Dietary drivers of taxonomic and functional diversity in the child gut microbiome

The human gut is home to trillions of microbial cells whose functions are essential for normal human physiology. However, quantitative linkages between diet and gut microbiome composition are lacking, particularly in post-weaned, pre-pubescent children. To address this knowledge gap, we conducted a community-based research project at a children's center located in Los Angeles, CA. Study participants (n=70, 2-8 years old) provided one fecal sample and three dietary recalls of the foods consumed over a 24-hour period. Dietary data was averaged across the three recalls to approximate the average daily intake of each child. Functional capacity of the gut microbiome was assessed using shotgun metagenomic sequencing on an Illumina HiSeq, yielding 334.3 Gbp of clean sequence data. Average dietary intake was disaggregated and converted into macro- and micronutrients using ASA24, a program developed by the USDA. Taxonomically, an individual's gut microbiome could be clustered into two groups based on the abundances of the Bacteroidetes and Firmicutes phyla. These taxonomic differences strongly correlate to functional differences such as the gut microbiomes ability to metabolize starch and synthesize vitamins. When we scale nutrient intake by the recommended daily allowance for each subject, many species level and functional attributes were correlated with consumption of specific dietary features such as processed grains, vegetables, B-vitamins, and zinc. The strongest relationships we observed were between microbiome features and a select set of micronutrients (zinc, folate, iron, Bvitamins). These nutrients co-varied suggesting a common food source, most likely enriched and fortified grains. Only by understanding relationships between diet and gut microbiome function in diverse populations of healthy individuals during different lifestages will we be able to link subtle changes in the gut microbiome with human health outcomes later in life.