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Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

Authors
  • Johnson, Abigail J1
  • Vangay, Pajau2
  • Al-Ghalith, Gabriel A2
  • Hillmann, Benjamin M3
  • Ward, Tonya L4
  • Shields-Cutler, Robin R1
  • Kim, Austin D5
  • Shmagel, Anna Konstantinovna6
  • Syed, Arzang N7
  • Walter, Jens8
  • Menon, Ravi9
  • Koecher, Katie9
  • Knights, Dan10
  • 1 BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA.
  • 2 Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA.
  • 3 Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
  • 4 CoreBiome Inc, St. Paul, MN 55114, USA.
  • 5 Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN 55105, USA.
  • 6 Division of Rheumatic and Autoimmune Diseases, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
  • 7 Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
  • 8 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada. , (Canada)
  • 9 Bell Institute of Health & Nutrition, General Mills Inc, Minneapolis, MN 55427, USA.
  • 10 BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: [email protected]
Type
Published Article
Journal
Cell host & microbe
Publication Date
Jun 12, 2019
Volume
25
Issue
6
Identifiers
DOI: 10.1016/j.chom.2019.05.005
PMID: 31194939
Source
Medline
Keywords
Language
English
License
Unknown

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. Copyright © 2019 Elsevier Inc. All rights reserved.

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