IBD-RESPONSE samples - methodology substudy. Evaluating intestinal biopsy tissue preservation methods to facilitate large-scale microbiome research

The gut microbiome is an important factor in inflammatory bowel disease. To maximise generalisability of results, and facilitate the necessary cohort stratification required to collect sufficiently granular data to inform precision medicine solutions, large-scale studies are required. The gold standard of sampling mucosal microbiomes requires understanding of which microbes are actively growing and interacting with the epithelium. Snap-freezing of biopsy tissue immediately following collection facilitates this but is often not pragmatic or achievable in large-scale studies. Instead, stool collection is often used as a proxy to characterise mucosal microbiomes. Furthermore, FFPE embedded tissue is often archived within the NHS and may represent an opportunity to characterise historical mucosal microbiomes in IBD patients where biopsy collection is not achievable. This study aims to validate different sample collection and storage conditions to identify pragmatic and cost-effective mucosal microbiome sampling techniques and compare these to the gold-standard.