Precision Nutrition: Transitioning from Diet-Microbiome Crosstalk to Personalized Microbiomics
Subject Areas : Food MicrobiologyAhmad gholami 1 , Alireza Ebrahiminezhad 2
1 - Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
2 - Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
Keywords: Precision nutrition, Personalized Microbiomics, diet-microbiome interactions, Microbial modulation. ,
Abstract :
The human gut microbiome is a dynamic, multispecies ecosystem that plays a crucial role in maintaining metabolic balance, regulating the immune system, and promoting overall health. In this systematic review, we examine the impact of various dietary patterns, including the Mediterranean, high-fiber, vegetarian, high-protein, ketogenic, and Western diets, on gut microbial composition, function, and diversity. We conducted comprehensive searches of PubMed/MEDLINE, Google Scholar, Web of Science, EMBASE, ISC, and SID up to June 2025, using relevant keywords in both Persian and English. Our findings indicate that diets rich in fiber and polyphenols enhance the production of short-chain fatty acids (SCFAs), modulate immune responses, and improve metabolic markers. In contrast, Western and high-protein diets are associated with decreased microbial diversity and increased production of potentially harmful metabolites, such as TMAO and hydrogen sulfide. The Mediterranean diet, especially its "green" variant, demonstrated the most significant positive effects, promoting the growth of anti-inflammatory bacteria (e.g., Faecalibacterium prausnitzii) and enhancing SCFA fermentation pathways. Advances in metagenomic sequencing and metabolic modeling have improved our understanding of the mechanisms underlying diet-microbiome interactions. Finally, we discuss the emerging potential of “next-generation” probiotics with combined diagnostic and therapeutic functions, as well as precision nutrition (PN) strategies tailored to individual microbial profiles. This review provides a scientific basis for translating microbiome research into targeted dietary recommendations and microbiome-based therapies for the prevention and treatment of chronic diseases.
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