Tree-based analysis of dietary diversity captures associations between fiber intake and gut microbiota composition in a healthy U.S. adult cohort

Authors: Kable, Mary; Chin, Elizabeth; Storms, David; Lemay, Danielle; Stephensen, Charles

Submitted to: Journal of Nutrition
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2021
Publication Date: 12/27/2021
Citation: Kable, M.E., Chin, E.L., Storms, D.H., Lemay, D.G., Stephensen, C.B. 2021. Tree-based analysis of dietary diversity captures associations between fiber intake and gut microbiota composition in a healthy U.S. adult cohort. Journal of Nutrition. 152(3):779-788. https://doi.org/10.1093/jn/nxab430.
DOI: https://doi.org/10.1093/jn/nxab430

Interpretive Summary: The types of food that humans consume impact the activities and survival of bacteria in our gut. These bacteria and their activities can in turn impact human health. Identifying relationships between consumption of specific foods/nutrients and expansion of specific bacteria within the gut could influence the development of future dietary guidelines. We examined the relationship between diet and gut bacteria by collecting 2 – 3 Automated Self-Administered 24-hour Dietary Recalls (ASA24) over the course of 10-14 days together with a single stool sample from each of 343 subjects in a multi-ethnic U.S. cohort balanced for age, sex, and BMI. The dietary data was organized into a tree format with similar foods arranged more closely together than dissimilar foods. For example, all fruits were connected to one branch, while milk products were connected to another. The identities of bacteria in the gut, collected by sequencing a bacterial marker gene from stool, were similarly arranged in a tree format. When the food tree was annotated with the amount of fiber contained in each food consumed by the participants in the study, we found that bacteria capable of consuming fiber from fruit, pectin, were significantly increased in individuals who consume diet patterns with significantly more fiber from “fruits excluding berries”.

Technical Abstract: Background. Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiome. Objective. We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy U.S. cohort (ClinicalTrials.gov Identifier: NCT02367287). Methods. Dietary data in the form of two to three Automated Self-Administered 24-hour Dietary Recalls (ASA24) were collected over 10-14 days together with a single stool sample from 343 subjects in a multi-ethnic cohort balanced for age, sex, and BMI. Dietary data was edited to a tree format according to methods published by Johnson et. al. and the 16S rRNA V4 region was sequenced from stool samples. Results. Dietary diversity, with abundance characterized by grams of each recorded food item consumed per day, was correlated with gut microbial community diversity. The association improved when diet was characterized using grams of carbohydrates or fiber. Total carbohydrate from level 3 categories “Mixtures-mainly grain pasta or bread”, “White potatoes fried” and “Carbonated soft drinks” was consumed in the highest amounts by individuals with gut microbiomes enriched for Bifidobacterium. Bacterial genus, Lachnospira, was significantly associated with diet patterns containing high consumption of fiber from “Fruits excluding berries”. Conclusion. Dietary data, organized in a tree structure annotated with grams of carbohydrate, especially fiber, is a robust analysis method for comparison of dietary data to gut microbial community composition. This analysis identified a reproducible association between consumption of fruit and relative abundance of pectinolytic bacterial genus, Lachnospira, in the gut microbial community.