Bioprocesses are increasingly used in many fields to produce, to extract, to transform or still to recover high added value substances in complex media. Yet, their functional heart, simplified or natural microbial ecosystems, are not well understood. Models are major tools to formalize the biological knowledge but they are of different - and sometimes fundamentally - different natures depending on the objective they are built for. In this presentation, we first propose a quick review of models for biological processes with respect to the questions they are supposed to contribute to give answers. Then, through several practical examples, we show how they can be successfully used to optimize biological systems or, on the opposite, how they help experimenters and theorician to exchange and confront different viewpoints. Then, their limits are highlighted and the actual research hotspots are presented.