Hospital treatments may alter the balance of bacteria in your body Trumzz/Getty Images

A trip to hospital can play havoc with your gut bacteria. People treated for several days in an intensive care unit had their guts quickly colonised by harmful pathogens, tests show. Healthier gut microbes were pushed out – a shift that may have long-term effects after someone is discharged.

Heavy use of broad-spectrum antibiotics, feeding people through a tube and using a ventilator to help them breathe could all contribute to the effect, say the team who carried out the study.

Gut health: from the inside out Megan Rossi at New Scientist Live

“It’s quite disconcerting,” says Mark Pallen, a microbial genomics researcher at the Quadram Institute, UK, who led the research. “I was surprised. I mean, I suspected that something like this was going on, but I was quite taken aback at the scale of the changes.”


To assess the impact of intensive care treatment on the gut microbiome, the team tracked 24 people admitted for trauma, heart attacks, cancer and other emergencies to Queen Elizabeth Hospital Birmingham, UK, over a 10-month period.

Many of those admitted, who were aged between 25 and 85, were unconscious or sedated. After getting permission from family members, the scientists took stool samples from those individuals.

Using a technique called shotgun metagenomics, they extracted and sequenced DNA from the samples to identify which microbes were present – and how that changed over the course of treatment.

Two-thirds of the patients showed a marked reduction in microbial diversity at some stage during their stay. The biggest changes were associated with intravenous use of the antibiotic meropenem.

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The gut is normally home to a rich and versatile set of microorganisms, says Pallen. “Whereas in these patients, we are seeing all that diversity collapsing down to domination of the gut microbiota by a single organism occurring at a very high abundance.”

Most frequently, the researchers found that patients’ guts were dominated by Enterococcus faecium, a common bacterial pathogen. That is a problem because this microbe can spread from the gut and damage other parts of the body, including the lungs. If it reaches the bloodstream, it can be fatal.

Particularly worrying, says Pallen, is that the study found evidence of a single strain of E. faecium spreading between three people.

It is a small number of patients to draw conclusions from, but the results align with other studies, says Joost Wiersinga at the Academic Medical Centre in Amsterdam, the Netherlands.

While the priority in intensive care is always to save lives, Wiersinga says medics could do more to minimise disruption to gut bacteria. “If you need to give antibiotics then give them. But think about which antibiotic, for how long and if you can stop earlier.”

Journal reference: Microbial Genomics, DOI: 10.1099/mgen.0.000293