Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome is mirrored by changes in gut microbiome

Irritable bowel syndrome (IBS) is a common disorder of the lower gastrointestinal tract. The pathophysiology is far from settled, and components of micro-inflammation, neuro-immunological signaling and gut microbial dysbiosis are frequently emphasized as causative factors. Here, we present fecal metagenomic sequencing data from our earlier published randomized double-blind placebo-controlled clinical trial on fecal microbiota transplantation (FMT) for IBS – the REFIT trial. Only samples from participants who received active fecal microbiota transplants were included in the present data set; 14 participants with effect of FMT (Effect) and 8 without (No effect) were chosen. Samples were collected at baseline before FMT, after 6 and 12 months. Also samples from the transplants (Donor) given to the participants were analyzed. In total 66 recipient samples and 17 donor samples were subjected to deep metagenomic sequencing (Illumina NextSeq550), generating on average 27.3 *106 reads. After in silico quality control, assembly and annotation, we generated taxonomic and functional profiles. Alpha diversity measures showed a significantly increased diversity and evenness in the IBS groups compared to the donors (P=0.0026 and 0.0046 for Effect and No effect groups by Simpson index, respectively). Taxonomic profiles showed higher relative abundance of phylum Firmicutes, and lower relative abundance of phylum Bacteroidetes, compared to donors at baseline. This profile was shifted towards the donor profile following FMT, and we derived, from the Effect group, a list of 170 species, differentially abundant, that were most prominent in this shift. Analysis of imputed growth rates showed that the resulting growth pattern was a conglomerate of donor and recipient activity. Thirty-four functional subclasses showed distinct differences between baseline samples and donors, most of which were shifted towards a donor-like profile after FMT. Functional systems involved in short chain fatty acid synthesis were detected, and also an increase in systems synthesizing growth factors like Menaquinone and scavenging metal ions like Zink and Manganese. We conclude that FMT induces long-term changes in gut microbiota, and these changes mirror the clinical effect of the treatment.