Potential of Clinical Care-Collected Gut Biopsies for Advancing Personalised Medicine in Inflammatory Bowel Disease

The management of inflammatory bowel disease (IBD) is challenged by significant patient diversity and a lack of effective profiling tools. This review evaluates the potential of archived formalin-fixed, paraffin-embedded (FFPE) gut biopsies as a resource for translational and precision medicine, given their global availability and associated long-term clinical data. Recent technical advances have expanded the molecular toolbox for FFPE samples to include proteomics, metabolomics, glycomics, spatial transcriptomics and characterising microbial components via 16S rRNA sequencing. Despite their potential, the use of FFPE materials is hindered using heterogeneous collection and storage methods. Consequently, the authors recommend implementing standardised guideline protocols for routine IBD biopsy management to facilitate high-quality research, improve disease understanding and support the identification of clinically translatable biomarkers.