{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:48:48Z","timestamp":1753890528511,"version":"3.41.2"},"reference-count":31,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"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. Cell. Infect. Microbiol."],"abstract":"<jats:p>Crohn\u2019s disease (CD) is associated with changes in the microbiome. The role of these changes and their precise association with disease course and activity remain ambiguous. In this prospective single-center study, the mucosal microbiome of surgical CD and non-CD patients was compared at the time of surgery. Microbial analyses were individually performed for ileal and colonic tissue samples obtained during surgery using 16S-rRNA-gene amplicon sequencing. Three groups out of the 46 included patients were formed: 1) a study group of CD of patients who received ileocecal resection due to CD involvement (CD study, n=10); 2) a control group of non-CD of patients who received intestinal resection due to indications other than CD (non-CD control, n=27); and 3) a second control group of CD who underwent resection of the intestine not affected by CD (CD non-affected control, n=9). Species richness and Shannon diversity were not different between all formed groups and regions analyzed (p&amp;gt;0.05). Several significant taxonomic differences were seen at the phylum-, order-, and genus-levels between the formed groups, such as a decrease of <jats:italic>Firmicutes<\/jats:italic> (phylum-level) and an increase of <jats:italic>Bacteroides<\/jats:italic> and <jats:italic>Escherichia\/Shigella\/Pseudescherichia<\/jats:italic> (genus-level) in CD study \u2013 colon vs. the non-CD control \u2013 colon (p \u2264 0.05). The CD non-affected control presented the largest amount of differentially abundant taxa in comparison to the other groups. These results underline that CD is accompanied by changes in affected and non-affected intestinal regions compared to non-CD controls. This study contributes the mucosal microbiome of a well-defined subset of surgical CD patients without confounding aspects of the fecal microbiome or regional microbial differences to the existing literature.<\/jats:p>","DOI":"10.3389\/fcimb.2023.1324668","type":"journal-article","created":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T04:38:46Z","timestamp":1705034326000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Mucosal microbiome of surgically treated terminal ileal Crohn\u2019s disease"],"prefix":"10.3389","volume":"13","author":[{"given":"Florian N.","family":"Loch","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carsten","family":"Kamphues","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Menzel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rolf","family":"Schwarzer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katharina","family":"Beyer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Schineis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,1,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"977","DOI":"10.3390\/microorganisms9050977","article-title":"Systematic review: the gut microbiome and its potential clinical application in inflammatory bowel disease","volume":"9","author":"Aldars-Garcia","year":"2021","journal-title":"Microorganisms"},{"key":"B2","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1016\/j.dld.2018.11.021","article-title":"Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota","volume":"51","author":"Altomare","year":"2019","journal-title":"Digestive Liver Disease."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1093\/ibd\/izaa071","article-title":"Microbiome-based biomarkers for IBD","volume":"26","author":"Ananthakrishnan","year":"2020","journal-title":"Inflammatory Bowel Diseases."},{"key":"B4","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\u2019s dis-ease","volume":"47","author":"Andoh","year":"2012","journal-title":"J. gastroenterology."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.1053\/j.gastro.2021.01.030","article-title":"Healthy cotwins share gut microbiome signatures with their inflammatory bowel disease twins and unrelated patients","volume":"160","author":"Brand","year":"2021","journal-title":"Gastroenterology"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf."},{"key":"B7","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1136\/gutjnl-2020-321106","article-title":"Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study","volume":"70","author":"Clooney","year":"2021","journal-title":"Gut"},{"key":"B8","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1053\/j.gastro.2011.01.055","article-title":"Epidemiology and natural history of inflammatory bowel diseases","volume":"140","author":"Cosnes","year":"2011","journal-title":"Gastroenterology"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-230X-13-131","article-title":"Association of gut microbiota with post-operative clinical course in Crohn\u2019s disease","volume":"13","author":"Dey","year":"2013","journal-title":"BMC gastroenterology."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/mBio.02120-17","article-title":"Fecal microbiota signa-tures are associated with response to ustekinumab therapy among Crohn\u2019s disease patients","volume":"9","author":"Doherty","year":"2018","journal-title":"MBio"},{"key":"B11","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. 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