The role of intestinal microbiota in the development of inflammatory bowel diseases: identification of potentially beneficial and harmful micorbiota through ex vivo organoid technology.

The exact pathogenesis of Crohn’s disease (CD) and ulcerative colitis (UC) remains incompletely understood, but a loss of tolerance to gut microbiota seems crucial. Interactions between host and microbiota take place at the intestinal surface which consists of intestinal stem cells (ISC), enterocytes, goblet, enteroendocrine, and Paneth cells. The differentiation of ISC into progeny cells is suggested to be disturbed in CD and UC. The impact of microbiota on ISC is unknown. We hypothesize that ISC behave differently upon stimulation with luminal microbiota leading to altered differentiation into progeny, altered release of antimicrobial peptides by Paneth cells, altered production of mucin by goblet cells, and altered epithelial barrier function. The behaviour and differentiation of ISC derived from human (UC, CD, and healthy control) and murine (IBD models) intestinal samples will be compared by using an ex vivo long-term culture model. In this model, ISC will grow out into mini-guts containing all differentiated epithelial cell types (organoids). Next, the influence of microbiota on ISC behaviour and differentiation, as well as barrier function, will be evaluated in a co-culture of such organoids in the presence of complete luminal microbiota (e.g. pro-inflammatory E. coli, anti-inflammatory microbes F. prausnitzii), microbial proteins, or cell wall components. Finally, the role of the host’s immune system will be assessed by adding dendritic cells to these co-cultures.