Programming the Infant Gut: How Maternal and Early Life Nutrition Shape the Infant Microbiome and Long-term Health—A Narrative Review

Childhood malnutrition, including undernutrition, obesity, and micronutrient deficiencies, remains a major global health burden. Emerging evidence points to the gut microbiome as a critical mediator linking maternal, prenatal, and early-life nutrition to long-term offspring health outcomes. From conception and through the first years of life, maternal diet, metabolic state, and environmental exposures shape offspring microbial colonization and maturation. Breastfeeding and consumption of fiber-rich and fermented foods (maternal and post-weaning) support beneficial microbiota, while high-fat, high-sugar diets, xenobiotics, and artificial additives may promote dysbiosis. The composition and diversity of the infant microbiome influence immune, metabolic, and neurodevelopmental processes and may also contribute to the intergenerational transmission of malnutrition. While commercial formulas increasingly include “biotics” to mimic human milk, exclusive breastfeeding remains the gold standard. Complementary feeding practices, including timing and diet quality, are known to modulate microbial maturation. Diet-based interventions in pregnancy show promise in improving microbiome function and preventing disease in offspring. Because the microbiome is highly plastic in the first years of life, this window offers unique opportunities for preventive strategies targeting maternal and child nutrition. Integrating microbiome science into public health and dietary guidelines could enhance current approaches to breaking the cycle of malnutrition and promoting lifelong health.