Leveraging a Biomarker-Based Dietary Assessment to Interrogate the Impacts of Global Complementary Feeding Diets on Gut Microbiome Development

Abstract

Between birth and adulthood, the human gut is colonized by a complex community of microorganisms. While the significance of the early life gut microbiome on human health is well established, knowledge is limited regarding what elements of early life complementary feeding diet govern microbiome colonization. Here, we use an objective and comprehensive dietary assessment technique, FoodSeq to interrogate diet across 1,063 samples from 0-3 year old children across 5 countries. We also performed 16S rRNA sequencing. We found that early life diet is highly diverse and region-specific: we detected 207 plant food sequence variants, of which, only 8 were significantly shared across all 5 countries. Acquisition of plant dietary diversity does not necessarily coincide with microbiome maturation, as diet diversifies soon after age 1, while the gut microbiome continues to increase in diversity until close to age 2. Plant diversity is positively correlated with microbial diversity in a context-dependent manner but does not appear to drive microbiome maturation. Nevertheless, specific adult-associated bacterial taxa were associated with plant intake. Preliminary data from an in vitro study support the hypothesis that plant diversity matters as a marker of plant intake. This study reveals that microbiome maturation following weaning is supported across diverse dietary compositions and that dietary diversity, previously known to be a biomarker for nutrition status, is also relevant for mature microbiome taxa abundance. The results described in this work lay the groundwork for future studies investigating diet-microbiome-health interactions in children.