The present Special Issue of the International Journal of Molecular Sciences focuses on the relevant and rapidly developing topic of gut microbiota research. As the articles within this issue highlight, the human gut microbiota plays a critical role in human health. Dietary intake directly influences gut microbiota composition, and the resulting changes in gut metabolites can have profound effects on the host. This Special Issue brings together the latest findings on the intricate relationship between bioactive food components, gut microbiota, colon health, and chronic metabolic diseases. The gut microbiota is a complex ecosystem composed of trillions of microorganisms, including bacteria, archaea, fungi, and viruses. These microbes play essential roles in digestion, nutrient absorption, immune function, and even mental health. Importantly, the composition of the gut microbiota is not static; it is constantly changing in response to diet, lifestyle factors, and medications. The articles within this issue highlight the vast potential of dietary interventions to modulate gut microbiota composition and promote health. As our understanding of this complex ecosystem continues to grow, we can expect to see the development of novel therapeutic strategies for a wide range of chronic diseases.