Metagenomics of the human intestinal tract: from who is there to what is done there

•The human intestinal microbiota catalog of genes account for 10 million non redundant genes.•Metagenomics is a powerful tool to study complex microbial communities.•Gut microbiota is shaped during the first years of life.•Immune response is shaped by gut microbiota and conditioned by diet.•Modulating gut microbiota is a challenging therapeutic approach.

The human gastro-intestinal tract is colonized by 106–1014 microorganisms from the three domains, eukaria, archaea and bacteria that are collectively referred as the human gut microbiota. Gut microbiota actively contributes to the digestion of the nutrients, mainly the fibers otherwise undigested by the host, and participate to the host capacity of energy recovery from food. It plays also a key role in gut homeostasis, impacting on its barrier function and regulating the immune and metabolic systems. The target of this review is the diet–microbiota–host immune response triad. Starting from the current knowledge based on intestinal metagenomics, we point out on the role of food in shaping gut microbiota composition and functions, which is therefore mirrored in its healthful or deleterious effect on host immune response.