This repository contains the supporting code for: Abdel-Rahman, LI and Morgan, XC
Searching for a consensus among inflammatory bowel disease studies: a systematic meta-analysis
Abstract:
Inflammatory Bowel Disease (IBD) encompasses Crohn’s Disease (CD) and Ulcerative colitis (UC), both of which are common chronic conditions in the western world with rates as high as 1 per 1000 individuals. Numerous studies have examined the gut microbial ecology of patients with CD and UC; however, many use substandard designs, resulting in inconsistent IBD-associated taxa and effect sizes. We systematically searched PubMed and Google Scholar and performed a meta-analysis using 13 studies to analyse how variables such as sample type (stool, biopsy, and lavage) affect widely held beliefs about the IBD gut microbiome. Reduced alpha diversity was consistent across CD studies, but not UC. Sample type contributed greatly to differences in alpha diversity between disease and control groups. Disease contributed to significant variation in beta diversity, however effect size varied across studies. Additionally, abundance changes of commonly associated CD and UC taxa at the genus level (e.g., a decrease in Faecalibacterium) were not consistent with previous literature. Our study concludes that previously described changes in IBD-associated taxa were inconsistent across studies, and variability in study design contributes greatly to results obtained.