The human intestinal microbiota is a complex microbial ecosystem that plays a crucial role in several aspects of human health. It is particularly involved in the metabolism of residual fibers, through anaerobic digestion, thus providing significant energy (Short Chain Fatty Acids, simple sugars) and vitamins to the host. Whole Genome Sequencing (WGS) data from metagenomic analyses give an insight of the content in terms of genes of an entire microbial community, even if the organisms that compose it cannot be cultivated. In addition to the potential of conventional molecular inventory techniques (such as targeting ADNr16s), which allows an analysis of diversity, WGS approaches provide an access to the functions. We show how these data can be used to analyse the structure of carbohydrates degradation-related functions. We show how the information obtained can be integrated in a high level mechanistic in silico model of the microbiota carbohydrate trophic chain.