Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

By A. Johnson, P. Vangay, Gabriel A. Al-Ghalith, Benjamin M Hillmann, Tonya L. Ward, Robin R. Shields-Cutler, Austin D. Kim, A. Shmagel, Arzang N Syed, J. Walter and 3 more. Cell Host and Microbe, 2019

609 citations recorded by the source corpus.

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.

Subfields: General Health Professions, Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/b70c0b18900f054f82cf2a15e3e1d29c08cb059b

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In General Health Professions

In Molecular Biology

In Public Health, Environmental and Occupational Health

Justin L. Sonnenburg

Citations in the corpus

Gut Microbiota-Targeted Diets Modulate Human Immune Status (2020, positive): “We found that in both diet arms participants’ gut microbiota composition stayed highly individualized during the intervention rather than clustering by diet at the end of the intervention, findings similar to those reported in previous human microbiota studies (Johnson et al., 2019; Wu et al., 2011)”
Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019, methodology): “Large day to day variations in diet are not reflected in the gut microbiota, suggesting that overall dietary habits have a greater impact on gut microbial composition [35].”
Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health (2020, background): “In addition to that the highly individual response to diet 88 89 highlights the need for personalised recommendations, based on different gut microbiota compositions, as well as on distinct metabolic phenotypes.”
DRAM for distilling microbial metabolism to automate the curation of microbiome function (2020, background): “We note, that this assignment is not unambiguous as some CAZymes are promiscuous for multiple substrates (79), a functionality DRAM accounts for in the Distillate and Product (Supplementary Figure S2, File S4).”
Gut Microbiome: Profound Implications for Diet and Disease (2019, background): “microbiome responses to different foods depending on their prior history of dietary diversity [322].”
Dietary lipids, gut microbiota and lipid metabolism (2019, background): “Even though efforts have been made to understand how dietary pattern affect the gut microbiota[138, 139], the importance of specific foods and combinations of nutrients in shaping microbial profile remains elusive.”