{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T07:00:57Z","timestamp":1780470057749,"version":"3.54.1"},"reference-count":78,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T00:00:00Z","timestamp":1780444800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Crohn\u2019s disease (CD) is a chronic inflammatory disease mainly characterized by chronic and relapsing intestinal inflammation. The pathogenesis of CD involves dysregulation of the immune response to commensal gut pro-inflammatory microbiota. Genome-wide association studies (GWAS) identified many genetic susceptibility loci associated with CD, such as\n                    <jats:italic>NOD2, CARD9, ATG16L1, IRGM<\/jats:italic>\n                    , and\n                    <jats:italic>FUT2<\/jats:italic>\n                    , etc. These risk genes are associated with the relative abundance of particular bacteria. The combined risk score was found to be predictive of disease severity. Moreover, the exact composition of microbiota is known to determine host phenotypes, including metabolic and immunological phenotypes. In this study, we elucidated the association between host genetics, gut microbiota, and host phenotypes. We propose that the pathogenesis of Crohn\u2019s disease is mediated by pro-inflammatory microbiota in genetically susceptible individuals.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1856205","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T06:01:29Z","timestamp":1780466489000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Pro-inflammatory microbiota mediates the effect of host risk genes in Crohn\u2019s disease"],"prefix":"10.3389","volume":"17","author":[{"given":"Dawei","family":"Gong","sequence":"first","affiliation":[{"name":"Department of Gastroenterology and Endoscopy Center, The Fourth People's Hospital of Jinan","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanshan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Medical and Health Laboratory of Blood Ecology and Biointelligence, Jinan Key Laboratory of Medical Cell Bioengineering, Science and Technology Innovation Center, The Fourth People\u2019s Hospital of Jinan Affiliated to Shandong Second Medical University","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Quality Management, The Fourth People's Hospital of Jinan Affiliated to Shandong Second Medical University","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jicai","family":"Lv","sequence":"additional","affiliation":[{"name":"Department of Hepatology II, Shandong Public Health Clinical Center, Shandong University","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liguo","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy Center, The Fourth People's Hospital of Jinan","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziying","family":"Chen","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Medical and Health Laboratory of Blood Ecology and Biointelligence, Jinan Key Laboratory of Medical Cell Bioengineering, Science and Technology Innovation Center, The Fourth People\u2019s Hospital of Jinan Affiliated to Shandong Second Medical University","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leisheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Medical and Health Laboratory of Blood Ecology and Biointelligence, Jinan Key Laboratory of Medical Cell Bioengineering, Science and Technology Innovation Center, The Fourth People\u2019s Hospital of Jinan Affiliated to Shandong Second Medical University","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shumin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Endoscopy Center, The Fourth People's Hospital of Jinan","place":["Jinan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,3]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.1007\/s00535-012-0605-0","article-title":"Multicenter analysis of fecal microbiota profiles in Japanese patients with Crohn's disease","volume":"47","author":"Andoh","year":"2012","journal-title":"J. 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Sci."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"4964","DOI":"10.1073\/pnas.1319114111","article-title":"Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in TMF\u2212\/\u2212 mice","volume":"111","author":"Bel","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"18933","DOI":"10.1073\/pnas.1007028107","article-title":"Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors","volume":"107","author":"Benson","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1017\/S0007114510001030","article-title":"Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects","volume":"104","author":"Benus","year":"2010","journal-title":"Br. J. Nutr."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"318","DOI":"10.3390\/ph19020318","article-title":"Diet and gut microbiota in inflammatory bowel disease: a clinical and nutritional perspective","volume":"19","author":"Bertin","year":"2026","journal-title":"Pharmaceuticals (Basel)"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"2645125","DOI":"10.1080\/19490976.2026.2645125","article-title":"A bile acid-GPBAR1 network supports anti-inflammatory and anti-fibrotic benefits of probiotics in colitis","volume":"18","author":"Biagioli","year":"2026","journal-title":"Gut Microbes"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1016\/j.cgh.2020.03.013","article-title":"Alterations in fecal microbiomes and serum metabolomes of fatigued patients with quiescent inflammatory bowel diseases","volume":"19","author":"Borren","year":"2021","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"555","DOI":"10.3389\/fimmu.2015.00555","article-title":"Mechanisms of microbe-host interaction in Crohn's disease: dysbiosis vs. pathobiont selection","volume":"6","author":"Butto","year":"2015","journal-title":"Front. Immunol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1111\/jgh.12592","article-title":"Imbalances of CD4(+) T-cell subgroups in Crohn's disease and their relationship with disease activity and prognosis","volume":"29","author":"Chao","year":"2014","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1128\/AEM.03301-15","article-title":"Host genetic control of the microbiota mediates the Drosophila nutritional phenotype","volume":"82","author":"Chaston","year":"2016","journal-title":"Appl. Environ. 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Bowel Dis."},{"key":"ref24","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":"ref25","doi-asserted-by":"publisher","first-page":"G1168","DOI":"10.1152\/ajpgi.00219.2004","article-title":"Butyrate specifically modulates MUC gene expression in intestinal epithelial goblet cells deprived of glucose","volume":"287","author":"Gaudier","year":"2004","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","article-title":"The treatment-naive microbiome in new-onset Crohn's disease","volume":"15","author":"Gevers","year":"2014","journal-title":"Cell Host Microbe"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.cell.2014.09.053","article-title":"Human genetics shape the gut microbiome","volume":"159","author":"Goodrich","year":"2014","journal-title":"Cell"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1136\/gutjnl-2015-311058","article-title":"Effects of enteral polymeric diet on gut microbiota in children with Crohn's disease","volume":"66","author":"Guinet-Charpentier","year":"2017","journal-title":"Gut"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.3748\/wjg.v10.i7.1069","article-title":"NOD2 3020insC frameshift mutation is not associated with inflammatory bowel disease in Chinese patients of Han nationality","volume":"10","author":"Guo","year":"2004","journal-title":"World J. 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Bowel Dis."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1578","DOI":"10.1136\/gutjnl-2013-306226","article-title":"Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn's disease and their unaffected siblings","volume":"63","author":"Hedin","year":"2014","journal-title":"Gut"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1136\/gutjnl-2014-308896","article-title":"Siblings of patients with Crohn's disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities","volume":"65","author":"Hedin","year":"2016","journal-title":"Gut"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"5201","DOI":"10.3748\/wjg.v22.i22.5201","article-title":"Faecalibacterium prausnitzii supernatant ameliorates dextran sulfate sodium induced colitis by regulating Th17 cell differentiation","volume":"22","author":"Huang","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"ref35","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":"ref36","doi-asserted-by":"publisher","first-page":"100084","DOI":"10.1016\/j.clinsp.2022.100084","article-title":"FOXP3 variants are independently associated with transforming growth factor \u03b21 plasma levels in female patients with inflammatory bowel disease","volume":"77","author":"Inoue","year":"2022","journal-title":"Clinics (Sao Paulo)"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1053\/gast.2002.34155","article-title":"Lack of common NOD2 variants in Japanese patients with Crohn's disease","volume":"123","author":"Inoue","year":"2002","journal-title":"Gastroenterology"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s13073-022-01099-7","article-title":"Crohn's disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome","volume":"14","author":"Jacobs","year":"2022","journal-title":"Genome Med."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"3258","DOI":"10.1128\/JCM.01396-12","article-title":"Microbial dysbiosis in pediatric patients with Crohn's disease","volume":"50","author":"Kaakoush","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref40","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 Med."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1038\/s41588-020-00763-1","article-title":"Large-scale association analyses identify host factors influencing human gut microbiome composition","volume":"53","author":"Kurilshikov","year":"2021","journal-title":"Nat. Genet."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1038\/nm.4102","article-title":"CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands","volume":"22","author":"Lamas","year":"2016","journal-title":"Nat. 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Hepatol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1038\/nature10208","article-title":"Intestinal homeostasis and its breakdown in inflammatory bowel disease","volume":"474","author":"Maloy","year":"2011","journal-title":"Nature"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"e39191","DOI":"10.1371\/journal.pone.0039191","article-title":"Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits","volume":"7","author":"McKnite","year":"2012","journal-title":"PLoS One"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1002\/ibd.22974","article-title":"IL-10R polymorphisms are associated with very-early-onset ulcerative colitis","volume":"19","author":"Moran","year":"2013","journal-title":"Inflamm. Bowel Dis."},{"key":"ref49","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 Biol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1111\/all.12549","article-title":"Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria","volume":"70","author":"Nylund","year":"2015","journal-title":"Allergy"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1097\/MPG.0000000000000302","article-title":"Exome sequencing identifies a novel FOXP3 mutation in a 2-generation family with inflammatory bowel disease","volume":"58","author":"Okou","year":"2014","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1558","DOI":"10.1101\/gr.194118.115","article-title":"Genetic and environmental control of host-gut microbiota interactions","volume":"25","author":"Org","year":"2015","journal-title":"Genome Res."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1016\/j.cell.2014.08.006","article-title":"Immunoglobulin a coating identifies colitogenic bacteria in inflammatory bowel disease","volume":"158","author":"Palm","year":"2014","journal-title":"Cell"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"e39242","DOI":"10.1371\/journal.pone.0039242","article-title":"Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease","volume":"7","author":"Papa","year":"2012","journal-title":"PLoS One"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"6548","DOI":"10.1073\/pnas.1302837110","article-title":"Diversity and heritability of the maize rhizosphere microbiome under field conditions","volume":"110","author":"Peiffer","year":"2013","journal-title":"Proc. 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Rep."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"1681","DOI":"10.1136\/gutjnl-2015-311004","article-title":"Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD","volume":"65","author":"Sabino","year":"2016","journal-title":"Gut"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"34","DOI":"10.3109\/00365521.2014.966320","article-title":"Contentious host-microbiota relationship in inflammatory bowel disease--can foes become friends again?","volume":"50","author":"Satokari","year":"2015","journal-title":"Scand. J. Gastroenterol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1136\/gutjnl-2015-309333","article-title":"Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence","volume":"65","author":"Schaubeck","year":"2016","journal-title":"Gut"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/0016-5085(92)91094-k","article-title":"Effect of butyrate enemas on the colonic mucosa in distal ulcerative colitis","volume":"103","author":"Scheppach","year":"1992","journal-title":"Gastroenterology"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"e108503","DOI":"10.1371\/journal.pone.0108503","article-title":"The NOD2 p.Leu1007fsX1008 mutation (rs2066847) is a stronger predictor of the clinical course of Crohn's disease than the FOXO3A intron variant rs12212067","volume":"9","author":"Schnitzler","year":"2014","journal-title":"PLoS One"},{"key":"ref64","doi-asserted-by":"publisher","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":"Infect. 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