Character of Microbial Engraftment Following the Fecal Microbiota Transplantation in Patients with Inflammatory Bowel Diseases

Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been applied in treatment of Crohn’s disease (CD) and ulcerative colitis (UC). However, only a fraction of patients respond positively to this therapy. In this regard, it is gaining popularity to study the combinations of approved medications and FMT to increase the effectiveness of therapy. Here we present a pilot longitude project for the study of FMT application combined with the anti-inflammatory therapy in CD (n = 8) and UC (n = 6) patients. Using the shotgun sequencing of stool samples (n = 56) we evaluated the temporal changes in the taxonomic and functional structure of the patients’ metagenomes and donor-derived microbes engraftment due to the FMT procedure. According to our analysis, the gut microbiota was changed both in CD and UC patients whereas reshaping nature in experimental groups was differ. Only in the UC group the shift of gut microbiota composition towards donor and the donor-derived microbes engraftment were more extensive in comparison with the CD group. Moreover, we observed that beneficial and prevailing in human population microbes such as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and others are the best colonizers. The difference in the microbial engraftment can be explained by differences in the pathogenesis of CD and UC. On the other hand, mucosal and intestinal lumen conditions in the UC group may have been better corrected due to the proposed treatment which allowed the donor microbes to colonize these patients more successfully. In addition, the evolutionary formed ecological relationship between the gut microbiota and the host can be linked with the FMT therapeutic effect.