{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T16:35:26Z","timestamp":1792427726447,"version":"4.5.0"},"reference-count":77,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:00:00Z","timestamp":1548115200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:00:00Z","timestamp":1548115200000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T00:00:00Z","timestamp":1548115200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA154426"],"award-info":[{"award-number":["CA154426"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK092405"],"award-info":[{"award-number":["DK092405"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK105653"],"award-info":[{"award-number":["DK105653"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001341","name":"Richard and Susan Smith Family Foundation","doi-asserted-by":"publisher","award":["Smith Family Foundation Award for Excellence in Biomedical Research"],"award-info":[{"award-number":["Smith Family Foundation Award for Excellence in Biomedical Research"]}],"id":[{"id":"10.13039\/100001341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK097485"],"award-info":[{"award-number":["DK097485"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK110499"],"award-info":[{"award-number":["DK110499"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Inflammatory bowel disease (IBD) is driven by dysfunction between host genetics, the microbiota, and immune system. Knowledge gaps remain regarding how IBD genetic risk loci drive gut microbiota changes. The Crohn\u2019s disease risk allele ATG16L1 T300A results in abnormal Paneth cells due to decreased selective autophagy, increased cytokine release, and decreased intracellular bacterial clearance. To unravel the effects of ATG16L1 T300A on the microbiota and immune system, we employed a gnotobiotic model using human fecal transfers into ATG16L1 T300A knock-in mice. We observed increases in Bacteroides ovatus and Th1 and Th17 cells in ATG16L1 T300A mice. Association of altered Schaedler flora mice with B. ovatus specifically increased Th17 cells selectively in ATG16L1 T300A knock-in mice. Changes occur before disease onset, suggesting that ATG16L1 T300A contributes to dysbiosis and immune infiltration prior to disease symptoms. Our work provides insight for future studies on IBD subtypes, IBD patient treatment and diagnostics.<\/jats:p>","DOI":"10.7554\/elife.39982","type":"journal-article","created":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T19:22:04Z","timestamp":1548098524000},"source":"Crossref","is-referenced-by-count":140,"title":["The Crohn\u2019s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1\/Th17 response"],"prefix":"10.7554","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2890-3634","authenticated-orcid":true,"given":"Sydney","family":"Lavoie","sequence":"first","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kara L","family":"Conway","sequence":"additional","affiliation":[{"name":"Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7023-461X","authenticated-orcid":true,"given":"Kara G","family":"Lassen","sequence":"additional","affiliation":[{"name":"Broad Institute of Harvard and MIT, Cambridge, United States"},{"name":"Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Humberto B","family":"Jijon","sequence":"additional","affiliation":[{"name":"Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Pan","sequence":"additional","affiliation":[{"name":"Joslin Diabetes Center, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunyoung","family":"Chun","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monia","family":"Michaud","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica K","family":"Lang","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carey Ann","family":"Gallini Comeau","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan M","family":"Dreyfuss","sequence":"additional","affiliation":[{"name":"Joslin Diabetes Center, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan N","family":"Glickman","sequence":"additional","affiliation":[{"name":"Department of Pathology, Harvard Medical School, Boston, United States"},{"name":"Beth Israel Deaconess Medical Center, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hera","family":"Vlamakis","sequence":"additional","affiliation":[{"name":"Broad Institute of Harvard and MIT, Cambridge, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashwin","family":"Ananthakrishnan","sequence":"additional","affiliation":[{"name":"Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksander","family":"Kostic","sequence":"additional","affiliation":[{"name":"Joslin Diabetes Center, Boston, United States"},{"name":"Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5092-0150","authenticated-orcid":true,"given":"Wendy S","family":"Garrett","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, United States"},{"name":"Broad Institute of Harvard and MIT, Cambridge, United States"},{"name":"Department and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramnik J","family":"Xavier","sequence":"additional","affiliation":[{"name":"Gastrointestinal Unit, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States"},{"name":"Broad Institute of Harvard and MIT, Cambridge, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4374","published-online":{"date-parts":[[2019,1,22]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"e1002358","DOI":"10.1371\/journal.pcbi.1002358","article-title":"Metabolic reconstruction for metagenomic data and its application to the human microbiome","volume":"8","author":"Abubucker","year":"2012","journal-title":"PLOS Computational Biology"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1053\/j.gastro.2005.06.071","article-title":"Interleukin-22, a member of the IL-10 subfamily, induces inflammatory responses in colonic subepithelial myofibroblasts","volume":"129","author":"Andoh","year":"2005","journal-title":"Gastroenterology"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1126\/science.aal4677","article-title":"Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine","volume":"357","author":"Bel","year":"2017","journal-title":"Science"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1016\/j.chom.2011.04.009","article-title":"Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease","volume":"9","author":"Bloom","year":"2011","journal-title":"Cell Host & Microbe"},{"key":"bib5","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1038\/nature07416","article-title":"A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells","volume":"456","author":"Cadwell","year":"2008","journal-title":"Nature"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"250","DOI":"10.4161\/auto.5.2.7560","article-title":"A common role for Atg16L1, Atg5 and Atg7 in small intestinal Paneth cells and Crohn disease","volume":"5","author":"Cadwell","year":"2009","journal-title":"Autophagy"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"1116","DOI":"10.1126\/science.aad9948","article-title":"Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease","volume":"352","author":"Chu","year":"2016","journal-title":"Science"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1053\/j.gastro.2013.08.035","article-title":"Atg16l1 is required for autophagy in intestinal epithelial cells and protection of mice from Salmonella infection","volume":"145","author":"Conway","year":"2013","journal-title":"Gastroenterology"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1038\/nm.2069","article-title":"NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation","volume":"16","author":"Cooney","year":"2010","journal-title":"Nature Medicine"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"6065","DOI":"10.3748\/wjg.v21.i19.6065","article-title":"Fecal stream diversion and mucosal cytokine levels in collagenous colitis: A case report","volume":"21","author":"Daferera","year":"2015","journal-title":"World Journal of Gastroenterology"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"24","DOI":"10.3109\/00365521.2014.966321","article-title":"The innate immune system and inflammatory bowel disease","volume":"50","author":"Davies","year":"2015","journal-title":"Scandinavian Journal of Gastroenterology"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1038\/ng.3760","article-title":"Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease","volume":"49","author":"de Lange","year":"2017","journal-title":"Nature Genetics"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1086\/510385","article-title":"The role of microbes in Crohn's disease","volume":"44","author":"Eckburg","year":"2007","journal-title":"Clinical Infectious Diseases"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1111\/j.0105-2896.2005.00291.x","article-title":"Experimental models of inflammatory bowel disease reveal innate, adaptive, and regulatory mechanisms of host dialogue with the microbiota","volume":"206","author":"Elson","year":"2005","journal-title":"Immunological Reviews"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1084\/jem.20092253","article-title":"Microbiota innate stimulation is a prerequisite for T cell spontaneous proliferation and induction of experimental colitis","volume":"207","author":"Feng","year":"2010","journal-title":"The Journal of Experimental Medicine"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"13780","DOI":"10.1073\/pnas.0706625104","article-title":"Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases","volume":"104","author":"Frank","year":"2007","journal-title":"PNAS"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1136\/gut.52.1.65","article-title":"Increased expression of interleukin 17 in inflammatory bowel disease","volume":"52","author":"Fujino","year":"2003","journal-title":"Gut"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1016\/j.cell.2010.01.023","article-title":"Homeostasis and inflammation in the intestine","volume":"140","author":"Garrett","year":"2010","journal-title":"Cell"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/j.chom.2010.08.004","article-title":"Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis","volume":"8","author":"Garrett","year":"2010","journal-title":"Cell Host & Microbe"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"4136","DOI":"10.1128\/JCM.01004-06","article-title":"Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis","volume":"44","author":"Gophna","year":"2006","journal-title":"Journal of Clinical Microbiology"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"3617","DOI":"10.1172\/JCI75436","article-title":"Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature","volume":"124","author":"Haberman","year":"2014","journal-title":"Journal of Clinical Investigation"},{"key":"bib22","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s13073-017-0490-5","article-title":"A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients","volume":"9","author":"Hall","year":"2017","journal-title":"Genome Medicine"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/nrg.2017.63","article-title":"Human genetic variation and the gut microbiome in disease","volume":"18","author":"Hall","year":"2017","journal-title":"Nature Reviews Genetics"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/ng1954","article-title":"A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1","volume":"39","author":"Hampe","year":"2007","journal-title":"Nature Genetics"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"1192","DOI":"10.3748\/wjg.v20.i5.1192","article-title":"Role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years?","volume":"20","author":"Hold","year":"2014","journal-title":"World Journal of Gastroenterology"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"1630","DOI":"10.1053\/j.gastro.2010.07.006","article-title":"ATG16L1 and NOD2 interact in an autophagy-dependent antibacterial pathway implicated in Crohn's disease pathogenesis","volume":"1392","author":"Homer","year":"2010","journal-title":"Gastroenterology"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1136\/gutjnl-2016-312135","article-title":"Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease","volume":"67","author":"Imhann","year":"2018","journal-title":"Gut"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"2441","DOI":"10.1111\/j.1572-0241.1999.01372.x","article-title":"Characterization of cytokine expression in the rectal mucosa of ulcerative colitis: correlation with disease activity","volume":"94","author":"Inoue","year":"1999","journal-title":"The American Journal of Gastroenterology"},{"key":"bib29","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"Jostins","year":"2012","journal-title":"Nature"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1038\/nature10209","article-title":"Genetics and pathogenesis of inflammatory bowel disease","volume":"474","author":"Khor","year":"2011","journal-title":"Nature"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1038\/ismej.2010.148","article-title":"Supervised classification of microbiota mitigates mislabeling errors","volume":"5","author":"Knights","year":"2011","journal-title":"The ISME Journal"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1038\/nmeth.1650","article-title":"Bayesian community-wide culture-independent microbial source tracking","volume":"8","author":"Knights","year":"2011","journal-title":"Nature Methods"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/s13073-014-0107-1","article-title":"Complex host genetics influence the microbiome in inflammatory bowel disease","volume":"6","author":"Knights","year":"2014","journal-title":"Genome Medicine"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"e00420","DOI":"10.1128\/IAI.00420-17","article-title":"Bacteroides fragilis Enterotoxin Induces Formation of Autophagosomes in Endothelial Cells but Interferes with Fusion with Lysosomes for Complete Autophagic Flux through a Mitogen-Activated Protein Kinase-, AP-1-, and C\/EBP Homologous Protein-Dependent Pathway","volume":"85","author":"Ko","year":"2017","journal-title":"Infection and Immunity"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/nrmicro2746","article-title":"How glycan metabolism shapes the human gut microbiota","volume":"10","author":"Koropatkin","year":"2012","journal-title":"Nature Reviews Microbiology"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.chom.2015.01.001","article-title":"The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes","volume":"17","author":"Kostic","year":"2015","journal-title":"Cell Host & Microbe"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nature Biotechnology"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1084\/jem.20041257","article-title":"IL-23 drives a pathogenic T cell population that induces autoimmune inflammation","volume":"201","author":"Langrish","year":"2005","journal-title":"The Journal of Experimental Medicine"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"7741","DOI":"10.1073\/pnas.1407001111","article-title":"Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense","volume":"111","author":"Lassen","year":"2014","journal-title":"PNAS"},{"key":"bib40","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1111\/cei.12996","article-title":"Enrichment of IL-17A+ IFN-\u03b3+ and IL-22+ IFN-\u03b3+ T cell subsets is associated with reduction of NKp44+ ILC3s in the terminal ileum of Crohn's disease patients","volume":"190","author":"Li","year":"2017","journal-title":"Clinical and Experimental Immunology"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1038\/ng.3359","article-title":"Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations","volume":"47","author":"Liu","year":"2015","journal-title":"Nature Genetics"},{"key":"bib42","doi-asserted-by":"publisher","first-page":"1296","DOI":"10.1172\/JCI200420295","article-title":"Bacterial flagellin is a dominant antigen in Crohn disease","volume":"113","author":"Lodes","year":"2004","journal-title":"Journal of Clinical Investigation"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/ng.3761","article-title":"Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7","volume":"49","author":"Luo","year":"2017","journal-title":"Nature Genetics"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1136\/gut.2005.073817","article-title":"Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach","volume":"55","author":"Manichanh","year":"2006","journal-title":"Gut"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/ismej.2011.139","article-title":"An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea","volume":"6","author":"McDonald","year":"2012","journal-title":"The ISME Journal"},{"key":"bib46","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1001\/archsurg.1971.01350080224035","article-title":"Diverting ileostomy or colostomy in the management of Crohn's disease of the colon","volume":"103","author":"McIlrath","year":"1971","journal-title":"Archives of Surgery"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"Morgan","year":"2012","journal-title":"Genome Biology"},{"key":"bib48","doi-asserted-by":"publisher","DOI":"10.1038\/s41575-018-0084-8","article-title":"IL-12, IL-23 and IL-17 in IBD: immunobiology and therapeutic targeting","volume":"314","author":"Moschen","year":"2018","journal-title":"Nature Reviews Gastroenterology & Hepatology"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"e132","DOI":"10.1038\/ctg.2017.58","article-title":"Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease","volume":"9","author":"Moustafa","year":"2018","journal-title":"Clinical and Translational Gastroenterology"},{"key":"bib50","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1038\/nature13044","article-title":"A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3","volume":"506","author":"Murthy","year":"2014","journal-title":"Nature"},{"key":"bib51","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1136\/gut.2003.025403","article-title":"Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease","volume":"53","author":"Ott","year":"2004","journal-title":"Gut"},{"key":"bib52","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.clim.2015.05.014","article-title":"Immune-microbiota interactions in health and disease","volume":"159","author":"Palm","year":"2015","journal-title":"Clinical Immunology"},{"key":"bib53","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1128\/IAI.59.6.2075-2082.1991","article-title":"Immunochemical characterization of two surface polysaccharides of Bacteroides fragilis","volume":"59","author":"Pantosti","year":"1991","journal-title":"Infection and Immunity"},{"key":"bib54","first-page":"823","article-title":"Type 1 T-helper cell predominance and interleukin-12 expression in the gut of patients with Crohn's disease","volume":"150","author":"Parronchi","year":"1997","journal-title":"The American Journal of Pathology"},{"key":"bib55","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1056\/NEJMra020831","article-title":"Inflammatory bowel disease","volume":"347","author":"Podolsky","year":"2002","journal-title":"New England Journal of Medicine"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1097\/MIB.0b013e31827fec6d","article-title":"Phylogenetic analysis of dysbiosis in ulcerative colitis during remission","volume":"19","author":"Rajili\u0107-Stojanovi\u0107","year":"2013","journal-title":"Inflammatory Bowel Diseases"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.immuni.2014.06.015","article-title":"Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus","volume":"41","author":"Ramanan","year":"2014","journal-title":"Immunity"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1099\/jmm.0.021170-0","article-title":"Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients","volume":"59","author":"Rehman","year":"2010","journal-title":"Journal of Medical Microbiology"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1038\/ng2032","article-title":"Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis","volume":"39","author":"Rioux","year":"2007","journal-title":"Nature Genetics"},{"key":"bib60","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1038\/ismej.2014.3","article-title":"Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission","volume":"8","author":"Rooks","year":"2014","journal-title":"The ISME Journal"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1016\/0140-6736(91)90663-A","article-title":"Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum","volume":"338","author":"Rutgeerts","year":"1991","journal-title":"The Lancet"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1038\/nature07383","article-title":"Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production","volume":"456","author":"Saitoh","year":"2008","journal-title":"Nature"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"3388","DOI":"10.1099\/mic.0.052332-0","article-title":"Identification and classification of the genus Bacteroides by multilocus sequence analysis","volume":"157","author":"Sakamoto","year":"2011","journal-title":"Microbiology"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1053\/j.gastro.2007.11.059","article-title":"Microbial influences in inflammatory bowel diseases","volume":"134","author":"Sartor","year":"2008","journal-title":"Gastroenterology"},{"key":"bib66","doi-asserted-by":"crossref","first-page":"5224","DOI":"10.1128\/IAI.66.11.5224-5231.1998","article-title":"Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-deficient mice","volume":"66","author":"Sellon","year":"1998","journal-title":"Infection and Immunity"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1053\/gast.2002.30294","article-title":"Mucosal flora in inflammatory bowel disease","volume":"122","author":"Swidsinski","year":"2002","journal-title":"Gastroenterology"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"3380","DOI":"10.1128\/JCM.43.7.3380-3389.2005","article-title":"Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease","volume":"43","author":"Swidsinski","year":"2005","journal-title":"Journal of Clinical Microbiology"},{"key":"bib69","doi-asserted-by":"publisher","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":"PNAS"},{"key":"bib70","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/ni.1823","article-title":"Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry","volume":"11","author":"Travassos","year":"2010","journal-title":"Nature Immunology"},{"key":"bib71","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"Truong","year":"2015","journal-title":"Nature Methods"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1093\/ibd\/izy085","article-title":"Determinants of IBD Heritability: Genes, Bugs, and More","volume":"24","author":"Turpin","year":"2018","journal-title":"Inflammatory bowel diseases"},{"key":"bib73","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1002\/ibd.20783","article-title":"Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease","volume":"15","author":"Willing","year":"2009","journal-title":"Inflammatory Bowel Diseases"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1038\/nature06005","article-title":"Unravelling the pathogenesis of inflammatory bowel disease","volume":"448","author":"Xavier","year":"2007","journal-title":"Nature"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"1310","DOI":"10.1172\/JCI21404","article-title":"IL-23 is essential for T cell-mediated colitis and promotes inflammation via IL-17 and IL-6","volume":"116","author":"Yen","year":"2006","journal-title":"Journal of Clinical Investigation"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"2133","DOI":"10.4049\/jimmunol.1601293","article-title":"Myeloid ATG16L1 Facilitates Host\u2013Bacteria Interactions in Maintaining Intestinal Homeostasis","volume":"198","author":"Zhang","year":"2017","journal-title":"The Journal of Immunology"},{"key":"bib77","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1126\/science.aad3369","article-title":"Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity","volume":"352","author":"Zhernakova","year":"2016","journal-title":"Science"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/39982\/elife-39982-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/39982\/elife-39982-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/39982","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,11]],"date-time":"2023-10-11T20:50:16Z","timestamp":1697057416000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/39982"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,22]]},"references-count":77,"alternative-id":["10.7554\/eLife.39982"],"URL":"https:\/\/doi.org\/10.7554\/elife.39982","archive":["CLOCKSS"],"relation":{"references":[{"id-type":"uri","id":"https:\/\/www.ncbi.nlm.nih.gov\/projects\/gap\/cgi-bin\/study.cgi?study_id=phs000130.v1.p1","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/www.ncbi.nlm.nih.gov\/projects\/gap\/cgi-bin\/study.cgi?study_id=phs000345.v1.p1","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"uri","id":"https:\/\/www.ncbi.nlm.nih.gov\/sra\/?term=4222585","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.7554\/eLife.39982.033","asserted-by":"object"},{"id-type":"doi","id":"10.7554\/eLife.39982.034","asserted-by":"object"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,22]]},"article-number":"e39982"}}