Comparative study of faecal microbiota in Crohn's disease patients in remission with and without surgical resection

Abstract Background Inflammatory bowel disease (IBD) is defined as a group of autoimmune diseases that affects the digestive tract by causing chronic inflammatory processes. Crohn’s disease (CD) is one of the major types of IBD. Although there are several efficient drugs for its treatment, almost 80% of patients will require an intestinal resection throughout their lives. Some bacterial species found in faecal samples can be used as indicators to diagnose and monitor activity in CD patients. However, this methodology has not yet been tested in patients that underwent an intestinal resection. The aim of this study was to investigate the changes in the abundance of these species associated with total or partial intestinal resection. Methods In this study, we used 30 faecal samples from patients diagnosed with CD in remission withdrawn from the Biobank of the Hospital Universitari Dr. Josep Trueta of Girona. Fifteen samples corresponded to patients who underwent an intestinal resection. The following markers were quantified by qPCR: Faecalibacterium prausnitzii (Fpra), F. prausnitzii phylogroup I (PHG-I), F. prausnitzii phylogrup II (PHG-II), Escherichia coli (Eco), Akkermansia muciniphila (Akk), Ruminococcus sp. (Rum), Bacteroidetes (Bac) and Methanobrevibacter smithii (Msm). Results The abundances of Fpra, PHG-I, PHG-II, Rum, and Msm were significantly lower (p < 0.05) in resected CD patients, whereas Eco was significantly more abundant in those patients. No significant differences were observed in the abundances of Akk and Bac. Conclusion In resected CD patients, beneficial butyrate-producing bacteria are underrepresented, whereas pro-inflammatory species are overpopulated. Any quantitative relationship of these indicators with the relapse probability would help to stratify these patients for a better orientation of therapeutic strategies.