Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease

The gut microbiome is an important contributor to the development and the course of inflammatory bowel disease (IBD). While changes in the gut microbiome composition were observed in response to IBD therapy using biologics, studies elucidating human and microbial proteins and pathways in dependence on therapy success are sparse. Fecal samples of a cohort of IBD patients were collected before and after 14 weeks of treatment with three different biologics. Clinical disease activity scores were used to determine the clinical response and remission. Fecal metaproteomes of remitting patients (n = 12) and of non-remitting patients (n = 12) were compared before treatment and changes within both groups were assessed over sampling time to identify functional changes and potential human and microbial biomarkers. The abundance of proteins associated with neutrophilic granulocytes, and immunoglobulins significantly decreased in remitting patients. There were changes in pathways of microbial metabolism in samples from patients with remission after therapy, including an increased butyrate fermentation. Distinct changes of proteins related to gut inflammation and gut microbiome metabolism showed whether IBD remission was achieved or not. This suggests that metaproteomics could be a useful tool for monitoring remission in IBD therapies. SIGNIFICANCE: IBD is rising in incidence, especially in newly industrialized countries, and the microbiome is an important contributor to its pathogenesis. Despite manifold therapeutical options, achieving remission is often ineffective, and choosing new alternative drugs remains often empirical. Therefore, efficient tools for monitoring therapeutic response and assessing the effectiveness of drugs in specific patients are mandatory. In the present study, we show that the use of metaproteomics is a promising avenue to address these challenges. We observed the amelioration of inflammation and restoration of a healthy microbiome in remitting patients in contrast to non-remitting patients. Therefore, metaproteomics is a valuable tool for monitoring the therapy success in IBD.