**Abstract**

Microbiomics represents a new science studying the microbiome, consisting of all the microorganisms of a given community. This new science collects data about all the members of the microbial community and quantifies the molecules responsible for the structure, function, and dynamics of the microbiome. The human microbiome plays a very important role in the healthy state and in a variety of disease states. The human microbiome knowledge has evolved during the last decades and nowadays one can consider that, in particular, the gut microbiota is seen as a significant organ holding 150 times more genes compared to the human genome. This chapter will focus on discussing the normal and modified phyla and species of the gut microbiome in a variety of conditions, providing a better understanding of host-microbiome interactions. We will highlight some new associations between intestinal dysbiosis and acute or chronic inflammatory and metabolic diseases.

**Keywords:** microbiomics, gut microbiome, microbiota, dysbiosis, eubiosis
