A functional perspective on probiotic interventions in the small intestine: dynamics and emergent properties of the microbial community

Our intestines are inhabited by bacteria, which form a network and keep us healthy. Simultaneously, too many bad bacteria can affect our health negatively. Luckily, many types of treatments targeting our gut bacteria are being developed, such as probiotics. However, most probiotics target the large intestine.In this thesis, we studied the effect of probiotics on the small intestinal bacteria. Since the bacterial community in the small intestine is not as easily accessible, we used two ways to circumvent this inaccessible organ. First we used content obtained from stoma bags of people without a large intestine. Secondly, we made a mock small intestinal community by growing three bacteria together. In both experiments we measured the number of bacteria, the pH and metabolites, which are compounds that can be used or produced by the bacteria. In both experiments, we observed an altered production of metabolites and growth of specific bacteria. Secondly, the probiotic bacteria mad a more connected network of metabolites, which indicates a higher resistance to perturbations of bad bacteria. When we compared the functionality, which are the metabolites each bacteria can produce, of the probiotic bacteria, and compared it to the bacteria in the community, we found that the probiotic bacteria with a different functionality from the community increased the usage of metabolites. Thus it is important to know the functionality of someone’s gut bacteria and find a probiotic with a functionality that is complementary. To do this, we describe how flux balance analysis, a simulation method, can be used to personalize probiotic treatment.

Dissertation: https://hdl.handle.net/11370/f435ecd7-7ef7-4571-aa7d-4a87ac0f3bff