{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:07:04Z","timestamp":1772168824097,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.108810.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,4]],"date-time":"2023-01-04T00:00:00Z","timestamp":1672790400000}}],"reference-count":13,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,1,4]],"date-time":"2023-01-04T00:00:00Z","timestamp":1672790400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011684","name":"Crohn's and Colitis Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011684","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gutsy Kids Fund"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    Patients with Crohn\u2019s disease (CD) have an altered intestinal microbiome, which may facilitate novel diagnostic testing. However, accuracy of microbiome classification models across geographic regions may be limited. Therefore, we sought to examine geographic variation in the microbiome of patients with CD from North America and test the performance of a machine learning classification model across geographic regions.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    The RISK cohort included 447 pediatric patients with CD and 221 non-inflammatory bowel disease controls from across North America. Terminal ileum, rectal and fecal samples were obtained prior to treatment for microbiome analysis. We divided study sites into 3 geographic regions to examine regional microbiome differences. We trained and tested the performance of a machine learning classification model across these regions.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    No differences were seen in the mucosal microbiome of patients with CD across regions or in either the fecal or mucosal microbiomes of controls. Machine learning classification algorithms for patients with CD performed well across regions (area under the receiver operating characteristic curve [AUROC] range of 0.85-0.91) with the best results from terminal ileum.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions:<\/ns4:bold>\n                    This study demonstrated the feasibility of microbiome based diagnostic testing in pediatric patients with CD within North America, independently from regional influences.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.108810.2","type":"journal-article","created":{"date-parts":[[2023,1,4]],"date-time":"2023-01-04T11:15:05Z","timestamp":1672830905000},"page":"156","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Mucosal microbiome is predictive of pediatric Crohn\u2019s disease across geographic regions in North America"],"prefix":"10.12688","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2318-3714","authenticated-orcid":false,"given":"Rajesh","family":"Shah","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristi","family":"Hoffman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lee","family":"Denson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Subramaniam","family":"Kugathasan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4146-1335","authenticated-orcid":false,"given":"Richard","family":"Kellermayer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2023,1,4]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"843-854","DOI":"10.1016\/j.immuni.2014.05.013","article-title":"Inflammatory Bowel Disease as a Model for Translating the Microbiome.","volume":"40","author":"C Huttenhower","year":"2014","journal-title":"Immunity."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"813-822","DOI":"10.1136\/gutjnl-2016-313235","article-title":"A microbial signature for Crohn\u2019s disease.","volume":"66","author":"V Pascal","year":"2017","journal-title":"Gut."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"382-392","DOI":"10.1016\/j.chom.2014.02.005","article-title":"The Treatment-Naive Microbiome in New-Onset Crohn\u2019s Disease.","volume":"15","author":"D Gevers","year":"2014","journal-title":"Cell Host Microbe."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"655-662","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.","volume":"569","author":"J Lloyd-Price","year":"2019","journal-title":"Nature."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1532-1535","DOI":"10.1038\/s41591-018-0164-x","article-title":"Regional variation limits applications of healthy gut microbiome reference ranges and disease models.","volume":"24","author":"Y He","year":"2018","journal-title":"Nat. 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Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"489-500","DOI":"10.1016\/j.chom.2015.09.008","article-title":"Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn\u2019s Disease.","volume":"18","author":"J Lewis","year":"2015","journal-title":"Cell Host Microbe."},{"key":"ref13","doi-asserted-by":"publisher","author":"S Rajesh","year":"2022","DOI":"10.6084\/m9.figshare.21727862.v1"}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/11-156\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/11-156\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/11-156\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,20]],"date-time":"2023-01-20T09:45:14Z","timestamp":1674207914000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/11-156\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,4]]},"references-count":13,"URL":"https:\/\/doi.org\/10.12688\/f1000research.108810.2","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.142172.r158956","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.142172.r158957","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.142172.r158957","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.142172.r158956","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,4]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/11-156\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.142172.r158957, Jonathan Braun, F. Widjaja IBD Institute, Cedars Sinai Medical Center, Los Angeles, CA, 90095-1732, USA, 05 Jan 2023, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/11-156\/v2#referee-response-158957","order":0,"name":"referee-response-158957","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.142172.r158956, Ranko Gacesa, Department of Gastroenterology and Hepatology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands, 20 Jan 2023, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/11-156\/v2#referee-response-158956","order":1,"name":"referee-response-158956","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"RK was supported by philanthropic donations through the Gutsy Kids Fund led by the Brock Wagner and Klaasmeyer families. The RISK consortium was supported by the Crohn\u2019s and Colitis Foundation.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}