Colonization and changes in potential functionality of the bacterial population in fecal microbiota transplantation

The human microbiota consists of trillions of microbes that inhabit different parts of the body. Most of them are bacteria that reside in the gastrointestinal tract, a place for complex molecular crosstalk between the host and microbes. Imbalance in microbial communities has been associated with multiple intra- and extraintestinal diseases, including inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Fecal microbiota transplantation (FMT) has been studied as a novel treatment option for these patients. However, clinical results in other indications have not reached the effect of FMT in recurrent Clostridioides difficile infection (rCDI), in which the efficacy is over 90% and recipients are efficiently colonized by donor microbiota. The studies in this thesis consist of one pre-clinical and two clinical FMT studies which examined the changes in microbiota composition and the potential functionality of the ecosystem after FMT treatment. In the first study, we evaluated the effect of pre-treatment with broad-spectrum antibiotics in donor microbiota engraftment using a mouse model. As a result, FMT corrected the antibiotic-perturbed microbiota efficiently. However, we found only a minor benefit of antibiotic pre-treatment in microbiota engraftment compared to mice receiving only lavage or no pre-treatments. The genus Bifidobacterium was enriched post-FMT in mice pre-treated with antibiotics. Next, we investigated IBS patients in two studies. First, we determined the clinical efficacy of FMT in 49 IBS patients who were randomized into either an FMT group (n = 23) or a placebo group (n = 26). Moreover, measures, including quality of life, mental health, and robust microbiota changes and stool water content, were studied. As a result, we did not find a significant difference in IBS symptom severity scores between the study groups, although FMT-treated patients experienced transient symptom relief at 12 weeks compared to the baseline. Nevertheless, bacterial richness increased significantly, and the overall microbiota composition shifted in the FMT group. The third study of this thesis was a follow-up study on these IBS patients, in which we analyzed the microbiota composition in more detail down to species and even strain level, and aimed to connect symptoms with the changes in the microbiota. Here, the donor-derived Prevotella copri strain dominated the microbiota of patients who had a low initial relative P. copri abundance. Additionally, we found a shift in the microbiotas’ functional capacity post-FMT, particularly in the pathways related to degradation of D-arabinose and biosynthesis of amino acids, especially branched-chain amino acids (BCAAs). Nevertheless, these changes were not associated with symptom relief in the IBS patients. In the fourth study, we studied the microbiota composition as well as the changes in host mucosal gene expression in 26 pouchitis patients randomized into an FMT group (n = 13) and a placebo group (n = 13). We detected low-level donor microbiota colonization among these patients. Moreover, patients had a high individuality and high temporal intra-individual variation in their microbiota composition. Most of the differentially expressed genes were found at baseline between two locations – terminal ileum and pouch. One year after FMT, changes were few compared to the baseline. However, the gene encoding a G-protein-coupled chemokine receptor, CXCR4, was downregulated in both study groups among non-relapsed patients, which may implicate that it is associated with sustained remission. Taken together, the results from the studies in this dissertation show that the use of broad-spectrum antibiotic pre-FMT may not be justified in patients who do not clinically need antibiotics. Moreover, microbiota changes in IBS patients were not associated with symptom relief. However, as donor-derived P. copri was effective in colonizing FMT-treated IBS patients, and as this bacterium has been associated with carbohydrate degradation, this may be useful in designing future FMT or microbiota modulation studies. Lastly, the level of donor microbiota colonization in pouchitis patients is low. Thus, modulation of pouchitis patients’ microbiota seems to be challenging due to the individuality of their microbiota composition, and host–microbe homeostasis may be better influenced by targeting therapies towards the host epithelium, such as via the CXCR4 gene.