Medicinal plants have been an important therapeutic option for the treatment of gastrointestinal disorders since ancient times. Among the wide range of diseases affecting the gastrointestinal tract, the main areas of application for medicinal plants are functional and chronic gastrointestinal disorders, such as functional dyspepsia and irritable bowel syndrome. Gut microbiota affects human behavior. This is thought to be mediated by hormones involved in brain-gut communication. The role of gut microbiota in the biotransformation of xenobiotics ingested by humans has received significant attention. It is widely acknowledged that gut microbiota can greatly influence the efficacy and toxicity of both synthetic drugs and natural products used to treat various diseases. Recent research has shown that gut microbiota plays a crucial role in maintaining normal brain function. The brain and gut have a bidirectional communication system that has been acknowledged for some time. It is suggested that gut microbiota is an important factor in how the body affects the brain, contributes to healthy homeostasis, and influences the risk of diseases such as anxiety and mood disorders.