The central objective of the MetaHit project is to establish associations between the genes of the human intestinal microbiota and human health and disease. The research work is focused on two disorders of increasing importance in Europe, Inflamatory Bowel Disease (IBD) and obesity. First, we need to establish an extensive reference catalog of microbial genes and genomes present in the human intestine. The second challenge is to develop tools to determine which genes and genomes of the reference catalog are present in different individuals and at what frequency. Third, it is necessary to gather cohorts of individuals, some sick and some healthy, and determine which genes and genomes they carry. Also, it is crucial to develop bioinformatic tools to store, organize and interpret this information, and thus establish associations between intestinal microbiota and health and disease.