Asking what the microbiome does, not what’s in it
Dr. Elena Verdú’s research is looking beyond which microbes are present to what they are doing, and what those signals could mean for more precise inflammatory bowel disease (IBD) care.
When researchers study the microbiome, one question is obvious: which bacteria are present in the gut?
The gut microbiome is a vast and complex community of microorganisms living in the digestive tract. It includes many different types of bacteria and other microbes, and its makeup can vary considerably from one person to another.
Because the microbiome is so complex, much research has focused on understanding which microbes are present and how those microbial communities may differ between people.
Dr. Elena Verdú is interested in another question: what are those microbes actually doing?
That question has shaped years of research by Dr. Verdú and her team at McMaster University, supported through two Crohn’s and Colitis Canada Grants-in-Aid of Research between 2016 and 2024.
Their work has explored whether the activity of certain gut bacteria may contribute to inflammation, whether changes in that activity can appear before ulcerative colitis is diagnosed, and whether those differences could eventually point toward more targeted approaches to care.
An enzyme and a brake
Dr. Verdú’s first project focused on microbial proteases, enzymes that break down proteins.
Her team studied whether bacteria with high protease activity could disrupt the intestinal barrier and contribute to inflammation.
But they also looked at the other side of the equation. Some beneficial bacteria naturally produce proteins that inhibit protease activity.
Some bacteria supply the enzyme, while others supply the brake.
That gives researchers something more specific to examine. Instead of only asking which microbes are associated with disease, they can begin asking what those microbes are doing and whether harmful activity could eventually be targeted.
Could the signal come before the diagnosis?
Dr. Verdú’s later research moved the question earlier in the disease journey.
Her team studied samples from people at risk for IBD who later developed ulcerative colitis, asking whether elevated microbial protease activity was already present before diagnosis.
In other words: could the gut leave biological clues before disease becomes clinically apparent?
This remains a future possibility. If reliable biological signals can be identified before diagnosis, they may one day contribute to new ways of identifying people at greater risk.
A census and an economy
Studying the composition of the microbiome tells researchers which microorganisms are present.
Studying its function asks what that community is actually doing.
Think of it as the difference between a census and an economy.
A census tells you who is there. An economy tells you what activity is taking place.
For precision medicine, that distinction matters.
Genetics remains an important part of understanding disease risk, but Dr. Verdú’s research adds another question: which microbial functions may be driving disease, and could those differences eventually help guide prevention or treatment?
Different patterns of microbial activity could help researchers identify people at greater risk, better understand biological differences between patients, and explore treatments aimed at harmful microbial activity while preserving what is beneficial.
Diet adds another possible layer. Dr. Verdú’s research has also examined how dietary protein interacts with proteolytic bacteria, raising the possibility that microbiome function could one day help inform more individualized nutritional approaches.
The goal is not simply to know more about the microbiome. It is to understand which differences matter enough to act on.
Nearly eight years, two grants, one line of inquiry
Across two Crohn’s and Colitis Canada-funded projects, Dr. Verdú’s research moved from a fundamental question about microbial enzymes and inflammation to questions about disease risk, biological signals and more targeted interventions.
These are potential future applications of the research. Together, they point toward the potential of precision medicine: identifying disease risk earlier, making treatment choices with greater precision, and ultimately tailoring care more closely to the biology of the individual.
Knowing which microbes are present may not tell us the whole story. What they are doing could tell us much more.
And understanding those differences could help bring us closer to a future where IBD care is more precisely matched to each person.