Microbial Immunomodulatory Function is Altered in Inflammatory Bowel Disease Independent of Microbial Composition

Abstract

Inflammatory bowel diseases (IBD) are chronic and relapsing immune-mediated conditions in which the NF-{kappa}B and STAT3 signalling pathways play central roles in pathogenesis. While gut microbiome dysbiosis is well described in IBD, its functional consequences, particularly microbial immunomodulatory function (MIF) remain poorly defined. Here, we integrated functional assays with metagenomic profiling to characterise microbiome-driven immune modulation in IBD. Faecal water from non-IBD controls and IBD patients was assessed using NF-{kappa}B and STAT3 reporter systems, alongside high-throughput screening of 2,820 bacterial isolates (94 per subject). Despite minimal differences in overall microbial composition, faecal water from patients with ulcerative colitis (UC) and Crohns disease (CD) significantly increased NF-{kappa}B activity under both basal and TNF-stimulated conditions. Non-IBD controls harboured a higher proportion of suppressive bacterial isolates (21.52%) compared to UC (5.64%) and CD (2.45%), whereas activating isolates were enriched in IBD (UC: 34.47%; CD: 39.36% vs. non-IBD: 5.35%). Similar trends were observed for IL-23-mediated STAT3 activation. Integration of metagenomic and pathway-level analyses identified 24 KEGG pathways associated with inflammatory signalling and faecal lipocalin-2, as well as amino acid, carbohydrate, lipid, cofactor, and nucleotide metabolism. These findings demonstrate that the IBD microbiome is functionally reprogrammed toward pro-inflammatory activity, independent of compositional changes. Defining patient-specific MIF profiles may provide a framework for precision microbiome-based therapeutic strategies in IBD.