Multi-omic remodeling of urine-exposed ileal mucosa after ileocystoplasty.

856 Background: Ileal segments are widely used for urinary diversion, yet long-term dysfunction (increased residual urine volume, low compliance, mucus burden, infections) persists. How chronic urine exposure remodels the mucosal microenvironment across histology, microbiome, and cellular programs remain unclear. Methods: Rat ileocystoplasty with assessments at 1 week, 1 month, and 6 months. Ultrasound measured reservoir size; In vitro length by ruler. H Masson quantified collagen fraction and total muscle thickness (blinded review). 16S rRNA sequencing at 1 month (ileum vs urine-exposed). Single-cell RNA-seq at 6 months (bladder/ileum/urine-exposed ileum). Statistics in R. Results: At 6 months, ileal segment length increased from 1.25 cm (1 week) to 1.62 cm (Δ 0.37 cm, +29.6%; p < 0.05). Goblet cells per 100 nuclei declined from 43 (normal) to 10 at 1 month and 9 at 6 months (−76.7%, −79.1%; p < 0.05 to < 0.01). Collagen fraction was 0.16 (normal), 0.17 (1 month; not significant), and 0.27 (6 months; Δ +0.11, +68.8%; p < 0.05). Total muscle thickness measured 1.12 at 1 month (vs 1.00; not significant) and 0.37 at 6 months (−63.0% vs normal; −67.0% vs 1 month; p < 0.001). At 1 month, α-diversity decreased (Chao1 22 vs 45, −51.1%; Simpson 0.705 vs 0.765, Δ −0.060; Shannon 2.05 vs 2.75, Δ −0.70) without β-diversity separation (PERMANOVA p = 0.304; PC1 39.9%, PC2 23.2%). Communities showed fewer spore-formers and Romboutsia, with Propionibacteriales enrichment (LEfSe LDA 3.0). Random forest ranked Cutibacterium acnes highest (MeanDecreaseGini 0.28). Single-cell RNA-seq at 6 months showed epithelial cells 70%→30% and fibroblasts 15%→55%, with B/T cells nearly absent. Pseudobulk correlations indicated urine-exposed epithelium was closer to bladder than native ileum (r = 0.80 vs 0.55; similar trends for fibroblast and smooth muscle). Marker programs supported mechanosensory–serotonergic rewiring with Cga, Slc6a4, Piezo1, Piezo2 up and Tph1 down; lineage specificity included Slc6a4 19% in epithelium, Piezo1 20% in neurons, and Piezo2 15% in endothelium (P < 0.001). Conclusions: Chronic urine exposure drives reservoir enlargement with fibrosis, goblet-cell loss, and microbiome simplification, alongside bladder-like and fibrosis cellular programs (extracellular matrix, Hippo activation). These data provide a new perspective and theoretical basis for the postoperative management of orthotopic ileal neobladder.