Hundreds of previously unknown viruses living inside bacteria in the human gut have been uncovered in a major new study from Monash University and the Hudson Institute of Medical Research.
The discovery, published in Nature, sheds light on how our bodies may shape, and be shaped by, the vast community of microbes living within us.
These viruses, called bacteriophages, are part of a largely uncharted ecosystem that affects how bacteria in the gut grow, interact, and respond to their environment. Until now, scientists lacked the tools to study these viruses in detail.
“We’ve known that the gut is full of viruses, but until now, we didn’t have the tools and experimental approaches to study them in the lab,” said Dr. Sofia Dahlman, first author of the study. “Our findings suggest that the human host isn’t just a passive environment, it’s actively influencing viral behavior.”
The team grew more than 250 bacterial samples from the human gut and tested how they responded to different foods and conditions. Surprisingly, Stevia, a popular plant-based sweetener, and natural compounds produced by human gut cells turned out to be strong activators, waking up otherwise dormant viruses inside gut bacteria.
“We found that compounds produced in human gut cells can wake up dormant viruses inside gut bacteria,” said senior author Professor Jeremy J. Barr. “This could have major implications for gut diseases like inflammatory bowel disease, where inflammation and cell death are common.”
Most of the gut viruses were dormant under normal conditions, but when exposed to human gut cells, their activity increased sharply. That finding suggests the human body itself plays a direct role in shaping the viral landscape of the gut.
Using CRISPR-based genetic tools, the researchers also identified viral gene mutations that prevent activation, revealing how some gut viruses may stay permanently “asleep.” These insights could eventually inform new microbiome-based therapies for digestive disorders and other diseases linked to gut health.
“This work lays the groundwork for future applications in synthetic biology, biotechnology and microbiome therapeutics,” Barr said. “It’s a major step forward in decoding the viral dark matter of the human gut.”
This research was supported by the Australian Research Council, the National Institutes of Health, CSL Centenary Fellowship, the National Health and Medical Research Council, and Monash University. Open access funding was provided by Monash University.