Abstract
Inflammatory bowel disease (IBD) is a chronic immune-mediated disease of the gastrointestinal tract that is associated with gut microbial dysbiosis. Medications such as corticosteroids and mesalamine are widely used to control inflammation and other IBD symptoms. However, their effects on the gut microbiome remain poorly understood. In this study, we reanalysed a published dataset of colonic biopsy samples from 130 patients with IBD to evaluate how pharmacological treatments influence microbial diversity, composition, and function. In inflamed tissues, alpha diversity showed no significant differences across treatment groups. However, beta diversity analysis revealed significant differences in microbial community composition between some medication groups, with corticosteroid-associated samples showing the strongest overall shifts relative to mesalamine-associated samples. In non-inflamed tissues, corticosteroid treatment was associated with reduced diversity and distinct taxonomic profiles, whereas inflamed tissues exhibited less variation across treatments. Differential abundance analyses identified depletion of commensal families (e.g. Lachnospiraceae and Marinilabiliaceae) and enrichment of dysbiosis-associated taxa (e.g. Enterobacteriaceae and Bacillaceae) in corticosteroid-treated groups. Predicted functional profiling further indicated increased abundance of two-component systems involved in anaerobic metabolism and osmotic stress in both inflamed and non-inflamed tissues of patients with IBD using corticosteroids. These findings suggest that corticosteroid treatments may have stronger microbiome-altering effects than mesalamine, highlighting the need to consider how various IBD treatment strategies influence the gut microbiota composition.