Unlike the known relationships between the essential nutrients and disease, which focus on single-nutrient relationships such as that between vitamin C and scurvy, these new diet-microbe-disease, and diet-metabolite-disease relationships are more complex. The microbes themselves and their metabolites signal the immune and nervous systems through known and unknown mechanisms, ultimately affecting human physiology, and disease development or progression. Microbes metabolize the end-products of human digestion and indigestible dietary substrates to produce a wide variety of diet-derived and secondary metabolites.

The microbes residing in the human gastrointestinal tract depend on their hosts for sources of fermentable substrate. Microbiome features and metabolites have been increasingly linked to states of health and disease ( 1, 2), and diet is appreciated as one of the key drivers of this relationship. Finally, recent studies demonstrating that diet-microbiome interactions are personalized suggest that diet-microbiome studies should either include longitudinal sampling within individuals to identify personalized responses, or should include an adequate number of participants spanning a range of microbiome types to identify generalized responses. We find evidence that direct effects of diet on the microbiome are likely to be observable within days, while the length of an intervention required for observing microbiome-mediated effects on the host phenotype or host biomarkers, depending on the outcome, may be much longer, on the order of weeks or months. We recommend that microbiome studies include multiple consecutive microbiome samples per study timepoint or phase and multiple days of dietary history prior to each microbiome sample whenever feasible. In this article, we review the current practices in diet-microbiome analysis and study design and make several recommendations for best practices to provoke broader discussion in the field.

Although an increasing number of microbiome studies are now collecting some form of dietary data or even performing diet interventions, there are no clear standards in the microbiome field for how to collect diet data or how to design a diet-microbiome study. Interestingly, despite the influence of diet on the gut microbiome, the majority of microbiome studies published to date contain little or no analysis of dietary intake. Diet is known to be a driver of microbiome variation, and yet the precise mechanisms by which certain dietary components modulate the microbiome, and by which the microbiome produces byproducts and secondary metabolites from dietary components, are not well-understood. Intense recent interest in understanding how the human gut microbiome influences health has kindled a concomitant interest in linking dietary choices to microbiome variation.

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