For decades, doctors have puzzled over why some gut bacteria outlast powerful antibiotics. Now a miniature laboratory that recreates the oxygen-free world of the intestine lets researchers watch gut bacteria in their natural element – and could help unravel many more health mysteries in the years ahead.
Hospitals worldwide report the same troubling pattern: people take antibiotics, improve for a few days and then relapse – sometimes so severely that their lives are at risk. Tests reveal that the culprit, the dangerous bacterium Clostridioides difficile, often bounces back with alarming speed. It thrives particularly among people whose normal gut flora has been wiped out by antibiotics given for other infections.
The study was led by Thomas Emil Andersen, working with doctors and microbiologists from Odense University Hospital and the University of Southern Denmark in Odense. The findings were published recently in npj Biofilms and Microbiomes.
“What makes this groundbreaking,” he explains, “is that, for the first time, we can grow oxygen-sensitive bacteria directly on living intestinal cells, keep them alive for days and do it all in a flowing environment that mimics the human gut.”
This has never been possible before and provides the researchers a tool to explore entirely new aspects of how gut bacteria interact with the body.
“This opens the door to solving many of the riddles doctors struggle with today, especially when infections recur after treatment.”
When gut bacteria suddenly turn dangerous
To grasp the significance of the breakthrough, picture the setting: the large intestine. There is no oxygen and billions of bacteria have adapted to live without. For them, even the tiniest trace is lethal. This extreme sensitivity has long made them almost impossible to study in an ordinary laboratory, where both researchers and test cells are surrounded by oxygen – which even seeps through materials such as plastic.
“For years it was a paradox,” says Thomas Emil Andersen. “Every time we tried to study these bacteria, our methods killed them. On the one hand we had to shield them from oxygen, on the other we had to keep the intestinal cells alive with oxygen. The two conditions contradicted each other – we simply could not keep the bacteria alive long enough to answer our questions.”
That is why he now welcomes the new set-up, which finally enables researchers to observe how anaerobic bacteria behave – and how they go about attacking the intestine.
When oxygen is vital for some – deadly for others
Researchers have previously tried organ-on-a-chip systems, but they never worked well. Flushing the oxygen out could take days, and even then it quickly seeped back in. With the new chip, the oxygen is gone within minutes, and the set-up stays stable and oxygen-free for several days.
The device is a specially designed plastic platform with two separate flow channels divided by a thin membrane. It is about 6–7 cm long and 3–4 cm wide. One channel supplies oxygen to the human intestinal cells from below – as they would receive it from the bloodstream. In the other, the bacteria grow on the cultured intestinal cells in a medium that has been stripped of oxygen using a special patent pending method.
“In practice we have built a miniature gut, where cells and bacteria live side by side exactly as they do in the body. That enables us to see how bacteria change their behaviour when they meet the host – and how they react to treatment,” explains Thomas Emil Andersen.
For the first time, the intestinal environment has been simulated this precisely over time. To prove that the system works, the researchers measured the oxygen levels directly inside the model.
“The results showed that conditions stayed well below 1% oxygen for weeks, and that once bacteria were introduced they continued to grow actively for up to five days – just as they do in the human gut,” Thomas Emil Andersen notes.
Why antibiotics fail against C. difficile
The researchers have already used the model to test how C. difficile responds to antibiotics. By tracking the number of bacteria before, during and after treatment, they found that the bacteria never really disappear, even at antibiotic concentrations that should be lethal. The infection simply flares up again.
The study shows exactly what doctors see in their patients: the bacteria often survive treatment because C. difficile entrenches itself in slimy structures called biofilms. Inside these biofilms, the bacteria can hide while the drugs are at work, only to launch new attacks on the gut once the danger has passed.
Using the model, the team could document the bacteria’s continued presence, their toxin secretion and the resulting damage to the intestinal cell barrier.
“This explains why patients fall ill again,” says Thomas Emil Andersen.
A chip that can change the treatment of infections
Every year, C. difficile strikes hundreds of thousands of hospital patients around the world, and the bacterium is now seen as one of the most persistent and costly hospital infections to treat.
The new model is therefore not just a technical achievement – it is a practical research tool for understanding disease and developing new therapies. In this study, the chip serves both as proof of a technical breakthrough and as a functional model that has solved a longstanding mystery: why some harmful gut bacteria survive antibiotics and return.
“We now have clear proof that the model works. It is a breakthrough because we have created a realistic alternative to animal testing – and something that, in the long term, can make developing new treatments easier and faster,” adds Thomas Emil Andersen.
For now, the system remains a prototype. It is complex and takes up considerable space. But with support from the Novo Nordisk Foundation, the team is working to compress the technology into a compact, user-friendly box that other laboratories can adopt. They expect to have a usable version within a year.
“We are already in dialogue with companies producing gut-on-a-chip technology. The plan is for our model to be offered as an upgrade to their systems. And we hope that, in the long term, it can be used both in research and in developing treatments – without relying on animal models, which raise ethical concerns and poorly reflect the human gut,” he says.
The research group is also working with the biotech company Bactolife, which develops molecules to neutralise the toxins released by C. difficile. The aim is to demonstrate how the model can be used to test entirely new treatment strategies before they reach patients.
In this way, the small plastic chip achieves what researchers have been striving for over decades: opening a window into the dark, oxygen-depleted world of the gut. C. difficile is still among the most feared and widespread hospital infections. With the new chip, researchers have opened a peephole into the hidden universe of the intestine – where bacteria hide, survive and strike again – and where they may one day be stopped.
