Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort

Background: Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiota. Objectives: We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy US adult cohort. Methods: We collected 2 to 3 automated self-administered 24-hour dietary recalls over 10-14 days, together with a single stool sample, from 343 healthy adults in a cross-sectional phenotyping study. This study examined a multi-ethnic cohort balanced for age (18-65 years), sex, and BMI (18.5-45 kg/m(2)). Dietary data were edited to a tree format according to published methods. The tree structure was annotated with the average total grams of dry weight, fat, protein, carbohydrate, or fiber from each food item reported. The alpha and beta diversity measurements, calculated using the tree structure, were analyzed relative to the microbial community diversity, determined by a Quantitative Insights Into Microbial Ecology (QIIME) 2 analysis of the bacterial 16S ribosomal RNA V4 region, sequenced from stool samples. K-means clustering was used to form groups of individuals consuming similar diets, and gut microbial communities were compared among groups using differential expression analysis for sequence count data. Results: The alpha diversity of diet dry weight was significantly correlated with the gut microbial community alpha diversity (r = 0.171). The correlation improved when diet was characterized using grams of carbohydrates (r = 0.186) or fiber (r= 0.213). Bifidobacterium was enriched with diets containing higher levels of total carbohydrate from cooked grains. Lachnospira, was enriched with diet patterns containing high consumption of fiber from fruits excluding berries. Conclusions: The tree structure, annotated with grams of carbohydrate, is a robust analysis method for comparing self-reported diet to the gut microbial community composition. This method identified consumption of fiber from fruit robustly associated with an abundance of pectinolytic bacterial genus, Lachnospira, in the guts of healthy adults.

Automated summary

This study investigated the relationship between diet patterns and gut microbial community composition in a diverse, healthy US adult cohort. Results showed significant correlations between diet dry weight, carbohydrates, fiber, and gut microbial diversity. Bifidobacterium and Lachnospira were found to be enriched in diets with specific nutrient profiles. The use of a tree structure annotated with grams of carbohydrates provided a robust method for comparing self-reported diet to gut microbial community composition.