The mammalian intestinal tract is heavily colonized with a complex community of micro-organisms, present at a very high density, and containing an estimated amount of 1014 bacteria. The microbiota generally benefits the host, as it plays a central role in maturing the immune system, protecting against infection by entero-pathogens such as Clostridium difficile, and favoring nutrient digestion/energy extraction in our intestine. An altered microbiota, however, can become detrimental and lead to inflammation, metabolic disorders, and even altered behavior/neuroinflammation. While there are many factors involved in regulating the intestinal microbiota composition and the way it interacts with its host, this review will focus on the role played by food additives on host/microbiota relationship.