{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T21:59:33Z","timestamp":1789077573007,"version":"build-2803163510"},"reference-count":119,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:00:00Z","timestamp":1722297600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Immune-mediated gastrointestinal (GI) diseases, including achalasia, celiac disease, and inflammatory bowel diseases, pose significant challenges in diagnosis and management due to their complex etiology and diverse clinical manifestations. While genetic predispositions and environmental factors have been extensively studied in the context of these conditions, the role of viral infections and virome dysbiosis remains a subject of growing interest. This review aims to elucidate the involvement of viral infections in the pathogenesis of immune-mediated GI diseases, focusing on achalasia and celiac disease, as well as the virome dysbiosis in IBD. Recent evidence suggests that viral pathogens, ranging from common respiratory viruses to enteroviruses and herpesviruses, may trigger or exacerbate achalasia and celiac disease by disrupting immune homeostasis in the GI tract. Furthermore, alterations in the microbiota and, specifically, in the virome composition and viral\u2013host interactions have been implicated in perpetuating chronic intestinal inflammation in IBD. By synthesizing current knowledge on viral contributions to immune-mediated GI diseases, this review aims to provide insights into the complex interplay between viral infections, host genetics, and virome dysbiosis, shedding light on novel therapeutic strategies aimed at mitigating the burden of these debilitating conditions on patients\u2019 health and quality of life.<\/jats:p>","DOI":"10.3390\/ijms25158301","type":"journal-article","created":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T17:08:34Z","timestamp":1722359314000},"page":"8301","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["The Role of Viruses in the Pathogenesis of Immune-Mediated Gastro-Intestinal Diseases"],"prefix":"10.3390","volume":"25","author":[{"given":"Francesca","family":"Bernardi","sequence":"first","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"},{"name":"Gastroenterology and Endoscopy, Vita-Salute San Raffaele University, Via Olgettina, 58, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Ungaro","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8591-6995","authenticated-orcid":false,"given":"Ferdinando","family":"D\u2019Amico","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandra","family":"Zilli","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommaso Lorenzo","family":"Parigi","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Massimino","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariangela","family":"Allocca","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvio","family":"Danese","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"},{"name":"Gastroenterology and Endoscopy, Vita-Salute San Raffaele University, Via Olgettina, 58, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4308-7295","authenticated-orcid":false,"given":"Federica","family":"Furfaro","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele, 20132 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1056\/NEJMra0804647","article-title":"Inflammatory Bowel Disease","volume":"361","author":"Abraham","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1111\/1751-2980.12973","article-title":"The Etiology of Achalasia: An Immune-Dominant Disease","volume":"22","author":"Wu","year":"2021","journal-title":"J. Dig. Dis."},{"key":"ref_3","first-page":"654143","article-title":"Immune Development and Intestinal Microbiota in Celiac Disease","volume":"2012","author":"Olivares","year":"2012","journal-title":"Clin. Dev. Immunol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"449","DOI":"10.5009\/gnl14446","article-title":"The Pathogenesis and Management of Achalasia: Current Status and Future Directions","volume":"9","author":"Ates","year":"2015","journal-title":"Gut Liver"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1640","DOI":"10.1056\/NEJMra1502863","article-title":"Eosinophilic Esophagitis","volume":"373","author":"Furuta","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nrgastro.2013.101","article-title":"Autoimmune Atrophic Gastritis--Pathogenesis, Pathology and Management","volume":"10","author":"Neumann","year":"2013","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1053\/j.gastro.2020.06.098","article-title":"Epidemiology, Presentation, and Diagnosis of Celiac Disease","volume":"160","author":"Lebwohl","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1111\/jgh.15692","article-title":"Gastrointestinal: Autoimmune Enteropathy Associated with Thymoma","volume":"37","author":"Gu","year":"2022","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2547","DOI":"10.1016\/S0140-6736(18)30300-3","article-title":"Primary Sclerosing Cholangitis","volume":"391","author":"Dyson","year":"2018","journal-title":"Lancet"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1016\/S0140-6736(20)31607-X","article-title":"Primary Biliary Cholangitis","volume":"396","author":"Lleo","year":"2020","journal-title":"Lancet"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e070201","DOI":"10.1136\/bmj-2022-070201","article-title":"Diagnosis and Management of Autoimmune Hepatitis","volume":"380","author":"Muratori","year":"2023","journal-title":"BMJ"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3801","DOI":"10.3748\/wjg.v21.i13.3801","article-title":"Gastrointestinal Beh\u00e7et\u2019s Disease: A Review","volume":"21","author":"Skef","year":"2015","journal-title":"World J. Gastroenterol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s11894-021-00809-2","article-title":"Eosinophilic Gastritis\/Gastroenteritis","volume":"23","author":"Chen","year":"2021","journal-title":"Curr. Gastroenterol. Rep."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1126\/science.aah5298","article-title":"Reovirus Infection Triggers Inflammatory Responses to Dietary Antigens and Development of Celiac Disease","volume":"356","author":"Bouziat","year":"2017","journal-title":"Science"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7892","DOI":"10.3748\/wjg.v22.i35.7892","article-title":"New Insights into the Pathophysiology of Achalasia and Implications for Future Treatment","volume":"22","author":"Valdovinos","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"S\u00e1nchez, D., Hoffmanov\u00e1, I., Szczepankov\u00e1, A., H\u00e1bov\u00e1, V., and Tlaskalov\u00e1-Hogenov\u00e1, H. (2021). Contribution of Infectious Agents to the Development of Celiac Disease. Microorganisms, 9.","DOI":"10.3390\/microorganisms9030547"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1111\/j.1572-0241.2006.00741.x","article-title":"Rotavirus Infection Frequency and Risk of Celiac Disease Autoimmunity in Early Childhood: A Longitudinal Study","volume":"101","author":"Stene","year":"2006","journal-title":"Am. J. Gastroenterol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1111\/j.1572-0241.2008.01956.x","article-title":"T Cells in the Myenteric Plexus of Achalasia Patients Show a Skewed TCR Repertoire and React to HSV-1 Antigens","volume":"103","author":"Facco","year":"2008","journal-title":"Am. J. Gastroenterol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1136\/gut.34.3.299","article-title":"Varicella-Zoster Virus DNA in the Oesophageal Myenteric Plexus in Achalasia","volume":"34","author":"Robertson","year":"1993","journal-title":"Gut"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1146\/annurev-immunol-040210-092915","article-title":"Integration of Genetic and Immunological Insights into a Model of Celiac Disease Pathogenesis","volume":"29","author":"Abadie","year":"2011","journal-title":"Annu. Rev. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1053\/j.gastro.2021.04.057","article-title":"Association of Achalasia with Active Varicella Zoster Virus Infection of the Esophagus","volume":"161","author":"Naik","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.coviro.2021.10.005","article-title":"The Gut Virome in Inflammatory Bowel Diseases","volume":"51","author":"Liang","year":"2021","journal-title":"Curr. Opin. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1016\/j.cell.2015.01.002","article-title":"Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease","volume":"160","author":"Norman","year":"2015","journal-title":"Cell"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/nri3738","article-title":"Regional Specialization within the Intestinal Immune System","volume":"14","author":"Mowat","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/s41577-020-0288-3","article-title":"RIG-I-like Receptors: Their Regulation and Roles in RNA Sensing","volume":"20","author":"Rehwinkel","year":"2020","journal-title":"Nat. Rev. Immunol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/nri2587","article-title":"A Cell Biological View of Toll-like Receptor Function: Regulation through Compartmentalization","volume":"9","author":"Barton","year":"2009","journal-title":"Nat. Rev. Immunol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"van Montfoort, N., van der Aa, E., and Woltman, A.M. (2014). Understanding MHC Class I Presentation of Viral Antigens by Human Dendritic Cells as a Basis for Rational Design of Therapeutic Vaccines. Front. Immunol., 5.","DOI":"10.3389\/fimmu.2014.00182"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1097\/MPG.0000000000002497","article-title":"European Society Paediatric Gastroenterology, Hepatology and Nutrition Guidelines for Diagnosing Coeliac Disease 2020","volume":"70","author":"Husby","year":"2020","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41586-020-2003-8","article-title":"IL-15, Gluten and HLA-DQ8 Drive Tissue Destruction in Coeliac Disease","volume":"578","author":"Abadie","year":"2020","journal-title":"Nature"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1001\/jama.2019.10329","article-title":"Association of Gluten Intake During the First 5 Years of Life with Incidence of Celiac Disease Autoimmunity and Celiac Disease Among Children at Increased Risk","volume":"322","author":"Lee","year":"2019","journal-title":"JAMA"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1515\/cclm-2019-0657","article-title":"Gut Microbiome Investigation in Celiac Disease: From Methods to Its Pathogenetic Role","volume":"58","author":"Sacchetti","year":"2020","journal-title":"Clin. Chem. Lab. Med."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1111\/cei.13369","article-title":"Serum Cytokines Elevated during Gluten-Mediated Cytokine Release in Coeliac Disease","volume":"199","author":"Goel","year":"2020","journal-title":"Clin. Exp. Immunol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"l231","DOI":"10.1136\/bmj.l231","article-title":"Enterovirus as Trigger of Coeliac Disease: Nested Case-Control Study within Prospective Birth Cohort","volume":"364","author":"Kahrs","year":"2019","journal-title":"BMJ"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.clim.2004.01.008","article-title":"Interferon Alpha\u2014A Potential Link in the Pathogenesis of Viral-Induced Type 1 Diabetes and Autoimmunity","volume":"111","author":"Devendra","year":"2004","journal-title":"Clin. Immunol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1016\/S0140-6736(00)02880-4","article-title":"Onset of Coeliac Disease during Treatment with Interferon for Chronic Hepatitis C","volume":"356","author":"Cammarota","year":"2000","journal-title":"Lancet"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1089\/107999099313424","article-title":"Effects of Oral Administration of Interferon-Alpha on Antibody Production in Mice with Induced Tolerance","volume":"19","author":"Takayama","year":"1999","journal-title":"J. Interferon Cytokine Res. Off. J. Int. Soc. Interferon Cytokine Res."},{"key":"ref_37","first-page":"303","article-title":"Celiac Disease and Hepatitis C Relationships in Transcriptional Regulatory Networks","volume":"10","author":"Izadi","year":"2017","journal-title":"Gastroenterol. Hepatol. Bed Bench"},{"key":"ref_38","first-page":"703","article-title":"Is Autoimmunity Infectious? The Effect of Gastrointestinal Viral Infections and Vaccination on Risk of Celiac Disease Autoimmunity","volume":"15","author":"Silvester","year":"2017","journal-title":"Clin. Gastroenterol. Hepatol. Off. Clin. Pract. J. Am. Gastroenterol. Assoc."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1111\/cei.12855","article-title":"Lack of Evidence of Rotavirus-Dependent Molecular Mimicry as a Trigger of Coeliac Disease","volume":"186","author":"Ziberna","year":"2016","journal-title":"Clin. Exp. Immunol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1080\/21645515.2017.1412019","article-title":"Report of the 5th European Expert Meeting on Rotavirus Vaccination (EEROVAC)","volume":"14","author":"Vesikari","year":"2018","journal-title":"Hum. Vaccines Immunother."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1097\/INF.0000000000002281","article-title":"Rotavirus Vaccination Does Not Increase Type 1 Diabetes and May Decrease Celiac Disease in Children and Adolescents","volume":"38","author":"Vesikari","year":"2019","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Zanoni, G., Navone, R., Lunardi, C., Tridente, G., Bason, C., Sivori, S., Beri, R., Dolcino, M., Valletta, E., and Corrocher, R. (2006). In Celiac Disease, a Subset of Autoantibodies against Transglutaminase Binds Toll-like Receptor 4 and Induces Activation of Monocytes. PLoS Med., 3.","DOI":"10.1371\/journal.pmed.0030358"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1007\/s12026-013-8420-0","article-title":"A Subset of Anti-Rotavirus Antibodies Directed against the Viral Protein VP7 Predicts the Onset of Celiac Disease and Induces Typical Features of the Disease in the Intestinal Epithelial Cell Line T84","volume":"56","author":"Dolcino","year":"2013","journal-title":"Immunol. Res."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e02062-17","DOI":"10.1128\/JVI.02062-17","article-title":"Reovirus-Induced Apoptosis in the Intestine Limits Establishment of Enteric Infection","volume":"92","author":"Brown","year":"2018","journal-title":"J. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"S484","DOI":"10.1016\/S0016-5085(16)31664-X","article-title":"Su1165 Virus-Enhanced Upregulation of Type-1 Interferon Promotes Loss of Oral Tolerance in Celiac Disease","volume":"150","author":"Discepolo","year":"2016","journal-title":"Gastroenterology"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e159823","DOI":"10.1172\/jci.insight.159823","article-title":"NK Cells Contribute to Reovirus-Induced IFN Responses and Loss of Tolerance to Dietary Antigen","volume":"7","author":"Brigleb","year":"2022","journal-title":"JCI Insight"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1056\/NEJMsa1206589","article-title":"Norovirus and Medically Attended Gastroenteritis in U.S. Children","volume":"368","author":"Payne","year":"2013","journal-title":"N. Engl. J. Med."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.chom.2018.10.004","article-title":"Murine Norovirus Infection Induces TH1 Inflammatory Responses to Dietary Antigens","volume":"24","author":"Bouziat","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Oikarinen, M., Puustinen, L., Lehtonen, J., Hakola, L., Simell, S., Toppari, J., Ilonen, J., Veijola, R., Virtanen, S.M., and Knip, M. (2020). Enterovirus Infections Are Associated with the Development of Celiac Disease in a Birth Cohort Study. Front. Immunol., 11.","DOI":"10.3389\/fimmu.2020.604529"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1136\/gutjnl-2019-319809","article-title":"Metagenomics of the Faecal Virome Indicate a Cumulative Effect of Enterovirus and Gluten Amount on the Risk of Coeliac Disease Autoimmunity in Genetically at Risk Children: The TEDDY Study","volume":"69","author":"Lindfors","year":"2020","journal-title":"Gut"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1002\/jmv.23305","article-title":"Type 1 Diabetes Associated and Tissue Transglutaminase Autoantibodies in Patients without Type 1 Diabetes and Coeliac Disease with Confirmed Viral Infections","volume":"84","author":"Sarmiento","year":"2012","journal-title":"J. Med. Virol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1007\/s10620-016-4403-z","article-title":"Circulating Zonulin Correlates with Density of Enteroviruses and Tolerogenic Dendritic Cells in the Small Bowel Mucosa of Celiac Disease Patients","volume":"62","author":"Vorobjova","year":"2017","journal-title":"Dig. Dis. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"788","DOI":"10.14309\/ajg.0000000000001003","article-title":"Parechovirus Infection in Early Childhood and Association with Subsequent Celiac Disease","volume":"116","author":"Tapia","year":"2021","journal-title":"Am. J. Gastroenterol."},{"key":"ref_54","first-page":"1216","article-title":"Detection of Active Epstein-Barr Virus Infection in Duodenal Mucosa of Patients with Refractory Celiac Disease","volume":"14","author":"Perfetti","year":"2016","journal-title":"Clin. Gastroenterol. Hepatol. Off. Clin. Pract. J. Am. Gastroenterol. Assoc."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1007\/s10654-010-9516-7","article-title":"The Generation R Study: Design and Cohort Update 2010","volume":"25","author":"Jaddoe","year":"2010","journal-title":"Eur. J. Epidemiol."},{"key":"ref_56","first-page":"191","article-title":"Autoimmune Diseases Co-Existing with Hepatitis C Virus Infection","volume":"9","author":"Jadali","year":"2010","journal-title":"Iran. J. Allergy Asthma Immunol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1016\/j.jhep.2014.05.020","article-title":"Prevalence of Celiac Disease in Cirrhosis and Outcome of Cirrhosis on a Gluten Free Diet: A Prospective Study","volume":"61","author":"Pagadala","year":"2014","journal-title":"J. Hepatol."},{"key":"ref_58","first-page":"763497","article-title":"Onset of Celiac Disease after Treatment of Chronic Hepatitis C with Interferon Based Triple Therapy","volume":"2015","author":"Singh","year":"2015","journal-title":"Case Rep. Hepatol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1080\/00365521.2017.1362464","article-title":"Influenza and Risk of Later Celiac Disease: A Cohort Study of 2.6 Million People","volume":"53","author":"Gunnes","year":"2018","journal-title":"Scand. J. Gastroenterol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1502","DOI":"10.1007\/s10620-014-3046-1","article-title":"Children with Celiac Disease Are More Likely to Have Attended Hospital for Prior Respiratory Syncytial Virus Infection","volume":"59","author":"Tjernberg","year":"2014","journal-title":"Dig. Dis. Sci."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.14309\/ajg.0000000000000731","article-title":"ACG Clinical Guidelines: Diagnosis and Management of Achalasia","volume":"115","author":"Vaezi","year":"2020","journal-title":"Am. J. Gastroenterol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1001\/jama.2015.2996","article-title":"Achalasia: A Systematic Review","volume":"313","author":"Pandolfino","year":"2015","journal-title":"JAMA"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e14058","DOI":"10.1111\/nmo.14058","article-title":"ESOPHAGEAL MOTILITY DISORDERS ON HIGH RESOLUTION MANOMETRY: CHICAGO CLASSIFICATION VERSION 4.0\u00a9","volume":"33","author":"Yadlapati","year":"2021","journal-title":"Neurogastroenterol. Motil. Off. J. Eur. Gastrointest. Motil. Soc."},{"key":"ref_64","first-page":"729217","article-title":"Achalasia\u2014An Autoimmune Inflammatory Disease: A Cross-Sectional Study","volume":"2015","author":"Valdovinos","year":"2015","journal-title":"J. Immunol. Res."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Furuzawa-Carballeda, J., Zu\u00f1iga, J., Hern\u00e1ndez-Zaragoza, D.I., Barquera, R., Marques-Garc\u00eda, E., Jim\u00e9nez-Alvarez, L., Cruz-Lagunas, A., Ram\u00edrez, G., Regino, N.E., and Espinosa-Soto, R. (2018). An Original Eurasian Haplotype, HLA-DRB1*14:54-DQB1*05:03, Influences the Susceptibility to Idiopathic Achalasia. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0201676"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1097\/MCG.0000000000000780","article-title":"Etiology and Pathogenesis of Idiopathic Achalasia","volume":"51","author":"Pressman","year":"2017","journal-title":"J. Clin. Gastroenterol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Verzosa, A.L., McGeever, L.A., Bhark, S.-J., Delgado, T., Salazar, N., and Sanchez, E.L. (2021). Herpes Simplex Virus 1 Infection of Neuronal and Non-Neuronal Cells Elicits Specific Innate Immune Responses and Immune Evasion Mechanisms. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.644664"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"806","DOI":"10.3109\/00365521003587804","article-title":"Enhanced Reactivity of Peripheral Blood Immune Cells to HSV-1 in Primary Achalasia","volume":"45","author":"Lau","year":"2010","journal-title":"Scand. J. Gastroenterol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1097\/01.aids.0000186820.22865.ce","article-title":"HIV and Achalasia","volume":"19","author":"Barrow","year":"2005","journal-title":"AIDS"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1111\/1751-2980.12287","article-title":"Achalasia Secondary to Cardial Tuberculosis Caused by AIDS","volume":"16","author":"Wang","year":"2015","journal-title":"J. Dig. Dis."},{"key":"ref_71","first-page":"2003","article-title":"Esophageal Motility in AIDS Patients with Symptomatic Opportunistic Infections of the Esophagus","volume":"89","author":"Fried","year":"1994","journal-title":"Am. J. Gastroenterol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"39","DOI":"10.32074\/1591-951X-235","article-title":"Histopathology of IBD Colitis. A Practical Approach from the Pathologists of the Italian Group for the Study of the Gastrointestinal Tract (GIPAD)","volume":"113","author":"Villanacci","year":"2021","journal-title":"Pathologica"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1093\/ibd\/izab192","article-title":"What Is a Flare? The Manitoba Living with IBD Study","volume":"28","author":"Witges","year":"2021","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1093\/ibd\/izz186","article-title":"The Changing Epidemiology of Inflammatory Bowel Disease: What Goes Up May Come Down","volume":"26","author":"Khalili","year":"2020","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1136\/gutjnl-2020-322129","article-title":"Emerging Treatment Options for Extraintestinal Manifestations in IBD","volume":"70","author":"Greuter","year":"2021","journal-title":"Gut"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.mayocp.2018.09.013","article-title":"Mechanisms of Disease: Inflammatory Bowel Diseases","volume":"94","author":"Ramos","year":"2019","journal-title":"Mayo Clin. Proc."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"19273","DOI":"10.1038\/s41598-020-76361-2","article-title":"Identifying Environmental Risk Factors for Inflammatory Bowel Diseases: A Mendelian Randomization Study","volume":"10","author":"Duell","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12328-017-0813-5","article-title":"Gut Microbiota in the Pathogenesis of Inflammatory Bowel Disease","volume":"11","author":"Nishida","year":"2018","journal-title":"Clin. J. Gastroenterol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Pargin, E., Roach, M.J., Skye, A., Papudeshi, B., Inglis, L.K., Mallawaarachchi, V., Grigson, S.R., Harker, C., Edwards, R.A., and Giles, S.K. (2023). The Human Gut Virome: Composition, Colonization, Interactions, and Impacts on Human Health. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.963173"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1097\/MIB.0b013e318292477c","article-title":"Bacteriophages in Gut Samples from Pediatric Crohn\u2019s Disease Patients: Metagenomic Analysis Using 454 Pyrosequencing","volume":"19","author":"Wagner","year":"2013","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/ecco-jcc\/jjaa094","article-title":"Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease","volume":"14","author":"Liang","year":"2020","journal-title":"J. Crohns Colitis"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1080\/19490976.2018.1511664","article-title":"Metagenomic Analysis of Intestinal Mucosa Revealed a Specific Eukaryotic Gut Virome Signature in Early-Diagnosed Inflammatory Bowel Disease","volume":"10","author":"Ungaro","year":"2019","journal-title":"Gut Microbes"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"7883945","DOI":"10.1155\/2022\/7883945","article-title":"Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases","volume":"2022","author":"Clinton","year":"2022","journal-title":"J. Immunol. Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/s43588-021-00114-y","article-title":"The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) Framework","volume":"1","author":"Massimino","year":"2021","journal-title":"Nat. Comput. Sci."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Nishiyama, H., Endo, H., Blanc-Mathieu, R., and Ogata, H. (2020). Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms, 8.","DOI":"10.3390\/microorganisms8111663"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Cornuault, J.K., Petit, M.-A., Mariadassou, M., Benevides, L., Moncaut, E., Langella, P., Sokol, H., and De Paepe, M. (2018). Phages Infecting Faecalibacterium Prausnitzii Belong to Novel Viral Genera That Help to Decipher Intestinal Viromes. Microbiome, 6.","DOI":"10.1186\/s40168-018-0452-1"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.jcmgh.2017.03.007","article-title":"Mend Your Fences: The Epithelial Barrier and Its Relationship with Mucosal Immunity in Inflammatory Bowel Disease","volume":"4","author":"Martini","year":"2017","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1038\/s41575-022-00675-x","article-title":"The Role of Goblet Cells and Mucus in Intestinal Homeostasis","volume":"19","author":"Gustafsson","year":"2022","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Metzger, R.N., Krug, A.B., and Eisen\u00e4cher, K. (2018). Enteric Virome Sensing-Its Role in Intestinal Homeostasis and Immunity. Viruses, 10.","DOI":"10.3390\/v10040146"},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Sinha, A., Li, Y., Mirzaei, M.K., Shamash, M., Samadfam, R., King, I.L., and Maurice, C.F. (2022). Transplantation of Bacteriophages from Ulcerative Colitis Patients Shifts the Gut Bacteriome and Exacerbates the Severity of DSS Colitis. Microbiome, 10.","DOI":"10.1186\/s40168-022-01275-2"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1838","DOI":"10.1136\/gutjnl-2022-328375","article-title":"Gut Virome-Colonising Orthohepadnavirus Genus Is Associated with Ulcerative Colitis Pathogenesis and Induces Intestinal Inflammation In Vivo","volume":"72","author":"Massimino","year":"2023","journal-title":"Gut"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"eaau4255","DOI":"10.1126\/sciadv.aau4255","article-title":"Type III Interferon Signaling Restricts Enterovirus 71 Infection of Goblet Cells","volume":"5","author":"Good","year":"2019","journal-title":"Sci. Adv."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"e00250-18","DOI":"10.1128\/JVI.00250-18","article-title":"Adenovirus Infection of Human Enteroids Reveals Interferon Sensitivity and Preferential Infection of Goblet Cells","volume":"92","author":"Holly","year":"2018","journal-title":"J. Virol."},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Kolawole, A.O., Mirabelli, C., Hill, D.R., Svoboda, S.A., Janowski, A.B., Passalacqua, K.D., Rodriguez, B.N., Dame, M.K., Freiden, P., and Berger, R.P. (2019). Astrovirus Replication in Human Intestinal Enteroids Reveals Multi-Cellular Tropism and an Intricate Host Innate Immune Landscape. PLoS Pathog., 15.","DOI":"10.1371\/journal.ppat.1008057"},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Kang, Y., Park, H., Choe, B.-H., and Kang, B. (2022). The Role and Function of Mucins and Its Relationship to Inflammatory Bowel Disease. Front. Med., 9.","DOI":"10.3389\/fmed.2022.848344"},{"key":"ref_96","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","year":"2013","journal-title":"Nat. Immunol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"eaat9691","DOI":"10.1126\/science.aat9691","article-title":"Bacteriophage Trigger Antiviral Immunity and Prevent Clearance of Bacterial Infection","volume":"363","author":"Sweere","year":"2019","journal-title":"Science"},{"key":"ref_98","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":"ref_99","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1016\/j.chom.2021.03.015","article-title":"Enteric Viruses Evoke Broad Host Immune Responses Resembling Those Elicited by the Bacterial Microbiome","volume":"29","author":"Dallari","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Carroll-Portillo, A., and Lin, H.C. (2019). Bacteriophage and the Innate Immune System: Access and Signaling. Microorganisms, 7.","DOI":"10.3390\/microorganisms7120625"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1007\/s10620-020-06090-z","article-title":"Microbial-Based and Microbial-Targeted Therapies for Inflammatory Bowel Diseases","volume":"65","author":"Oka","year":"2020","journal-title":"Dig. Dis. Sci."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"2174","DOI":"10.1053\/j.gastro.2019.03.017","article-title":"Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-Based Therapies for Inflammatory Bowel Diseases","volume":"156","author":"Cohen","year":"2019","journal-title":"Gastroenterology"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Zuo, T., and Ng, S.C. (2018). The Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02247"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"119622","DOI":"10.1016\/j.lfs.2021.119622","article-title":"Restoration of Dysbiotic Human Gut Microbiome for Homeostasis","volume":"278","author":"Dixit","year":"2021","journal-title":"Life Sci."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1093\/jhmas\/48.3.275","article-title":"Cholera and Plague in India: The Bacteriophage Inquiry of 1927\u20131936","volume":"48","author":"Summers","year":"1993","journal-title":"J. Hist. Med. Allied Sci."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1136\/gutjnl-2017-314903","article-title":"Adherent-Invasive Escherichia coli in Inflammatory Bowel Disease","volume":"67","author":"Palmela","year":"2018","journal-title":"Gut"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/j.cell.2017.07.008","article-title":"Fusobacterium Nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy","volume":"170","author":"Yu","year":"2017","journal-title":"Cell"},{"key":"ref_108","doi-asserted-by":"crossref","unstructured":"Chervy, M., Barnich, N., and Denizot, J. (2020). Adherent-Invasive E. coli: Update on the Lifestyle of a Troublemaker in Crohn\u2019s Disease. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21103734"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1053\/j.gastro.2016.10.012","article-title":"Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches","volume":"152","author":"Sartor","year":"2017","journal-title":"Gastroenterology"},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Vahedi, A., Soltan Dallal, M.M., Douraghi, M., Nikkhahi, F., Rajabi, Z., Yousefi, M., and Mousavi, M. (2018). Isolation and Identification of Specific Bacteriophage against Enteropathogenic Escherichia coli (EPEC) and In Vitro and In Vivo Characterization of Bacteriophage. FEMS Microbiol. Lett., 365.","DOI":"10.1093\/femsle\/fny136"},{"key":"ref_111","first-page":"840","article-title":"Bacteriophages Targeting Adherent Invasive Escherichia coli Strains as a Promising New Treatment for Crohn\u2019s Disease","volume":"11","author":"Galtier","year":"2017","journal-title":"J. Crohns Colitis"},{"key":"ref_112","doi-asserted-by":"crossref","unstructured":"Febvre, H.P., Rao, S., Gindin, M., Goodwin, N.D.M., Finer, E., Vivanco, J.S., Lu, S., Manter, D.K., Wallace, T.C., and Weir, T.L. (2019). PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults. Nutrients, 11.","DOI":"10.3390\/nu11030666"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"2879","DOI":"10.1016\/j.cell.2022.07.003","article-title":"Targeted Suppression of Human IBD-Associated Gut Microbiota Commensals by Phage Consortia for Treatment of Intestinal Inflammation","volume":"185","author":"Federici","year":"2022","journal-title":"Cell"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.1128\/AAC.49.7.2874-2878.2005","article-title":"Human Volunteers Receiving Escherichia coli Phage T4 Orally: A Safety Test of Phage Therapy","volume":"49","author":"Bruttin","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1080\/07315724.2018.1483783","article-title":"Bacteriophage for Gastrointestinal Health (PHAGE) Study: Evaluating the Safety and Tolerability of Supplemental Bacteriophage Consumption","volume":"38","author":"Gindin","year":"2019","journal-title":"J. Am. Coll. Nutr."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"eabn6660","DOI":"10.1126\/sciimmunol.abn6660","article-title":"Human Enteric Viruses Autonomously Shape Inflammatory Bowel Disease Phenotype through Divergent Innate Immunomodulation","volume":"7","author":"Adiliaghdam","year":"2022","journal-title":"Sci. Immunol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"2236750","DOI":"10.1080\/19490976.2023.2236750","article-title":"Fecal Virome Transplantation Is Sufficient to Alter Fecal Microbiota and Drive Lean and Obese Body Phenotypes in Mice","volume":"15","author":"Borin","year":"2023","journal-title":"Gut Microbes"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1053\/j.gastro.2016.11.010","article-title":"Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients with Clostridium Difficile Infection","volume":"152","author":"Ott","year":"2017","journal-title":"Gastroenterology"},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Wu, Z., Huang, S., Li, T., Li, N., Han, D., Zhang, B., Xu, Z.Z., Zhang, S., Pang, J., and Wang, S. (2021). Gut Microbiota from Green Tea Polyphenol-Dosed Mice Improves Intestinal Epithelial Homeostasis and Ameliorates Experimental Colitis. 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