Host diets drive microbiome evolution and functional divergence

Substantial variation in gut microbiome function across individuals underscores the pivotal role of the host in shaping microbial diversity. Increasing evidence indicates that diet is a major selective force driving the evolutionary trajectory of the gut microbiome. In response to dietary inputs, the microbiome adapts by shifting the relative abundance of taxa, species, and sub-strains. The gut microbiome also acquires novel genetic features through selecting advantageous mutations and genes, as well as colonizing exogenous bacterial species that enhance nutrient utilization. These adaptive processes occur not only across human evolutionary history but also within an individual's lifetime, consequently generating functionally divergent microbiomes with important consequences for health. Diets of poor nutritional quality, such as the Western-style diet, foster disease-permissive microbial functions. Understanding how dietary patterns and components influence microbiome evolution, and thereby affect health, is essential for developing diet-based strategies to modulate microbial functions. This review presents compelling evidence to demonstrate how host diet shapes gut microbiome evolution and leads to a functionally divergent gut microbiome that impacts human health.