Microbes in the inflamed gut

This thesis investigates the gut microbiome's role in inflammatory bowel disease (IBD). The research emphasizes the importance of a multifactorial understanding of IBD that includes microbiome interactions, immune responses, and patient metabolism. Part I focuses on the microbiome in pediatric patients with Crohn's disease and ulcerative colitis. Multi-omics techniques are used to gain insight in the differences between active disease and remission. In addition, literature on the role of serotonin in gut homeostasis is reviewed. Part II explores the sporobiota in the gut in health and disease, and their potential therapeutic roles in IBD. Literature on the role of the sporobiota in the gut is reviewed and we investigated whether metagenomics analysis of fecal samples can be used to predict the potential of an individual’s microbiota to sporulate based on the presence of sporobiota associated genes. Additionally, the origins of fecal transplantation practices are investigated, debunking a popular anecdote regarding the use of dromedary feces for treating dysentery. Overall, the findings underscore the microbiota's significant role in IBD, highlighting the potential for microbiome-targeted therapies and the necessity for personalized treatment strategies to improve patient outcomes.