{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T04:23:07Z","timestamp":1784694187000,"version":"3.55.0"},"reference-count":50,"publisher":"OAE Publishing Inc.","issue":"1","content-domain":{"domain":["oaepublish.com"],"crossmark-restriction":false},"short-container-title":["Microbiome Res Rep."],"abstract":"<jats:p>Background: Inflammatory bowel diseases (IBDs) are complex conditions marked by chronic inflammation in the gastrointestinal tract. Traditional classification separates IBD into Crohn\u2019s disease and ulcerative colitis, but this division may not fully capture disease heterogeneity. Here, we examine whether microbiome-driven subtyping can describe novel clinical IBD phenotypes. To achieve this, we applied unsupervised clustering to fecal microbiota profiles from the population-based Inflammatory Bowel Disease in South-Eastern Norway III (IBSEN III) cohort.<\/jats:p>\n                  <jats:p>Methods: A Gaussian Mixture Model (GMM) was used to cluster participants with IBD based on microbiome composition and examine associations between clusters and clinical outcomes, including inflammatory markers and disease severity during the first year after inclusion.<\/jats:p>\n                  <jats:p>Results: Three microbiome-based clusters were identified: CLO (dominated by Clostridia UCG-014), ALF (Agathobacter, Lachnoclostridium, and Faecalibacterium), and RUM (Ruminococcus gnavus). Participants in the RUM cluster had a higher risk of future severe disease than those in the CLO cluster, even among participants with remission-to-mild disease at inclusion (21% vs. 6%, P &lt; 0.00001). This association could not be explained by antibiotic use or baseline disease severity. Cluster membership alone performed comparably to fecal calprotectin in distinguishing severe disease, and a combined model significantly improved accuracy (P &lt; 0.0001).<\/jats:p>\n                  <jats:p>Conclusion: Our findings demonstrate a connection between microbiome composition and the risk of severe disease development, which is partly independent of inflammation levels at the time of sampling. Microbiome-informed subgrouping could lead to more personalized treatment strategies. Further validation is needed to determine the clinical utility of these clusters.<\/jats:p>","DOI":"10.20517\/mrr.2025.96","type":"journal-article","created":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:51:03Z","timestamp":1774317063000},"update-policy":"https:\/\/doi.org\/10.20517\/oae.crossmark.policy","source":"Crossref","is-referenced-by-count":1,"title":["Bacterial clusters are associated with the risk of severe disease progression in inflammatory bowel disease irrespective of conventional disease categories"],"prefix":"10.20517","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0156-9875","authenticated-orcid":true,"given":"Simen Hyll","family":"Hansen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-6503-7677","authenticated-orcid":true,"given":"Niharika","family":"Bhattacharjee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chang","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3053-0267","authenticated-orcid":true,"given":"Maria Gjerstad","family":"Maseng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4329-1659","authenticated-orcid":true,"given":"Olle","family":"Grann\u00f6","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6814-6151","authenticated-orcid":true,"given":"Corinna","family":"Bang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5680-4313","authenticated-orcid":true,"given":"Christine","family":"Olbj\u00f8rn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4158-372X","authenticated-orcid":true,"given":"G\u00f8ri","family":"Perminow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7193-7069","authenticated-orcid":true,"given":"J\u00f8rgen","family":"Valeur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5615-7141","authenticated-orcid":true,"given":"May-Bente","family":"Bengtson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7841-608X","authenticated-orcid":true,"given":"Svein Oskar","family":"Frigstad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0283-2789","authenticated-orcid":true,"given":"Svend","family":"Andersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-4933-5580","authenticated-orcid":true,"given":"Tone Bergene","family":"Aabrekk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1576-5298","authenticated-orcid":true,"given":"Trond Espen","family":"Detlie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1530-5811","authenticated-orcid":true,"given":"Andre","family":"Franke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0876-8634","authenticated-orcid":true,"given":"Vendel A.","family":"Kristensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0122-7234","authenticated-orcid":true,"given":"Jonas","family":"Halfvarson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0104-465X","authenticated-orcid":true,"given":"Marte Lie","family":"H\u00f8ivik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ravishankar K.","family":"Iyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5900-8096","authenticated-orcid":true,"given":"Johannes","family":"Hov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"8410","published-online":{"date-parts":[[2026,3,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2020.09.056"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3390\/nu12040944"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2013.80"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1128\/iai.00302-24"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2021.12.246"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(15)00465-1"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1002\/ueg2.12485"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1002\/ueg2.12338"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1093\/ibd\/izaf060"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)30317-3"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1080\/00365521.2021.1922746"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1136\/gut.43.1.29"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(80)92767-1"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-6"},{"key":"B15","unstructured":"BBTools software package. Available from http:\/\/sourceforge. net\/projects\/bbmap. [accessed 17 March 2026]"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0185056"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00191-16"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0209-9"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0470-z"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.5555\/1593511"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1029\/2021ea001680"},{"key":"B24","unstructured":"R Core Team. R: A language and environment for statistical computing; 2021. Vienna: R Foundation for Statistical Computing; 2021. Available from https:\/\/cran.rstudio.com\/manuals.html. [accessed 17 March 2026]"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1002\/wics.147"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1016\/j.cgh.2015.06.001"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1016\/j.crohns.2013.09.010"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1111\/apt.18154"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1982.tb01195.x"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02224"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1904099116"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.2147\/ceg.s186235"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.3390\/genes11111245"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuad014"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1002\/ibd.21625"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.13205"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2020-321106"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2269-x"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.09.013"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2023.11.304"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0483-9"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1002\/acn3.51004"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines10010016"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1007\/s10482-018-1104-y"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01199-3"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002863"},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.1038\/nature24460"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1038\/nature09944"},{"key":"B49","unstructured":"Modulation of human gut microbiota by linear and branched fructooligosaccharides in an in vitro colon model (TIM-2)"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2021.1987783"}],"container-title":["Microbiome Research Reports"],"original-title":[],"link":[{"URL":"https:\/\/www.oaepublish.com\/articles\/mrr.2025.96","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.oaepublish.com\/articles\/mrr.2025.96","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:51:07Z","timestamp":1774317067000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.oaepublish.com\/articles\/mrr.2025.96"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,18]]},"references-count":50,"journal-issue":{"issue":"1"},"URL":"https:\/\/doi.org\/10.20517\/mrr.2025.96","relation":{},"ISSN":["2771-5965"],"issn-type":[{"value":"2771-5965","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,18]]}}}