The review explores the relationship between nutrition, gut microbiota, and epigenetics. It highlights how dietary nutrients can influence the gut microbiota, which in turn affects epigenetic regulation, impacting overall health. The gut microbiota, a complex community of microorganisms, plays a crucial role in immune function, nutrient metabolism, and intestinal barrier integrity. Epigenetic mechanisms, such as DNA methylation, histone modification, and RNA interference, regulate gene expression without altering DNA sequences. The review discusses how nutrients like vitamin D, iron, short-chain fatty acids (SCFAs), and magnesium can modulate the gut microbiota through epigenetic pathways. Vitamin D influences immune function and microbiota composition, while iron affects iron homeostasis and microbiota diversity. SCFAs, produced by gut bacteria, inhibit histone deacetylases, promoting gene expression and reducing inflammation. Magnesium supports microbial diversity and SCFA production, which are essential for gut health. Zinc is essential for microbial growth and immune function. The review emphasizes the interplay between diet, microbiota, and epigenetics in maintaining systemic health and preventing diseases. Further research is needed to fully understand these interactions and their implications for therapeutic interventions.The review explores the relationship between nutrition, gut microbiota, and epigenetics. It highlights how dietary nutrients can influence the gut microbiota, which in turn affects epigenetic regulation, impacting overall health. The gut microbiota, a complex community of microorganisms, plays a crucial role in immune function, nutrient metabolism, and intestinal barrier integrity. Epigenetic mechanisms, such as DNA methylation, histone modification, and RNA interference, regulate gene expression without altering DNA sequences. The review discusses how nutrients like vitamin D, iron, short-chain fatty acids (SCFAs), and magnesium can modulate the gut microbiota through epigenetic pathways. Vitamin D influences immune function and microbiota composition, while iron affects iron homeostasis and microbiota diversity. SCFAs, produced by gut bacteria, inhibit histone deacetylases, promoting gene expression and reducing inflammation. Magnesium supports microbial diversity and SCFA production, which are essential for gut health. Zinc is essential for microbial growth and immune function. The review emphasizes the interplay between diet, microbiota, and epigenetics in maintaining systemic health and preventing diseases. Further research is needed to fully understand these interactions and their implications for therapeutic interventions.