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Abstract
Introduction Great progress has been made in understanding the pathophysiology of Crohn’s disease (CD) and ulcerative colitis (UC), and it is now widely believed that dysregulation of the relationship between the gut microbiota and the host immune system is central to both diseases. Most published studies to date have focused on assessing the microbiota found in faecal samples, but it is increasingly recognised that this may not be an accurate reflection of what is happening at the mucosal level.
The Aims of this study were to establish a bioresource of IBD patients and controls, and to use this to assess differences in gut microbiota between cases and controls and between different IBD subphenotypes.
Methods Patients undergoing colonoscopy and flexible sigmoidoscopy were recruited to the South East Scotland IBD bioresource. Mucosal biopsies were obtained and snap-frozen using dry ice. DNA was then extracted using a QIAGEN spin column-based method. Blood and serum samples were also biobanked for genetic, epigenetic and metabolomics analysis. Quantitative PCR was used to measure the relative abundance of different bacterial classes compared to the total measured with universal primers. Statistical analysis was done using Mann Whitney U, chi squared and Fisher’s exact tests using R 2.15.2.
Results After quality control, results were available from 147 biopsies taken from 84 patients. There were 20 patients with CD, 26 with UC, 2 IBD-U, 20 healthy controls (HC) and 16 with other diagnoses. Median age was 45 years (interquartile range [IQR] 28–50) in the CD group, 51 y (38–63) in the UC group and 39 (30–49) in the HC group. There were no significant differences in age or sex distribution between the CD, UC and HC groups.
There was a statistically significant reduction in CD compared with HC in Ruminococcaceae (p = 0.002, figure 1), Lachnospiraceae (p = 0.046) and Bacteroides (0.024) and an increase in Enterobacteriaceae (p = 0.046). Comparing UC with HC, there was a significant increase in Enterobacteriaceae (p = 0.025), but no difference in the other classes. There were no significant differences in any bacterial class between biopsies taken from inflamed and non-inflamed sites in IBD patients.
Conclusion This study confirms reductions in Ruminococcaceae described previously in CD, and increased Enterobacteriaceae in both CD and UC. The presence of paired DNA and serum samples offers the exciting potential to explore the relationship between the gut microbiota, epigenetic and metabolomics changes.
Disclosure of Interest None Declared.