The thesis project aims to interface multiple in silico models describing host-microbiota interaction at different scales. While the developed models encompass various living entities, the focus will primarily be on mice and humans due to the availability of extensive data. At the microscopic level, these novel advancements will involve coupling a spatially distributed model of colon fluid mechanics with a crypt model, simulating interactions between the host and the microbiota. Thus, effects generated at the microscopic scale will influence the behavior of the host's digestive and cardiovascular systems at the macroscopic scale. Modeling these macroscopic systems is crucial for integrating individual-specific data or biological measurements, which will be compared with simulation results from the model.