Bile acid diarrhoea is a poorly understood gastroenterological condition despite it affecting an estimated 1% of the general population. It can present concomitantly in other conditions such as post-cholecystectomy and Crohn's disease, where it is found in over 90% of patients following a terminal ileal resection. A major limitation to recognising and acknowledging this disease is the lack of available diagnostic modalities. The treatment for this condition is bile acid sequestrants although the National Institute for Health and Care Excellence recommend further research to assess treatment response and quality of life outcomes. Furthermore, the aetiology has only recently gained attention with a greater understanding in bile acid modulation and its relationship with the microbiome. There is now increasing evidence that bile acid sequestrants may also alter the composition of intestinal microbial species, thus manipulating disease activity in Crohn's disease. In this thesis, we first set out to investigate the use of a single random stool sample in the diagnosis of bile acid diarrhoea. Secondly, we aimed to profile the gut microbiome in patients with bile acid diarrhoea and determine if bile acid sequestrants altered the microbiome following treatment. Lastly, we investigated whether this treatment could manipulate the gut microbiome and consequently prevent the clinical and endoscopic recurrence of post-operative Crohn's disease. The results of these studies demonstrated that a single random stool test can be used in patients to diagnose severe bile acid diarrhoea and in those with terminal ileal resected Crohn's disease. Our study further demonstrated significantly reduced bacterial diversity in patients with idiopathic bile acid diarrhoea and in patients with severe disease. In patients with a negative diagnosis of bile acid diarrhoea, we found an abundance of bacteria that express enzymes that convert primary to secondary bile acids, thereby reducing the symptoms of diarrhoea. Following treatment in those with a positive diagnosis of BAD, we demonstrated an increase in these same bacteria in patients who clinically responded to treatment. Furthermore, in post-operative Crohn's disease patients, not only were patients more likely to be in clinical and endoscopic remission if taking long-term bile acid sequestrants but they were also found to have a higher abundance of bacteria that exhibit anti-inflammatory properties and reduced abundance of bacteria that is associated with Crohn's disease pathogenesis. This has important implications in our Crohn's cohort as not only did we demonstrate disease remission and an improvement in their microbiome following treatment, we further demonstrated this cohort to have the greatest improvement in their clinical symptoms and QoL outcomes. Future work is now needed with larger mechanistic studies exploring the relationship of bile acid sequestrants on bile acid metabolism and microbial composition.