Ileal microbial and luminal biomarker dysbiosis precede acute cellular rejection following intestinal transplantation.

The role of gut microbiota in acute cellular rejection (ACR) after intestinal transplantation (ITx) remains poorly defined. This study investigated whether ileal microbial dysbiosis precedes ACR and is associated with barrier injury. We conducted a longitudinal and cross-sectional analysis of 16 ITx recipients. Ileal effluents were profiled via 16S ribosomal RNA gene sequencing, short-chain fatty acid quantification, complemented by graft histopathology and assessment of systemic biomarkers of barrier dysfunction. Eight recipients (50.0%) developed biopsy-proven ACR (median 25.5 days post-ITx). Recipients who developed ACR exhibited early and sustained microbial divergence, characterized by Enterobacteriaceae dominance and loss of diversity. Samples collected at a median of 7.0 days before ACR diagnosis revealed a prerejection dysbiotic state marked by reduced microbial diversity, diminished short-chain fatty acid levels, enrichment of Enterobacteriaceae, and depletion of Enterococcaceae and Bacteroidaceae. Functional profiling indicated pre-ACR upregulation of bacterial motility, flagellar assembly, and lipopolysaccharide biosynthesis pathways. These microbial shifts correlated with mucosal injury (mucus thinning, goblet cell loss, and bacterial adherence) and elevated systemic barrier dysfunction biomarkers. Collectively, ileal microbial and metabolic dysbiosis precede clinical ACR and correlate with barrier injury, nominating the ileal microbiota as a predictive biomarker source and therapeutic target in ITx.