Gut Microbiome Alterations in Inflammatory Bowel Disease: A Narrative Review of Sequencing Studies

Abstract

Inflammatory bowel disease, which includes Crohn s disease and ulcerative colitis, is consistently accompanied by a shift in the composition of the intestinal microbial community, and sequencing has made that shift measurable. This narrative review asks what the sequencing literature does and does not establish. It draws on published work on amplicon and shotgun methods, on cross-sectional and longitudinal cohorts, on fungal and viral communities, and on microbial metabolites and immune signalling, and it reports no new data. The most repeated observations are lower diversity, fewer butyrate-producing Firmicutes and a relative gain of facultative anaerobes such as Enterobacteriaceae, with differences between Crohn s disease and ulcerative colitis and between ileal and colonic disease. Much of this signal is entangled with inflammation, diet, medication and bowel habit, and most studies are cross-sectional, so cause and consequence are hard to separate. Compositional data, small cohorts, contamination and uneven methods add further uncertainty. The review concludes that dysbiosis is a robust description but a weak explanation, and it lists the designs that would move the field from association towards mechanism and clinical use.