In a groundbreaking study, scientists have discovered more than 100 new human viruses in 252 different gut microbes, providing a remarkable look at our bacteria and forming the very first living model of the “gut virome,” which until now has been just DNA fragments and markers. And it has real-world implications for treating some of the most puzzling chronic human health conditions.
Scientists already know that the human gut is packed with bacteriophages (phages) – viruses that infect bacteria – but most of this knowledge comes from metagenomics. This means that what we’ve understood, until now, came from DNA sequencing directly from samples, not from growing the viruses in a lab. That’s given researchers lots of hypotheses, but not a lot of experimental proof of how these phages behave or interact with bacteria (and, in turn, our health).
In this study, an international team led by researchers from Monash University and the Hudson Institute of Medical Research have grown, isolated and triggered these new viruses to wake up from their dormant – “prophage” – state, marking a major step toward understanding and engineering the gut virome for health and medicine.
The team took 252 bacterial strains from the human gut, sourced from the Australian Microbiome Culture Collection (AusMiCC). Then, they had to grow each one (an isolate), housed in anaerobic chambers, to produce a living culture of each pure strain. Once their numbers were sufficient, each isolate was exposed to 10 different treatments – compounds, foods, conditions like changes in oxygen.
Through this process, the team managed to “wake up” 134 phages, essentially switching on the activity and replication of viruses inside the bacteria. Interestingly, only 18% of the phages that had been predicted by models could be induced in the pure living cultures. Basically, most of what was expected to happen didn’t work in the real world, showing that computational predictions alone appear to overestimate viral activity.
“This is a foundational study that changes how we think about and study the viruses within the human gut,” said senior author Professor Jeremy J. Barr, from Monash University’s School of Biological Sciences. “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.”
The team found that artificial sweetener Stevia, as well as compounds released by our own gut cells, were the main instigators in activating these gut phages. Then, building a synthetic gut microbiome made up of 78 species of bacteria that had been co-cultured with human cells modeling the intestinal lining of the gut, the researchers found that 35% of the phage species became active when our gut cells were present.
Now, before we go further we should explain that phages only infect bacteria, not human cells – they don’t have the right molecular machinery to attach to or replicate beyond their microbial hosts. However, because the viruses can change the genetic behavior of bacteria and change the species makeup of the microbiome – which does affect us – they’re extremely relevant when it comes to the gut’s influence on the immune system, metabolism and mental health, for example.
And the compounds released from gut cells when cells are dying or damaged proved to be the most effective at activating phages. Diet, such as processed foods, medications, alcohol, stress, poor sleep and pathogens can all damage gut cells.
“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 first author Dr Sofia Dahlman. “Our findings suggest that the human host isn’t just a passive environment, it’s actively influencing viral behavior.”
In one of the most fascinating discoveries, CRISPR-based genetic engineering identified specific mutations and deletions in the DNA of inactive phages that had caused them to remain permanently dormant. The team directly compared the DNA of inducible (active) and non-inducible (dormant) viruses to see whether dormant ones might someday reawaken. What they found was that the dormant phages had damaging mutations in their own integration and excision genes – the machinery that allows a phage to cut itself out of the bacterial genome and start replicating.
Basically, it had evolved to become trapped forever inside its bacterial host. Further testing confirmed that the genetic changes came from within the phage itself, as the host remained unchanged when viral genetic mutations were knocked out. This part of the study provided the first direct functional proof that mutations within the phage genome can permanently silence its ability to reactivate.
On face value, this seems counterproductive for even a microorganism, where replication and in turn genetic survival is a driving force. However, such dormancy could be a life strategy too, keeping the bacterium stable with its DNA replicated (albeit with next to no chance of mutating or evolving) every time the host divides. So while some viruses become activated when exposed to the right compounds produced in the gut from external triggers like medications, these dormant phages have simply evolved to become genetic hitchhikers inside bacteria.
Inactive or “domesticated” phages may still subtly shape our gut health, however. Even though they can no longer replicate, the viral genes embedded in bacterial DNA can influence how those microbes behave – helping friendly strains succeed or suppressing harmful ones. Meanwhile, active phages may one day be used to better shape the microbiome, targeting harmful bacteria or delivering helpful genes to beneficial strains that protect against conditions like IBD. Basically, this discovery could inform future therapeutic strategies aimed at manipulating the gut microbiome for human health.
This monumental research has been eight years in the making for the Monash and Hudson Institute teams, as well as other collaborating Australian and international scientists. Having cultivated a collection of gut phages and bacterial hosts, scientists now have tangible targets to study and manipulate.
“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,” said Associate Professor Sam Forster from the Hudson Institute. “This technology also provides a capacity to engineer probiotic strains with tailored viral functions.”
And because the team successfully cultured and characterized so many bacterial viruses, these methods now make it possible to engineer phages and probiotics for a vast range of human therapies.
“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,” added Barr.
The study was published in the journal Nature.
Source: Monash University