Polyphenols and gut microbiota in precision nutrition: Epigenetic mechanisms and dietary strategies

Abstract

Objective

Understand how the interaction between polyphenols and gut microbiota influences the metabolic response and which dietary strategies modulate this relationship.

Understand how the interaction between polyphenols and gut microbiota influences the metabolic response and which dietary strategies modulate this relationship.

Methods

A review of articles selected from January to June 2026 from the PubMed, SciELO and ScienceDirect databases was conducted using the descriptors ‘gut microbiome’, ‘microbiota’, ‘polyphenols’ and ‘bioactive compounds’. Original articles published between 2010 and 2026 in English with a human or experimental design were included.

A review of articles selected from January to June 2026 from the PubMed, SciELO and ScienceDirect databases was conducted using the descriptors ‘gut microbiome’, ‘microbiota’, ‘polyphenols’ and ‘bioactive compounds’. Original articles published between 2010 and 2026 in English with a human or experimental design were included.

Results

Between 90% and 95% of dietary polyphenols reach the colon intact, where they are metabolised by the microbiota into bioactive low-molecular-weight metabolites, such as urolithins. These metabolites have greater bioavailability and biological activity than their parent compounds. This interaction is bidirectional. While microbes process polyphenols, they act as ‘bioactive prebiotics’, modulating intestinal ecology by stimulating the growth of beneficial bacteria such as Akkermansia muciniphila, Bifidobacterium, and Faecalibacterium prausnitzii, while also inhibiting pathogens. This modulation favours the production of short-chain fatty acids (SCFAs), which are essential for the integrity of the intestinal barrier and the regulation of the inflammatory response. Dietary strategies involving varied consumption of foods such as fruits, coffee, chocolate and wine, as observed in dietary patterns like the Mediterranean diet, have been shown to improve insulin sensitivity and reduce the risk of metabolic syndrome and endotoxemia by decreasing circulating lipopolysaccharides. However, the metabolic response is individualised depending on specific metabolites (producers vs. non-producers), which highlights the importance of applying precision nutrition to optimise clinical benefits.

Between 90% and 95% of dietary polyphenols reach the colon intact, where they are metabolised by the microbiota into bioactive low-molecular-weight metabolites, such as urolithins. These metabolites have greater bioavailability and biological activity than their parent compounds. This interaction is bidirectional. While microbes process polyphenols, they act as ‘bioactive prebiotics’, modulating intestinal ecology by stimulating the growth of beneficial bacteria such as Akkermansia muciniphila, Bifidobacterium, and Faecalibacterium prausnitzii, while also inhibiting pathogens. This modulation favours the production of short-chain fatty acids (SCFAs), which are essential for the integrity of the intestinal barrier and the regulation of the inflammatory response. Dietary strategies involving varied consumption of foods such as fruits, coffee, chocolate and wine, as observed in dietary patterns like the Mediterranean diet, have been shown to improve insulin sensitivity and reduce the risk of metabolic syndrome and endotoxemia by decreasing circulating lipopolysaccharides. However, the metabolic response is individualised depending on specific metabolites (producers vs. non-producers), which highlights the importance of applying precision nutrition to optimise clinical benefits.

Conclusion

The interaction between polyphenols and gut microbiota is fundamental to metabolic health, as it mediates systemic antioxidant and anti- inflammatory effects. The effectiveness of dietary strategies hinges on individual microbial composition, underscoring the importance of personalised approaches and dietary diversity in chronic disease prevention.

The interaction between polyphenols and gut microbiota is fundamental to metabolic health, as it mediates systemic antioxidant and anti- inflammatory effects. The effectiveness of dietary strategies hinges on individual microbial composition, underscoring the importance of personalised approaches and dietary diversity in chronic disease prevention.