Representative Fna C1 and Fna C2 strains co-cultured with human colon cancer cells. The grid shows the results of computational analysis of confocal imaging. Independent masks for cancer epithelial cells (grey), and intracellular bacterial cells (Fna C1 green, Fna C2 lavender) were generated. The masks were used to calculate the percent of cancer cells with intracellular Fna. The scale bar is 20 μm.
| Photo Credit: Zepeda-Rivera, M., Minot, S.S., Bouzek, H. et al. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 628, 424–432 (2024).
The bacteria known as Fusobacterium nucleatum live in the human mouth and are rarely found elsewhere. But in cases of cancer of the colon or the rectum, the bacteria are found in tumours in the gut, where they help cancer cells escape from the immune system and spread to other parts of the body.
In a new study, a group of researchers from the Fred Hutchinson Cancer Center in the U.S. has identified a distinct subtype of the bacterium that’s found in relatively greater quantities in colorectal cancer (CRC) tumours.
CRC is the seventh most common type of cancer in India, where the number of cases rose by 20% from 2004 to 2014. Worldwide, the overall CRC incidence has declined but, experts wrote in the journal Science last year, the incidence of age-adjusted early-onset CRC “has risen at an alarming rate of 2-4% in many countries, with even sharper increases in individuals younger than 30 years.”
According to the team’s experiments, described in a paper in Naturein March, some genetic factors could be boosting Fusobacterium’s ability to associate with cancers of the gut. The team also showed that when mice were infected with this type of Fusobacterium, their intestines developed precancerous formations called adenomas.
Experts said the study’s findings could be used in future to develop tests to detect CRC early and develop targeted treatment options.
A clade of its own
The researchers began by culturing Fusobacterium bacteria collected from 130 human CRC tumours in the laboratory. Then they mapped the entire genetic composition of the isolated bacteria and found that out of the four known Fusobacterium nucleatum subspecies, only Fusobacterium nucleatum animalis (Fna) was significantly associated with CRC tumours.
Individual members of the same species have slightly different DNA. Pangenomic analysis helps researchers map all the genes in a species as well as those parts of the genome that some but not all members of the species have. This part is called the accessory genome. The members of a species can be further subclassified depending on the accessory genomes they have.
In their analysis, the researchers found Fna has the smallest core genome (the part that all members of the species have), indicating there could be different subtypes of Fna. In response, they traced the evolutionary history of the bacteria by tracing the changes in its genes. This analysis revealed that Fna, instead of being one homogenous group, is composed of bacteria from two different evolutionary lineages.
Scientists call a group of life-forms belonging to one evolutionary lineage a clade. Thus, the researchers had identified two different clades of Fna: they called these Fna C1 and Fna C2. They further found Fna C2 bacteria are significantly associated with CRC tumours and that they have extra genetic factors to help them in this regard.
Colonising the gut
Both physical and genetic differences between the two clades seemed to contribute to Fna C2 bacteria’s ability to associate with CRC tumours. Physically, the Fna C2 bacteria looked longer and thinner than Fna C1 bacteria. Such differences can affect how bacteria are able to live in host tissue as well as evade the body’s immune system, the authors wrote in their paper.
Genetically, Fna C2 bacteria had genes required to munch two compounds for energy in the human gut: ethanolamine and 1,2-propanediol. These genes were missing in Fna C1. So the researchers concluded Fna C2 bacteria’s ability to associate with CRC tumours was at least partly contingent on them “having increased nutrient scavenging mechanisms and enhanced metabolic potential”.
The researchers validated their findings by analysing genomes present in more than 1,200 human stool samples, roughly half of which were from people with CRC while others were from healthy individuals. They found that the Fna genes required to metabolise ethanolamine and 1,2-propanediol were more enriched in stool samples from CRC patients than in samples from people without CRC.
Mouth to gut
Scientists previously believed Fusobacterium bacteria could go from the mouth to the gut by infecting the bloodstream when, say, someone brushed their gums too hard or during routine dental procedures. The authors of the new Nature paper pitched a new route: that the bacteria could have descended through the gastrointestinal tract to reach the colon.
Bacteria don’t usually take this path because they can’t survive the highly acidic environment of the stomach.
But the researchers found Fna C2 could. These bacteria could grow in more acidic conditions than could Fna C1 bacteria — and they also had specific genes that could resist the effects of acids. These genes came online when the acidity was comparable to that of stomach acid.
In mice as in humans
Next, the researchers investigated whether Fna C2 could induce the development of tumours in the gut. For this, they introduced Fna C1 bacteria in the inflamed guts of some mice and Fna C2 bacteria in the inflamed guts of others. (These mice are a common animal model used to investigate conditions that also affect humans.) They found a significantly higher incidence of adenomas in the intestines the mice treated with Fna C2 bacteria.
They also noted that the intestines of Fna C2-treated mice had different metabolic profiles — changes consistent with previously reported associations between differential metabolite levels and tumour progression.
“Overall, our results demonstrate the ability of Fna C2, but not Fna C1, to metabolically affect the intestinal milieu towards” conditions conducive to CRC, the authors wrote.
Finally, the researchers tested their hypotheses in a cohort of human patients. Working with CRC tissue and non-cancerous tissues from the same individual, the authors confirmed that Fna C2 was the only Fusobacterium subtype enriched in CRC tissues. They found similar results in stool samples from those with CRC but not in those from healthy individuals.
Long road to clinical trials
According to Neetu Kalra, a cancer therapeutics researcher at Azim Premji University, Bhopal, “The study presents promising prospects for the advancements of microbial cellular therapies, which involve the use of modified bacterial strains to directly administer treatments into tumours.”
Varun Aggarwala is an assistant professor at Jio Institute, Mumbai, who also works on faecal transplants for infectious and inflammatory bowel diseases. He called the study “comprehensive” and said “studies like this provide a solid foundation for the broader community to design targeted microbial interventions and diagnostics for CRC.”
He added that future research should track the gut and oral microbiome of high-risk individuals and their tumour microbiome after a CRC diagnosis to understand how certain strains of bacteria can cause cancer.
Similarly, Dr. Kalra said studies to come could look at the “colonisation timeline” of Fna C2 bacteria: the CRC stage at which the bacteria become associated with the tumours. “If colonisation occurs early,” she explained, “it could facilitate early CRC diagnosis”.
On the flip side, she also said developing a drug that could selectively target Fna C2 bacteria without affecting Fna C1 or other gut bacteria “presents a significant challenge”.
Sayantan Datta is a science journalist and a faculty member at Krea University. They tweet at @queersprings.
