Comparing apples to apples: Evaluating foodomics in precision nutrition research featuring the influence of polyphenols on the gut microbiome

Abstract

This review aimed to evaluate the use of advanced omics methodologies in dietary intervention clinical trials investigating the influence of polyphenols on the gut microbiome. All published clinical studies in the Cochrane Library database from 2014 to 2024 containing the keywords “polyphenols” and “gut microbiome” were compiled and categorized based on experimental design, analytical methodologies, and findings. We found that despite known variability in food composition across agricultural and processing parameters, omics analysis of the food used in clinical nutrition interventions has not been widely embraced. None of the studies evaluated employed untargeted omics approaches for food composition analysis, while 5 of the 38 studies used untargeted omics for clinical samples analysis. Targeted analytical methods focused on known compounds or proxies were more commonly used for food composition analysis (18 of 38 studies) and clinical samples (24 of 38 studies), though analysis of clinical samples focused on a greater number of target compounds. Data from these studies support relationships between the gut microbiome, clinical outcomes, and specific metabolites. However, several studies highlight inconsistencies between their findings and previous literature, which may be attributed to unrealized differences in polyphenol composition. We propose that inclusion of comprehensive omics-based food composition analyses in dietary intervention clinical trials may increase study value by accounting for variability in food composition and enabling novel discovery. Such data would support the emerging fields of personalized and precision nutrition, aimed at understanding the influence of individual human characteristics on physiological responses to foods, nutrients, phytochemicals, and dietary patterns.