Developing an in vitro dosing model to analyse the fermentation processes of the gut microbiota

The gut microbiota contains approximately 1014 bacteria that live in a mutual symbiosis with their host. These bacteria are involved in the fermentation of the indigestible fraction of our food (mostly made up of resistant polysaccharides). This fermentation leads to the production of several metabolites such as short chain fatty acids (SCFAs) and branched chain fatty acid (BCFAs). These metabolites have been recently linked to several pathologies such as inflammatory bowel disease, depression, diabetes, and colorectal cancer. For the moment it is not clearly understood how these metabolites affect our health. Indeed, there is a lack of information concerning the metabolic pathways involved in the transformation of the substrate into metabolites. In this context, we decided to study the impact that different doses of fibers or amino acids could have on the production rate of these metabolites. The hypotheses made at the beginning were that a substrate supplementation would lead to an increase in metabolite levels and that this increase would be linear. For this purpose, we developed an in vitro dosing model to analyse the fermentation processes of the gut microbiota. This model is based on an in vitro model developed for a single dose of dietary fiber and that has never been tested for amino acids. The results demonstrated that the in vitro dosing model works for both fibers and amino acids. Indeed, this model allowed us to explore the production rate of both SCAFs and BCFAs. Throughout this study we discovered that the metabolic pathways of the microbiota involved probably several mechanisms of action. Indeed, an increase in the substrate dose was not always corelated to an increase of the metabolite production rate and were never linear, thus suggesting the existence of other metabolic pathways involved in the fermentation processes