Abstract
Iron supplementation studies in children under five suggest potentially adverse gut microbiota shifts. Given iron's importance during early childhood, food-based approaches may offer a more viable supplementation strategy. Using shotgun metagenomics, we examined the effects of 9 months' daily consumption of iron/zinc-biofortified pearl millet (FeZnPM; 8.70 mg/100 g iron) versus control pearl millet (CPM; 3 mg/100 g iron) on the gut microbiome in 12-18-month-old children without severe anemia (hemoglobin ≥9.0 g/dL) from Mumbai urban slums through a randomized controlled trial, the primary outcomes of which were iron status biomarkers and infant growth (ClinicalTrials.gov ID: NCT02233764). In paired (n = 81) and endpoint (n = 108) analyses, FeZnPM consumption was not associated with detectable adverse effects on developing microbiomes and exploratory analyses suggest that it may support beneficial metabolic adaptations via direct modulation of antibiotic, antioxidant, and pollutant degradation pathways. This suggests biofortified crops could provide a sustainable approach to addressing iron deficiency while maintaining healthy microbiome development in early life.