The gut microbiota and inflammatory bowel disease
The human gut microbiome is influenced by numerous factors including commonly used drugs, but it has also been shown that the gut microbiome by itself influences drug responses and efficacy. We studied the relations between commonly used drugs and microbial changes considering factors like polypharmacy and multi-morbidity. We performed metagenomics sequencing of 1883 faecal samples from three cohorts: 1) a population-based cohort, 2) patients with inflammatory bowel diseases and 3) patients with irritable bowel syndrome. Differences between drug users and non-users were analysed per cohort, followed by a meta-analysis. 17 of 41 drugs were associated with changes in microbial features. For example, metformin users showed enrichment of Escherichia-coli -derived metabolic pathways and methanogenic pathways were increased in oral steroid users in patients with IBD. Due the importance of the gut microbiome in health and the widespread use of drugs, we here provide evidence for extensive changes in taxonomy, metabolic activity and resistome in relation to commonly used drugs. This research paves the way to further mechanistic studies for drug response and side effects and has implications on future microbiome studies, underlining the need for correcting for multiple drug use in both general population and in GI disease cohorts.