Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

Abigail J. Johnson, Personalized Microbiome Class Students, Anna K Shmagel

Research output: Contribution to journalArticlepeer-review

74 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)789-802.e5
JournalCell Host and Microbe
Volume25
Issue number6
DOIs
StatePublished - Jun 12 2019

Bibliographical note

Funding Information:
We thank the study subjects for their dedication to this study. The citizen science course associated with this study was supported by the College of Biological Sciences and the BioTechnology Institute, both at the University of Minnesota. We thank the Personalized Microbiome Class students who contributed to early analysis of this dataset and were the source of fruitful discussions related to these data. We specifically thank Abdirahman Sheikh-Mohamed and Patrick Johnson for their volunteer contributions to this study. We are thankful to the Knights Lab members and collaborators who provided early insight into analysis and interpretation of the data during early manuscript development. We thank the study's reviewers, who greatly improved the quality of the manuscript during review. This study was supported by General Mills. Conceptualization, D.K. and A.J.J.; Methodology, D.K. and A.J.J.; Software, A.J.J, P.V. G.A.-G. B.H. T.W. and A.D.K.; Formal Analysis, A.J.J.; Investigation, A.J.J. R.S.C. and A.N.S.; Resources, D.K.; Data Curation, A.J.J.; Writing – Original Draft, A.J.J.; Writing – Review & Editing, D.K. G.A.-G. B.H. P.V. R.M. K.K. R.S.C. T.W. A.J.J. and J.W.; Visualization, A.J.J.; Supervision, D.K.; Project Administration, A.J.J. and D.K.; Funding Acquisition, D.K. R.M. and K.K. All authors read and approved the final manuscript. Personal Microbiome Class students (Jesse Abelson, Breann Elise Abernathy, Kasey Ah Pook, Adam Rashid Ahmed, Khadir Tababouanga Albert, Samantha Tappe Brook, Drew Benjamin Carter, Elizabeth S. Dean, Tong Ding, Grant Andrew Hedblom, Laura Beth Jore, Vasanth Lakshmipathy, Leeore Levinstein, Sarah Anna Marie Lucas, Morrine Auma Omolo, Kayla Donnelle Pederson, Philips,Kinsey H. Austin Michael Schachtner, Reed Grace Owens-Kurtz, Justin Wiertzema, Sambhawa Priya, and Serina Lee Robinson) provided ideas for analysis. D.K. serves as CEO of CoreBiome, a company involved in the commercialization of microbiome analysis. CoreBiome is now a wholly owned subsidiary of OraSure. These interests have been reviewed and managed by the University of Minnesota in accordance with its conflict-of-interest policies. T.W. is an employee of CoreBiome. R.M. and K.K. are employees of General Mills.

Funding Information:
We thank the study subjects for their dedication to this study. The citizen science course associated with this study was supported by the College of Biological Sciences and the BioTechnology Institute, both at the University of Minnesota. We thank the Personalized Microbiome Class students who contributed to early analysis of this dataset and were the source of fruitful discussions related to these data. We specifically thank Abdirahman Sheikh-Mohamed and Patrick Johnson for their volunteer contributions to this study. We are thankful to the Knights Lab members and collaborators who provided early insight into analysis and interpretation of the data during early manuscript development. We thank the study’s reviewers, who greatly improved the quality of the manuscript during review. This study was supported by General Mills .

Funding Information:
We thank the study subjects for their dedication to this study. The citizen science course associated with this study was supported by the College of Biological Sciences and the BioTechnology Institute, both at the University of Minnesota. We thank the Personalized Microbiome Class students who contributed to early analysis of this dataset and were the source of fruitful discussions related to these data. We specifically thank Abdirahman Sheikh-Mohamed and Patrick Johnson for their volunteer contributions to this study. We are thankful to the Knights Lab members and collaborators who provided early insight into analysis and interpretation of the data during early manuscript development. We thank the study's reviewers, who greatly improved the quality of the manuscript during review. This study was supported by General Mills. Conceptualization, D.K. and A.J.J.; Methodology, D.K. and A.J.J.; Software, A.J.J, P.V. G.A.-G. B.H. T.W. and A.D.K.; Formal Analysis, A.J.J.; Investigation, A.J.J. R.S.C. and A.N.S.; Resources, D.K.; Data Curation, A.J.J.; Writing ? Original Draft, A.J.J.; Writing ? Review & Editing, D.K. G.A.-G. B.H. P.V. R.M. K.K. R.S.C. T.W. A.J.J. and J.W.; Visualization, A.J.J.; Supervision, D.K.; Project Administration, A.J.J. and D.K.; Funding Acquisition, D.K. R.M. and K.K. All authors read and approved the final manuscript. Personal Microbiome Class students (Jesse Abelson, Breann Elise Abernathy, Kasey Ah Pook, Adam Rashid Ahmed, Khadir Tababouanga Albert, Samantha Tappe Brook, Drew Benjamin Carter, Elizabeth S. Dean, Tong Ding, Grant Andrew Hedblom, Laura Beth Jore, Vasanth Lakshmipathy, Leeore Levinstein, Sarah Anna Marie Lucas, Morrine Auma Omolo, Kayla Donnelle Pederson, Philips,Kinsey H. Austin Michael Schachtner, Reed Grace Owens-Kurtz, Justin Wiertzema, Sambhawa Priya, and Serina Lee Robinson) provided ideas for analysis. D.K. serves as CEO of CoreBiome, a company involved in the commercialization of microbiome analysis. CoreBiome is now a wholly owned subsidiary of OraSure. These interests have been reviewed and managed by the University of Minnesota in accordance with its conflict-of-interest policies. T.W. is an employee of CoreBiome. R.M. and K.K. are employees of General Mills.

Publisher Copyright:
© 2019 Elsevier Inc.

Keywords

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

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