Dietary plant diversity predicts early life microbiome maturation

Between birth and adulthood, the human gut is colonized by a complex microbial community. Despite established links between the infant gut microbiome and health, knowledge is limited for how complementary feeding influences colonization. Using FoodSeq, an objective DNA-based dietary assessment technique, we analyzed 1,036 fecal samples from 729 children aged 0-3 years across countries in North America, Central America, Africa, and Asia. We detected a wide diversity of 199 unique plant food sequences, of which only eight staple foods were consistently present across all countries. Despite this variation in global diet, we identified universal trajectories in early life dietary exposure: weaning stage, which tracked with dietary diversity, emerged as the dominant dietary signature across populations. Still, dietary diversity did not correlate with gut microbial diversity. Instead, dietary diversity and weaning stage specifically predicted the abundance of adult-like bacterial taxa, including known fiber-degrading taxa, which colonized after age 1. Our findings support a two-stage model of microbiome maturation: an early phase dominated by milk-adapted taxa independent of complementary feeding, followed by a maturation phase where diet shapes adult-like microbiota colonization. This model suggests that tracking and promoting plant dietary diversity may support the timely emergence of an adult-like microbiome.