Whole foods, especially vegetables, fruits, and whole grains, are important parts of a healthy diet and have preventive effects against various chronic diseases. In recent years, gut microbiota-oriented studies describing the relationship between whole foods and gut microbiota have validated the benefits of whole foods from a new perspective. The microbiota-accessible components, such as carbohydrates and polyphenols, contribute to a higher gut microbial diversity, richer probiotics, and more regulated metabolites, including short-chain fatty acids and secondary bile acids. Moreover, the food matrix often contributes to this intestinal regulation with synergistic effects between nutrients. Although the correlation between different diseases and specific gut microbiota requires more clinical data validation, the ever-infnovating metagenomic sequencing and foodomics will provide the support for gut microbiota-based personalized dietary nutrition. This review highlights the recent research progress on how whole foods regulate gut microbiota and metabolites to promote human health. All rights reserved, Elsevier.

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