Coevolution of Human Diet and Gut Microbiome: Implications for Nutrigenomics and Cross-Population Health

The coevolution of the human diet and gut microbiome has played a pivotal role in shaping metabolic, immune, and epigenetic functions across human history. Dietary transitions from high-fiber ancestral patterns to modern ultraprocessed diets have markedly influenced microbial diversity and functionality, contributing to the emergence of chronic diseases such as obesity, Type 2 diabetes, and inflammatory conditions. Recognizing the significance of gut microbial patterns in humans, this review explores the coevolution of diet and gut microbiota, especially on how gut microbiota influences human gene regulation, and the implications of these interactions for personalized nutrition and global health strategies. Comparative insights across populations in different periods reveal that geography, dietary practices, and host genetics interact to shape distinct microbiome configurations and disease susceptibility. Therefore, implementing a nutrigenomics and nutrigenetics approach might provide a molecular framework to understand these interactions and to develop personalized nutrition strategies. Though several clinical implementations utilizing genomic data have been embedded in several countries, global implementation remains challenging due to population-specific genetic variability, cultural dietary preferences, cost limitations, and ethical considerations. Integrating microbiome and genetic data into clinical practice and public health policy offers a promising path to mitigate diet-related health disparities that is tailored to individual and population-level needs.