The human gut harbors a complex bacterial community that maintains a symbiotic relationship with its host. An increasing number of studies highlight its implication in the maintain of the host's health, but also in various disorders such as inflammatory bowel disease, allergic or metabolic disorders. We propose to integrate in the same model different micriobiological or biophysical informations related to the microbiota structure and functions and to the gut environment. A population dynamics model of functional microbial populations involved in fibre degradation is coupled to a fluid mechanic model of the intestinal fluids. This model is simplified through asymptotic analysis and is used to study the mechanisms that impact the spatial structure of the gut microbiota.