# The Polyphenol–Microbiota Axis: Molecular Mechanisms, Metabolic Pathways, and Therapeutic Perspectives in Human Health

**Authors:** Andrea Ballini, Simona Nicole Barile, Alfredo De Rosa, Maria Eleonora Bizzoca, Mariarosaria Boccellino, Salvatore Scacco, Stefania Cantore, Lorenzo Lo Muzio, Francesco Massimo Lasorsa, Roberto Arrigoni

PMC · DOI: 10.3390/jpm16030142 · Journal of Personalized Medicine · 2026-03-02

## TL;DR

This review explores how polyphenols interact with gut microbes to produce beneficial compounds that impact health through various biological pathways.

## Contribution

The paper provides a comprehensive synthesis of the bidirectional relationship between polyphenols and gut microbiota, emphasizing their therapeutic potential.

## Key findings

- Polyphenols are metabolized by gut microbes into bioactive compounds like urolithins and phenolic acids.
- These microbial metabolites influence pathways related to inflammation, oxidative stress, and metabolic regulation.
- The polyphenol–microbiota–metabolite axis is proposed as a target for precision nutrition and personalized therapies.

## Abstract

Polyphenols are a diverse class of bioactive phytochemicals increasingly recognized for their ability to modulate human physiology through extensive interactions with the gut microbiota. This review provides a comprehensive and updated synthesis of the bidirectional polyphenol–microbiota relationship, emphasizing how dietary polyphenols reshape microbial community structure while intestinal microorganisms metabolize polyphenols into smaller, more bioavailable derivatives. These microbial metabolites—such as urolithins, phenolic acids, and dihydroresveratrol—exert amplified biological activities compared to their parent molecules, acting on key molecular pathways linked to oxidative stress, inflammation, energy homeostasis, and metabolic regulation. Through integration of mechanistic studies, multi-omics analyses, and emerging clinical evidence, this review outlines the potential of the polyphenol–microbiota–metabolite axis as a target for precision nutrition and microbiota-informed therapeutic interventions. The manuscript highlights ongoing challenges, including inter-individual variability in polyphenol metabolism, and proposes future research directions to advance the field of personalized nutrition.

## Linked entities

- **Chemicals:** dihydroresveratrol (PubChem CID 185914)

## Full-text entities

- **Genes:** NFKBIA (NFKB inhibitor alpha) [NCBI Gene 4792] {aka EDAID2, IKBA, MAD-3, NFKBI}, FFAR3 (free fatty acid receptor 3) [NCBI Gene 2865] {aka FFA3R, GPR41}, SLC2A4 (solute carrier family 2 member 4) [NCBI Gene 6517] {aka GLUT4}, PRKN (parkin RBR E3 ubiquitin protein ligase) [NCBI Gene 5071] {aka AR-JP, LPRS2, PARK2, PDJ}, PPARGC1A (PPARG coactivator 1 alpha) [NCBI Gene 10891] {aka LEM6, PGC-1(alpha), PGC-1alpha, PGC-1v, PGC1, PGC1A}, NOS2 (nitric oxide synthase 2) [NCBI Gene 4843] {aka HEP-NOS, INOS, NOS, NOS2A}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, SREBF1 (sterol regulatory element binding transcription factor 1) [NCBI Gene 6720] {aka HMD, IFAP2, SREBP1, bHLHd1}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, HMOX1 (heme oxygenase 1) [NCBI Gene 3162] {aka HMOX1D, HO-1, HSP32, bK286B10}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, PINK1 (PTEN induced kinase 1) [NCBI Gene 65018] {aka BRPK, PARK6}, COX2 (cytochrome c oxidase subunit II) [NCBI Gene 4513] {aka COII, MTCO2}, CCL2 (C-C motif chemokine ligand 2) [NCBI Gene 6347] {aka GDCF-2, HC11, HSMCR30, MCAF, MCP-1, MCP1}, ULK1 (unc-51 like autophagy activating kinase 1) [NCBI Gene 8408] {aka ATG1, ATG1A, UNC51, Unc51.1, hATG1}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, KEAP1 (kelch like ECH associated protein 1) [NCBI Gene 9817] {aka INrf2, KLHL19}, TLR4 (toll like receptor 4) [NCBI Gene 7099] {aka ARMD10, CD284, TLR-4, TOLL}, NQO1 (NAD(P)H quinone dehydrogenase 1) [NCBI Gene 1728] {aka DHQU, DIA4, DTD, NMOR1, NMORI, QR1}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, STK11 (serine/threonine kinase 11) [NCBI Gene 6794] {aka LKB1, PJS, hLKB1}, FFAR2 (free fatty acid receptor 2) [NCBI Gene 2867] {aka FFA2R, GPR43}, NFE2L2 (NFE2 like bZIP transcription factor 2) [NCBI Gene 4780] {aka IMDDHH, NRF2, Nrf-2}, SOD1 (superoxide dismutase 1) [NCBI Gene 6647] {aka ALS, ALS1, HEL-S-44, IPOA, SOD, STAHP}, CAMKK2 (calcium/calmodulin dependent protein kinase kinase 2) [NCBI Gene 10645] {aka CAMKK, CAMKKB}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}
- **Diseases:** chronic inflammation (MESH:D007249), neurodegenerative disorders (MESH:D019636), colon cancer (MESH:D015179), cognitive impairment (MESH:D003072), rectal cancer (MESH:D012004), cardiometabolic disease (MESH:D024821), cardiovascular disease (MESH:D002318), dysbiosis (MESH:D064806), Cancer (MESH:D009369), type 2 diabetes (MESH:D003924), obese (MESH:D009765), chronic disease (MESH:D002908), metabolic dysfunction (MESH:D008659), injury to (MESH:D014947), differentiated thyroid cancer (MESH:D013964), IBD (MESH:D015212)
- **Chemicals:** glucose (MESH:D005947), flavan-3-ols (MESH:C404987), lipid (MESH:D008055), butyrate (MESH:D002087), enterolactone (MESH:C029497), acetate (MESH:D000085), quercetin (MESH:D011794), Flavonols (MESH:D044948), Isoflavones (MESH:D007529), polysaccharides (MESH:D011134), vitamin K (MESH:D014812), propionate (MESH:D011422), delphinidin (MESH:C017185), FOS (MESH:C116580), kaempferol (MESH:C006552), O-desmethylangolensin (MESH:C050052), Curcuminoids (MESH:D036381), SCFA (MESH:D005232), NO (MESH:D009614), urolithin A (MESH:C026423), LPS (MESH:D008070), Polyphenol (MESH:D059808), ATP (MESH:D000255), green (MESH:C024537), flavones (MESH:D047309), protocatechuic acid (MESH:C009091), carbohydrates (MESH:D002241), enterodiol (MESH:C029498), Catechins (MESH:D002392), tannins (MESH:D013634), iron (MESH:D007501), resveratrol (MESH:D000077185), Flavonoids (MESH:D005419), equol (MESH:D060754), acids (MESH:D000143), cysteine (MESH:D003545), luteolin (MESH:D047311), glutathione (MESH:D005978), Anthocyanins (MESH:D000872), fatty acid (MESH:D005227), lignans (MESH:D017705), ellagitannins (MESH:D047348), flavanones (MESH:D044950), ACC (MESH:C023863), cyanidin (MESH:C017154), dihydroresveratrol (MESH:C544754), AMP (MESH:D000249), cholesterol (MESH:D002784), enterolignans (-), tetrahydrocurcumin (MESH:C096277), nitric oxide (MESH:D009569), Phenolic acids (MESH:C017616), gallic acid (MESH:D005707), proanthocyanidins (MESH:D044945), Curcumin (MESH:D003474), Stilbenes (MESH:D013267), apigenin (MESH:D047310), ellagitannin (MESH:C013515)
- **Species:** Bacteroides (genus) [taxon 816], Echinacea (genus) [taxon 53747], Escherichia coli (E. coli, species) [taxon 562], Lactobacillus (genus) [taxon 1578], Homo sapiens (human, species) [taxon 9606], Clostridioides difficile (species) [taxon 1496], Faecalibacterium prausnitzii (species) [taxon 853], Eggerthella lenta (species) [taxon 84112], Bacillota (clostridial firmicutes, phylum) [taxon 1239], Sesamum indicum (beniseed, species) [taxon 4182], Lagerstroemia speciosa (giant crepe-myrtle, species) [taxon 122810], Akkermansia muciniphila (species) [taxon 239935], Bifidobacterium adolescentis (species) [taxon 1680]

## Full text

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## Figures

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## References

116 references — full list in the complete paper: https://tomesphere.com/paper/PMC13028265/full.md

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Source: https://tomesphere.com/paper/PMC13028265