{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T06:10:48Z","timestamp":1792649448507,"version":"4.5.0"},"reference-count":130,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,1,27]],"date-time":"2022-01-27T00:00:00Z","timestamp":1643241600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"content-domain":{"domain":["mucosalimmunology.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Mucosal Immunology"],"published-print":{"date-parts":[[2022,11]]},"DOI":"10.1038\/s41385-022-00562-3","type":"journal-article","created":{"date-parts":[[2022,9,5]],"date-time":"2022-09-05T02:02:39Z","timestamp":1662343359000},"page":"1085-1094","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":43,"title":["From germ-free to wild: modulating microbiome complexity to understand mucosal immunology"],"prefix":"10.1016","volume":"15","author":[{"given":"Carolyn A.","family":"Thomson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney C.","family":"Morgan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Ohland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathy D.","family":"McCoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1038\/s41385-022-00562-3_bib1","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrmicro2536","article-title":"Shifting the balance: antibiotic effects on host-microbiota mutualism","volume":"9","author":"Willing","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib2","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria","volume":"139","author":"Ivanov","year":"2009","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib3","doi-asserted-by":"crossref","unstructured":"Flannigan K. L. & Denning T.L. Segmented filamentous bacteria-induced immune responses: a balancing act between host protection and autoimmunity. Immunology154, 537\u2013546 (2018).","DOI":"10.1111\/imm.12950"},{"key":"10.1038\/s41385-022-00562-3_bib4","first-page":"114","article-title":"Lost in translation: animal models and clinical trials in cancer treatment","volume":"6","author":"Mak","year":"2014","journal-title":"Am. J. Transl. Res."},{"key":"10.1038\/s41385-022-00562-3_bib5","doi-asserted-by":"crossref","first-page":"3507","DOI":"10.1073\/pnas.1222878110","article-title":"Genomic responses in mouse models poorly mimic human inflammatory diseases","volume":"110","author":"Seok","year":"2013","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1038\/s41385-022-00562-3_bib6","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/nature17655","article-title":"Normalizing the environment recapitulates adult human immune traits in laboratory mice","volume":"532","author":"Beura","year":"2016","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib7","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1038\/s41564-021-00912-0","article-title":"Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance","volume":"6","author":"Liu","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib8","doi-asserted-by":"crossref","unstructured":"Scott N. A. et al. Antibiotics induce sustained dysregulation of intestinal T cell immunity by perturbing macrophage homeostasis. Sci. Transl. Med. 10, eaao4755 (2018).","DOI":"10.1126\/scitranslmed.aao4755"},{"key":"10.1038\/s41385-022-00562-3_bib9","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-020-00991-x","article-title":"Antibiotic-associated dysbiosis affects the ability of the gut microbiota to control intestinal inflammation upon fecal microbiota transplantation in experimental colitis models","volume":"9","author":"Strati","year":"2021","journal-title":"Microbiome"},{"key":"10.1038\/s41385-022-00562-3_bib10","doi-asserted-by":"crossref","unstructured":"Ashley S. L. et al. Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice. Sci. Transl. Med. 12, eaau9959 (2020).","DOI":"10.1126\/scitranslmed.aau9959"},{"key":"10.1038\/s41385-022-00562-3_bib11","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-017-01803-x","article-title":"The microbiota protects against respiratory infection via GM-CSF signaling","volume":"8","author":"Brown","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1038\/s41385-022-00562-3_bib12","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41586-022-04427-4","article-title":"The lung microbiome regulates brain autoimmunity","volume":"603","author":"Hosang","year":"2022","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib13","doi-asserted-by":"crossref","first-page":"5354","DOI":"10.1073\/pnas.1019378108","article-title":"Microbiota regulates immune defense against respiratory tract influenza A virus infection","volume":"108","author":"Ichinohe","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1038\/s41385-022-00562-3_bib14","doi-asserted-by":"crossref","first-page":"16465","DOI":"10.1073\/pnas.2003022117","article-title":"Immunity to commensal skin fungi promotes psoriasiform skin inflammation","volume":"117","author":"Hurabielle","year":"2020","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1038\/s41385-022-00562-3_bib15","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/nature14052","article-title":"Commensal-dendritic-cell interaction specifies a unique protective skin immune signature","volume":"520","author":"Naik","year":"2015","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib16","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.jaut.2016.05.001","article-title":"Different immunological responses to early-life antibiotic exposure affecting autoimmune diabetes development in NOD mice","volume":"72","author":"Hu","year":"2016","journal-title":"J. Autoimmun."},{"key":"10.1038\/s41385-022-00562-3_bib17","doi-asserted-by":"crossref","first-page":"4176","DOI":"10.4049\/jimmunol.1500884","article-title":"Maternal Antibiotic Treatment Protects Offspring from Diabetes Development in Nonobese Diabetic Mice by Generation of Tolerogenic APCs","volume":"195","author":"Hu","year":"2015","journal-title":"J. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib18","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.3389\/fphys.2018.01534","article-title":"Mouse Microbiota Models: comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria","volume":"9","author":"Kennedy","year":"2018","journal-title":"Front. Physiol."},{"key":"10.1038\/s41385-022-00562-3_bib19","first-page":"337","article-title":"Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host","volume":"164","author":"Sender","year":"2016","journal-title":"Cells Hum. Cell"},{"key":"10.1038\/s41385-022-00562-3_bib20","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrmicro2974","article-title":"The gut microbiota\u2013masters of host development and physiology","volume":"11","author":"Sommer","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib21","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","year":"2011","journal-title":"Nat. Rev. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib22","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1126\/science.1127119","article-title":"Symbiotic bacteria direct expression of an intestinal bactericidal lectin","volume":"313","author":"Cash","year":"2006","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib23","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-018-0404-9","article-title":"Commensal microbiota modulate gene expression in the skin","volume":"6","author":"Meisel","year":"2018","journal-title":"Microbiome"},{"key":"10.1038\/s41385-022-00562-3_bib24","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/ni.1684","article-title":"RORgammat and commensal microflora are required for the differentiation of mucosal interleukin 22-producing NKp46+ cells","volume":"10","author":"Sanos","year":"2009","journal-title":"Nat. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib25","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/ni.2967","article-title":"Constant replenishment from circulating monocytes maintains the macrophage pool in the intestine of adult mice","volume":"15","author":"Bain","year":"2014","journal-title":"Nat. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib26","doi-asserted-by":"crossref","unstructured":"Chen Q., Nair S. & Ruedl C. Microbiota regulates the turnover kinetics of gut macrophages in health and inflammation. Life Sci Alliance.5, e202101178 (2022).","DOI":"10.26508\/lsa.202101178"},{"key":"10.1038\/s41385-022-00562-3_bib27","unstructured":"Constantinides M. G. et al. MAIT cells are imprinted by the microbiota in early life and promote tissue repair. Science366, eaax6624 (2019)."},{"key":"10.1038\/s41385-022-00562-3_bib28","doi-asserted-by":"crossref","first-page":"205","DOI":"10.3389\/fimmu.2019.00205","article-title":"Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy","volume":"10","author":"Schwarzer","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib29","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1084\/jem.20180019","article-title":"Tissue-resident macrophages in the intestine are long lived and defined by Tim-4 and CD4 expression","volume":"215","author":"Shaw","year":"2018","journal-title":"J. Exp. Med."},{"key":"10.1038\/s41385-022-00562-3_bib30","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1126\/science.aaw2719","article-title":"Microbial metabolites control the thymic development of mucosal-associated invariant T cells","volume":"366","author":"Legoux","year":"2019","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib31","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1016\/j.immuni.2008.11.001","article-title":"Microbial flora drives interleukin 22 production in intestinal NKp46+ cells that provide innate mucosal immune defense","volume":"29","author":"Satoh-Takayama","year":"2008","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib32","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1093\/intimm\/dxq449","article-title":"Commensal microbiota induce LPS hyporesponsiveness in colonic macrophages via the production of IL-10","volume":"22","author":"Ueda","year":"2010","journal-title":"Int. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib33","doi-asserted-by":"crossref","first-page":"2519","DOI":"10.4049\/jimmunol.1701776","article-title":"The Impact of Maternal Microbes and Microbial Colonization in Early Life on Hematopoiesis","volume":"200","author":"McCoy","year":"2018","journal-title":"J. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib34","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1016\/j.jaci.2016.09.019","article-title":"Skin microbiome promotes mast cell maturation by triggering stem cell factor production in keratinocytes","volume":"139","author":"Wang","year":"2017","journal-title":"J. Allergy Clin. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib35","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.immuni.2012.05.020","article-title":"Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota","volume":"37","author":"Ganal","year":"2012","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib36","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1016\/j.jhep.2021.10.015","article-title":"Hallmarks of the human intestinal microbiome on liver maturation and function","volume":"76","author":"Almeida","year":"2022","journal-title":"J. Hepatol."},{"key":"10.1038\/s41385-022-00562-3_bib37","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1038\/nn.4030","article-title":"Host microbiota constantly control maturation and function of microglia in the CNS","volume":"18","author":"Erny","year":"2015","journal-title":"Nat. Neurosci."},{"key":"10.1038\/s41385-022-00562-3_bib38","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1016\/j.immuni.2011.03.021","article-title":"Intestinal bacterial colonization induces mutualistic regulatory T cell responses","volume":"34","author":"Geuking","year":"2011","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib39","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1126\/science.aac5560","article-title":"Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine","volume":"351","author":"Kim","year":"2016","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib40","doi-asserted-by":"crossref","first-page":"1723","DOI":"10.1084\/jem.20120914","article-title":"Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells","volume":"209","author":"Weiss","year":"2012","journal-title":"J. Exp. Med."},{"key":"10.1038\/s41385-022-00562-3_bib41","doi-asserted-by":"crossref","unstructured":"Bunker J. J. et al. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science358, eaan6619 (2017).","DOI":"10.1126\/science.aan6619"},{"key":"10.1038\/s41385-022-00562-3_bib42","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.chom.2013.10.004","article-title":"Intestinal microbial diversity during early-life colonization shapes long-term IgE levels","volume":"14","author":"Cahenzli","year":"2013","journal-title":"Cell Host Microbe"},{"key":"10.1038\/s41385-022-00562-3_bib43","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1164\/rccm.201010-1574OC","article-title":"Dysregulation of allergic airway inflammation in the absence of microbial colonization","volume":"184","author":"Herbst","year":"2011","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1038\/s41385-022-00562-3_bib44","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.immuni.2019.02.014","article-title":"A Weaning Reaction to Microbiota Is Required for Resistance to Immunopathologies in the Adult","volume":"50","author":"Al Nabhani","year":"2019","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib45","doi-asserted-by":"crossref","unstructured":"Knoop K. A. et al. Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria. Sci. Immunol.2, eaao1314 (2017).","DOI":"10.1126\/sciimmunol.aao1314"},{"key":"10.1038\/s41385-022-00562-3_bib46","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1126\/science.1219328","article-title":"Microbial exposure during early life has persistent effects on natural killer T cell function","volume":"336","author":"Olszak","year":"2012","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib47","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1164\/rccm.201104-0655OC","article-title":"Topographical continuity of bacterial populations in the healthy human respiratory tract","volume":"184","author":"Charlson","year":"2011","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1038\/s41385-022-00562-3_bib48","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1164\/rccm.201711-2180OC","article-title":"The Lung Microbiota of Healthy Mice Are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity","volume":"198","author":"Dickson","year":"2018","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1038\/s41385-022-00562-3_bib49","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1038\/nm.3568","article-title":"Lung microbiota promotes tolerance to allergens in neonates via PD-L1","volume":"20","author":"Gollwitzer","year":"2014","journal-title":"Nat. Med."},{"key":"10.1038\/s41385-022-00562-3_bib50","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1016\/j.cell.2018.12.040","article-title":"Commensal Microbiota Promote Lung Cancer Development via gammadelta T Cells","volume":"176","author":"Jin","year":"2019","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib51","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1164\/rccm.201809-1650OC","article-title":"Lung Microbiota Contribute to Pulmonary Inflammation and Disease Progression in Pulmonary Fibrosis","volume":"199","author":"O'Dwyer","year":"2019","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1038\/s41385-022-00562-3_bib52","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/1471-2172-9-65","article-title":"Gut microbiota and lipopolysaccharide content of the diet influence development of regulatory T cells: studies in germ-free mice","volume":"9","author":"Hrncir","year":"2008","journal-title":"BMC Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib53","doi-asserted-by":"crossref","first-page":"e0167786","DOI":"10.1371\/journal.pone.0167786","article-title":"Diet Matters: Endotoxin in the Diet Impacts the Level of Allergic Sensitization in Germ-Free Mice","volume":"12","author":"Schwarzer","year":"2017","journal-title":"PLoS ONE"},{"key":"10.1038\/s41385-022-00562-3_bib54","doi-asserted-by":"crossref","first-page":"eaaw1507","DOI":"10.1126\/sciadv.aaw1507","article-title":"Food antigens drive spontaneous IgE elevation in the absence of commensal microbiota","volume":"5","author":"Hong","year":"2019","journal-title":"Sci. Adv."},{"key":"10.1038\/s41385-022-00562-3_bib55","doi-asserted-by":"crossref","first-page":"2432","DOI":"10.3389\/fimmu.2019.02432","article-title":"Dietary Antigens Induce Germinal Center Responses in Peyer's Patches and Antigen-Specific IgA Production","volume":"10","author":"Hara","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib56","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/nature12721","article-title":"Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells","volume":"504","author":"Furusawa","year":"2013","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib57","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.3389\/fimmu.2017.01036","article-title":"The Microbial Metabolite Butyrate Induces Expression of Th1-Associated Factors in CD4(+) T Cells","volume":"8","author":"Kespohl","year":"2017","journal-title":"Front. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib58","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.immuni.2018.06.016","article-title":"Detection of Succinate by Intestinal Tuft Cells Triggers a Type 2 Innate Immune Circuit","volume":"49","author":"Nadjsombati","year":"2018","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib59","doi-asserted-by":"crossref","first-page":"263ra158","DOI":"10.1126\/scitranslmed.3009759","article-title":"The gut microbiota influences blood-brain barrier permeability in mice","volume":"6","author":"Braniste","year":"2014","journal-title":"Sci. Transl. Med."},{"key":"10.1038\/s41385-022-00562-3_bib60","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1016\/j.cell.2016.11.018","article-title":"Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease","volume":"167","author":"Sampson","year":"2016","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib61","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/s41586-019-1125-3","article-title":"Compartmentalized gut lymph node drainage dictates adaptive immune responses","volume":"569","author":"Esterhazy","year":"2019","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib62","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1038\/mi.2015.77","article-title":"The lymph nodes draining the small intestine and colon are anatomically separate and immunologically distinct","volume":"9","author":"Houston","year":"2016","journal-title":"Mucosal. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib63","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1126\/science.1188454","article-title":"Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses","volume":"328","author":"Hapfelmeier","year":"2010","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib64","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1126\/science.aad2571","article-title":"The maternal microbiota drives early postnatal innate immune development","volume":"351","author":"Gomez de Aguero","year":"2016","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib65","doi-asserted-by":"crossref","unstructured":"Fonseca, W. et al. Maternal gut microbiome regulates immunity to RSV infection in offspring. J. Exp. Med. 218, e20210235 (2021).","DOI":"10.1084\/jem.20210235"},{"key":"10.1038\/s41385-022-00562-3_bib66","unstructured":"Kimura, I. et al. Maternal gut microbiota in pregnancy influences offspring metabolic phenotype in mice. Science367, eaaw8429 (2020)."},{"key":"10.1038\/s41385-022-00562-3_bib67","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.cell.2015.08.058","article-title":"Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells","volume":"163","author":"Atarashi","year":"2015","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib68","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.jim.2015.03.020","article-title":"Induction of Th17 cells by segmented filamentous bacteria in the murine intestine","volume":"421","author":"Farkas","year":"2015","journal-title":"J. Immunol. Methods"},{"key":"10.1038\/s41385-022-00562-3_bib69","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1016\/j.immuni.2014.03.009","article-title":"Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses","volume":"40","author":"Lecuyer","year":"2014","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib70","doi-asserted-by":"crossref","first-page":"E8141","DOI":"10.1073\/pnas.1617460113","article-title":"Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice","volume":"113","author":"Tan","year":"2016","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1038\/s41385-022-00562-3_bib71","doi-asserted-by":"crossref","first-page":"12204","DOI":"10.1073\/pnas.0909122107","article-title":"Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota","volume":"107","author":"Round","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1038\/s41385-022-00562-3_bib72","unstructured":"Verma, R. et al. Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3(+) regulatory T cells. Sci. Immunol. 3, eaat6975 (2018)."},{"key":"10.1038\/s41385-022-00562-3_bib73","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1038\/s41385-020-00335-w","article-title":"Microbial modulation of intestinal T helper cell responses and implications for disease and therapy","volume":"13","author":"Geuking","year":"2020","journal-title":"Mucosal Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib74","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1038\/s41586-021-03727-5","article-title":"Acetate differentially regulates IgA reactivity to commensal bacteria","volume":"595","author":"Takeuchi","year":"2021","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib75","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1126\/science.abc3421","article-title":"Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy","volume":"369","author":"Mager","year":"2020","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib76","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1016\/j.cell.2017.01.022","article-title":"Mining the Human Gut Microbiota for Immunomodulatory Organisms","volume":"168","author":"Geva-Zatorsky","year":"2017","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib77","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","year":"2012","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib78","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.immuni.2009.08.020","article-title":"The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses","volume":"31","author":"Gaboriau-Routhiau","year":"2009","journal-title":"Immunity"},{"key":"10.1038\/s41385-022-00562-3_bib79","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.jcmgh.2014.11.004","article-title":"Microbial activities and intestinal homeostasis: a delicate balance between health and disease","volume":"1","author":"Ohland","year":"2015","journal-title":"Cell Mol. Gastroenterol. Hepatol."},{"key":"10.1038\/s41385-022-00562-3_bib80","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/s41586-020-2634-9","article-title":"Gut microorganisms act together to exacerbate inflammation in spinal cords","volume":"585","author":"Miyauchi","year":"2020","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib81","doi-asserted-by":"crossref","first-page":"4615","DOI":"10.1073\/pnas.1000082107","article-title":"Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis","volume":"108","author":"Lee","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1038\/s41385-022-00562-3_bib82","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/ilar\/ilv012","article-title":"The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community","volume":"56","author":"Wymore Brand","year":"2015","journal-title":"ILAR J."},{"key":"10.1038\/s41385-022-00562-3_bib83","doi-asserted-by":"crossref","first-page":"16215","DOI":"10.1038\/nmicrobiol.2016.215","article-title":"Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium","volume":"2","author":"Brugiroux","year":"2016","journal-title":"Nat. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib84","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.3389\/fmicb.2019.02999","article-title":"Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities","volume":"10","author":"Eberl","year":"2019","journal-title":"Front. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib85","doi-asserted-by":"crossref","first-page":"3107","DOI":"10.3389\/fimmu.2019.03107","article-title":"Using Precisely Defined in vivo Microbiotas to Understand Microbial Regulation of IgE","volume":"10","author":"Wyss","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib86","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/19490976.2020.1854008","article-title":"The gut bacterium Extibacter muris produces secondary bile acids and influences liver physiology in gnotobiotic mice","volume":"13","author":"Streidl","year":"2021","journal-title":"Gut Microbes"},{"key":"10.1038\/s41385-022-00562-3_bib87","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41586-019-0878-z","article-title":"A defined commensal consortium elicits CD8 T cells and anti-cancer immunity","volume":"565","author":"Tanoue","year":"2019","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib88","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-26963-9","article-title":"A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF\/SPF phenotypes","volume":"12","author":"Darnaud","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1038\/s41385-022-00562-3_bib89","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science"},{"key":"10.1038\/s41385-022-00562-3_bib90","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"Atarashi","year":"2013","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib91","article-title":"Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria","volume":"8","author":"Shetty","year":"2022","journal-title":"NPJ Biofilms Microbiomes"},{"key":"10.1038\/s41385-022-00562-3_bib92","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1111\/jvim.14875","article-title":"The gastrointestinal microbiome: a review","volume":"32","author":"Barko","year":"2018","journal-title":"J. Vet. Intern. Med."},{"key":"10.1038\/s41385-022-00562-3_bib93","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.mib.2021.04.004","article-title":"The intestinal mycobiome as a determinant of host immune and metabolic health","volume":"62","author":"Gutierrez","year":"2021","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib94","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1038\/s41579-021-00536-5","article-title":"The human virome: assembly, composition and host interactions","volume":"19","author":"Liang","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib95","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.cell.2022.01.017","article-title":"Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity","volume":"185","author":"Leonardi","year":"2022","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib96","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-16431-1","article-title":"Intestinal fungi are causally implicated in microbiome assembly and immune development in mice","volume":"11","author":"van Tilburg Bernardes","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1038\/s41385-022-00562-3_bib97","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/nature13960","article-title":"An enteric virus can replace the beneficial function of commensal bacteria","volume":"516","author":"Kernbauer","year":"2014","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib98","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.chom.2019.01.008","article-title":"Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis","volume":"25","author":"Gogokhia","year":"2019","journal-title":"Cell Host Microbe"},{"key":"10.1038\/s41385-022-00562-3_bib99","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1093\/biostatistics\/kxx069","article-title":"Estimation of clinical trial success rates and related parameters","volume":"20","author":"Wong","year":"2019","journal-title":"Biostatistics"},{"key":"10.1038\/s41385-022-00562-3_bib100","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-017-0284-4","article-title":"Transplanted human fecal microbiota enhanced Guillain Barre syndrome autoantibody responses after Campylobacter jejuni infection in C57BL\/6 mice","volume":"5","author":"Brooks","year":"2017","journal-title":"Microbiome"},{"key":"10.1038\/s41385-022-00562-3_bib101","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-015-0097-2","article-title":"Humanized microbiota mice as a model of recurrent Clostridium difficile disease","volume":"3","author":"Collins","year":"2015","journal-title":"Microbiome"},{"key":"10.1038\/s41385-022-00562-3_bib102","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/ismej.2016.151","article-title":"Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans","volume":"11","author":"Zhang","year":"2017","journal-title":"ISME J."},{"key":"10.1038\/s41385-022-00562-3_bib103","doi-asserted-by":"crossref","first-page":"1933","DOI":"10.1038\/ismej.2013.89","article-title":"A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice","volume":"7","author":"Marcobal","year":"2013","journal-title":"ISME J."},{"key":"10.1038\/s41385-022-00562-3_bib104","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nature17940","article-title":"Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice","volume":"534","author":"Planer","year":"2016","journal-title":"Nature"},{"key":"10.1038\/s41385-022-00562-3_bib105","doi-asserted-by":"crossref","unstructured":"Round J. L. & Palm N. W. Causal effects of the microbiota on immune-mediated diseases. Sci. Immunol.3, eaao1603 (2018).","DOI":"10.1126\/sciimmunol.aao1603"},{"key":"10.1038\/s41385-022-00562-3_bib106","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.cell.2019.12.025","article-title":"Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents","volume":"180","author":"Walter","year":"2020","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib107","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1016\/j.chom.2021.10.001","article-title":"Mice with diverse microbial exposure histories as a model for preclinical vaccine testing","volume":"29","author":"Fiege","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1038\/s41385-022-00562-3_bib108","doi-asserted-by":"crossref","first-page":"1729","DOI":"10.1016\/j.celrep.2019.07.028","article-title":"Microbial Exposure Enhances Immunity to Pathogens Recognized by TLR2 but Increases Susceptibility to Cytokine Storm through TLR4 Sensitization","volume":"28","author":"Huggins","year":"2019","journal-title":"Cell Rep."},{"key":"10.1038\/s41385-022-00562-3_bib109","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1016\/j.chom.2016.04.003","article-title":"Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response","volume":"19","author":"Reese","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.1038\/s41385-022-00562-3_bib110","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-12311-5","article-title":"Human PI3Kgamma deficiency and its microbiota-dependent mouse model reveal immunodeficiency and tissue immunopathology","volume":"10","author":"Takeda","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1038\/s41385-022-00562-3_bib111","doi-asserted-by":"crossref","unstructured":"Rosshart S. P. et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science365, eaaw4361 (2019).","DOI":"10.1126\/science.aaw4361"},{"key":"10.1038\/s41385-022-00562-3_bib112","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1016\/j.cell.2017.09.016","article-title":"Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance","volume":"171","author":"Rosshart","year":"2017","journal-title":"Cell"},{"key":"10.1038\/s41385-022-00562-3_bib113","doi-asserted-by":"crossref","unstructured":"Kreisinger J., Bastien G., Hauffe H. C., Marchesi J. & Perkins S. E. Interactions between multiple helminths and the gut microbiota in wild rodents. Philos. Trans. R Soc. Lond B. Biol. Sci. 370, 20140295 (2015).","DOI":"10.1098\/rstb.2014.0295"},{"key":"10.1038\/s41385-022-00562-3_bib114","doi-asserted-by":"crossref","first-page":"e0134643","DOI":"10.1371\/journal.pone.0134643","article-title":"The Gut Microbiota of Wild Mice","volume":"10","author":"Weldon","year":"2015","journal-title":"PLoS ONE"},{"key":"10.1038\/s41385-022-00562-3_bib115","doi-asserted-by":"crossref","first-page":"2423","DOI":"10.1038\/ismej.2015.53","article-title":"Marked seasonal variation in the wild mouse gut microbiota","volume":"9","author":"Maurice","year":"2015","journal-title":"ISME J."},{"key":"10.1038\/s41385-022-00562-3_bib116","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/s43705-021-00053-9","article-title":"Effects of laboratory domestication on the rodent gut microbiome","volume":"1","author":"Bowerman","year":"2021","journal-title":"ISME Commun."},{"key":"10.1038\/s41385-022-00562-3_bib117","doi-asserted-by":"crossref","first-page":"596149","DOI":"10.3389\/fcimb.2020.596149","article-title":"Metagenomic Analysis of the Gut Microbiota of Wild Mice, a Newly Identified Reservoir of Campylobacter","volume":"10","author":"Song","year":"2020","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10.1038\/s41385-022-00562-3_bib118","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14811","article-title":"The comparative immunology of wild and laboratory mice, Mus musculus domesticus","volume":"8","author":"Abolins","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1038\/s41385-022-00562-3_bib119","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1111\/j.1365-294X.2010.04910.x","article-title":"Measures of immune function of wild mice, Mus musculus","volume":"20","author":"Abolins","year":"2011","journal-title":"Mol. Ecol."},{"key":"10.1038\/s41385-022-00562-3_bib120","doi-asserted-by":"crossref","first-page":"5103","DOI":"10.1111\/j.1365-294X.2011.05269.x","article-title":"Natural killer cells in free-living Mus musculus have a primed phenotype","volume":"20","author":"Boysen","year":"2011","journal-title":"Mol. Ecol."},{"key":"10.1038\/s41385-022-00562-3_bib121","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1016\/j.ijpara.2018.04.003","article-title":"Antibodies and coinfection drive variation in nematode burdens in wild mice","volume":"48","author":"Clerc","year":"2018","journal-title":"Int. J. Parasitol."},{"key":"10.1038\/s41385-022-00562-3_bib122","doi-asserted-by":"crossref","first-page":"e2004108","DOI":"10.1371\/journal.pbio.2004108","article-title":"Rapid environmental effects on gut nematode susceptibility in rewilded mice","volume":"16","author":"Leung","year":"2018","journal-title":"PLoS Biol."},{"key":"10.1038\/s41385-022-00562-3_bib123","doi-asserted-by":"crossref","first-page":"736692","DOI":"10.3389\/fimmu.2021.736692","article-title":"Mast Cells Are Identified in the Lung Parenchyma of Wild Mice, Which Can Be Recapitulated in Naturalized Laboratory Mice","volume":"12","author":"Yeh","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1038\/s41385-022-00562-3_bib124","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1016\/j.chom.2020.02.015","article-title":"Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization","volume":"27","author":"Yeung","year":"2020","journal-title":"Cell Host Microbe."},{"key":"10.1038\/s41385-022-00562-3_bib125","doi-asserted-by":"crossref","first-page":"e113466","DOI":"10.1371\/journal.pone.0113466","article-title":"Environmentally determined differences in the murine lung microbiota and their relation to alveolar architecture","volume":"9","author":"Yun","year":"2014","journal-title":"PLoS ONE"},{"key":"10.1038\/s41385-022-00562-3_bib126","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1136\/thx.2008.101683","article-title":"Novel site-specific mast cell subpopulations in the human lung","volume":"64","author":"Andersson","year":"2009","journal-title":"Thorax"},{"key":"10.1038\/s41385-022-00562-3_bib127","doi-asserted-by":"crossref","first-page":"2367","DOI":"10.1038\/s41396-020-0690-7","article-title":"Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice","volume":"14","author":"Belheouane","year":"2020","journal-title":"ISME J."},{"key":"10.1038\/s41385-022-00562-3_bib128","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.imlet.2005.06.012","article-title":"CD28 superagonists: mode of action and therapeutic potential","volume":"100","author":"Hunig","year":"2005","journal-title":"Immunol. Lett."},{"key":"10.1038\/s41385-022-00562-3_bib129","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1056\/NEJMoa063842","article-title":"Cytokine storm in a phase 1 trial of the anti-CD28 monoclonal antibody TGN1412","volume":"355","author":"Suntharalingam","year":"2006","journal-title":"N. Engl. J. Med."},{"key":"10.1038\/s41385-022-00562-3_bib130","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1056\/NEJM199606273342603","article-title":"Treatment of septic shock with the tumor necrosis factor receptor:Fc fusion protein. The Soluble TNF Receptor Sepsis Study Group","volume":"334","author":"Fisher","year":"1996","journal-title":"N. Engl. J. Med."}],"container-title":["Mucosal Immunology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41385-022-00562-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41385-022-00562-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S193302192201738X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S193302192201738X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41385-022-00562-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T13:31:14Z","timestamp":1761831074000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S193302192201738X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11]]},"references-count":130,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,11]]}},"alternative-id":["S193302192201738X"],"URL":"https:\/\/doi.org\/10.1038\/s41385-022-00562-3","relation":{},"ISSN":["1933-0219"],"issn-type":[{"value":"1933-0219","type":"print"}],"subject":[],"published":{"date-parts":[[2022,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"From germ-free to wild: modulating microbiome complexity to understand mucosal immunology","name":"articletitle","label":"Article Title"},{"value":"Mucosal Immunology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1038\/s41385-022-00562-3","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2022 \u00a9 Society for Mucosal Immunology. Published by Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}