This section explores the bidirectional relationship between the human microbiota and functional nutrition through a multidimensional lens. The human body is defined as a superorganism composed not only of human cells but also of microbial cells, with the gut microbiota in particular playing a critical role in individual health. Functional foods are defined as those that go beyond basic nutritional functions, containing bioactive components that regulate physiological processes and contribute to the prevention of chronic diseases. In this context, the systemic health effects of microbiota-modulating components such as prebiotics, probiotics, and postbiotics are examined in detail. Additionally, the chapter highlights the importance of nutrigenetic and epigenetic factors in designing personalized nutritional strategies based on an individual’s genetic makeup. The effects of functional foods on gene expression and epigenetic mechanisms are also discussed. Through clinical case studies, the complementary role of functional foods is demonstrated in conditions such as obesity, diabetes, irritable bowel syndrome, and neuropsychiatric disorders. In conclusion, microbiota-focused functional nutrition emerges as a preventive and therapeutic approach within modern health strategies. When integrated with personalized dietary models, it offers sustainable solutions for public health.