The pathogenesis of inflammatory bowel disease (IBD) involves the interaction between an individual’s genes, gut microbiota and environmental factors. The Crohn’s disease (CD) microbiome is characterised by a reduction in Firmicutes and an increase in Proteobacteria. The CD metabonome consistently shows a reduction in secondary bile acids (SBAs) and an increase in stool and serum primary bile acids (PBAs). Very few studies have examined the multiomic profile in patients with Crohn’s disease-intestinal failure (CD-IF).

I present two retrospective case-control studies and one prospective multiomics study. I identified the following risk factors for the development of IF in patients with CD: female gender, ileocolonic involvement, penetrating disease and non-exposure to biologic medications. Patients with CD-IF are twice as likely to be in remission compared to patients with CD (without IF) and the strongest factor associated with active disease, was the presence of a surgical anastomosis to colon in continuity compared to those with an end enterostomy.

For the multiomics study, stool, serum and urine samples from CD-IF patients were analysed. 16s rRNA sequencing demonstrated an expansion of aerotolerant and facultative anaerobic microorganisms, with a decrease in obligate anaerobes; the CD-IF gut luminal environment has a higher oxygen content. Metabonomic profiling showed a higher serum and faecal cholic acid and chenodeoxycholic acid in active disease compared to remission; this is in keeping with the theory that loss of bowel length leads to loss of farnesoid X receptor (FXR) and Fibroblast growth factor 19 (FGF19) and an increase in hepatic synthesis of PBAs. Expectedly, an almost absence of serum SBAs was observed in CD-IF. Multiomics changes seen with active disease could be a cause or a consequence of disease activity, or secondary to the anatomic changes or changes in diet and parenteral nutrition.