Uncovering a whole new world inside the gut

10 November 2025

By Rob Clancy, staff writer. Reviewed by Associate Professor Samuel Forster

Microbiome medicine has been described as having the potential to revolutionise healthcare.

Thanks to a team from Hudson Institute and Monash University, that revolution just came a whole lot closer, promising a new range of possibilities.

Hudson Institute’s own Associate Professor Sam Forster working with Professor Jeremy J. Barr from Monash University’s School of Biological Sciences and PhD student Dr Sofia Dahlman, who published a ground-breaking study in the journal Nature, identifying hundreds of previously unknown gut viruses.

These viruses, known as bacteriophages, infect the bacteria in the gut. They offer the potential to reshape the gut microbiome, influencing gut health and the progression of various disease states.

Waking dormant viruses

They found that compounds produced in human gut cells can wake up dormant viruses inside gut bacteria. This could have major implications for gut diseases like inflammatory bowel disease (IBD), where inflammation and cell death are common.

“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,” explained Dr Dahlman, “…but our findings suggest that the human host isn’t just a passive environment, it’s actively influencing viral behaviour.”

The research represents over eight years of collaborative work, and A/Prof Forster believes it will have significant implications for health translation.

“Being able to grow these viruses allows us to understand their function and provides the opportunity to develop microbiome therapeutics for diseases from inflammatory bowel disease to cancers. This technology will provide the opportunity for targeted removal of detrimental species from the microbiome using phage.” he said.

Decoding mysteries of the human gut

But this work – described as “a major step forward in decoding the viral dark matter of the human gut” – is far from the only breakthrough to come from the Forster lab in the past year.

As part of a joint project between A/Prof Forster, PhD Student Dr Caitlin Welsh and Professor Chris Greening from Monash University’s Biomedicine Discovery Institute, they have revealed for the first time how hydrogen is made and used in the human gut – including the positive role it plays in supporting gut health.

Dr Caitlin Welsh

Their work, published in Nature Microbiology, analysed how microbes control hydrogen levels in the gut.

Hudson Institute post-doctoral researcher, Dr Caitlin Welsh said the results revealed hydrogen had an even bigger role in gut function than previously thought.

“Most people release about a litre of gas per day and half of that is hydrogen. But hydrogen is more than just the gas behind flatulence – it’s a hidden driver of gut health,” Dr Welsh said. “Our study shows hydrogen shapes the gut microbiome in surprising and varied ways. It helps some beneficial bacteria thrive in the gut and keeps digestion going.”

This research highlights the need to expand fundamental knowledge of how our gut works so it can be used to design new treatments for gastrointestinal issues.