Different levels of gut microbiota modeling are introduced. Functional metagenomic data are analyzed through non-negative matrix factorization (NMF) to identify metabolic profiles that are interpreted as functional potential of microbial meta-populations. Metabolic models of the meta-populations are built to predict the metabolite consumptions and the growth rates, and are plugged to a PDE population dynamics model to account for the interactions between the bacterial populations and the intestinal environment. Conversely, the model outputs can be interpreted as synthetic metagenomic counts that can be compared to experimental data. 

This work is a collaboration with B. Laroche, and with M. Ribot, B. Polizzi, T. Phan and T. Goudon for the population/fluid dynamics of the microbiota and its environment, and with L. Darrigade and M.Leclerc for the metapopulation construction.