The human gut harbors a complex bacterial community, the gut microbiota, that maintains a symbiotic relationship with its host: the microbiota ecology is then linked to the host’s health. Mathematical models of the microbial population dynamics are therefore a promising tool to study the mechanisms driving the homeostasis or the dysbiosis of the microbiota. We couple a PDE population dynamics model of functional microbial meta-populations involved in fibre degradation to a fluid mechanic model of the intestinal content. The metabolic capabilities of the meta-populations are inferred from functional metagenomic data through NMF (non-negative matrix factorization). Metabolic models of the meta-populations are built to predict the metabolite consumptions and the growth rates, and are plugged to the PDE population dynamics model to account for the interactions between the bacterial populations and the intestinal environment. Additionally, the taxonomic composition of the meta-populations is derived from the comparison of their functional potential with the genome of 190 bacterial strains of the human gut microbiota. This approach makes possible direct comparisons between the model outputs and both gene (shotgun) or bacterial (16s) counts. This work is a collaboration with B. Laroche, and with M. Ribot, B. Polizzi, T. Phan and T. Goudon for the population/fluid dynamics model of the microbiota and its environment, and with L. Darrigade for the metapopulations construction.