Single course of antibiotics may cause irreversible damage to crucial gut bacteria

Taking just a single course of antibiotics can damage the healthy bacteria in the gut for at least a year and possibly permanently, scientists have warned.

Researchers at University College London (UCL) found that just one prescription can change the composition of the microbiome - the collection of trillions of bacteria, fungi and microbes, which live in the body and help regulate the immune system, aid digestion and produce vitamins.

In a healthy human gut there are around 1,000 different kinds of bacteria in the gut, and greater diversity of species has been linked to better health.

But the new study found that antibiotics caused the gut microbiome to change to a less diverse state with fewer types of bacterial species, potentially raising the risk of disease.

In recent years problems with gut bacteria have been linked to obesity, the development of Parkison’s disease, Chron’s disease, asthma, allergies, inflammatory bowel, diabetes, multiple sclerosis, autism, cancer, and even HIV.

“People have known that antibiotics decrease the diversity of microbes in the gut before it recovers, but the model we’ve developed suggests that the disturbance may transition the microbiome to a new composition, perhaps permanently,” said first author Dr Liam Shaw, of UCL Genetics Institute.

“If you picture the state of the microbiome as a ball resting in a valley, antibiotics can ‘kick’ the ball up and out of the valley into a different valley, where it may not be able to return to the first one.”

The NHS is currently trying to limit the number of antibiotics given by doctors, over fears it over-use is causing bacteria to evolve into untreatable strains.

But the research suggests too many drugs could also be harming patients from the inside out, and the researchers say GPs should also take that into account when prescribing.

“We do know that where gut populations of microbes take a long time to recover, or sometimes don’t recover at all, individuals are likely to be at more risk from colonisation and overgrowth of pathogenic species,” added Dr Shaw.

“Antibiotics are sometimes extremely necessary, but this kind of ‘collateral damage’ – which varies by antibiotic – should probably be considered more in the future when making prescribing decisions.”

For the study, published in The ISME Journal, the researchers developed a computer model to predict the changing diversity of microbes in the body over time, following a course of antibiotics.

They used data from previous studies which had measured the changes to 40 people who had taken four common antibiotics – ciprofloxacin, clindamycin, minocyline and amoxicillin - then used their model to fast forward and see what happened to the microbial soup after a year.

The biggest disturbance to the gut was seen in individuals given ciprofloxacin and clindamycin which are usually given for urinary tract, skin and respiratory tract infections.

In those cases the gut microbiome changed to a less diverse state with fewer types of bacterial species, and in the case of clindamycin persisted for a year after exposure.

“Though we don’t fully understand the exact role the microbiome plays in maintaining health, the effect of antibiotics is dramatic and are likely to be of some importance,” explained study author Professor Francois Balloux  of the UCL Genetics Institute.

“The impact we saw raises concerns about the length of antibiotic courses and the long-term impacts of antibiotic use.”

The gut is now thought to be so pivotal to human health, and even mood, that some scientists have now dubbed it ‘the second brain’ and are concerned that children are particularly sensitive to upsets in the microbiome.

Have you experienced damage to your gut after taking antibiotics? Share your experiences in the comments section below. 

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