This dissertation includes six papers relating to the treatment of intestinal diseases through faecal microbiota transplantation (FMT) plus one paper examining bacteriophage therapy, which is another way of manipulating the human microbiome. A correlation has been reported between the gut microbiome and numerous diseases that affect both the gut and other organs. FMT is therefore seen as a potential treatment for an increasing number of diseases. The cure rate of FMT as a treatment of recurrent Clostridioides difficile infection (rCDI) is higher than antibiotics and FMT has therefore become part of treatment guidelines. In the treatment of all other conditions, FMT is still only being used on a research basis. FMT can be administered through different routes. The focus in this dissertation is on FMT delivered through capsules, which for safety, patient comfort and logistical reasons will probably become the preferred administration form in future. Through clinical studies we report that FMT capsules is effective in the treatment of rCDI and promising in the treatment of Ulcerative Colitis (UC). In systematic reviews the effects of FMT as treatment of rCDI and various other diseases are reported. Following a meta-analysis of all published studies in which FMT capsules were used to treat rCDI, the treatment is reported to be highly effective across studies, with differences in the way the treatment was produced and delivered between the studies not significantly affecting cure rates. The safety following FMT has primarily been reported from studies without a control group and often only reported for up to one year following treatment. A study involving the long-term follow-up of 280 patients for up to five years following treatment of rCDI found that there was no increased risk of long-term adverse effects when compared to a similar control group treated with 12 bacterial strains. This was in relation to mortality, the risk of hospital admission and the onset of certain diseases such as cancer and inflammatory bowel disease. Changes in the recipients’ gut microbiome following FMT are not fully understood. In a study investigating the effects on the gut microbiome following 12 days of FMT capsule treatment for patients with irritable bowel syndrome, FMT was reported to cause major changes in the recipients’ gut microbiome, with a significant engraftment of donor bacteria and loss of pre- treatment bacteria for a minimum of six months. These changes were not correlated with any beneficial effects. Based on the knowledge gained from experience with the FMT treatment, potential directions for future microbiome-modulating treatments are given. One of these is bacteriophage therapy and current evidence has been reviewed.