The trillions of microbes that live in the human gut may play a bigger role in health than previously thought, according to new research by the University of Hawaiʻi at Mānoa. The article, published in September 2025 in the International Journal of Molecular Sciences, explores how gut bacteria interact with human genes in ways that could shape disease risk, aging, and even future medical treatments.
The review highlights how the gut microbiome (the collection of bacteria, viruses, and fungi that live in the digestive system) can affect epigenetics, the process that turns genes on or off without changing the DNA itself. These changes happen through chemical tags such as DNA or RNA methylation, which control when and how genes are expressed.
Everyday factors—such as diet, stress, medications, and aging—can influence these microbial interactions. For example, gut bacteria produce short-chain fatty acids, nutrient,s and other chemical signals that may reprogram gene activity linked to immunity, metabolism or brain health. In turn, a person’s lifestyle and genetic makeup can shape which microbes thrive in the gut, creating a feedback loop between humans and their microbes.
The researchers point to future possibilities where understanding this loop could help doctors design personalized treatments. Potential applications include using microbial biomarkers (biological signals that indicate health or disease), developing “live biotherapeutics” (beneficial bacteria given like medicine) or refining fecal microbiota transplants, which transfer gut microbes from healthy donors to patients. Advances in artificial intelligence and single-cell analysis are helping scientists model these complex relationships at an unprecedented scale.
By mapping out how gut microbes communicate with human genes, the review underscores both the promise and responsibility of this emerging science. The insights could open the door to precision health strategies that tailor prevention and treatment to each individual’s unique microbial and epigenetic makeup.
Ref: Rubas, N.C.; Torres, A.; Maunakea, A.K. The Gut Microbiome and Epigenomic Reprogramming: Mechanisms, Interactions, and Implications for Human Health and Disease. Int. J. Mol. Sci. 2025, 26, 8658. https://doi.org/10.3390/ijms26178658
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