Models of microbial community dynamics generally rely on some sub- system scale model for microbial metabolisms. Here we propose a model which combines cellular level metabolic flux analysis with macroscale microbial community models. The methodology allows coupling of macroscale information with cell-scale metabolism. In particular, we present a forward problem model which aims at predicting the system pro- file, and an inverse problem model which aims at providing uncertainty estimates when only partial data of the system is available.