The consumption of probiotics may minimize disturbances of the intestinal microbiota. The health effects of probiotic strains are known to be strain dependent. Hence, it is crucial to select probiotic strains for their tolerance to acid and bile salts and their ability to survive transit through the stomach and small intestine in order to reach the large intestine. Lactobacilli and bifidobacteria are the main strains present in commercial probiotic products. Probiogenomics and functional genomics allow the determination of the molecular mechanisms by which the functional activities of probiotics are achieved and in understanding their roles. Yogurt and fermented milk products are generally the most commercialized probiotic products. The minimum dose required for a probiotic effect depends on the probiotic strain used as well as the type of food. In healthy individuals, probiotic strains should reinforce populations of autochtonous bifidobacteria or lactobacilli without altering the balanced microbial ecosystem. Evaluation of the safety of probiotic strains should consider many factors, including the ability of probiotic strains to deconjugate bile salts and the discrimination of probiotics strains (genus, species, subspecies, and bacterial strain) by classical and molecular methods.