Discovery of new gut viruses opens doors to therapeutics targeting the microbiome

A new study has discovered hundreds of new viruses living inside bacteria in the human gut, which could potentially influence health and disease outcomes.

The publication in Nature used a large-scale, culture-based approach and isolated bacteriophages in the human gut, which could be used to reshape the microbiome. The researchers found that the human gut environment directly shaped the viral landscape of the gut, which has the potential to shape future therapeutic strategies. 

“This is a foundational study that changes how we think about and study the viruses within the human gut,” says senior author professor Jeremy Barr from Monash University’s School of Biological Sciences, Australia.

“We 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.”

Human biology activates viruses

The study, touted as the “first of its kind,” examined 252 bacterial isolates sourced from the Australian Microbiome Culture Collection.

It found that most gut bacteriophages are dormant, and only a small percentage can be activated under the tested conditions. When they were exposed to human cells, the virus’ activation rate spiked significantly.  

From these results, the researchers infer that human biology plays an important role in activating viruses that shape the viral-gut landscape. 

The study, touted as the “first of its kind,” examined 252 bacterial isolates sourced from the Australian Microbiome Culture Collection.“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,” comments first author Dr. Sofia Dahlman, research fellow at the School of Biological Sciences, at Monash University.

“Our findings suggest that the human host isn’t just a passive environment. It’s actively influencing viral behavior.”

Years of research to potential therapeutics

Monash University and Hudson Institute of Medical Research, collaborating over eight years with other international experts, have also discovered mutations in gut viruses that prevent activation, using CRISPR-based genetic engineering. This revealed how some gut viruses become permanently dormant.

The team believes its findings hold potential for therapeutics that target the gut microbiome for health benefits. “This work lays the groundwork for future applications in synthetic biology, biotechnology, and microbiome therapeutics; it’s a major step forward in decoding the viral dark matter of the human gut,” says Barr.

Associate professor Sam Forster at the Hudson Institute of Medical Research comments: “Being able to grow these viruses allows us to understand their function and provides the opportunity to develop microbiome therapeutics for diseases from IBD to cancers. This technology also provides a capacity to engineer probiotic strains with tailored viral functions.”