor hypoxia. Cancer science. 2009; 100:1366–1373. [PubMed: 19459851] 16. Maslowski KM, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009; 461:1282–1286. [PubMed: 19865172] 17. Millard AL, et al. 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