Various microorganisms such as archaea, bacteria, fungi and viruses inhabit the gastrointestinal tract, where bacterial communities form one of the most densely populated bacterial populations in the world involved in many essential processes: metabolism of nutrients, protection against pathogens, maintenance of the structural integrity of the intestinal mucosal barrier and immunomodulation. Also, many things influence the development and change of the intestinal microbiota during life, of which we particularly single out nutrition. The Western type of diet, rich in animal proteins, saturated fats, simple sugars, and very little food of plant origin, is spreading more and more in the world; for these reasons there are more and more chronic diseases in the world. The Mediterranean diet, which contains a high intake of fiber and other carbohydrates, is rich in mono- and poly-unsaturated fatty acids, high levels of polyphenols and other antioxidants, and has a higher intake of vegetable than animal proteins, is presented as a better choice of diet. Everyone has a unique intestinal microbiota, and therefore one type of diet cannot suit everyone, and for this reason, personalized approach should be practiced, with the use of antibiotics as rarely as possible and the use of probiotics and prebiotics to restore lost good bacteria.