The gut microbial community is a highly complex ecosystem, harboring a high taxonomic diversity. The gut microbiota plays an important role in the health and well-being of its host. Our aim is to develop mathematical, data analysis and modelling approaches to help integrate knowledge and data. We work on knowledge based dynamic models but also design new models, hypothesis driven, to analyze metagenomic datasets. Our team and B?atrice Laroche (MAIAGE) have been collaborating since 2007 and we co-supervise S?bastien Raguideau’s PhD.