Searching for a consensus among inflammatory bowel disease studies: a systematic meta-analysis

Numerous studies have examined the gut microbial ecology of patients with Crohn’s disease and ulcerative colitis, but IBD-associated taxa and ecological effect sizes are not consistent between studies. We have systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyse how variables such as sample type (stool, biopsy, and lavage) affect results in IBD gut microbiome studies. Reduced alpha diversity was a consistent feature of both CD and UC, but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD. Our results indicate that sample type variation is an important contributor to study variability.