Research highlights how the gut microbiome can affect epigenetics

The trillions of microbes that live in the human gut may play a bigger role in health than previously thought, according to a 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.

"By understanding how gut microbes influence our genes, we can begin to imagine new ways to prevent disease and promote health in a way that gets us closer to personalized medicine," said Alika K. Maunakea, a co-author of the study and professor at the UH Mānoa John A. Burns School of Medicine.

Everyday factors-such as diet, stress, medications and aging-can influence these microbial interactions. For example, gut bacteria produce short-chain fatty acids, nutrients 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.

The paper also stresses the importance of setting clear standards and ethical safeguards as this field develops. Frameworks such as the FAIR principles (Findable, Accessible, Interoperable and Reusable data) and CARE principles (Collective benefit, Authority to control, Responsibility and Ethics) are needed to ensure that data from microbiome research benefits diverse populations equitably.

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.