The gut microbiota is considered an essential “organ” due to its various functions and significance for human health, and its altered composition and function have been linked with various disease states of the host. Over the years, different strategies aimed at targeting the gut microbiota have emerged as promising tools for the prevention and management of several human disorders. This review summarizes notable findings from studies published between April 2021 and March 2022 evaluating the therapeutic potential of microbiota-modulatory agents, including prebiotics, probiotics, and synbiotics in intestinal and cardiometabolic diseases.