{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:58:57Z","timestamp":1785419937999,"version":"3.56.0"},"posted":{"date-parts":[[2025,5,10]]},"group-title":"Microbiology","reference-count":44,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,10]],"date-time":"2025-05-10T00:00:00Z","timestamp":1746835200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["DK134043"],"award-info":[{"award-number":["DK134043"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["DK108901"],"award-info":[{"award-number":["DK108901"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["AI162787"],"award-info":[{"award-number":["AI162787"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["AI124255"],"award-info":[{"award-number":["AI124255"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/04cheq228","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,10]]},"abstract":"<jats:title>Summary<\/jats:title>\n                <jats:p>\n                  Alterations in the gut microbiota, known as gut dysbiosis, are associated with inflammatory bowel disease (IBD). There is a need for model systems that can recapitulate the IBD gut microbiome to better understand the mechanistic impact of differences in microbiota composition and its functional consequences in a controlled laboratory setting. To this end, we introduced fecal samples from patients with Crohn\u2019s disease (CD) and ulcerative colitis (UC), as well as from healthy control subjects, to miniature bioreactor arrays (MBRAs) and analyzed the microbial communities over time. We then performed two functional assessments. First, we evaluated the colitogenic potential of the CD microbiotas in genetically susceptible germ-free IL-10-deficient mice and found that colitogenic capacity was preserved in a bioreactor-cultivated CD microbiota. Second, we tested impaired colonization resistance against\n                  <jats:italic>Clostridioides difficile<\/jats:italic>\n                  in UC microbiotas using the MBRA system and found that UC microbiotas were innately susceptible to\n                  <jats:italic>C. difficile<\/jats:italic>\n                  colonization while healthy microbiotas were resistant, consistent with what is seen clinically. Overall, our results demonstrate that IBD microbiotas perform comparably to healthy donor microbiotas in the MBRA system, successfully recapitulating microbial structure while preserving IBD-specific functional characteristics. These findings establish a foundation for further mechanistic research into the IBD microbiota using MBRAs.\n                <\/jats:p>","DOI":"10.1101\/2025.05.09.653173","type":"posted-content","created":{"date-parts":[[2025,5,11]],"date-time":"2025-05-11T02:05:23Z","timestamp":1746929123000},"source":"Crossref","is-referenced-by-count":3,"title":["Miniature bioreactor arrays for modeling functional and structural dysbiosis in inflammatory bowel disease"],"prefix":"10.64898","author":[{"given":"Kira L.","family":"Newman","sequence":"first","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra K.","family":"Standke","sequence":"additional","affiliation":[{"name":"Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabrielle","family":"James","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberly C.","family":"Vendrov","sequence":"additional","affiliation":[{"name":"Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naohiro","family":"Inohara","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid L.","family":"Bergin","sequence":"additional","affiliation":[{"name":"The Unit for Laboratory Animal Medicine, University of Michigan Medical, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter D.R.","family":"Higgins","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishna","family":"Rao","sequence":"additional","affiliation":[{"name":"Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent B.","family":"Young","sequence":"additional","affiliation":[{"name":"Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"},{"name":"Department of Microbiology and Immunology, University of Michigan, Ann Arbor, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1980-4178","authenticated-orcid":false,"given":"Nobuhiko","family":"Kamada","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, USA"},{"name":"Department of Pathology, University of Michigan, Ann Arbor, USA"},{"name":"WPI Immunology Frontier Research Center, The University of Osaka, Suita, Japan"},{"name":"Center for Infectious Disease Education and Research, The University of Osaka, Suita, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041121192639000_2025.05.09.653173v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2017.4"},{"key":"2026041121192639000_2025.05.09.653173v1.2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.54.2.354-358.1986"},{"key":"2026041121192639000_2025.05.09.653173v1.3","doi-asserted-by":"publisher","DOI":"10.1007\/s002489900072"},{"key":"2026041121192639000_2025.05.09.653173v1.4","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkg267"},{"key":"2026041121192639000_2025.05.09.653173v1.5","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dki321"},{"key":"2026041121192639000_2025.05.09.653173v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkn358"},{"key":"2026041121192639000_2025.05.09.653173v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dku324"},{"key":"2026041121192639000_2025.05.09.653173v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks529"},{"key":"2026041121192639000_2025.05.09.653173v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkv108"},{"key":"2026041121192639000_2025.05.09.653173v1.10","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-6361-4_18"},{"key":"2026041121192639000_2025.05.09.653173v1.11","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-015-0106-5"},{"key":"2026041121192639000_2025.05.09.653173v1.12","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00387-20"},{"key":"2026041121192639000_2025.05.09.653173v1.13","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00996-6"},{"key":"2026041121192639000_2025.05.09.653173v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-65253-0"},{"key":"2026041121192639000_2025.05.09.653173v1.15","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.01049-24"},{"key":"2026041121192639000_2025.05.09.653173v1.16","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkq345"},{"key":"2026041121192639000_2025.05.09.653173v1.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2018.08.003"},{"key":"2026041121192639000_2025.05.09.653173v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-020-0764-0"},{"key":"2026041121192639000_2025.05.09.653173v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2013.89"},{"key":"2026041121192639000_2025.05.09.653173v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-018-0324-z"},{"key":"2026041121192639000_2025.05.09.653173v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.07.008"},{"key":"2026041121192639000_2025.05.09.653173v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2018.12.015"},{"key":"2026041121192639000_2025.05.09.653173v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcmgh.2016.02.003"},{"key":"2026041121192639000_2025.05.09.653173v1.24","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-309333"},{"key":"2026041121192639000_2025.05.09.653173v1.25","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2017.04.044"},{"key":"2026041121192639000_2025.05.09.653173v1.26","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2025.2476570"},{"key":"2026041121192639000_2025.05.09.653173v1.27","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.021170-0"},{"key":"2026041121192639000_2025.05.09.653173v1.28","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2014-308341"},{"key":"2026041121192639000_2025.05.09.653173v1.29","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2265028"},{"key":"2026041121192639000_2025.05.09.653173v1.30","doi-asserted-by":"publisher","DOI":"10.1038\/s41575-025-01041-3"},{"key":"2026041121192639000_2025.05.09.653173v1.31","unstructured":"On the Protection of Animals Used for Scientific Purposes, (2010)."},{"key":"2026041121192639000_2025.05.09.653173v1.32","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2024-333925"},{"key":"2026041121192639000_2025.05.09.653173v1.33","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02928-22"},{"key":"2026041121192639000_2025.05.09.653173v1.34","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202400078"},{"key":"2026041121192639000_2025.05.09.653173v1.35","doi-asserted-by":"publisher","DOI":"10.1007\/s10620-025-08946-8"},{"key":"2026041121192639000_2025.05.09.653173v1.36","doi-asserted-by":"publisher","DOI":"10.14309\/ajg.0000000000002584"},{"key":"2026041121192639000_2025.05.09.653173v1.37","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2015.03.045"},{"key":"2026041121192639000_2025.05.09.653173v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0209-9"},{"key":"2026041121192639000_2025.05.09.653173v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"2026041121192639000_2025.05.09.653173v1.40","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbiotec.2017.06.1198"},{"key":"2026041121192639000_2025.05.09.653173v1.41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1209"},{"key":"2026041121192639000_2025.05.09.653173v1.42","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"2026041121192639000_2025.05.09.653173v1.43","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0470-z"},{"key":"2026041121192639000_2025.05.09.653173v1.44","doi-asserted-by":"publisher","DOI":"10.1128\/mSphereDirect.00698-18"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.05.09.653173","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:10:11Z","timestamp":1782277811000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.05.09.653173"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,10]]},"references-count":44,"URL":"https:\/\/doi.org\/10.1101\/2025.05.09.653173","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1080\/19490976.2025.2604875","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,5,10]]},"subtype":"preprint"}}