Evidence has shown that human gut microbiota has an important effect on many aspects of human physiology including metabolism, nutrient absorption and immune function. Perturbation of the intestinal microbiota could lead to chronic diseases, such as inflammatory bowel diseases, obesity, diabetes, and colon cancer. Modulation of the microbiota by dietary interventions, especially by the use of probiotics, prebiotics and synbiotics has shown its potential for the treatment and prevention of diseases. Hence, the number of studies aimed to research the therapeutic effect of probiotic strains and prebiotics as well as the molecular mechanisms involved in the modulation of microbial populations and their environment by dietary intervention had increased considerably in the last 10 years. On the other hand, the current omics technologies are providing the tools needed to examine the community structure and function of the gut microbiota and therefore, understand its role in health and disease. The aim of this chapter is to provide a comprehensive overview of the research carried out on probiotics, prebiotics and synbiotics in the last 10 years as well as present the new biotechnologies that are contributing to the understanding of the host-microbiota interactions and the mechanisms of actions of pro-, pre- and synbiotics.