The human intestinal ecosystem hosts a dynamic and complex community of microorganisms, both from a taxonomic and functional point of view. The interaction between this microbiota and the host significantly influences the digestive tract's functionality and plays a key role in many immunological and physiological responses. Many bacteria and their metabolites have been positively correlated with the prevention of various diseases such as diabetes, obesity, ulcerative colitis, colon cancer, irritable bowel syndrome, and neurodegenerative and cardiovascular diseases. Diet plays a central role in determining the assembly and evolution of gut microbiota. Consequently, modulation of the gut microbiota is considered a promising strategy to protect health. Although fermentation is a process known for improving the bioavailability of nutrients, bioactive compounds and prebiotics, the effect of fermented foods and individual ingredients on the gut ecosystem remains to be further investigated. 

In this context, the Centre aims to open a window on the gut microbiome ecological evolution and its plausible assembly mechanisms using the Human Intestinal Microbial Ecosystem Simulator (SHIME). The SHIME simulator represents a dynamic, representative and scientifically tested model of the human gastrointestinal tract in which the gut microbiota is reproduced from a faecal sample. In vitro research using the SHIME model is not only a complement to in vivo studies, but it is, to date, the most promising method for mapping the effect of individual foods, ingredients or probiotics while excluding a priori interference from other dietary factors and mitigating conditioning due to human physiology. This technology will make it possible to study thoroughly, both in the short and medium term, the ecosystem changes orchestrated by the intake of fermented foods at the level of microbiome composition and functionality. Furthermore, the digestibility of new fermented foods in terms of bioaccessibility and bioavailability of nutrients will be fully characterised through the ESIN model, which today represents the most advanced computer-controlled in vitro dynamic model of the human stomach and small intestine.