{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:22:19Z","timestamp":1787008939537,"version":"build-2736575974"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T00:00:00Z","timestamp":1757635200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Right on Time","award":["WO 19-25"],"award-info":[{"award-number":["WO 19-25"]}]},{"name":"The Dutch Digestive Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background and Aims<\/jats:title>\n                    <jats:p>Microbiome studies reveal distinct microbial differences in inflammatory bowel disease (IBD), indicating its potential role in pathophysiology and as a noninvasive diagnostic biomarker. This study aims to profile the gut microbiome in children with IBD, compared to both healthy controls (HC) and controls with gastrointestinal symptoms (CGI), and to assess the potential of microbiome profiles as noninvasive diagnostic markers for de novo treatment-na\u00efve pediatric IBD, and as early predictive markers for therapy response.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analyzed baseline fecal samples and clinical data from 103 therapy-na\u00efve children with IBD, 75 CGI, and 356 age and sex matched HC. Metagenomic sequencing was performed, and prediction models assessed diagnostic potential and prediction of induction therapy response at 3 months.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Alpha diversity progressively decreased from HC to CGI (P\u2009&amp;lt;\u2009.001) and decreased even further in IBD patients (P\u2009=\u2009.0056). Beta diversity analysis showed significant clustering differences (P\u2009&amp;lt;\u2009.001, R2 = 0.045). Differential abundance analysis revealed 116 species differing between HC and IBD, and 30 species between CGI and IBD. Prediction models based on microbiome features accurately distinguished IBD from HC (area under the curve [AUC]\u2009=\u20090.96) and from CGI (AUC\u2009=\u20090.71). However, these models were outperformed by clinical features, such as fecal calprotectin. Microbiome-based prediction of response to induction therapy in general showed limited accuracy (AUC\u2009=\u20090.63), as well as for response to nutritional induction therapy (AUC\u2009=\u20090.67).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We observed profound gut microbiome differences between de novo, therapy-na\u00efve pediatric IBD patients and controls. While microbiome profiles hold promise for improving diagnostic precision, their predictive value for therapy response seems limited.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ibd\/izaf184","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T11:53:46Z","timestamp":1753271626000},"page":"207-219","source":"Crossref","is-referenced-by-count":4,"title":["Metagenomic Sequencing Reveals Distinct Gut Microbiome Profiles in Therapy-Na\u00efve de Novo Pediatric Inflammatory Bowel Disease"],"prefix":"10.1093","volume":"32","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-4335-0100","authenticated-orcid":false,"given":"Eva","family":"Vermeer","sequence":"first","affiliation":[{"name":"Department of Pediatric Gastroenterology and Hepatology, Emma Children\u2019s Hospital, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, 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Groningen,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0417-7121","authenticated-orcid":false,"given":"Jasmijn Z","family":"Jagt","sequence":"additional","affiliation":[{"name":"Department of Pediatric Gastroenterology and Hepatology, Emma Children\u2019s Hospital, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3454-0094","authenticated-orcid":false,"given":"Robert","family":"de Jonge","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9406-9188","authenticated-orcid":false,"given":"Marc A","family":"Benninga","sequence":"additional","affiliation":[{"name":"Department of Pediatric Gastroenterology and Hepatology, Emma Children\u2019s Hospital, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2119-0539","authenticated-orcid":false,"given":"Ranko","family":"Gacesa","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, University Medical Centre Groningen , Groningen,","place":["The Netherlands"]},{"name":"Department of Genetics, University Medical Centre Groningen , Groningen,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7928-7371","authenticated-orcid":false,"given":"Rinse K","family":"Weersma","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, University Medical Centre Groningen , Groningen,","place":["The Netherlands"]},{"name":"Department of Genetics, University Medical Centre Groningen , Groningen,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8357-9887","authenticated-orcid":false,"given":"Nanne K H","family":"de Boer","sequence":"additional","affiliation":[{"name":"Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Department of Gastroenterology and Hepatology, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7556-5896","authenticated-orcid":false,"given":"Tim G J","family":"de Meij","sequence":"additional","affiliation":[{"name":"Department of Pediatric Gastroenterology and Hepatology, Emma Children\u2019s Hospital, Amsterdam University Medical Centre , Amsterdam,","place":["The Netherlands"]},{"name":"Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Research Institute, 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