This article deals with the inclusion of microbial ecology measurements such as abundances of operational taxonomic units in bioprocess modelling. The first part presents the mathematical analysis of a model that may be framed within the class of Lotka-Volterra models fitted to experimental data in a chemostat setting where a nitrification process was operated for over 500 days. The limitations and the insights of such an approach are discussed. In the second part, the use of an optimal tracking technique (developed within the framework of control theory) for the integration of data from genetic sequencing in chemostat models is presented. The optimal tracking revisits the data used in the aforementioned chemostat setting. The resulting model is an explanatory model, not a predictive one, it is able to reconstruct the different forms of nitrogen in the reactor by using the abundances of the operational taxonomic units, providing some insights into the growth rate of microbes in a complex community.
Keywords: bifurcation analysis; chemostat theory; generalized Lotka–Volterra; microbal interactions; microbial growth rate; optimal control.