Scientists in Denmark say that a newly discovered virus hiding inside a common gut bacterium could help explain one of medicine’s long-standing mysteries: why a microbe found in both healthy people and cancer patients is linked to colorectal cancer.
Their research suggests that the interaction between bacteria and the viruses they carry may be key to understanding disease risk. It may even lead to future screening tests that detect cancer risk earlier, according to their findings, published in Communications Medicine.
Colorectal cancer is among the most common cancers in Western countries and remains a major cause of cancer-related deaths. While factors like age, diet and lifestyle are known to influence risk, the exact triggers behind the disease are still not fully understood.
In recent years, scientists have increasingly focused on the gut microbiome, the vast ecosystem of bacteria, viruses and other microorganisms living in the digestive system.
Now, researchers from the University of Southern Denmark and Odense University Hospital have identified a previously unknown virus inside a common gut bacterium. This virus appears more often in people with colorectal cancer, offering a new clue about how the disease may develop.
Common gut bacterium with a longstanding mystery
For years, researchers have linked one specific bacterium, Bacteroides fragilis, to colorectal cancer. However, this connection has been difficult to explain because the same bacterium is also found in most healthy individuals.
“It has been a paradox that we repeatedly find the same bacterium in connection with colorectal cancer, while at the same time it is a completely normal part of the gut in healthy people,” said Flemming Damgaard, medical doctor and PhD at the Department of Clinical Microbiology at Odense University Hospital and the University of Southern Denmark.
To resolve this contradiction, the team investigated whether there might be important differences within the bacterium itself.
They found that there were.
The key difference turned out to be a virus living inside the bacterium. In patients who later developed colorectal cancer, Bacteroides fragilis was much more likely to carry a specific bacteriophage, a virus that infects bacteria.
“We found a virus that has not previously been described and which appears to be closely linked to the bacteria we find in patients with colorectal cancer,” said Damgaard.
The researchers believe this virus represents entirely new types that have not been identified before.
“It is not just the bacterium itself that seems interesting. It is the bacterium in interaction with the virus it carries,” he added.
Although the study shows a strong statistical link between the virus and colorectal cancer, it does not prove that the virus causes the disease.
“We do not yet know whether the virus is a contributing cause, or whether it is simply a sign that something else in the gut has changed,” he noted.
Large-scale data and clear pattern
The discovery began with data from a large Danish population study involving about 2m people. Researchers focused on patients who had experienced serious bloodstream infections caused by Bacteroides fragilis. A small portion of them were diagnosed with colorectal cancer within weeks.
By comparing bacterial samples from patients with and without cancer, the team identified a clear pattern. Bacteria from cancer patients were more likely to contain specific viruses.
The initial findings came from a relatively small group of Danish samples, but they provided a strong starting point for further investigation.
Confirmed across nearly 900 patients worldwide
To test whether the pattern held up globally, the researchers analysed stool samples from 877 individuals across Europe, the United States and Asia. The results were consistent.
People with colorectal cancer were about twice as likely to carry these viruses in their gut.
“It was important for us to examine whether the association could be reproduced in completely independent data. And it could,” said Damgaard.
While this strengthens the link, it still does not show that the virus directly causes cancer.
New way to look at cancer risk
Up to 80% of colorectal cancer risk is thought to be influenced by environmental factors, including the microorganisms in the gut.
The gut microbiome is incredibly complex, containing thousands of bacterial species and even more genetic variation. This complexity has made it difficult to pinpoint what separates healthy individuals from those who develop disease.
“The number and diversity of bacteria in the gut is enormous. Previously, it has been like looking for a needle in a haystack. Instead, we have investigated whether something inside the bacteria – namely viruses – might help explain the difference,” Damgaard said.
If the virus changes how the bacterium behaves, it could alter the gut environment in ways that influence cancer risk. This possibility is now being explored.
New screening tests?
Currently, colorectal cancer screening often involves stool tests seeking hidden blood.
In the future, researchers believe it may be possible to screen for these newly identified viruses as well.
Damgaard said in the short term, “we can investigate whether the virus can be used to identify individuals at increased risk”.
Early analyses suggest that certain viral markers could identify about 40% of cancer cases, while most healthy individuals do not carry them.
However, the researchers stress that this work is still in its early stages. More studies are needed before it could be used in clinical practice.
Study details
Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis
Flemming Damgaard, Magnus Jespersen, Jens Møller et al.
Published in Communications Medicine on 7 February 2026
Abstract
Background
Colorectal cancer (CRC) patients exhibit distinct gut microbiota disruption, known as dysbiosis, which is believed to play a causative role in CRC. One of the key bacterial species implicated in CRC dysbiosis is Bacteroides fragilis, which presents a paradox as it is also present in most healthy individuals. This discrepancy underscores the need for analysis beyond species-level associations and to investigate intraspecies variation within B. fragilis.
Methods
From a highly specific collection of B. fragilis isolates from CRC patients and controls, a pangenome-wide association study was conducted, identifying intraspecies genetic variations associated with CRC. The CRC association of these genetic variations were then validated in a metagenome sequencing cohort of faecal samples from 877 individuals, with and without CRC. To test group differences a mixed effects logistic regression with cohort as a random effect was performed for each genetic variation.
Results
Here we show that CRC-associated B. fragilis isolates are infected with specific Caudoviricetes prophages, significantly more often than negative controls. The initial discovery was made in our highly specific isolate collection and then validated in an independent metagenome sequencing cohort, finding that CRC patients were twice as likely to have detectable levels of these phages (OR = 2.05, p = 2.522E-7, SE = 0.139).
Conclusions
To our knowledge, these findings mark the first link between one of the most implicated driver bacteria and phages in CRC and suggest a more complex role of phages in CRC dysbiosis than current models suggest and highlights the potential of phages as CRC biomarkers.
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