Many of us are familiar with the situation: The doctor prescribes antibiotics for strep throat, sinusitis, or another infection, and within minutes, the recommendation from friends or family members arrives: "Don't forget to take probiotics to protect your stomach."
But according to experts in the field of gastroenterology, it is possible that this habit is not only not particularly beneficial, but that in certain cases, it might even delay gut recovery.
Although antibiotics save lives and are considered one of the greatest breakthroughs in modern medicine, at the same time, they also affect the natural bacterial population living in our gut, known as the "microbiome."
The microbiome includes trillions of bacteria and microorganisms that live in the digestive system and fulfill particularly important roles: Assisting in digestion, breaking down dietary fiber, producing anti–inflammatory substances, and strengthening the immune system.
Why do antibiotics cause damage to the intestines?
When antibiotics go into action, they do not always distinguish between "bad bacteria" and beneficial bacteria. Therefore, many people experience side effects during the treatment, such as abdominal pain, diarrhea, nausea, or cramping.
In some cases, this is also a direct effect of the medication itself on the digestive system. For example, the antibiotic azithromycin, known among other things as part of "Zifac," binds to receptors in the digestive system that can cause cramping and abdominal pain.
Nevertheless, experts emphasize that digestive symptoms during antibiotic use are not necessarily a sign that the microbiome is permanently "destroyed," as many fear.
Years of damage from a single use of antibiotics
In fact, for years, researchers believed that in most cases, the microbiome manages to rehabilitate itself naturally within a few short weeks after ending the treatment, even after using relatively strong antibiotics.
However, a new Swedish study published recently in the journal Nature Medicine found that for some people, even a single antibiotic treatment can cause prolonged changes in the microbiome, sometimes even years later.
The researchers analyzed data from nearly 15,000 people and compared different types of antibiotics. According to the findings, some of the broad–spectrum drugs, including clindamycin and fluoroquinolones, were linked to a more significant and continuous effect on the gut bacteria population.
In contrast, other common antibiotics like amoxicillin, macrolides, and cephalosporins were found to have a relatively more moderate effect.
The implication, experts explain, is that not every antibiotic affects the body in the same way, and not every person responds identically either. People with a weakened immune system or those taking certain medications, such as medications to reduce stomach acidity, may be more sensitive to changes in the microbiome.
Do probiotics really help?
According to a large review of studies published in 2023, the answer is apparently much more complex than is commonly thought. The researchers found that probiotic supplements during antibiotic treatment provide very limited benefit for most people.
An additional study, published as early as 2018 in the journal Cell, raised an even more surprising finding: Participants who took probiotics after antibiotics recovered slower in terms of their microbiome composition, compared to people who did not take probiotics at all.
At the same time, there are cases where the use of probiotics is considered, mainly in people at increased risk for infection with the bacterium Clostridioides difficile, such as hospitalized or immunosuppressed patients.
What can actually be done to help the gut recover?
The experts point to three main strategies that are based on stronger studies.
The first is ensuring a diet rich in dietary fiber. The gut bacteria "feed" on fiber, and in the process of its breakdown, important substances with an anti–inflammatory effect are formed. The recommendation is not only to consume a sufficient amount of fiber, but also to diversify plant sources as much as possible.
A large study from 2018 found that a wide variety of plant foods was one of the best metrics for a diverse and healthy microbiome.
The third strategy is the daily incorporation of fermented foods like Greek yogurt, kimchi, or sauerkraut.
In a controlled study conducted at Stanford University, it was found that people who consumed a large amount of fermented foods showed an increase in gut bacteria diversity and even a decrease in various inflammatory markers in the blood.
Alongside all of these, doctors emphasize a particularly important message: Antibiotics are an essential and sometimes life–saving treatment, and therefore should not be avoided when there is a real medical need.
However, it is important to use antibiotics only when they are truly necessary, and not to demand antibiotic treatment for viral illnesses like a cold or the flu, because antibiotics do not work against viruses. The experts also remind that once you start an antibiotic treatment, it is important to complete it to the end, in order to prevent a recurrence of the infection and the development of antibiotic–resistant bacteria.