In this talk, we present the construction of PDE model describing the evolution of microalgae or bacteria interacting together and in interaction with their environment. These models are based on the mixture theory and are coupled with reaction-diffusion equations or fluid mechanics equations. We begin with the description of micro-algae biofilms in fountains, then the description of photosynthetic biofilms of micro-algae producing lipids and finally, the evolution of gut microbiota in interaction with the colon rheology.