- Some probiotics (e.g., L. rhamnosus GG, S. boulardii) may reduce the risk of diarrhoea when taking antibiotics.
- Not all probiotics work in the same way – it depends on the specific strain, dose and timing.
- Restoring the gut microbiome with probiotics is not guaranteed – they are more likely to help mitigate the effects than to "repair" the microbiome.
Antibiotic treatment and the gut: what can go wrong?
Antibiotics are an effective weapon against bacterial infections – but at the same time, they also interfere with the complex ecosystem of microorganisms that inhabit our digestive tract. This microbiome is composed mainly of bacteria, but also yeasts, viruses and fungi. In healthy individuals, it functions as a dynamic yet stable community that participates in fibre digestion, vitamin production, protection against pathogens and the modulation of immunity.
When this balance is disrupted by antibiotics, there is often a sharp reduction in bacterial diversity. This means not only a decrease in the total number of species, but also a change in their relative proportions. Particularly sensitive to antibiotics are bacteria that support our health – for example, those from the genera Bifidobacterium and Lactobacillus.
This state, known as dysbiosis, can have several unpleasant consequences:
- Antibiotic‑associated diarrhoea (AAD): the most common adverse effect. It affects up to a third of adults treated with antibiotics.
- Overgrowth of pathogens: reduced competition allows harmful microorganisms, such as Clostridioides difficile, to develop, which can cause severe colitis.
- Decrease in SCFA production: these substances have an anti‑inflammatory effect and support the absorption of water and minerals in the intestine. A deficiency can worsen diarrhoea and disrupt the intestinal barrier.
- Changes in bile acid and carbohydrate metabolism: this can lead to increased osmolarity of the intestinal contents and worsening symptoms.
The consequences of dysbiosis can also be long‑term. With repeated courses or broad‑spectrum antibiotics (e.g., clindamycin and cephalosporins), restoration of the microbiome can be slow and incomplete – especially if there is not enough time between individual courses.
What are probiotics, and why is there so much talk about them?
The word ‘probiotic’ can now be found on the shelves of pharmacies, supermarkets and nutrition e‑shops. It is often offered as an answer to any digestive problem – from diarrhoea to bloating. But what exactly are probiotics?
According to the definition of the World Health Organization (WHO) and FAO, probiotics are "live microorganisms which, when administered in adequate amounts, confer a health benefit on the host". The key words here are ‘live’ and ‘adequate amounts’. It is not enough for a product simply to be ‘natural’ or ‘fermented’. It must contain specific microorganisms in an effective dose that have proven effects.
There is no universal probiotic that works for everything
One of the most common misconceptions about probiotics is the idea that "a probiotic is a probiotic" – that you can choose any product with this label and expect the same effect. But the reality is more complex, and we can compare it, for example, to vitamins. You distinguish between taking vitamin C and vitamin D and choose them based on the effect you expect.
Probiotics are not all the same product
Each probiotic is characterised by a three‑part name:
- Genus (e.g., Lactobacillus)
- Species (e.g., rhamnosus)
- Strain designation (e.g., GG)
This gives us, for example, Lacticaseibacillus rhamnosus GG – a specific probiotic that has been thoroughly clinically tested. Another strain of the same species, e.g., L. rhamnosus GR‑1, may have completely different effects, while a third strain may have none at all.
So, if you are offered probiotics in a pharmacy without any mention of the specific genera, species and strains of bacteria, it is likely to be money wasted.
Can probiotics prevent antibiotic‑associated diarrhoea?
One of the mainreasons people reach for probiotics during antibiotic treatment is the fear of antibiotic‑associated diarrhoea (AAD). According to studies, this type of diarrhoea affects 5–39% of adult patients, with the risk depending on the type of antibiotic, dose, duration of treatment and other factors.
How effective are probiotics for diarrhoea caused by antibiotics?
A comprehensive analysis of 36 randomised, placebo‑controlled studies involving more than 9,000 participants showed that probiotics can reduce the risk of AAD by 38%. This effect was consistent across different types of antibiotics and durations of probiotic use.
Moreover, it was not only about reducing diarrhoea, but also about lowering the risk of infection with Clostridioides difficile – a serious pathogen that can cause severe pseudomembranous colitis and, in severe cases, can even lead to life‑threatening conditions. There is also evidence that a properly chosen probiotic can reduce this risk.
Which probiotics work best?
Not all probiotics are equal. Among the most well‑studied are:
- Lacticaseibacillus rhamnosus GG: one of the most extensively studied strains, with a proven effect on the prevention of AAD in both children and adults.
- Saccharomyces boulardii CNCM I-745: a yeast that, unlike bacteria, survives antibiotic treatment.
- A combination of L. casei LBC80R + L. acidophilus CL1285: effective in several studies involving hospitalised patients.
How should you take probiotics with antibiotics to reduce the risk of diarrhoea?
- Start as soon as possible. The greatest benefit is seen when the probiotic is started as early as possible – ideally within the first two days of starting antibiotics. The sooner, the better in terms of diarrhoea prevention.
- It is sufficient to take them during the course of antibiotic treatment. Analysis shows that the most effective strategy was to take probiotics alongside antibiotics for the entire duration of treatment. If probiotics were continued for significantly longer after finishing antibiotics (e.g., for another week or more), the protective effect against diarrhoea was no better – in fact, it was somewhat weaker.
What is important to keep in mind?
- Not every probiotic sold on the market contains these proven strains.
- The effect is strain‑specific – you cannot expect the same effect from other strains, even if they are from the same genus.
- In healthy adults, taking probiotics with antibiotics is generally safe, although the effect may vary from person to person.
- On the other hand, probiotics may not be suitable for high‑risk patients – for example, those who are severely immunocompromised, critically ill or have a central venous catheter.
How do probiotics work?
Although we have quite a lot of clinical data showing that probiotics can reduce the risk of antibiotic‑associated diarrhoea, we still do not know exactly how they achieve this. The mechanisms of their action are largely hypothetical and probably differ from strain to strain. Nevertheless, based on available studies, several key pathways can be identified through which probiotics may positively influence the intestinal environment:
1. Competition with pathogens
Probiotics can compete with undesirable microorganisms for nutrients and binding sites on the intestinal mucosa. This reduces the chance that pathogens such as Clostridioides difficile or Klebsiella spp. will overgrow.
2. Production of antimicrobial substances
Some probiotic strains (e.g., Lactobacillus and E. coli Nissle 1917) produce substances called bacteriocins – natural antibiotic peptides that can suppress the growth of other bacteria.
3. Changing the composition of intestinal contents
Probiotics can influence the metabolism of bile acids or carbohydrates, thereby changing the chemical environment in the intestine. This can help reduce osmolarity and alleviate diarrhoea.
4. Increasing production of SCFA (short‑chain fatty acids)
Some strains support the fermentation of fibre and therefore the formation of SCFAs – especially butyrate, propionate and acetate. These substances improve the absorption of ions and water, have anti‑inflammatory effects and strengthen the intestinal barrier.
5. Modulation of immune response
Probiotics can influence the activity of immune‑system cells in the gut, for example by suppressing excessive inflammatory responses or supporting the production of protective mucus.
6. Temporary help, not permanent colonisation
It is important to understand that most probiotics do not create a new permanent microbiota. They usually act in the digestive tract only temporarily, for the duration of use. During this transient presence, however, they can positively, but also negatively, influence the composition and behaviour of other microorganisms – e.g., through the "cross‑feeding" effect, meaning the creation of substances that other bacteria use.
Probiotics may not have only positive effects
Marketing slogans may make it seem as though probiotics have almost magical powers to restore the natural balance of the gut microbiome after antibiotic treatment. But what does science say?
What happens to the microbiome during antibiotic treatment?
Antibiotics can cause dramatic changes in the composition and diversity of the gut microbiome. Some types of bacteria disappear almost completely, others overgrow, and the result is often a state of low diversity. In healthy adults, the microbiome usually partially recovers within a few weeks, but a complete return to the ‘baseline state’ is more the exception than the rule – especially after repeated courses of antibiotics.
Can probiotics worsen microbiome regeneration?
Specific types of probiotics have a proven positive effect on the occurrence of diarrhoea, but their effect on restoring the original microbiome is largely negligible and sometimes even negative.
According to a recent review of studies evaluating the effect of probiotics on the microbiome, rather than only clinical symptoms such as diarrhoea, the results were inconsistent:
- One study showed that probiotics mitigated the decline in diversity.
- Another study found that probiotics delayed spontaneous microbiome regeneration.
- Most studies showed no significant effect of probiotics on the composition or function of the microbiome.
Another meta‑analysis from 2023 concluded that probiotics do not provide any measurable benefit in maintaining microbial diversity during antibiotic therapy. Differences between groups, with and without probiotics, were statistically insignificant across several indicators.
The authors of these studies therefore point out that, even though probiotics may improve clinical symptoms, such as alleviating diarrhoea, their effect on actual microbial restoration is uncertain – and sometimes possibly even undesirable.
Bottom line
- Antibiotics disrupt the gut microbiome, which can lead to unpleasant side effects, most commonly diarrhoea, but also other long‑term problems.
- Some probiotics may help reduce this risk – especially Lacticaseibacillus rhamnosus GG and Saccharomyces boulardii.
- Not every probiotic works in the same way. The effect is strain‑specific – just as with vitamins, it depends on the specific type. When choosing probiotics, make sure you know what they contain.
- Probiotics generally do not ‘repair’ the microbiome, but rather help bridge the period of disruption. Some may even slow down spontaneous regeneration.
- Safety is generally good, but for at‑risk groups, including immunocompromised and hospitalised patients, caution and consultation with a doctor are advised.
