{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,13]],"date-time":"2026-09-13T05:05:00Z","timestamp":1789275900660,"version":"build-2803163510"},"reference-count":94,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Italian Ministry of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Inflammatory bowel diseases (IBD) arise from complex interactions among the immune system, intestinal microbiota, and host metabolism. However, how different intestinal compartments contribute to disease activity and phenotype in paediatric IBD remains incompletely understood. Children with Crohn\u2019s disease (CD) and ulcerative colitis (UC) were stratified according to disease phenotype and inflammatory activity to distinguish disease-associated signatures from dynamic inflammatory processes. We performed an integrated multi-omics analysis combining luminal and mucosal bacterial and fungal metataxonomy, faecal metabolomics, and microbial- and host-derived biomarkers, including IgA, lysozyme, bile acids, and urinary indican. Luminal bacterial communities largely preserved their ecological structure, while disease activity was associated with coordinated taxonomic, metabolic, and interactional remodelling. These changes were accompanied by alterations in microbial metabolites and host biomarkers consistent with altered fermentation, proteolytic metabolism, and immune\u2013metabolic coupling. In contrast, phenotype-associated ecological differences were more evident in the mucosal compartment, particularly within the fungal community, whereas mucosal bacterial changes were more limited. Together, these findings suggest that luminal and mucosal host\u2013microbiome interactions provide complementary information on inflammatory activity and disease phenotype in paediatric IBD, highlighting the value of integrated multi-omic approaches to investigate compartment-specific host\u2013microbiome interactions in paediatric IBD.<\/jats:p>","DOI":"10.3390\/microorganisms14092027","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T13:29:29Z","timestamp":1789133369000},"page":"2027","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Multi-Omics Reveals Complementary Luminal and Mucosal Host\u2013Microbiome Interactions Associated with Disease Activity and Phenotype in Paediatric Inflammatory Bowel Disease"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8976-9013","authenticated-orcid":false,"given":"Francesca","family":"Toto","sequence":"first","affiliation":[{"name":"Research Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00165 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pamela","family":"Vernocchi","sequence":"additional","affiliation":[{"name":"Research Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00165 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"De Angelis","sequence":"additional","affiliation":[{"name":"Gastroenterology, Digestive Endoscopy and Nutrition Unit, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00165 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Isoldi","sequence":"additional","affiliation":[{"name":"Pediatric Gastroenterology Unit, Santobono Pediatric Hospital, 80122 Naples, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salvatore","family":"Cucchiara","sequence":"additional","affiliation":[{"name":"Pediatric Gastroenterology and Liver Unit, Maternal Child Health Department, Sapienza University of Rome, 00161 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Stronati","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0134-2830","authenticated-orcid":false,"given":"Lorenza","family":"Putignani","sequence":"additional","affiliation":[{"name":"Department of Life Science, Health, and Health Professions, Link Campus University, 00165 Rome, Italy"},{"name":"Unit of Microbiomics and Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00146 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4204-4736","authenticated-orcid":false,"given":"Federica","family":"Del Chierico","sequence":"additional","affiliation":[{"name":"Research Unit of Microbiome, Bambino Ges\u00f9 Children\u2019s Hospital, IRCCS, 00165 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/s41590-025-02197-5","article-title":"Gene-Environment Interactions Shape the Host-Microbial Interface in Inflammatory Bowel Disease","volume":"26","author":"Cadwell","year":"2025","journal-title":"Nat. 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