Abstract
Altered gut microbiota‒metabolite interactions may result in intestinal inflammation severity variation in Crohn's disease (CD). Magnetic resonance enterography (MRE) advances anti-inflammatory strategy development. We aimed to identify inflammation-related multiomics factors and MRE interactions for CD management, analyzing 425 CD patients and 42 healthy controls undergoing MRE, ileocolonoscopy, and fecal/blood sampling (microbiota/metabolite analyses), with intestinal inflammation categorized by MRE and ileocolonoscopy. Ruminococcus species were enriched in CD patients versus healthy controls, while Pseudomonas and Staphylococcus dominated moderate-severe versus no-mild inflammation groups, suggesting inflammation-level associations. Ruminococcus gauvreauii suppressed intestinal inflammation by regulating serum PC(O-34:3), ePE(38:6), and ceramides (all p < 0.05). Serum N-acetylneuraminic acid and guanidinoacetic acid correlated with intestinal morphological changes (e.g., MRE-detectable effusion and wall thickness) and inflammation severity (P (ACME) < 0.05). A link was established between microscopic microbiota-metabolite markers and macroscopic imaging of inflammatory features, which could offer valuable insights into inflammation management.