Clemente JC , Ursell LK , Parfrey LW , Knight R . The impact of the gut microbiota on human health: an integrative view. Cell 2012; 148: 1258–1270. https://doi.org/10.1016/j.cell.2012.01.035.

• Crossref
Clemente JC , Ursell LK , Parfrey LW , Knight R . The impact of the gut microbiota on human health: an integrative view. Cell 2012; 148: 1258–1270. https://doi.org/10.1016/j.cell.2012.01.035.10.1016/j.cell.2012.01.035)| false
• Search Google Scholar
• Export Citation

Dzutsev A , Badger JH , Perez-Chanona E , Roy S , Salcedo R , Smith CK , et al.. Microbes and Cancer. Annu Rev Immunol 2017; 35: 199–228. https://doi.org/10.1146/annurev-immunol-051116-052133.

• Crossref
Dzutsev A , Badger JH , Perez-Chanona E , Roy S , Salcedo R , Smith CK , . Microbes and Cancer. Annu Rev Immunol 2017; 35: 199–228. https://doi.org/10.1146/annurev-immunol-051116-052133.10.1146/annurev-immunol-051116-052133)| false
• Search Google Scholar
• Export Citation

Belkaid Y , Hand TW . Role of the microbiota in immunity and inflammation. Cell 2014; 157: 121–141. https://doi.org/10.1016/j.cell.2014.03.011.

• Crossref
Belkaid Y , Hand TW . Role of the microbiota in immunity and inflammation. Cell 2014; 157: 121–141. https://doi.org/10.1016/j.cell.2014.03.011.10.1016/j.cell.2014.03.011)| false
• Search Google Scholar
• Export Citation

Blekhman R , Goodrich JK , Huang K , Sun Q , Bukowski R , Bell JT , et al.. Host genetic variation impacts microbiome composition across human body sites. Genome Biol 2015; 16: 191. https://doi.org/10.1186/s13059-015-0759-1.

• Crossref
Blekhman R , Goodrich JK , Huang K , Sun Q , Bukowski R , Bell JT , . Host genetic variation impacts microbiome composition across human body sites. Genome Biol 2015; 16: 191. https://doi.org/10.1186/s13059-015-0759-1.10.1186/s13059-015-0759-1)| false
• Search Google Scholar
• Export Citation

Flandroy L , Poutahidis T , Berg G , Clarke G , Dao M-C , Decaestecker E , et al.. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci Total Environ 2018; 627: 1018–1038. https://doi.org/10.1016/j.scitotenv.2018.01.288.

• Crossref
Flandroy L , Poutahidis T , Berg G , Clarke G , Dao M-C , Decaestecker E , . The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci Total Environ 2018; 627: 1018–1038. https://doi.org/10.1016/j.scitotenv.2018.01.288.10.1016/j.scitotenv.2018.01.288)| false
• Search Google Scholar
• Export Citation

Zheng D , Liwinski T , Elinav E . Interaction between microbiota and immunity in health and disease. Cell Res. 2020; 30: 492–506. https://doi.org/10.1038/s41422-020-0332-7.

• Crossref
Zheng D , Liwinski T , Elinav E . Interaction between microbiota and immunity in health and disease. Cell Res. 2020; 30: 492–506. https://doi.org/10.1038/s41422-020-0332-7.10.1038/s41422-020-0332-7)| false
• Search Google Scholar
• Export Citation

Belkaid Y , Harrison OJ . Homeostatic immunity and the microbiota. Immunity 2017; 46: 562–576. https://doi.org/10.1016/j.immuni.2017.04.008.

• Crossref
Belkaid Y , Harrison OJ . Homeostatic immunity and the microbiota. Immunity 2017; 46: 562–576. https://doi.org/10.1016/j.immuni.2017.04.008.10.1016/j.immuni.2017.04.008)| false
• Search Google Scholar
• Export Citation

Levy M , Blacher E , Elinav E . Microbiome, metabolites and host immunity. Curr Opin Microbiol 2017; 35: 8–15. https://doi.org/10.1016/j.mib.2016.10.003.

• Crossref
Levy M , Blacher E , Elinav E . Microbiome, metabolites and host immunity. Curr Opin Microbiol 2017; 35: 8–15. https://doi.org/10.1016/j.mib.2016.10.003.10.1016/j.mib.2016.10.003)| false
• Search Google Scholar
• Export Citation

Wen L , Ley RE , Volchkov PV , Stranges PB , Avanesyan L , Stonebraker AC , et al.. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008; 455: 1109–1113. https://doi.org/10.1038/nature07336.

• Crossref
Wen L , Ley RE , Volchkov PV , Stranges PB , Avanesyan L , Stonebraker AC , . Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008; 455: 1109–1113. https://doi.org/10.1038/nature07336.10.1038/nature07336)| false
• Search Google Scholar
• Export Citation

Chassaing B , Ley RE , Gewirtz AT . Intestinal epithelial cell toll-like receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice. Gastroenterology 2014; 147: 1363–1377.e17. https://doi.org/10.1053/j.gastro.2014.08.033.

• Crossref
Chassaing B , Ley RE , Gewirtz AT . Intestinal epithelial cell toll-like receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice. Gastroenterology 2014; 147: 1363–1377.e17. https://doi.org/10.1053/j.gastro.2014.08.033.10.1053/j.gastro.2014.08.033)| false
• Search Google Scholar
• Export Citation

Carvalho FA , Koren O , Goodrich JK , Johansson MEV , Nalbantoglu I , Aitken JD , et al.. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 2012; 12: 139–152. https://doi.org/10.1016/j.chom.2012.07.004.

• Crossref
Carvalho FA , Koren O , Goodrich JK , Johansson MEV , Nalbantoglu I , Aitken JD , . Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell Host Microbe 2012; 12: 139–152. https://doi.org/10.1016/j.chom.2012.07.004.10.1016/j.chom.2012.07.004)| false
• Search Google Scholar
• Export Citation

Vijay-Kumar M , Aitken JD , Carvalho FA , Cullender TC , Mwangi S , Srinivasan S , et al.. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010; 328: 228–231. https://doi.org/10.1126/science.1179721.

• Crossref
Vijay-Kumar M , Aitken JD , Carvalho FA , Cullender TC , Mwangi S , Srinivasan S , . Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010; 328: 228–231. https://doi.org/10.1126/science.1179721.10.1126/science.1179721)| false
• Search Google Scholar
• Export Citation

Vijay-Kumar M , Sanders CJ , Taylor RT , Kumar A , Aitken JD , Sitaraman SV , et al.. Deletion of TLR5 results in spontaneous colitis in mice. J Clin Invest 2007; 117: 3909–3921. https://doi.org/10.1172/JCI33084.

Vijay-Kumar M , Sanders CJ , Taylor RT , Kumar A , Aitken JD , Sitaraman SV , . Deletion of TLR5 results in spontaneous colitis in mice. J Clin Invest 2007; 117: 3909–3921. https://doi.org/10.1172/JCI33084.)| false
• Search Google Scholar
• Export Citation

Valentini M , Piermattei A , Di Sante G , Migliara G , Delogu G , Ria F . Immunomodulation by gut microbiota: role of Toll-like receptor expressed by T cells. J Immunol Res 2014; 2014: 586939. https://doi.org/10.1155/2014/586939.

• Crossref
Valentini M , Piermattei A , Di Sante G , Migliara G , Delogu G , Ria F . Immunomodulation by gut microbiota: role of Toll-like receptor expressed by T cells. J Immunol Res 2014; 2014: 586939. https://doi.org/10.1155/2014/586939.10.1155/2014/586939)| false
• Search Google Scholar
• Export Citation

Lee J , Mo J-H , Katakura K , Alkalay I , Rucker AN , Liu Y-T , et al.. Maintenance of colonic homeostasis by distinctive apical TLR9 signalling in intestinal epithelial cells. Nat Cell Biol 2006; 8: 1327–1336. https://doi.org/10.1038/ncb1500.

• Crossref
Lee J , Mo J-H , Katakura K , Alkalay I , Rucker AN , Liu Y-T , . Maintenance of colonic homeostasis by distinctive apical TLR9 signalling in intestinal epithelial cells. Nat Cell Biol 2006; 8: 1327–1336. https://doi.org/10.1038/ncb1500.10.1038/ncb1500)| false
• Search Google Scholar
• Export Citation

Round JL , Lee SM , Li J , Tran G , Jabri B , Chatila TA , et al.. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011; 332: 974–977. https://doi.org/10.1126/science.1206095.

• Crossref
Round JL , Lee SM , Li J , Tran G , Jabri B , Chatila TA , . The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 2011; 332: 974–977. https://doi.org/10.1126/science.1206095.10.1126/science.1206095)| false
• Search Google Scholar
• Export Citation

Zou S , Fang L , Lee M-H . Dysbiosis of gut microbiota in promoting the development of colorectal cancer. Gastroenterol Rep 2018; 6: 1–12. https://doi.org/10.1093/gastro/gox031.

• Crossref
Zou S , Fang L , Lee M-H . Dysbiosis of gut microbiota in promoting the development of colorectal cancer. Gastroenterol Rep 2018; 6: 1–12. https://doi.org/10.1093/gastro/gox031.10.1093/gastro/gox031)| false
• Search Google Scholar
• Export Citation

Dalby MJ , Aviello G , Ross AW , Walker AW , Barrett P , Morgan PJ . Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N. Sci Rep 2018; 8. https://doi.org/10.1038/s41598-018-33928-4.

• Crossref
Dalby MJ , Aviello G , Ross AW , Walker AW , Barrett P , Morgan PJ . Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N. Sci Rep 2018; 8. https://doi.org/10.1038/s41598-018-33928-4.10.1038/s41598-018-33928-4)| false
• Search Google Scholar
• Export Citation

Bereswill S , Kühl AA , Alutis M , Fischer A , Möhle L , Struck D , et al.. The impact of Toll-like-receptor-9 on intestinal microbiota composition and extra-intestinal sequelae in experimental Toxoplasma gondii induced ileitis. Gut Pathog 2014; 6: 19. https://doi.org/10.1186/1757-4749-6-19.

• Crossref
Bereswill S , Kühl AA , Alutis M , Fischer A , Möhle L , Struck D , . The impact of Toll-like-receptor-9 on intestinal microbiota composition and extra-intestinal sequelae in experimental Toxoplasma gondii induced ileitis. Gut Pathog 2014; 6: 19. https://doi.org/10.1186/1757-4749-6-19.10.1186/1757-4749-6-19)| false
• Search Google Scholar
• Export Citation

Ubeda C , Lipuma L , Gobourne A , Viale A , Leiner I , Equinda M , et al.. Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J Exp Med 2012; 209: 1445–1456. https://doi.org/10.1084/jem.20120504.

• Crossref
Ubeda C , Lipuma L , Gobourne A , Viale A , Leiner I , Equinda M , . Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J Exp Med 2012; 209: 1445–1456. https://doi.org/10.1084/jem.20120504.10.1084/jem.20120504)| false
• Search Google Scholar
• Export Citation

Moreira LO , Zamboni DS . NOD1 and NOD2 signaling in infection and inflammation. Front Immunol 2012; 3. https://doi.org/10.3389/fimmu.2012.00328.

• Crossref
Moreira LO , Zamboni DS . NOD1 and NOD2 signaling in infection and inflammation. Front Immunol 2012; 3. https://doi.org/10.3389/fimmu.2012.00328.10.3389/fimmu.2012.00328)| false
• Search Google Scholar
• Export Citation

Bouskra D , Brézillon C , Bérard M , Werts C , Varona R , Boneca IG , et al.. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 2008; 456: 507–510. https://doi.org/10.1038/nature07450.

• Crossref
Bouskra D , Brézillon C , Bérard M , Werts C , Varona R , Boneca IG , . Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 2008; 456: 507–510. https://doi.org/10.1038/nature07450.10.1038/nature07450)| false
• Search Google Scholar
• Export Citation

Petnicki-Ocwieja T , Hrncir T , Liu Y-J , Biswas A , Hudcovic T , Tlaskalova-Hogenova H , et al.. Nod2 is required for the regulation of commensal microbiota in the intestine. Proc Natl Acad Sci U S A 2009; 106: 15813–15818. https://doi.org/10.1073/pnas.0907722106.

• Crossref
Petnicki-Ocwieja T , Hrncir T , Liu Y-J , Biswas A , Hudcovic T , Tlaskalova-Hogenova H , . Nod2 is required for the regulation of commensal microbiota in the intestine. Proc Natl Acad Sci U S A 2009; 106: 15813–15818. https://doi.org/10.1073/pnas.0907722106.10.1073/pnas.0907722106)| false
• Search Google Scholar
• Export Citation

Robertson SJ , Zhou JY , Geddes K , Rubino SJ , Cho JH , Girardin SE , et al.. Nod1 and Nod2 signaling does not alter the composition of intestinal bacterial communities at homeostasis. Gut Microbes 2013; 4: 222–231. https://doi.org/10.4161/gmic.24373.

• Crossref
Robertson SJ , Zhou JY , Geddes K , Rubino SJ , Cho JH , Girardin SE , . Nod1 and Nod2 signaling does not alter the composition of intestinal bacterial communities at homeostasis. Gut Microbes 2013; 4: 222–231. https://doi.org/10.4161/gmic.24373.10.4161/gmic.24373)| false
• Search Google Scholar
• Export Citation

Lu W-G , Zou Y-F , Feng X-L , Yuan F-L , Gu Y-L , Li X , et al.. Association of NOD1 (CARD4) insertion/deletion polymorphism with susceptibility to IBD: a meta-analysis. World J Gastroenterol WJG 2010; 16: 4348–4356. https://doi.org/10.3748/wjg.v16.i34.4348.

• Crossref
Lu W-G , Zou Y-F , Feng X-L , Yuan F-L , Gu Y-L , Li X , . Association of NOD1 (CARD4) insertion/deletion polymorphism with susceptibility to IBD: a meta-analysis. World J Gastroenterol WJG 2010; 16: 4348–4356. https://doi.org/10.3748/wjg.v16.i34.4348.10.3748/wjg.v16.i34.4348)| false
• Search Google Scholar
• Export Citation

Li E , Hamm CM , Gulati AS , Sartor RB , Chen H , Wu X , et al.. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One 2012; 7: e26284. https://doi.org/10.1371/journal.pone.0026284.

• Crossref
Li E , Hamm CM , Gulati AS , Sartor RB , Chen H , Wu X , . Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One 2012; 7: e26284. https://doi.org/10.1371/journal.pone.0026284.10.1371/journal.pone.0026284)| false
• Search Google Scholar
• Export Citation

Glas J , Seiderer J , Tillack C , Pfennig S , Beigel F , Jürgens M , et al.. The NOD2 single nucleotide polymorphisms rs2066843 and rs2076756 are novel and common crohn’s disease susceptibility gene variants. PLoS One 2010; 5: e14466. https://doi.org/10.1371/journal.pone.0014466.

• Crossref
Glas J , Seiderer J , Tillack C , Pfennig S , Beigel F , Jürgens M , . The NOD2 single nucleotide polymorphisms rs2066843 and rs2076756 are novel and common crohn’s disease susceptibility gene variants. PLoS One 2010; 5: e14466. https://doi.org/10.1371/journal.pone.0014466.10.1371/journal.pone.0014466)| false
• Search Google Scholar
• Export Citation

Levy M , Thaiss CA , Zeevi D , Dohnalová L , Zilberman-Schapira G , Mahdi JA , et al.. Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Cell. 2015; 163: 1428–1443. https://doi.org/10.1016/j.cell.2015.10.048.

• Crossref
Levy M , Thaiss CA , Zeevi D , Dohnalová L , Zilberman-Schapira G , Mahdi JA , . Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Cell. 2015; 163: 1428–1443. https://doi.org/10.1016/j.cell.2015.10.048.10.1016/j.cell.2015.10.048)| false
• Search Google Scholar
• Export Citation

Wlodarska M , Thaiss CA , Nowarski R , Henao-Mejia J , Zhang J-P , Brown EM , et al.. NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion. Cell 2014; 156: 1045–1059. https://doi.org/10.1016/j.cell.2014.01.026.

• Crossref
Wlodarska M , Thaiss CA , Nowarski R , Henao-Mejia J , Zhang J-P , Brown EM , . NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion. Cell 2014; 156: 1045–1059. https://doi.org/10.1016/j.cell.2014.01.026.10.1016/j.cell.2014.01.026)| false
• Search Google Scholar
• Export Citation

Hu B , Elinav E , Huber S , Strowig T , Hao L , Hafemann A , et al.. Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer. Proc Natl Acad Sci USA 2013; 110: 9862–9867. https://doi.org/10.1073/pnas.1307575110.

• Crossref
Hu B , Elinav E , Huber S , Strowig T , Hao L , Hafemann A , . Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer. Proc Natl Acad Sci USA 2013; 110: 9862–9867. https://doi.org/10.1073/pnas.1307575110.10.1073/pnas.1307575110)| false
• Search Google Scholar
• Export Citation

Elinav E , Strowig T , Kau AL , Henao-Mejia J , Thaiss CA , Booth CJ , et al.. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 2011; 145: 745–757. https://doi.org/10.1016/j.cell.2011.04.022.

• Crossref
Elinav E , Strowig T , Kau AL , Henao-Mejia J , Thaiss CA , Booth CJ , . NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 2011; 145: 745–757. https://doi.org/10.1016/j.cell.2011.04.022.10.1016/j.cell.2011.04.022)| false
• Search Google Scholar
• Export Citation

Mamantopoulos M , Ronchi F , Van Hauwermeiren F , Vieira-Silva S , Yilmaz B , Martens L , et al.. Nlrp6- and ASC-dependent inflammasomes do not shape the commensal gut microbiota composition. Immunity 2017; 47: 339–348.e4. https://doi.org/10.1016/j.immuni.2017.07.011.

• Crossref
Mamantopoulos M , Ronchi F , Van Hauwermeiren F , Vieira-Silva S , Yilmaz B , Martens L , . Nlrp6- and ASC-dependent inflammasomes do not shape the commensal gut microbiota composition. Immunity 2017; 47: 339–348.e4. https://doi.org/10.1016/j.immuni.2017.07.011.10.1016/j.immuni.2017.07.011)| false
• Search Google Scholar
• Export Citation

Seregin SS , Golovchenko N , Schaf B , Chen J , Pudlo NA , Mitchell J , et al.. NLRP6 protects IL10−/− mice from colitis by limiting colonization of Akkermansia muciniphila. Cell Rep 2017; 19: 733–745. https://doi.org/10.1016/j.celrep.2017.03.080.

• Crossref
Seregin SS , Golovchenko N , Schaf B , Chen J , Pudlo NA , Mitchell J , . NLRP6 protects IL10−/− mice from colitis by limiting colonization of Akkermansia muciniphila. Cell Rep 2017; 19: 733–745. https://doi.org/10.1016/j.celrep.2017.03.080.10.1016/j.celrep.2017.03.080)| false
• Search Google Scholar
• Export Citation

Levy M , Shapiro H , Thaiss CA , Elinav E . NLRP6: a multifaceted innate immune sensor. Trends Immunol 2017; 38: 248–260. https://doi.org/10.1016/j.it.2017.01.001.

• Crossref
Levy M , Shapiro H , Thaiss CA , Elinav E . NLRP6: a multifaceted innate immune sensor. Trends Immunol 2017; 38: 248–260. https://doi.org/10.1016/j.it.2017.01.001.10.1016/j.it.2017.01.001)| false
• Search Google Scholar
• Export Citation

Salzman NH , Hung K , Haribhai D , Chu H , Karlsson-Sjöberg J , Amir E , et al.. Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol 2010; 11: 76–83. https://doi.org/10.1038/ni.1825.

• Crossref
Salzman NH , Hung K , Haribhai D , Chu H , Karlsson-Sjöberg J , Amir E , . Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol 2010; 11: 76–83. https://doi.org/10.1038/ni.1825.10.1038/ni.1825)| false
• Search Google Scholar
• Export Citation

Elphick D , Liddell S , Mahida YR . Impaired luminal processing of human defensin-5 in Crohn’s disease: persistence in a complex with chymotrypsinogen and trypsin. Am J Pathol 2008; 172: 702–713. https://doi.org/10.2353/ajpath.2008.070755.

• Crossref
Elphick D , Liddell S , Mahida YR . Impaired luminal processing of human defensin-5 in Crohn’s disease: persistence in a complex with chymotrypsinogen and trypsin. Am J Pathol 2008; 172: 702–713. https://doi.org/10.2353/ajpath.2008.070755.10.2353/ajpath.2008.070755)| false
• Search Google Scholar
• Export Citation

Wehkamp J , Salzman NH , Porter E , Nuding S , Weichenthal M , Petras RE , et al.. Reduced Paneth cell alpha-defensins in ileal Crohn’s disease. Proc Natl Acad Sci U S A 2005; 102: 18129–18134. https://doi.org/10.1073/pnas.0505256102.

• Crossref
Wehkamp J , Salzman NH , Porter E , Nuding S , Weichenthal M , Petras RE , . Reduced Paneth cell alpha-defensins in ileal Crohn’s disease. Proc Natl Acad Sci U S A 2005; 102: 18129–18134. https://doi.org/10.1073/pnas.0505256102.10.1073/pnas.0505256102)| false
• Search Google Scholar
• Export Citation

Vaishnava S , Yamamoto M , Severson KM , Ruhn KA , Yu X , Koren O , et al.. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 2011; 334: 255–258. https://doi.org/10.1126/science.1209791.

• Crossref
Vaishnava S , Yamamoto M , Severson KM , Ruhn KA , Yu X , Koren O , . The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 2011; 334: 255–258. https://doi.org/10.1126/science.1209791.10.1126/science.1209791)| false
• Search Google Scholar
• Export Citation

Honda M , Surewaard BGJ , Watanabe M , Hedrick CC , Lee W-Y , Brown K , et al.. Perivascular localization of macrophages in the intestinal mucosa is regulated by Nr4a1 and the microbiome. Nat Commun 2020; 11: 1329. https://doi.org/10.1038/s41467-020-15068-4.

• Crossref
Honda M , Surewaard BGJ , Watanabe M , Hedrick CC , Lee W-Y , Brown K , . Perivascular localization of macrophages in the intestinal mucosa is regulated by Nr4a1 and the microbiome. Nat Commun 2020; 11: 1329. https://doi.org/10.1038/s41467-020-15068-4.10.1038/s41467-020-15068-4)| false
• Search Google Scholar
• Export Citation

Kim M , Galan C , Hill AA , Wu W-J , Fehlner-Peach H , Song HW , et al.. Critical role for the microbiota in CX3CR1+ intestinal mononuclear phagocyte regulation of intestinal T cell responses. Immunity 2018; 49: 151–163.e5. https://doi.org/10.1016/j.immuni.2018.05.009.

• Crossref
Kim M , Galan C , Hill AA , Wu W-J , Fehlner-Peach H , Song HW , . Critical role for the microbiota in CX3CR1+ intestinal mononuclear phagocyte regulation of intestinal T cell responses. Immunity 2018; 49: 151–163.e5. https://doi.org/10.1016/j.immuni.2018.05.009.10.1016/j.immuni.2018.05.009)| false
• Search Google Scholar
• Export Citation

Diehl GE , Longman RS , Zhang J-X , Breart B , Galan C , Cuesta A , et al.. Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX(3)CR1(hi) cells. Nature 2013; 494: 116–120. https://doi.org/10.1038/nature11809.

• Crossref
Diehl GE , Longman RS , Zhang J-X , Breart B , Galan C , Cuesta A , . Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX(3)CR1(hi) cells. Nature 2013; 494: 116–120. https://doi.org/10.1038/nature11809.10.1038/nature11809)| false
• Search Google Scholar
• Export Citation

Chang PV , Hao L , Offermanns S , Medzhitov R . The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci U S A 2014; 111: 2247–2252. https://doi.org/10.1073/pnas.1322269111.

• Crossref
Chang PV , Hao L , Offermanns S , Medzhitov R . The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition. Proc Natl Acad Sci U S A 2014; 111: 2247–2252. https://doi.org/10.1073/pnas.1322269111.10.1073/pnas.1322269111)| false
• Search Google Scholar
• Export Citation

Ji J , Shu D , Zheng M , Wang J , Luo C , Wang Y , et al.. Microbial metabolite butyrate facilitates M2 macrophage polarization and function, Sci Rep 2016; 6: 24838. https://doi.org/10.1038/srep24838.

• Crossref
Ji J , Shu D , Zheng M , Wang J , Luo C , Wang Y , . Microbial metabolite butyrate facilitates M2 macrophage polarization and function, Sci Rep 2016; 6: 24838. https://doi.org/10.1038/srep24838.10.1038/srep24838)| false
• Search Google Scholar
• Export Citation

Skelly AN , Sato Y , Kearney S , Honda K . Mining the microbiota for microbial and metabolite-based immunotherapies. Nat Rev Immunol 2019; 19: 305–323. https://doi.org/10.1038/s41577-019-0144-5.

• Crossref
Skelly AN , Sato Y , Kearney S , Honda K . Mining the microbiota for microbial and metabolite-based immunotherapies. Nat Rev Immunol 2019; 19: 305–323. https://doi.org/10.1038/s41577-019-0144-5.10.1038/s41577-019-0144-5)| false
• Search Google Scholar
• Export Citation

Zhang D , Chen G , Manwani D , Mortha A , Xu C , Faith JJ , et al.. Neutrophil ageing is regulated by the microbiome. Nature 2015; 525: 528–532. https://doi.org/10.1038/nature15367.

• Crossref
Zhang D , Chen G , Manwani D , Mortha A , Xu C , Faith JJ , . Neutrophil ageing is regulated by the microbiome. Nature 2015; 525: 528–532. https://doi.org/10.1038/nature15367.10.1038/nature15367)| false
• Search Google Scholar
• Export Citation

Clarke TB , Davis KM , Lysenko ES , Zhou AY , Yu Y , Weiser JN . Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat Med 2010; 16: 228–231. https://doi.org/10.1038/nm.2087.

• Crossref
Clarke TB , Davis KM , Lysenko ES , Zhou AY , Yu Y , Weiser JN . Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat Med 2010; 16: 228–231. https://doi.org/10.1038/nm.2087.10.1038/nm.2087)| false
• Search Google Scholar
• Export Citation

Rescigno M , Urbano M , Valzasina B , Francolini M , Rotta G , Bonasio R , et al.. Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nat Immunol 2001; 2: 361–367. https://doi.org/10.1038/86373.

• Crossref
Rescigno M , Urbano M , Valzasina B , Francolini M , Rotta G , Bonasio R , . Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nat Immunol 2001; 2: 361–367. https://doi.org/10.1038/86373.10.1038/86373)| false
• Search Google Scholar
• Export Citation

Konieczna P , Ferstl R , Ziegler M , Frei R , Nehrbass D , Lauener RP , et al.. Immunomodulation by Bifidobacterium infantis 35624 in the murine lamina propria requires retinoic acid-dependent and independent mechanisms. PLoS One 2013; 8: e62617. https://doi.org/10.1371/journal.pone.0062617.

• Crossref
Konieczna P , Ferstl R , Ziegler M , Frei R , Nehrbass D , Lauener RP , . Immunomodulation by Bifidobacterium infantis 35624 in the murine lamina propria requires retinoic acid-dependent and independent mechanisms. PLoS One 2013; 8: e62617. https://doi.org/10.1371/journal.pone.0062617.10.1371/journal.pone.0062617)| false
• Search Google Scholar
• Export Citation

Rubic T , Lametschwandtner G , Jost S , Hinteregger S , Kund J , Carballido-Perrig N , et al.. Triggering the succinate receptor GPR91 on dendritic cells enhances immunity. Nat Immunol 2008; 9: 1261–1269. https://doi.org/10.1038/ni.1657.

• Crossref
Rubic T , Lametschwandtner G , Jost S , Hinteregger S , Kund J , Carballido-Perrig N , . Triggering the succinate receptor GPR91 on dendritic cells enhances immunity. Nat Immunol 2008; 9: 1261–1269. https://doi.org/10.1038/ni.1657.10.1038/ni.1657)| false
• Search Google Scholar
• Export Citation

Zheng Y , Valdez PA , Danilenko DM , Hu Y , Sa SM , Gong Q , et al.. Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens. Nat Med 2008; 14: 282–289. https://doi.org/10.1038/nm1720.

• Crossref
Zheng Y , Valdez PA , Danilenko DM , Hu Y , Sa SM , Gong Q , . Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens. Nat Med 2008; 14: 282–289. https://doi.org/10.1038/nm1720.10.1038/nm1720)| false
• Search Google Scholar
• Export Citation

Hughes T , Becknell B , Freud AG , McClory S , Briercheck E , Yu J , et al.. Interleukin-1beta selectively expands and sustains interleukin-22+ immature human natural killer cells in secondary lymphoid tissue. Immunity 2010; 32: 803–814. https://doi.org/10.1016/j.immuni.2010.06.007.

• Crossref
Hughes T , Becknell B , Freud AG , McClory S , Briercheck E , Yu J , . Interleukin-1beta selectively expands and sustains interleukin-22+ immature human natural killer cells in secondary lymphoid tissue. Immunity 2010; 32: 803–814. https://doi.org/10.1016/j.immuni.2010.06.007.10.1016/j.immuni.2010.06.007)| false
• Search Google Scholar
• Export Citation

Qiu J , Guo X , Chen ZE , He L , Sonnenberg GF , Artis D , et al.. Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora. Immunity 2013; 39: 386–399. https://doi.org/10.1016/j.immuni.2013.08.002.

• Crossref
Qiu J , Guo X , Chen ZE , He L , Sonnenberg GF , Artis D , . Group 3 innate lymphoid cells inhibit T-cell-mediated intestinal inflammation through aryl hydrocarbon receptor signaling and regulation of microflora. Immunity 2013; 39: 386–399. https://doi.org/10.1016/j.immuni.2013.08.002.10.1016/j.immuni.2013.08.002)| false
• Search Google Scholar
• Export Citation

Sonnenberg GF , Monticelli LA , Alenghat T , Fung TC , Hutnick NA , Kunisawa J , et al.. Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science 2012; 336: 1321–1325. https://doi.org/10.1126/science.1222551.

• Crossref
Sonnenberg GF , Monticelli LA , Alenghat T , Fung TC , Hutnick NA , Kunisawa J , . Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria. Science 2012; 336: 1321–1325. https://doi.org/10.1126/science.1222551.10.1126/science.1222551)| false
• Search Google Scholar
• Export Citation

Zenewicz LA , Yin X , Wang G , Elinav E , Hao L , Zhao L , et al.. Interleukin-22 deficiency alters colonic microbiota to be transmissible and colitogenic. J Immunol Baltim Md 2013; 1950(190): 5306–5312. https://doi.org/10.4049/jimmunol.1300016.

Zenewicz LA , Yin X , Wang G , Elinav E , Hao L , Zhao L , . Interleukin-22 deficiency alters colonic microbiota to be transmissible and colitogenic. J Immunol Baltim Md 2013; 1950(190): 5306–5312. https://doi.org/10.4049/jimmunol.1300016.)| false
• Search Google Scholar
• Export Citation

Clark E , Hoare C , Tanianis-Hughes J , Carlson GL , Warhurst G . Interferon γ induces translocation of commensal Escherichia coli across gut epithelial cells via a lipid raft–mediated process. Gastroenterology 2005; 128: 1258–1267. https://doi.org/10.1053/j.gastro.2005.01.046.

• Crossref
Clark E , Hoare C , Tanianis-Hughes J , Carlson GL , Warhurst G . Interferon γ induces translocation of commensal Escherichia coli across gut epithelial cells via a lipid raft–mediated process. Gastroenterology 2005; 128: 1258–1267. https://doi.org/10.1053/j.gastro.2005.01.046.10.1053/j.gastro.2005.01.046)| false
• Search Google Scholar
• Export Citation

Kubinak JL , Round JL . Do antibodies select a healthy microbiota? Nat Rev Immunol 2016; 16: 767–774. https://doi.org/10.1038/nri.2016.114.

• Crossref
Kubinak JL , Round JL . Do antibodies select a healthy microbiota? Nat Rev Immunol 2016; 16: 767–774. https://doi.org/10.1038/nri.2016.114.10.1038/nri.2016.114)| false
• Search Google Scholar
• Export Citation

Palm NW , de Zoete MR , Cullen TW , Barry NA , Stefanowski J , Hao L , et al.. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 2014; 158: 1000–1010. https://doi.org/10.1016/j.cell.2014.08.006.

• Crossref
Palm NW , de Zoete MR , Cullen TW , Barry NA , Stefanowski J , Hao L , . Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 2014; 158: 1000–1010. https://doi.org/10.1016/j.cell.2014.08.006.10.1016/j.cell.2014.08.006)| false
• Search Google Scholar
• Export Citation

Peterson DA , McNulty NP , Guruge JL , Gordon JI . IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe 2007; 2: 328–339. https://doi.org/10.1016/j.chom.2007.09.013.

• Crossref
Peterson DA , McNulty NP , Guruge JL , Gordon JI . IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe 2007; 2: 328–339. https://doi.org/10.1016/j.chom.2007.09.013.10.1016/j.chom.2007.09.013)| false
• Search Google Scholar
• Export Citation

Shulzhenko N , Morgun A , Hsiao W , Battle M , Yao M , Gavrilova O , et al.. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat Med 2011; 17: 1585–1593. https://doi.org/10.1038/nm.2505.

• Crossref
Shulzhenko N , Morgun A , Hsiao W , Battle M , Yao M , Gavrilova O , . Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat Med 2011; 17: 1585–1593. https://doi.org/10.1038/nm.2505.10.1038/nm.2505)| false
• Search Google Scholar
• Export Citation

Catanzaro JR , Strauss JD , Bielecka A , Porto AF , Lobo FM , Urban A , et al.. IgA-deficient humans exhibit gut microbiota dysbiosis despite production of compensatory IgM. BioRxiv 2018; 446724. https://doi.org/10.1101/446724.

Catanzaro JR , Strauss JD , Bielecka A , Porto AF , Lobo FM , Urban A , . IgA-deficient humans exhibit gut microbiota dysbiosis despite production of compensatory IgM. BioRxiv 2018; 446724. https://doi.org/10.1101/446724.)| false
• Search Google Scholar
• Export Citation

Kim M , Qie Y , Park J , Kim CH . Gut microbial metabolites fuel host antibody responses. Cell Host Microbe 2016; 20: 202–214. https://doi.org/10.1016/j.chom.2016.07.001.

• Crossref
Kim M , Qie Y , Park J , Kim CH . Gut microbial metabolites fuel host antibody responses. Cell Host Microbe 2016; 20: 202–214. https://doi.org/10.1016/j.chom.2016.07.001.10.1016/j.chom.2016.07.001)| false
• Search Google Scholar
• Export Citation

Tanoue T , Morita S , Plichta DR , Skelly AN , Suda W , Sugiura Y , et al.. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 2019; 565: 600–605. https://doi.org/10.1038/s41586-019-0878-z.

• Crossref
Tanoue T , Morita S , Plichta DR , Skelly AN , Suda W , Sugiura Y , . A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 2019; 565: 600–605. https://doi.org/10.1038/s41586-019-0878-z.10.1038/s41586-019-0878-z)| false
• Search Google Scholar
• Export Citation

Luu M , Weigand K , Wedi F , Breidenbend C , Leister H , Pautz S , et al.. Regulation of the effector function of CD8 + T cells by gut microbiota-derived metabolite butyrate. Sci Rep 2018; 8: 1–10. https://doi.org/10.1038/s41598-018-32860-x.

• Crossref
Luu M , Weigand K , Wedi F , Breidenbend C , Leister H , Pautz S , . Regulation of the effector function of CD8 + T cells by gut microbiota-derived metabolite butyrate. Sci Rep 2018; 8: 1–10. https://doi.org/10.1038/s41598-018-32860-x.10.1038/s41598-018-32860-x)| false
• Search Google Scholar
• Export Citation

Brown EM , Kenny DJ , Xavier RJ . Gut microbiota regulation of T cells during inflammation and autoimmunity. Annu Rev Immunol 2019; 37: 599–624. https://doi.org/10.1146/annurev-immunol-042718-041841.

• Crossref
Brown EM , Kenny DJ , Xavier RJ . Gut microbiota regulation of T cells during inflammation and autoimmunity. Annu Rev Immunol 2019; 37: 599–624. https://doi.org/10.1146/annurev-immunol-042718-041841.10.1146/annurev-immunol-042718-041841)| false
• Search Google Scholar
• Export Citation

Sallusto F . Heterogeneity of human CD4(+) T cells against microbes. Annu Rev Immunol 2016; 34: 317–334. https://doi.org/10.1146/annurev-immunol-032414-112056.

• Crossref
Sallusto F . Heterogeneity of human CD4(+) T cells against microbes. Annu Rev Immunol 2016; 34: 317–334. https://doi.org/10.1146/annurev-immunol-032414-112056.10.1146/annurev-immunol-032414-112056)| false
• Search Google Scholar
• Export Citation

Atarashi K , Suda W , Luo C , Kawaguchi T , Motoo I , Narushima S , et al.. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science 2017; 358: 359–365. https://doi.org/10.1126/science.aan4526.

• Crossref
Atarashi K , Suda W , Luo C , Kawaguchi T , Motoo I , Narushima S , . Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science 2017; 358: 359–365. https://doi.org/10.1126/science.aan4526.10.1126/science.aan4526)| false
• Search Google Scholar
• Export Citation

von Moltke J , Ji M , Liang H-E , Locksley RM . Tuft-cell-derived IL-25 regulates an intestinal ILC2-epithelial response circuit. Nature 2016; 529: 221–225. https://doi.org/10.1038/nature16161.

• Crossref
von Moltke J , Ji M , Liang H-E , Locksley RM . Tuft-cell-derived IL-25 regulates an intestinal ILC2-epithelial response circuit. Nature 2016; 529: 221–225. https://doi.org/10.1038/nature16161.10.1038/nature16161)| false
• Search Google Scholar
• Export Citation

Gerbe F , Jay P . Intestinal tuft cells: epithelial sentinels linking luminal cues to the immune system. Mucosal Immunol 2016; 9: 1353–1359. https://doi.org/10.1038/mi.2016.68.

• Crossref
Gerbe F , Jay P . Intestinal tuft cells: epithelial sentinels linking luminal cues to the immune system. Mucosal Immunol 2016; 9: 1353–1359. https://doi.org/10.1038/mi.2016.68.10.1038/mi.2016.68)| false
• Search Google Scholar
• Export Citation

Atarashi K , Nishimura J , Shima T , Umesaki Y , Yamamoto M , Onoue M , et al.. ATP drives lamina propria T(H)17 cell differentiation. Nature 2008; 455: 808–812. https://doi.org/10.1038/nature07240.

• Crossref
Atarashi K , Nishimura J , Shima T , Umesaki Y , Yamamoto M , Onoue M , . ATP drives lamina propria T(H)17 cell differentiation. Nature 2008; 455: 808–812. https://doi.org/10.1038/nature07240.10.1038/nature07240)| false
• Search Google Scholar
• Export Citation

Ivanov II , Atarashi K , Manel N , Brodie EL , Shima T , Karaoz U , et al.. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009; 139: 485–498. https://doi.org/10.1016/j.cell.2009.09.033.

• Crossref
Ivanov II , Atarashi K , Manel N , Brodie EL , Shima T , Karaoz U , . Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009; 139: 485–498. https://doi.org/10.1016/j.cell.2009.09.033.10.1016/j.cell.2009.09.033)| false
• Search Google Scholar
• Export Citation

Schnupf P , Gaboriau-Routhiau V , Sansonetti PJ , Cerf-Bensussan N . Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world. Curr Opin Microbiol 2017; 35: 100–109. https://doi.org/10.1016/j.mib.2017.03.004.

• Crossref
Schnupf P , Gaboriau-Routhiau V , Sansonetti PJ , Cerf-Bensussan N . Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world. Curr Opin Microbiol 2017; 35: 100–109. https://doi.org/10.1016/j.mib.2017.03.004.10.1016/j.mib.2017.03.004)| false
• Search Google Scholar
• Export Citation

Tan TG , Sefik E , Geva-Zatorsky N , Kua L , Naskar D , Teng F , et al.. Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proc Natl Acad Sci U S A 2016; 113: E8141–E8150. https://doi.org/10.1073/pnas.1617460113.