Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

TLDR

Diet is a key determinant of human gut microbiome variation, yet the fine‑scale relationships between daily food choices and microbiome composition remain unexplored. The study integrated 24‑hour food records with daily fecal shotgun metagenomes from 34 healthy subjects over 17 days using multivariate methods. Microbiome composition was more strongly linked to specific food choices than to nutrient profiles, varied across multiple days, and showed highly personalized responses; monotonous diets did not stabilize the microbiome, whereas dietary diversity promoted stability, indicating that interventions must be individualized. Trial registered at ClinicalTrials.gov: NCT03610477.

Abstract

Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.