Background
Crohn’s disease (CD) is a chronic inflammatory gastro-intestinal condition with a variable disease course. Medical drugs are the most important treatment regimen to induce and maintain remission. However, a substantial number of patients experience adverse effects and non-response. As the intestinal microbiota can interact with xenobiotics and is involved in CD pathophysiology, the aim of this study is to explore the effect of common CD drugs on the patient’s microbiome ex vivo.

Methods
Five CD patients donated a fecal sample, which was anaerobically collected and used for the experiments on the same day. The individual fecal microbiota was exposed to budesonide, 6-mercaptopurine, tofacitinib, or DMSO-control for 24 hours. Subsequently, DNA and proteins were isolated and subjected to 16 rRNA gene amplicon sequencing and HPLC-MS proteomic analysis, respectively.

Results
Metagenomic and metaproteomic analyses revealed larger differences between donors as between drug exposures. Preliminary metaproteomic analyses could discriminate between 6-MP, tofacitinib, and the control condition, but not between budesonide and control. Due to 6-MP exposure 18 proteins were upregulated and 22 downregulated in all cultures. Further, preliminary metagenomic analyses could detect no drug-related shifts in overall microbiota diversity.

Conclusion
Although the origin of the fecal bacteria has a higher impact on microbiota composition and function, 6-MP and tofacitinib exposure significantly impacts bacterial protein expression in vitro. Further research is needed about the impact of drug-induced functional microbial alterations on the host and a potential relation with treatment outcomes in CD.