225 Supplementary Table Index Supplementary Table S1. Differential gene expression analyses between non-inflamed and inflamed biopsies from ileal CD (group 1), colonic CD (group 2) and UC (group 3). Supplementary Table S2. Differential gene expression analysis between inflamed biopsies from patients with CD (reference) and patients with UC. Supplementary Table S3. Differential expression analysis of deconvoluted cell types between inflamed colonic biopsies of patients with CD (reference) and patients with UC. Supplementary Table S4. Relative abundances of mucosal bacterial groups in different groups (CD, UC and non-IBD controls) and biopsy locations (ileum or colon). Supplementary Table S5. Comparison of relative abundances of bacterial groups between nonIBD controls and ileal CD (group 1), colonic CD (group 2) and UC (group 3). Supplementary Table S6. Hierarchical analysis performed using an end-to-end statistical algorithm (HAllA) demonstrating the main associations between mucosal bacterial groups and clinical phenotypes. Supplementary Table S7. Genes and bacteria contained in component pair 1 from sparse-CCA analysis (FDR<0.05). Supplementary Table S8. Pathway annotation of genes involved in component pair 1 from sparse-CCA analysis (FDR<0.05). Supplementary Table S9. Genes and bacteria contained in component pair 3 from sparse-CCA analysis (FDR<0.05). Supplementary Table S10. Pathway annotation of genes involved in component pair 3 from sparse-CCA analysis (FDR<0.05). Supplementary Table S11. Genes and bacteria contained in component pair 7 from sparse-CCA analysis (FDR<0.05). Supplementary Table S12. Pathway annotation of genes involved in component pair 7 from sparse-CCA analysis (FDR<0.05). Supplementary Table S13. Genes and bacteria contained in component pair 8 from sparse-CCA analysis (FDR<0.05). Supplementary Table S14. Pathway annotation of genes involved in component pair 8 from sparse-CCA analysis (FDR<0.05). Supplementary Table S15. Genes and bacteria contained in component pair 5 from sparse-CCA analysis (FDR<0.05). Supplementary Table S16. Pathway annotation of genes involved in component pair 5 from sparse-CCA analysis (FDR<0.05). Supplementary Table S17. Genes and bacteria contained in component pair 9 from sparse-CCA analysis (FDR<0.05). Supplementary Table S18. Pathway annotation of genes involved in component pair 9 from sparse-CCA analysis (FDR<0.05). Supplementary Table S19. Individual pairwise gene-bacteria associations. Supplementary Table S20. Genes and bacteria associated with fibrostenotic CD/Montreal B2 (reference: Montreal B1). Mucosal host-microbe interactions in IBD
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