It is now becoming feasible to determine the composition of an individual gut microbiota (gut microflora), as well as the individual genome. In addition, whole genome scale metabolic models (GEMs) exist for a range of bacteria, and also for human. In principle this enables us to build models for gut microbiota by aggregating strain-specific models and also place this within the human context, and to make predictions on a personalised basis of the influence of gut microbiota on human metabolism, and how the interactions between these microbiota and also the human may evolve. Such aggregation, however, raises several challenges, which we discuss in this paper.
Furthermore, we present techniques and supporting tools which permit the development of personlised models for human – gut microbiota interaction. The construction of such models is supported by a suite of modelling and analysis tools which permit the exploration of the dynamic behaviour of the very large metabolic models, comprising Snoopy, Charlie, Prolog, MC2, and Marcie.
Our tools could be applied to populations of models in the context of human - gut microbiota in- teractions. Our approach that we have developed permits the description of the dynamic behavioural interaction between different bacterial strains and their human host on a personalised level within one aggregated model represented as a coloured Petri net. We use simulative model checking techniques over coloured traces to analyse the huge amounts of data generated by the dynamic simulation of these very large and hierarchically structured models.