1. Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans
- Author
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Abigail J. Johnson, Arzang N Syed, Robin R. Shields-Cutler, Anna Shmagel, Tonya Ward, Benjamin Hillmann, Pajau Vangay, Dan Knights, Austin D. Kim, Gabriel A. Al-Ghalith, Katie Koecher, Jens Walter, Personalized Microbiome Class Students, and Ravi Menon
- Subjects
Adult ,Male ,Multiple days ,Meal replacement ,Biology ,Gut flora ,Microbiology ,03 medical and health sciences ,Feces ,Young Adult ,0302 clinical medicine ,Human gut ,Virology ,Environmental health ,Food choice ,Humans ,Microbiome ,Longitudinal Studies ,030304 developmental biology ,0303 health sciences ,Microbiota ,digestive, oral, and skin physiology ,Middle Aged ,biology.organism_classification ,Diet ,Gastrointestinal Microbiome ,Metagenomics ,Dietary history ,Parasitology ,Female ,030217 neurology & neurosurgery - Abstract
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 .
- Published
- 2018