Dietary Habits of 2- to 9-Year-Old American Children Are Associated with Gut Microbiome Composition

Abstract

Background The human gut microbiome is recognized as an important determinant of human health, yet little is known about how dietary habits are related to the microbiome in post-weaned, pre-pubescent children. Objective The goal of this work was to link quantitative dietary intake with microbiome features in a diverse population of children consuming a predominantly Western diet. Design This was a cross-sectional study. Participants/settings English- or Spanish-speaking families with healthy children between the ages of 2 and 9 years were recruited from a community-based, early childhood learning center in suburban Los Angeles, California between June and September 2014. Main outcome measures Children included in the analyses (n=75) contributed three fecal samples and three quantitative 24-hour dietary recalls using the multiple-pass method with an average of 5.7 days between samples. Microbial communities of each fecal sample were characterized using Illumina sequencing of the 16S ribosomal RNA gene. Dietary recalls were analyzed using the Automated Self-Administered 24-Hour Recall Dietary Assessment Tool. Statistical analysis performed Associations between dietary factors and microbiome features were assessed using the Kruskal-Wallis test, Spearman rank correlations, or permutational multivariate analysis of variance. For demographic and health-related variables, χ 2 analyses were used to test for differences between age groups for categorical variables. Results Our results show that age is correlated with three metrics of microbiome diversity ( P <0.05) and is associated with both community structure ( P =0.0488) and membership ( P =0.0002). Several dietary food groups and nutrients were likewise associated with microbiome features. For example, consumption of non–whole-grain foods was associated with community structure ( P =0.0089) and membership ( P =0.0057), but not diversity ( P >0.05). Likewise, the relative abundance of several bacterial taxa were linked to consumption of particular food groups and/or nutrients, as illustrated by the positive associations between total fruit ( P false discovery rate <0.05) and fiber ( P false discovery rate <0.05) consumption with the relative abundance of the Lachnospira genera. Conclusions This hypothesis-generating study demonstrates that the composition of the child gut microbiome remains dynamic beyond the age of 3 years and responds to dietary differences across individuals. In particular, non–whole-grain foods fortified with vitamins and minerals appear to be associated with the composition of the microbiome. Future interventional or model organism-based studies will be needed to test these associations between diet and microbiome composition.