Antibiotics are a basic ingredient of modern medicine and save millions of lives every year, but they can be harmful to the normal bacterial system on which our health is based.
Our body hosts billions of bacteria that we cannot live without, and most of them are in the intestines.
Are we permanently damaging this vital part of our body every time we take an antibiotic?
"The gut microbiome is a complex network of microbial life forms and all the things that are necessary to feed them in different parts of the body," says James Kinross, a colorectal surgeon at Imperial College London.
The gut microbiome plays a huge role in maintaining our health, among other things it regulates the immune system and helps with digestion.
Experts claim that antibiotics are one of the biggest threats to the microbiome of our intestines.
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Antibiotics, often prescribed to treat and prevent bacterial infections, are a cornerstone of modern medicine.
But when attacking the bacteria that cause infections in our body, antibiotics can inadvertently kill other bacteria from our bodies.
There is growing concern among scientists about the health consequences of our increasing dependence on antibiotics.
Between 2000 and 2015, global antibiotic prescribing increased by 65 percent.
The problem with the increase in the use of antibiotics is twofold: the damage they do to the microbiome of our intestines and the increasing bacterial resistance to antibiotics.
"Antibiotics disrupt the sensitive ecosystem of our gut microbiome, which puts surviving bacteria at greater risk of donating resistant genes to pathogens," says Gautam Dantas, professor of laboratory and genomic medicine at Washington University School of Medicine in St. Louis, USA.
We know that the more diverse the bacterial population of our intestines, the better for us.
But any antibiotic therapy destroys their numbers, because the antibiotics are not targeted precisely enough to kill only the pathogenic bacteria that cause the infection.
Instead, they attack all the bacteria in our intestines.
"Collateral damage is occurring.
"Imagine a forest where you are trying to get rid of a weed infestation. We use antibiotics by carpet-bombing that entire forest, killing both good and bad bacteria," says Dantas.
When scientists looked retrospectively at the microbiomes of people who had been treated with antibiotics, they found that the diversity of the microbiome generally recovered within a few months, the professor adds.
In some people, however, some good bacteria never reappear, he notes.
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Dantas and his team of researchers are studying stool samples from children treated at a pediatric hospital affiliated with the lab.
The samples were collected routinely, before any antibiotics and infections, which allowed his team to observe changes in children who get infections and later antibiotics.
Dantas used these samples to compare changes in the gut microbiome after antibiotics in two groups of infants: premature babies, those born before 36 weeks, and babies born after 36 weeks.
"What we know happens in adults after taking antibiotics is even more dramatic in babies: lower microbiome density and huge jumps in drug-resistant genes," he says.
Although the consequences differ from person to person and depend on our age, the consensus among scientists is that the effects of just one course of antibiotics can be permanent.
"Some people are very susceptible to damage to their microbiome from antibiotics, and the ecology of their microbiome will change dramatically and never return to what it was before the antibiotic dose.
"We are losing diversity in our guts and key microbes that have sustained us for hundreds of thousands of years are disappearing on unprecedented timescales," says James Kinross.
Scientists are still trying to understand the long-term health consequences of antibiotic use on our gut microbiomes.
"We know that antibiotics have the ability to affect every domain of microbiome function.
"They don't reduce the number of bacteria, but they affect the role of microbes in complex and individualized ways that we don't really understand," says Kinross.
He adds that it is not only their impact on the bacteria in the intestines that worries him, but also the secondary consequences of the development of the immune system.
Studies show that taking constant doses of antibiotics has a cumulative effect, and the consequences are greater if you take doses of a wider spectrum.
This is often called the "multiple hits hypothesis".
"This is a strange evolutionary experiment that we do to ourselves every time we take an antibiotic," says Dantas.
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Another consequence of long-term antibiotic use is the risk of resistance.
When a bacterial population is exposed to an antibiotic, those that do not have the genes for antibiotic resistance usually die out.
But those who have it either through genes picked up from the environment or spontaneous mutations survive.
In this way, the drugs actively select bacteria that are resistant to antibiotics.
This is a problem when pathogenic bacteria take advantage of this adaptation.
"Every time we drink antibiotics, the proportional risk that the gut microbiome is enriched with drug-resistant genes increases.
"The next time the parasite comes along, it might pick up some of those selective resistance genes from the gut," says Dantas.
And that process doesn't just take place in our intestines, says Craig McLean, professor of evolution and microbiology at the University of Oxford.
"Resistant bacteria can move from the gut to other parts of the body, so what happens in the gut affects the rest of the body," he says.
The harmful and saving influence of antibiotics is one of the biggest puzzles that plague scientists from all over the world.
Although there is no single solution, there are approaches that could mitigate the harmful effects of antibiotics on our health.
"Antibiotics are fantastic drugs that have saved millions of lives.
"They are very valuable resources and should be used, but we need to find a way to target them precisely," says Kinross.
Scientists are now looking at antibiotics that target more specific parts of the body, as well as those that target specific bacteria, McLean says, with the idea of getting rid of only the bacteria they want to get rid of, while leaving the beneficial bacteria in the gut intact.
Anthony Buckley, Associate Professor of Gut Microbiology at the University of Leeds, says the most powerful weapon we currently have is our diet.
"Nutrition is one of the biggest fuels that builds the human microbiome," he says.
A research group from the University of Leeds dealing with healthcare-associated infections has been analyzing the effects of antibiotics on the microbiome over the past two decades.
"The greater variety of food we eat tends to be associated with a greater diversity of microbes in the gut, and fiber in particular seems to have a positive effect," says Ines Moura, a research associate at the University of Leeds' School of Medicine and Health, who is currently investigating the effects of different nutrients on gut microbiome and how they can reduce the negative effects of antibiotics.
Dietary fiber is especially important because microbes in our bodies digest it and produce short-chain fatty acids, which provide energy to the cells lining the gut, says Buckley.
"When you take antibiotics, the number of microbes that produce short-chain fatty acids is reduced and it takes time for them to recover.
"Our theory is that by introducing fiber in the diet, it provides a replacement for those microbes where they can grow and produce fatty acids, and with any luck rebalance," he says.
The irony of antibiotic use is that with each new therapy we take, our body's ability to fight infections potentially decreases, and our dependence on antibiotics increases.
"It's much better not to depend on antibiotics, but to focus on bio-resilience of our internal ecology by eating healthy, especially early in life, because that's where antibiotics do the most damage," says Kinross.
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