Metabonomic profiling in inflammatory bowel disease: application to real-life population of patients

Abstract

Previous studies have demonstrated the importance of the microbiome in the pathogenesis of inflammatory bowel disease (IBD), with a dysbiosis being a common feature. This change in the microcbiome has metabolic consequences, and metabonomic profiling can be used to detect these metabolic signals along with changes in the patient’s own metabolic profile.

Metabonomics have been applied clinically in oncology to augment diagnosis, treatment, and prognostication, and the aim is for it to have a similar role in IBD. Most studies in IBD have been performed on stool, and have observed a number of discriminatory metabolites, but more recently urinary metabonomics has been studied, as this is a much more convenient biofluid to use both in terms of sample collection and preparation. Here too, discriminatory metaboliteshave been observed, several of which are produced by intestinal microbial or host-microbial metabolism. These changes in the IBD metabolome give an insight into the complex pathophysiology of this disease, and have significant potential impact in both diagnosis and stratification of patients into different disease phenotypes and in the assessment of treatment outcome.

However, up until now IBD metabonomic research has been restricted to homogeneous clinical cohorts where subjects with comorbidities have been excluded, and for the technique to be clinically useful it has to provide consistent results in real-life cohorts, including factors that may influence the metabolome such as obesity and the effects of bowel cleansing pre-colonoscopy, both of which apply to a real-life IBD clinical population. This project assessed these factors on the IBD metabolome, examining principally urine due to its ease of use.

Multivariate analysis showed that changes seen in the IBD metabolome are present with the inclusion of subjects with comorbidities in IBD and Crohn’s disease cohorts relative to controls. Targeted analysis showed differences in hippurate and 4-cresol sulfate between IBD cohorts relative to controls, likely associated with reduced abundance of Clostridia species seen on microbiomic analysis. No changes could be seen in ulcerative colitis (UC) cohorts, but UC participant numbers were relatively low following removal of patients taking 5- aminosalicylates that influenced the NMR spectrum.

Obesity may have an effect on the urinary IBD metabolome, as although there was no clustering on unsupervised multivariate analysis, a reduction in hippurate excretion was not seen in the obese IBD relative to control cohorts, and hippurate has been the most consistently reported discriminatory metabolite associated with IBD. Longitudinal analysis of the urinary and faecal metabolome showed resistance at day 3 and week 6 following bowel cleansing; a temporary reduction of alpha diversity was observed on microbiomic analysis.

Overall, this project has shown that whilst many elements of the IBD related urinary metabolome are preserved when patients with comorbidities are included into analysis, obesity may be a significant confounder. The studies of the urinary and faecal metabolome after bowel cleansing show that the metabolome appears resistant to significant changes at day 3 following bowel cleansing, which may be helpful in analysing future metabolic and microbiomic studies after colonoscopy, and help to associate changes identified from sampling during those procedures.