Temporal nutrition analysis associates dietary regularity and quality with gut microbiome diversity: insights from the Food & You digital cohort

Rohan Singh, Daniel McDonald, Alejandra Rios Hernandez, Se Jin Song, Andrew Bartko, Rob Knight and Marcel Salathé ()
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Rohan Singh: EPFL
Daniel McDonald: University of California
Alejandra Rios Hernandez: University of California
Se Jin Song: University of California San Diego
Andrew Bartko: University of California
Rob Knight: University of California
Marcel Salathé: EPFL

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract The gut microbiota is profoundly influenced by dietary choices, with emerging evidence linking it to various health outcomes. Here, we investigate diet-microbiota associations using detailed temporal nutrition intake data captured through real-time food logging via a smartphone app and gut microbiota profiles from 16S rDNA sequencing in ~ 1,000 participants from a digital cohort on personalized nutrition (“Food & You” - clinicaltrials.gov NCT03848299). The primary outcome of the parental trial was to investigate post-meal glucose response variations between individuals in function of their individual factors such as diet, microbiome composition and lifestyle. Our analysis reaffirms that high-quality diets rich in vegetables, fruits, nuts, micronutrients, and favorable dietary indices like HEI (calculated both as standard HEI and daily HEI to capture day-to-day diet quality regularity) correlate with increased microbial diversity and improved stool quality, while fast food-rich diets show opposite effects. Regular consumption of beneficial food groups emerges as a key factor, with regularity in both food intake and diet quality sometimes showing stronger associations than average intake quantities. Machine learning analyses reveal strong bidirectional predictability between gut microbiota composition and dietary factors (ROC AUC up to ~ 0.85-0.9). These findings highlight the critical role of both diet quality and regularity in shaping gut microbiota, the importance of temporal nutrition tracking in offering insights for targeted nutritional strategies, and suggest that the gut microbiota can be used to estimate dietary indices.

Date: 2025
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DOI: 10.1038/s41467-025-63799-z

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