The gut microbiota is being recognized as a factor with a significant influence on host physiology, health maintenance, and disease prevention. Distinct alterations of the gut microbiota are correlated with several chronic diseases. Currently, gut microbiota can be modulated by diet, probiotics, prebiotics, postbiotics, pharmabiotics, and fecal microbiota transplantation. An effective strategy in gut microbiota modulation is needed for the prevention and supportive treatment of chronic diseases. New and more effective approaches toward gut microbiota modulation are emerging, namely personalization and targeted modulation. The composition of novel products and treatments based on the individual gut microbiome, metabolome, strain specificity, and clinical data analysis can reveal and address specific changes to the diversity, composition, and function of gut microbiota. These analyses enable the development of personalized and targeted gut microbiota modulation, by the application of beneficial microorganisms, their consortia, their metabolites, and their effective combination.