Recent research increasingly highlights the connection between diet, the gut microbiome, and overall human health. It has been established that the gut microbiome functions as an independent “organ” and its metabolic activity influences the overall metabolism of the body. This paper emphasizes the key roles of the gut microbiome, its composition, and its importance in maintaining the body’s health, as well as the changes that occur under pathological conditions. Our study includes recent in vivo and in vitro findings that demonstrate a direct link between microbiome imbalances and various diseases. Changes in microbiome composition have been observed in conditions such as Alzheimer’s disease, gastrointestinal disorders, and skin diseases. This paper provides an overview of the fundamental concepts and relationships between the health of the gut microbiota and the health of the human body.