Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

Management of terminal ileal Crohn's disease (CD) is difficult due to fibrotic prognosis and failure to achieve mucosal healing. A limited number of synchronous analyses have been conducted on the transcriptome and microbiome in unpaired terminal ileum tissues. Therefore, our study focused on the transcriptome and mucosal microbiome in terminal ileal tissues of CD patients with the aim of determining the role of cross-talk between the microbiome and transcriptome in the pathogenesis of terminal ileal CD. Mucosa-attached microbial communities were significantly associated with segmental inflammation status. Interaction-related transcription factors (TFs) are the panel nodes for crosstalk between the gene patterns and microbiome for terminal ileal CD. The transcriptome and microbiome in terminal ileal CD can be different related to local inflammatory status, and specific differentially expressed genes (DEGs) may be targeted for mucosal healing. TFs connect gene patterns with the microbiome by reflecting environmental stimuli and signals from microbiota. Approximately 5 mg (four mucosal biopsies) of tissue samples were extracted from the inflamed and proximal non-inflamed ileum of CD patients (n=10). IMCD and NMCD were extracted from the biopsy samples, and they were confirmed by light microcopy. Three months prior to recruitment, all patients were instructed to avoid antibiotics, steroids, immunosuppressants, and biologics.