Cell Host & Microbe
Volume 25, Issue 6, 12 June 2019, Pages 789-802.e5
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Article
Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

https://doi.org/10.1016/j.chom.2019.05.005Get rights and content
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Highlights

  • Daily microbiome variation is related to food choices, but not to conventional nutrients

  • Daily microbiome variation depends on at least two days of dietary history

  • Similar foods have different effects on different people’s microbiomes

Summary

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.

Keywords

microbiome
diet
metagenomics
shotgun sequencing
diversity
stability
fiber
dynamics
microbial ecology

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