It has become clear that food components, including micronutrients, and gut microbiota are involved in the control of health conditions. Further, there has been growing interest in food products and drug development targeting the gut environment. Particularly, precision nutrition, which proposes optimal diets based on an individual’s gut environment, genetic information, and lifestyle, has gained importance. In this article, we discuss the relationship between the gut environment, which is shaped in collaboration of diets and gut microbiota, and its immune functions and health, using examples such as vitamin B1 and dietary oils. Furthermore, we explore the potential for developing a personalized nutritional guidance system through the advancement of precision nutrition and the utilization of gut environment databases, as well as the possibilities for drug development and healthcare targeting beneficial gut bacteria.