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Cell Host Microbe. 2019 Jun 12;25(6):789-802.e5. doi: 10.1016/j.chom.2019.05.005.

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

Author information

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
Microbial Engineering Program, Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA.
9
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
10
Bell Institute of Health & Nutrition, General Mills Inc, Minneapolis, MN 55427, USA.
11
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: dknights@umn.edu.

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.

KEYWORDS:

diet; diversity; dynamics; fiber; metagenomics; microbial ecology; microbiome; shotgun sequencing; stability

PMID:
31194939
DOI:
10.1016/j.chom.2019.05.005

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