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Controlled microbial activity is the core of many industrial processes. Such dynamic microbial processes must be carefully studied to optimize their application. They are usually tackled by means of continuous mathematical modelling at the population level (top-down). An alternative approach is individual-based modelling (IbM) (bottom-up). INDISIM is a discrete and spatially explicit IbM. It sets the rules that govern each microbe and its interaction with its local environment, as well as the significant environmental processes. Then it performs simulations that include a large number of microbes, and the behaviour of the whole system emerges. The rules are changed to reproduce the behaviour of microbes depending on the system to be studied. Two adaptations of INDISIM to study yeast fermentations and multi-species composting are presented in this article (INDISIM-YEAST and INDISIM-COMP), proof of INDISIM's versatility. A few representative results are also shown. [ABSTRACT FROM AUTHOR]