{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:43:29Z","timestamp":1790815409838,"version":"4.1.0"},"reference-count":56,"publisher":"National Academy of Sciences","issue":"7","license":[{"start":{"date-parts":[[2015,8,17]],"date-time":"2015-08-17T00:00:00Z","timestamp":1439769600000},"content-version":"vor","delay-in-days":188,"URL":"http:\/\/www.pnas.org\/site\/misc\/userlicense.xhtml"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["DK071754"],"award-info":[{"award-number":["DK071754"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI046688"],"award-info":[{"award-number":["AI046688"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI089771"],"award-info":[{"award-number":["AI089771"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2015,2,17]]},"abstract":"<jats:title>Significance<\/jats:title>\n                  <jats:p>The mammalian intestine provides a key interface with several essential environmental factors, including nutrients, toxins, resident microbiota, and pathogens. Consequently, the intestine undergoes major developmental transitions that correspond to dramatic changes in the environment: one at birth and the other at weaning. These transitions reflect both developmental and environmentally induced changes in intestinal gene expression. Here, we performed a systematic analysis of global gene expression that is associated with developmental timing versus the changes that are due to the innate immune signaling pathways mediated by toll-like receptor (TLR) and IL-1 receptor families. The results reveal distinct roles of these pathways in intestinal adaptation throughout postnatal development.<\/jats:p>","DOI":"10.1073\/pnas.1424886112","type":"journal-article","created":{"date-parts":[[2015,2,17]],"date-time":"2015-02-17T12:52:24Z","timestamp":1424177544000},"page":"1929-1936","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":94,"title":["Analysis of gene\u2013environment interactions in postnatal development of the mammalian intestine"],"prefix":"10.1073","volume":"112","author":[{"given":"Seth","family":"Rakoff-Nahoum","sequence":"first","affiliation":[{"name":"Howard Hughes Medical Institute,"},{"name":"Department of Immunobiology,"},{"name":"Division of Infectious Diseases, Department of Medicine, Boston Children\u2019s Hospital and Harvard Medical School, Boston, MA 02115"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Kong","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, W. M. Keck Foundation Biotechnology Resource Laboratory, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven H.","family":"Kleinstein","sequence":"additional","affiliation":[{"name":"Interdepartmental Program in Computational Biology and Bioinformatics and Department of Pathology, Yale University School of Medicine, New Haven, CT 06510;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sathish","family":"Subramanian","sequence":"additional","affiliation":[{"name":"Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip P.","family":"Ahern","sequence":"additional","affiliation":[{"name":"Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey I.","family":"Gordon","sequence":"additional","affiliation":[{"name":"Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruslan","family":"Medzhitov","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute,"},{"name":"Department of Immunobiology,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2015,2,10]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195122343.001.0001","volume-title":"Developmental Plasticity and Evolution","author":"West-Eberhard MJ","year":"2003","unstructured":"MJ West-Eberhard Developmental Plasticity and Evolution (Oxford Univ Press, Oxford, UK, 2003)."},{"key":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"8420","DOI":"10.1073\/pnas.95.15.8420","article-title":"Evolvability","volume":"95","author":"Kirschner M","year":"1998","unstructured":"M Kirschner, J Gerhart, Evolvability. Proc Natl Acad Sci USA 95, 8420\u20138427 (1998).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1016\/j.ejphar.2011.07.006","article-title":"The gut as communicator between environment and host: immunological consequences","volume":"668","author":"Brandtzaeg P","year":"2011","unstructured":"P Brandtzaeg, The gut as communicator between environment and host: immunological consequences. Eur J Pharmacol 668, S16\u2013S32 (2011).","journal-title":"Eur J Pharmacol"},{"key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/nature10213","article-title":"Human nutrition, the gut microbiome and the immune system","volume":"474","author":"Kau AL","year":"2011","unstructured":"AL Kau, PP Ahern, NW Griffin, AL Goodman, JI Gordon, Human nutrition, the gut microbiome and the immune system. Nature 474, 327\u2013336 (2011).","journal-title":"Nature"},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1159\/000354907","article-title":"Initial intestinal colonization in the human infant and immune homeostasis","volume":"63","author":"Walker WA","year":"2013","unstructured":"WA Walker, Initial intestinal colonization in the human infant and immune homeostasis. Ann Nutr Metab 63, 8\u201315 (2013).","journal-title":"Ann Nutr Metab"},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrmicro2974","article-title":"The gut microbiota\u2014masters of host development and physiology","volume":"11","author":"Sommer F","year":"2013","unstructured":"F Sommer, F B\u00e4ckhed, The gut microbiota\u2014masters of host development and physiology. Nat Rev Microbiol 11, 227\u2013238 (2013).","journal-title":"Nat Rev Microbiol"},{"key":"e_1_3_4_7_2","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.cell.2014.06.037","article-title":"Conducting a microbiome study","volume":"158","author":"Goodrich JK","year":"2014","unstructured":"JK Goodrich, , Conducting a microbiome study. Cell 158, 250\u2013262 (2014).","journal-title":"Cell"},{"key":"e_1_3_4_8_2","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1084\/jem.20120504","article-title":"Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice","volume":"209","author":"Ubeda C","year":"2012","unstructured":"C Ubeda, , Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J Exp Med 209, 1445\u20131456 (2012).","journal-title":"J Exp Med"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/j.immuni.2006.06.010","article-title":"Role of toll-like receptors in spontaneous commensal-dependent colitis","volume":"25","author":"Rakoff-Nahoum S","year":"2006","unstructured":"S Rakoff-Nahoum, L Hao, R Medzhitov, Role of toll-like receptors in spontaneous commensal-dependent colitis. Immunity 25, 319\u2013329 (2006).","journal-title":"Immunity"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.smim.2006.10.002","article-title":"Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota","volume":"19","author":"Smith K","year":"2007","unstructured":"K Smith, KD McCoy, AJ Macpherson, Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 19, 59\u201369 (2007).","journal-title":"Semin Immunol"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.cell.2006.08.043","article-title":"Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection","volume":"127","author":"Rawls JF","year":"2006","unstructured":"JF Rawls, MA Mahowald, RE Ley, JI Gordon, Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127, 423\u2013433 (2006).","journal-title":"Cell"},{"key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.1016\/j.cell.2012.04.037","article-title":"Gut immune maturation depends on colonization with a host-specific microbiota","volume":"149","author":"Chung H","year":"2012","unstructured":"H Chung, , Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149, 1578\u20131593 (2012).","journal-title":"Cell"},{"key":"e_1_3_4_13_2","first-page":"1.7.1","article-title":"Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype","volume":"25","author":"Shaw DR","year":"2009","unstructured":"DR Shaw, Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. Curr Protoc Bioinformatics 25, 1.7.1\u20131.7.14 (2009).","journal-title":"Curr Protoc Bioinformatics"},{"key":"e_1_3_4_14_2","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.clp.2012.12.012","article-title":"A clinical perspective of necrotizing enterocolitis: Past, present, and future","volume":"40","author":"Sharma R","year":"2013","unstructured":"R Sharma, ML Hudak, A clinical perspective of necrotizing enterocolitis: Past, present, and future. Clin Perinatol 40, 27\u201351 (2013).","journal-title":"Clin Perinatol"},{"key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"6294","DOI":"10.1128\/MCB.00939-09","article-title":"Hepatocyte nuclear factor 4alpha, a key factor for homeostasis, cell architecture, and barrier function of the adult intestinal epithelium","volume":"29","author":"Cattin A-L","year":"2009","unstructured":"A-L Cattin, , Hepatocyte nuclear factor 4alpha, a key factor for homeostasis, cell architecture, and barrier function of the adult intestinal epithelium. Mol Cell Biol 29, 6294\u20136308 (2009).","journal-title":"Mol Cell Biol"},{"key":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1093\/glycob\/cwi004","article-title":"Regulation of intestinal ontogeny: Effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice","volume":"15","author":"Nanthakumar NN","year":"2005","unstructured":"NN Nanthakumar, , Regulation of intestinal ontogeny: Effect of glucocorticoids and luminal microbes on galactosyltransferase and trehalase induction in mice. Glycobiology 15, 221\u2013232 (2005).","journal-title":"Glycobiology"},{"key":"e_1_3_4_17_2","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1126\/science.273.5280.1380","article-title":"A model of host-microbial interactions in an open mammalian ecosystem","volume":"273","author":"Bry L","year":"1996","unstructured":"L Bry, PG Falk, T Midtvedt, JI Gordon, A model of host-microbial interactions in an open mammalian ecosystem. Science 273, 1380\u20131383 (1996).","journal-title":"Science"},{"key":"e_1_3_4_18_2","doi-asserted-by":"crossref","first-page":"1254009","DOI":"10.1126\/science.1254009","article-title":"Innate lymphoid cells regulate intestinal epithelial cell glycosylation","volume":"345","author":"Goto Y","year":"2014","unstructured":"Y Goto, , Innate lymphoid cells regulate intestinal epithelial cell glycosylation. Science 345, 1254009 (2014).","journal-title":"Science"},{"key":"e_1_3_4_19_2","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nature13823","article-title":"Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness","volume":"514","author":"Pickard JM","year":"2014","unstructured":"JM Pickard, , Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature 514, 638\u2013641 (2014).","journal-title":"Nature"},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1097\/MOG.0b013e32835c9cb3","article-title":"Indoleamine 2,3 dioxygenase in intestinal disease","volume":"29","author":"Ciorba MA","year":"2013","unstructured":"MA Ciorba, Indoleamine 2,3 dioxygenase in intestinal disease. Curr Opin Gastroenterol 29, 146\u2013152 (2013).","journal-title":"Curr Opin Gastroenterol"},{"key":"e_1_3_4_21_2","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.2741\/3792","article-title":"Channelling of arginine in NO and polyamine pathways in colonocytes and consequences","volume":"16","author":"Blachier F","year":"2011","unstructured":"F Blachier, AM Davila, R Benamouzig, D Tome, Channelling of arginine in NO and polyamine pathways in colonocytes and consequences. Front Biosci (Landmark Ed) 16, 1331\u20131343 (2011).","journal-title":"Front Biosci (Landmark Ed)"},{"key":"e_1_3_4_22_2","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1152\/physrev.2000.80.4.1633","article-title":"Development of intestinal transport function in mammals","volume":"80","author":"P\u00e1cha J","year":"2000","unstructured":"J P\u00e1cha, Development of intestinal transport function in mammals. Physiol Rev 80, 1633\u20131667 (2000).","journal-title":"Physiol Rev"},{"key":"e_1_3_4_23_2","doi-asserted-by":"crossref","first-page":"G484","DOI":"10.1152\/ajpgi.00477.2011","article-title":"The role and pathophysiological relevance of membrane transporter PepT1 in intestinal inflammation and inflammatory bowel disease","volume":"302","author":"Ingersoll SA","year":"2012","unstructured":"SA Ingersoll, , The role and pathophysiological relevance of membrane transporter PepT1 in intestinal inflammation and inflammatory bowel disease. Am J Physiol Gastrointest Liver Physiol 302, G484\u2013G492 (2012).","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"e_1_3_4_24_2","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/ng1339","article-title":"Functional variants of OCTN cation transporter genes are associated with Crohn disease","volume":"36","author":"Peltekova VD","year":"2004","unstructured":"VD Peltekova, , Functional variants of OCTN cation transporter genes are associated with Crohn disease. Nat Genet 36, 471\u2013475 (2004).","journal-title":"Nat Genet"},{"key":"e_1_3_4_25_2","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.cmet.2013.01.003","article-title":"Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist","volume":"17","author":"Sayin SI","year":"2013","unstructured":"SI Sayin, , Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 17, 225\u2013235 (2013).","journal-title":"Cell Metab"},{"key":"e_1_3_4_26_2","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nri3112","article-title":"The impact of perinatal immune development on mucosal homeostasis and chronic inflammation","volume":"12","author":"Renz H","year":"2012","unstructured":"H Renz, P Brandtzaeg, M Hornef, The impact of perinatal immune development on mucosal homeostasis and chronic inflammation. Nat Rev Immunol 12, 9\u201323 (2012).","journal-title":"Nat Rev Immunol"},{"key":"e_1_3_4_27_2","article-title":"Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88","author":"Larsson E","year":"2011","unstructured":"E Larsson, , Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut, 2011).","journal-title":"Gut"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1186\/1471-2164-13-335","article-title":"A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development","volume":"13","author":"Yamamoto M","year":"2012","unstructured":"M Yamamoto, , A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. BMC Genomics 13, 335 (2012).","journal-title":"BMC Genomics"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1038\/ni.2614","article-title":"Resident viruses and their interactions with the immune system","volume":"14","author":"Duerkop BA","year":"2013","unstructured":"BA Duerkop, LV Hooper, Resident viruses and their interactions with the immune system. Nat Immunol 14, 654\u2013659 (2013).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_30_2","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.coi.2012.05.002","article-title":"Viral interactions with the host and microbiota in the intestine","volume":"24","author":"Moon C","year":"2012","unstructured":"C Moon, TS Stappenbeck, Viral interactions with the host and microbiota in the intestine. Curr Opin Immunol 24, 405\u2013410 (2012).","journal-title":"Curr Opin Immunol"},{"key":"e_1_3_4_31_2","doi-asserted-by":"crossref","first-page":"20858","DOI":"10.1073\/pnas.0808723105","article-title":"Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface","volume":"105","author":"Vaishnava S","year":"2008","unstructured":"S Vaishnava, CL Behrendt, AS Ismail, L Eckmann, LV Hooper, Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proc Natl Acad Sci USA 105, 20858\u201320863 (2008).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_32_2","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1084\/jem.20070563","article-title":"MyD88-mediated signals induce the bactericidal lectin RegIII gamma and protect mice against intestinal Listeria monocytogenes infection","volume":"204","author":"Brandl K","year":"2007","unstructured":"K Brandl, G Plitas, B Schnabl, RP DeMatteo, EG Pamer, MyD88-mediated signals induce the bactericidal lectin RegIII gamma and protect mice against intestinal Listeria monocytogenes infection. J Exp Med 204, 1891\u20131900 (2007).","journal-title":"J Exp Med"},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/mi.2012.23","article-title":"Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides","volume":"5","author":"Frantz AL","year":"2012","unstructured":"AL Frantz, , Targeted deletion of MyD88 in intestinal epithelial cells results in compromised antibacterial immunity associated with downregulation of polymeric immunoglobulin receptor, mucin-2, and antibacterial peptides. Mucosal Immunol 5, 501\u2013512 (2012).","journal-title":"Mucosal Immunol"},{"key":"e_1_3_4_34_2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1159\/000341630","article-title":"Bacterial stimulation of the TLR-MyD88 pathway modulates the homeostatic expression of ileal Paneth cell \u03b1-defensins","volume":"5","author":"Menendez A","year":"2013","unstructured":"A Menendez, , Bacterial stimulation of the TLR-MyD88 pathway modulates the homeostatic expression of ileal Paneth cell \u03b1-defensins. J Innate Immun 5, 39\u201349 (2013).","journal-title":"J Innate Immun"},{"key":"e_1_3_4_35_2","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1097\/01.shk.0000239774.02904.65","article-title":"The role of the intestinal barrier in the pathogenesis of necrotizing enterocolitis","volume":"27","author":"Anand RJ","year":"2007","unstructured":"RJ Anand, CL Leaphart, KP Mollen, DJ Hackam, The role of the intestinal barrier in the pathogenesis of necrotizing enterocolitis. Shock 27, 124\u2013133 (2007).","journal-title":"Shock"},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: A new phylogenetic method for comparing microbial communities","volume":"71","author":"Lozupone C","year":"2005","unstructured":"C Lozupone, R Knight, UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228\u20138235 (2005).","journal-title":"Appl Environ Microbiol"},{"key":"e_1_3_4_37_2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1126\/science.1209791","article-title":"The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine","volume":"334","author":"Vaishnava S","year":"2011","unstructured":"S Vaishnava, , The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255\u2013258 (2011).","journal-title":"Science"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","first-page":"15451","DOI":"10.1073\/pnas.202604299","article-title":"Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells","volume":"99","author":"Stappenbeck TS","year":"2002","unstructured":"TS Stappenbeck, LV Hooper, JI Gordon, Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci USA 99, 15451\u201315455 (2002).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/nature10893","article-title":"Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling","volume":"483","author":"Reinhardt C","year":"2012","unstructured":"C Reinhardt, , Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling. Nature 483, 627\u2013631 (2012).","journal-title":"Nature"},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","first-page":"1672","DOI":"10.1136\/gut.29.12.1672","article-title":"Maturation of the rat small intestine at weaning: Changes in epithelial cell kinetics, bacterial flora, and mucosal immune activity","volume":"29","author":"Cummins AG","year":"1988","unstructured":"AG Cummins, TW Steele, JT LaBrooy, DJ Shearman, Maturation of the rat small intestine at weaning: Changes in epithelial cell kinetics, bacterial flora, and mucosal immune activity. Gut 29, 1672\u20131679 (1988).","journal-title":"Gut"},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1128\/MCB.26.6.2387-2398.2006","article-title":"Regulation of PCNA and cyclin D1 expression and epithelial morphogenesis by the ZO-1-regulated transcription factor ZONAB\/DbpA","volume":"26","author":"Sourisseau T","year":"2006","unstructured":"T Sourisseau, , Regulation of PCNA and cyclin D1 expression and epithelial morphogenesis by the ZO-1-regulated transcription factor ZONAB\/DbpA. Mol Cell Biol 26, 2387\u20132398 (2006).","journal-title":"Mol Cell Biol"},{"key":"e_1_3_4_42_2","article-title":"The gut microbiota engages different signaling pathways to induce Duox2 expression in the ileum and colon epithelium","author":"Sommer F","year":"2014","unstructured":"F Sommer, F B\u00e4ckhed, The gut microbiota engages different signaling pathways to induce Duox2 expression in the ileum and colon epithelium. Mucosal Immunol, 2014).","journal-title":"Mucosal Immunol"},{"key":"e_1_3_4_43_2","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1038\/ni.1765","article-title":"Coordination of multiple dual oxidase-regulatory pathways in responses to commensal and infectious microbes in drosophila gut","volume":"10","author":"Ha E-M","year":"2009","unstructured":"E-M Ha, , Coordination of multiple dual oxidase-regulatory pathways in responses to commensal and infectious microbes in drosophila gut. Nat Immunol 10, 949\u2013957 (2009).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nature08119","article-title":"A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish","volume":"459","author":"Niethammer P","year":"2009","unstructured":"P Niethammer, C Grabher, AT Look, TJ Mitchison, A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish. Nature 459, 996\u2013999 (2009).","journal-title":"Nature"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.cell.2004.07.002","article-title":"Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis","volume":"118","author":"Rakoff-Nahoum S","year":"2004","unstructured":"S Rakoff-Nahoum, J Paglino, F Eslami-Varzaneh, S Edberg, R Medzhitov, Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118, 229\u2013241 (2004).","journal-title":"Cell"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1073\/pnas.0405979102","article-title":"Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury","volume":"102","author":"Pull SL","year":"2005","unstructured":"SL Pull, JM Doherty, JC Mills, JI Gordon, TS Stappenbeck, Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc Natl Acad Sci USA 102, 99\u2013104 (2005).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1126\/science.1140488","article-title":"Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88","volume":"317","author":"Rakoff-Nahoum S","year":"2007","unstructured":"S Rakoff-Nahoum, R Medzhitov, Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88. Science 317, 124\u2013127 (2007).","journal-title":"Science"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1016\/j.gde.2004.08.003","article-title":"Control of smooth muscle development by the myocardin family of transcriptional coactivators","volume":"14","author":"Wang D-Z","year":"2004","unstructured":"D-Z Wang, EN Olson, Control of smooth muscle development by the myocardin family of transcriptional coactivators. Curr Opin Genet Dev 14, 558\u2013566 (2004).","journal-title":"Curr Opin Genet Dev"},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1053\/j.gastro.2012.06.034","article-title":"Gut microbial products regulate murine gastrointestinal motility via Toll-like receptor 4 signaling","volume":"143","author":"Anitha M","year":"2012","unstructured":"M Anitha, M Vijay-Kumar, SV Sitaraman, AT Gewirtz, S Srinivasan, Gut microbial products regulate murine gastrointestinal motility via Toll-like receptor 4 signaling. Gastroenterology 143, 1006\u201316.e4 (2012).","journal-title":"Gastroenterology"},{"key":"e_1_3_4_50_2","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.cell.2014.04.050","article-title":"Crosstalk between muscularis macrophages and enteric neurons regulates gastrointestinal motility","volume":"158","author":"Muller PA","year":"2014","unstructured":"PA Muller, , Crosstalk between muscularis macrophages and enteric neurons regulates gastrointestinal motility. Cell 158, 300\u2013313 (2014).","journal-title":"Cell"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"2984","DOI":"10.4049\/jimmunol.1401056","article-title":"MyD88 signaling inhibits protective immunity to the gastrointestinal helminth parasite Heligmosomoides polygyrus","volume":"193","author":"Reynolds LA","year":"2014","unstructured":"LA Reynolds, , MyD88 signaling inhibits protective immunity to the gastrointestinal helminth parasite Heligmosomoides polygyrus. J Immunol 193, 2984\u20132993 (2014).","journal-title":"J Immunol"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1111\/j.0105-2896.2005.00277.x","article-title":"Mucosal immunity and allergic responses: Lack of regulation and\/or lack of microbial stimulation?","volume":"206","author":"Prioult G","year":"2005","unstructured":"G Prioult, C Nagler-Anderson, Mucosal immunity and allergic responses: Lack of regulation and\/or lack of microbial stimulation? Immunol Rev 206, 204\u2013218 (2005).","journal-title":"Immunol Rev"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1084\/jem.127.4.783","article-title":"Lasting biological effects of early environmental influences. I. Conditioning of adult size by prenatal and postnatal nutrition","volume":"127","author":"Dubos R","year":"1968","unstructured":"R Dubos, RW Schaedler, R Costello, Lasting biological effects of early environmental influences. I. Conditioning of adult size by prenatal and postnatal nutrition. J Exp Med 127, 783\u2013799 (1968).","journal-title":"J Exp Med"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1038\/nature09199","article-title":"Viruses in the faecal microbiota of monozygotic twins and their mothers","volume":"466","author":"Reyes A","year":"2010","unstructured":"A Reyes, , Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334\u2013338 (2010).","journal-title":"Nature"},{"key":"e_1_3_4_55_2","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1038\/nrmicro1978","article-title":"Worlds within worlds: Evolution of the vertebrate gut microbiota","volume":"6","author":"Ley RE","year":"2008","unstructured":"RE Ley, CA Lozupone, M Hamady, R Knight, JI Gordon, Worlds within worlds: Evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6, 776\u2013788 (2008).","journal-title":"Nat Rev Microbiol"},{"key":"e_1_3_4_56_2","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1126\/science.1223490","article-title":"Interactions between the microbiota and the immune system","volume":"336","author":"Hooper LV","year":"2012","unstructured":"LV Hooper, DR Littman, AJ Macpherson, Interactions between the microbiota and the immune system. Science 336, 1268\u20131273 (2012).","journal-title":"Science"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.pnas.org\/syndication\/doi\/10.1073\/pnas.1424886112","content-type":"unspecified","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1424886112","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T09:35:22Z","timestamp":1654594522000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1424886112"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,10]]},"references-count":56,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2015,2,17]]}},"alternative-id":["10.1073\/pnas.1424886112"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1424886112","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,2,10]]},"assertion":[{"value":"2015-02-10","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}