The epigenetic influence of diet-induced gut microbiome changes in precision nutrition – a systematic review
Gastroenterology and Hepatology from Bed to Bench,
Vol. 18 No. 3 (2025),
26 August 2025
https://doi.org/10.22037/ghfbb.v18i3.3136
Abstract
Aim: This systematic review aimed to comprehensively evaluate the existing literature on the epigenetic influence of diet-induced gut microbiome changes in the context of precision nutrition.
Background: Diet influences gut microbiome composition, which regulates epigenetic modifications affecting inflammation, metabolism, and disease susceptibility. Precision nutrition seeks to personalize dietary strategies based on these interactions, yet the role of microbiome-driven epigenetic regulation remains under investigation.
Methods: A systematic review was conducted in 2025 following PRISMA guidelines. Studies exploring the relationship between dietary interventions, gut microbiome composition, and epigenetic changes were identified via PubMed and Google Scholar. Thirty-five studies, including randomized controlled trials, cohort studies, and observational research, met the inclusion criteria. Data on dietary interventions, microbial composition, epigenetic modifications, and health outcomes were synthesized.
Results: Diets rich in fiber and polyphenols enhanced microbial diversity, increased short-chain fatty acid production, and positively influenced epigenetic markers related to metabolic health. In contrast, Western-style and high-fat diets were associated with gut dysbiosis, inflammation, and negative epigenetic changes linked to metabolic disorders. Dietary interventions impacted DNA methylation, histone modifications, and microRNA expression, influencing long-term health.
Conclusion: This review highlights the key role of diet-induced changes in the gut microbiome in modulating epigenetic mechanisms like DNA methylation and histone modifications. These alterations influence metabolic health, disease risk, and precision nutrition strategies. While dietary interventions show promise, challenges such as individual variability and methodological inconsistencies require further research to refine clinical applications of microbiome-driven nutrition.
- Diet
- gut microbiome
- epigenetics
- DNA methylation
- histone modification
- precision nutrition
- microbiota
- metabolic health
- inflammation
- personalized nutrition
How to Cite
References
Bianchetti G, De Maio F, Abeltino A, Serantoni C, Riente A, Santarelli G, et al. Unraveling the gut microbiome–diet connection: exploring the impact of digital precision and personalized nutrition on microbiota composition and host physiology. Nutrients 2023;15:3931.
Jackson S, Frame LA, Costas E. Current explorations of nutrition and the gut microbiome: a systematic review. Nutr Rev 2020;78:798–812.
Sanz Y, Cryan JF, Deschasaux-Tanguy M, Elinav E, Lambrecht R, Veiga P. The gut microbiome connects nutrition and human health. Nat Rev Gastroenterol Hepatol 2025.
Ross FC, Patangia D, Grimaud G, Lavelle A, Dempsey EM, Ross RP, Stanton C. The interplay between diet and the gut microbiome: implications for health and disease. Nat Rev Microbiol 2024;22:671–86.
Li X, Qi L. Epigenetics in precision nutrition. J Pers Med 2022;12:533.
Missong H, Joshi R, Khullar N, Thareja S, Navik U, Bhatti GK, et al. Nutrient-epigenome interactions: implications for personalized nutrition against aging-associated diseases. J Nutr Biochem 2024;127:109592.
Shock T, Badang L, Ferguson B, Martinez-Guryn K. The interplay between diet, gut microbes, and host epigenetics in health and disease. J Nutr Biochem 2021;95:108631.
Fu Y, Gou W, Zhong H, Tian Y, Zhao H, Liang X, et al. Diet–gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials. EBioMedicine 2025;111:105483.
Kaczmarczyk M, Löber U, Adamek K, Węgrzyn D, Skonieczna-Żydecka K, Malinowski D, et al. The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. J Transl Med 2021;19:177.
Allison J, Kaliszewska A, Uceda S, Reiriz M, Arias N. Targeting DNA methylation in the adult brain through diet. Nutrients 2021;13:3979.
Shang Z, Pai L, Patil S. Unveiling the dynamics of gut microbial interactions: a review of dietary impact and precision nutrition in gastrointestinal health. Front Nutr 2024;11:1395664.
Gonçalves CL, Doifode T, Rezende VL, Costa MA, Rhoads JM, Soutullo CA. The many faces of microbiota–gut–brain axis in autism spectrum disorder. Life Sci 2024;337:122596.
Zhu G, Zhao J, Zhang H, Wang G, Chen W. Gut microbiota and its metabolites: bridge of dietary nutrients and Alzheimer’s disease. Adv Nutr 2023;14:819–39.
Hermanson JB, Tolba SA, Chrisler EA, Leone VA. Gut microbes, diet, and genetics as drivers of metabolic liver disease: a narrative review outlining implications for precision medicine. J Nutr Biochem 2024;133:109704.
Li D, Li Y, Yang S, Lu J, Jin X, Wu M. Diet–gut microbiota–epigenetics in metabolic diseases: from mechanisms to therapeutics. Biomed Pharmacother 2022;153:113290.
Jardon KM, Canfora EE, Goossens GH, Blaak EE. Dietary macronutrients and the gut microbiome: a precision nutrition approach to improve cardiometabolic health. Gut 2022;71:1214–26.
Aleksandrova K, Romero-Mosquera B, Hernandez V. Diet, gut microbiome and epigenetics: emerging links with inflammatory bowel diseases and prospects for management and prevention. Nutrients 2017;9:962.
Greathouse KL, Choudhury A. Precision nutrition and the gut microbiome: harnessing AI to revolutionize cancer prevention and therapy. Cell Host Microbe 2025;33:766–76.
Hill EB, Konigsberg IR, Ir D, Frank DN, Jambal P, Litkowski EM, et al. The microbiome, epigenome, and diet in adults with obesity during behavioral weight loss. Nutrients 2023;15:3588.
Turchi R, Sciarretta F, Ceci V, Tiberi M, Audano M, Pedretti S, et al. Butyrate prevents visceral adipose tissue inflammation and metabolic alterations in a Friedreich’s ataxia mouse model. iScience 2023;26:107713.
Sun A, Park P, Cole L, Vaidya H, Maegawa S, Keith K, et al. Non-pathogenic microbiota accelerate age-related CpG island methylation in colonic mucosa. Epigenetics 2023;18:2160568.
Fawad JA, Luzader DH, Hanson GF, Moutinho TJ Jr, McKinney CA, Mitchell PG, et al. Histone deacetylase inhibition by gut microbe-generated short-chain fatty acids entrains intestinal epithelial circadian rhythms. Gastroenterology 2022;163:1377–90.
Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, et al. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut 2016;65:1973–80.
Chleilat F, Schick A, Deleemans JM, Reimer RA. Paternal methyl donor supplementation in rats improves fertility, physiological outcomes, gut microbial signatures and epigenetic markers altered by high fat/high sucrose diet. Int J Mol Sci 2021;22:689.
Goni L, Cuervo M, Milagro FI, Martinez JA. Future perspectives of personalized weight loss interventions based on nutrigenetic, epigenetic, and metagenomic data. J Nutr 2015;146:905S–12S.
Lilja S, Stoll C, Krammer U, Hippe B, Duszka K, Debebe T, et al. Five days periodic fasting elevates levels of longevity related Christensenella and sirtuin expression in humans. Int J Mol Sci 2021;22:2331.
Chen L, Tan KML, Xu J, Mishra P, Mir SA, Gong M, et al. Exploring multi-omics and clinical characteristics linked to accelerated biological aging in Asian women of reproductive age: insights from the S-PRESTO study. Genome Med 2024;16:128.
Kawakami S, Ninomiya R, Maeda Y. Improvement in epigenetic aging clock induced by BioBran containing rice kefiran in relation to various biomarkers: a pilot study. Int J Mol Sci 2024;25:6332.
Miller CB, Benny P, Riel J, Boushey C, Perez R, Khadka V, et al. Adherence to Mediterranean diet impacts gastrointestinal microbial diversity throughout pregnancy. BMC Pregnancy Childbirth 2021;21:558.
Ugai T, Akimoto N, Haruki K, Harrison TA, Cao Y, Qu C, et al. Prognostic role of detailed colorectal location and tumor molecular features: analyses of 13,101 colorectal cancer patients including 2994 early-onset cases. J Gastroenterol 2023;58:229–45.
Louveau C, Brookes KJ, Schumann G, Walters JTR, Buitelaar J, Gozzi A, et al. Neurodevelopmental disorders without boundaries: research and interventions beyond classifications. J Neural Transm 2023;130:473–9.
Baumann-Dudenhoeffer AM, D’Souza AW, Tarr PI, Warner BB, Dantas G. Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. Nat Med 2018;24:1822–9.
Murga-Garrido SM, Hong Q, Cross T-WL, Hutchison ER, Han J, Thomas S, et al. Gut microbiome variation modulates the effects of dietary fiber on host metabolism. Microbiome 2021;9:117.
Ahmed I, Roy BC, Khan SA, Sepesy LM, Hurst KE, Bernier-Latmani J, et al. Dietary interventions ameliorate infectious colitis by restoring the microbiome and promoting stem cell proliferation in mice. Int J Mol Sci 2021;23:173.
Khan AI, Zhang Y, Abid MU, Yang S, Li Z, Wang B, et al. Effects of shrimp peptide hydrolysate on intestinal microbiota restoration and immune modulation in cyclophosphamide-treated mice. Molecules 2022;27:1600.
Chleilat F, Klancic T, Ma K, Armet AM, Kasaian J, Samanfar B, et al. Paternal high-protein diet modulates body composition, insulin sensitivity, epigenetics, and gut microbiota intergenerationally in rats. FASEB J 2021;35:e21847.
Ogrodowczyk AM, Zakrzewska M, Romaszko E, Wroblewska B. Gestational dysfunction-driven diets and probiotic supplementation correlate with allergen-specific antibodies in allergy sufferers. Nutrients 2020;12:2389.
Xie Y, Ding F, Di W. Impact of a high-fat diet on intestinal stem cells and epithelial barrier function in middle-aged female mice. Mol Med Rep 2020;21:1133–44.
Soldado-Gordillo A, Alvarez-Mercado AI. Epigenetics, microbiota, and breast cancer: a systematic review. Life 2024;14:905.
Notarbartolo V, Carta M, Accomando S, Giuffrè M. First 1000 days of life: how microbiota changes can influence food allergy onset in children. Life 2023;13:244.
Coppola S, Bianchi F, Vigano C, Morelli L, Zuccotti G, Agostoni C, et al. Effects of the Mediterranean diet during pregnancy on the onset of allergy in at-risk children: PREMEDI study protocol. Front Nutr 2022;9:951223.
Makki K, Deehan EC, Walter J, Bäckhed F. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 2018;23:705–15.
Severino A, Milani C, Duranti S, Turroni F, Ventura M. The microbiome-driven impact of Western diet in the development of noncommunicable chronic disorders. Best Pract Res Clin Gastroenterol 2024;68:101891.
Cardona F, Andrés-Lacueva C, Tulipani S, Tinahones FJ, Queipo-Ortuño MI. Benefits of polyphenols on gut microbiota and implications in human health. J Nutr Biochem 2013;24:1415–22.
Zhao Y, Jiang Q. Roles of the polyphenol–gut microbiota interaction in alleviating colitis and preventing colitis-associated colorectal cancer. Adv Nutr 2021;12:546–65.
Chandrasekaran P, Weiskirchen S, Weiskirchen R. Effects of probiotics on gut microbiota: an overview. Int J Mol Sci 2024;25:6350.
González-Becerra K, Ramos-Lopez O, Barrón-Cabrera E, Riezu-Boj JI, Milagro FI, Martínez-López E, et al. Fatty acids, epigenetic mechanisms and chronic diseases: a systematic review. Lipids Health Dis 2019;18:178.
Číž M, Dvořáková A, Skočková V, Kubala L. Dietary phenolic compounds in epigenetic modulation involved in inflammatory processes. Antioxidants 2020;9:874.
Mazziotta C, Tognon M, Martini F, Torreggiani E, Rotondo JC. Probiotics mechanism of action on immune cells and beneficial effects on human health. Cells 2023;12:159.
Singh VK, Kumar N, Ahmad M, Singh P, Nagar S, Alam I, et al. Precision nutrition-based strategy for management of human diseases and healthy aging: current progress and challenges forward. Front Nutr 2024;11:1390279.
Davis C. The gut microbiome and its role in obesity. Nutr Today 2016;51:160–2.
Geng J, Ni Q, Sun W, Li L, Feng X. Links between gut microbiota and obesity and obesity-related diseases. Biomed Pharmacother 2022;147:112678.
Chu NHS, Chow E, Chan JCN. Therapeutic potential of the Specific Intestinal Microbiome (SIM) diet on metabolic diseases. Biology 2024;13:577.
Chaudhary D, Srivastava A, Rai A, Sharma R, Gupta N, Kumar P, et al. Nutrigenomics and personalized diets: tailoring nutrition for optimal health. Appl Food Res 2025;5:100306.
Seidel M, Schuch B, Nischwitz V, Kollmann M, Wagner G, Holz B, et al. Study protocol of comprehensive risk evaluation for anorexia nervosa in twins (CREAT): discordant monozygotic twins. BMC Psychiatry 2020;20:507.
Bittinger K, Zhao C, Li Y, Ford E, Friedman ES, Ni J, et al. Bacterial colonization reprograms the neonatal gut metabolome. Nat Microbiol 2020;5:838–47.
Goni L, Cuervo M, Milagro FI, Martinez JA. Future perspectives of personalized weight loss interventions based on nutrigenetic, epigenetic, and metagenomic data. J Nutr 2015;146:905–12.
Notarbartolo V, Carta M, Accomando S, Giuffrè M. The First 1000 days of life: how microbiota changes can influence food allergy onset in children. Life 2023;14:244.
Xie Y, Ding F, Di W., Lv Y, Xia F, Sheng Y, et al. Impact of a high-fat diet on intestinal stem cells and epithelial barrier function in middle-aged female mice. Mol Med Rep 2020;21:1133–44.
Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA et al.. Fusobacterium nucleatum incolorectal carcinoma tissue and patient prognosis. Gut 2016;65:1973–80.
Hill EB, Konigsberg IR, Ir D, Frank DN, Jambal P, Litkowski EM, et al. The microbiome, epigenome, and diet in adults with obesity during behavioral weight loss. Nutrients 2023;15:442.
Fawad JA, Luzader DH, Hanson GF, Pickard JM, Kearns DB, Herring CA, et al. Histone deacetylase inhibition by gut microbe-generated short-chain fatty acids entrains intestinal epithelial circadian rhythms. Gastroenterology 2022;163:1377–90.e11.
Chen Y, Li X, Yang M., Chen J, Zhenghao H, Suqing Z et al. Time-restricted eating reveals a “younger” immune system and reshapes the intestinal microbiome in humans. Redox Biol 2024;78:103422.
Miller CB, Benny P, Riel J, Boushey C, Perez R, Khadka V, et al. Adherence to Mediterranean diet impacts gastrointestinal microbial diversity throughout pregnancy. BMC Pregnancy Childbirth 2021;21:558.
Stobernack T, Rombouts S, van Rooij D, Pelsser LM, Franke B, Buitelaar JK, et al. Biomarker research in ADHD: the impact of nutrition (BRAIN) study protocol of a few-foods diet trial. BMJ Open 2019;9:e029422.
Malcomson FC, Mathers JC. Translation of nutrigenomic research for personalised and precision nutrition for cancer ptrvention and for cancer survivors. Radox Biol 2023;62.
- Abstract Viewed: 236 times
- PDF Downloaded: 113 times