Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

Abigail J Johnson; Pajau Vangay; Gabriel A Al-Ghalith; Benjamin M Hillmann; Tonya L Ward; Robin R Shields-Cutler; Austin D Kim; Anna Konstantinovna Shmagel; Arzang N Syed; Personalized Microbiome Class Students; Jens Walter; Ravi Menon; Katie Koecher; Dan Knights

doi:10.1016/j.chom.2019.05.005

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

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

Authors

Affiliations

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.

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

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Diet*
Feces / microbiology
Female
Gastrointestinal Microbiome*
Humans
Longitudinal Studies
Male
Metagenomics
Microbiota*
Middle Aged
Young Adult

Associated data

ClinicalTrials.gov/NCT03610477