Will probiotics help your gut recover from antibiotics?

Should you be taking probiotics after antibiotics to protect the health of your gut microbiome? Let’s dig in.

Your gut microbiome is home to trillions of microorganisms, such as fungi, yeasts, viruses, and many species of bacteria.

These microbes help you break down food, fight off infections, and produce chemicals that are good for your health.

Antibiotics are antimicrobial medicines that work by killing bacteria. In fact, the word “antibiotic” comes from the Greek language and means “against life,” referring to the ability to destroy other living organisms.  

Conversely, probiotics are living microbes that provide health benefits.

In this article, we’ll explain how antibiotics affect your gut microbiome. Then, we’ll look at what the research says — is taking probiotics after a course of antibiotics a good idea?

Lastly, we’ll give you some top tips about supporting your gut health. 

Antibiotics and the gut microbiome

Many people credit Alexander Fleming with discovering the first antibiotic, penicillin, in 1928. However, scientists have found traces of antimicrobials in human skeletons dating as far back as 350 A.D.

Antibiotics are brilliant at destroying harmful bacteria, which is why doctors prescribe them to treat infections. 

They have saved millions of lives and are particularly important for treating dangerous diseases like pneumonia, meningitis, and sepsis. 

There are two main types:

  • Narrow-spectrum antibiotics are used to target specific bacteria.

  • Broad-spectrum antibiotics are used to kill a wide range of bacteria.

Broad-spectrum antibiotics are particularly useful for fighting infections when it’s unclear what type of bacteria is responsible. 

However, these powerful medicines take out lots of “good” bugs in the process. This scattershot approach can disrupt the delicate balance of your gut microbiome. Experts call this disruption microbial dysbiosis

While killing large quantities of bacteria may sound like a good thing, there are some inescapable downsides. With large swathes of “good” bugs gone, there’s more room for less desirable bacteria to set up camp and multiply. 

When colonies of “bad” bugs rapidly increase, you may experience unpleasant side effects, including:  

  • nausea

  • vomiting

  • loss of appetite

  • stomach pain

  • bloating

One of the most common side effects is antibiotic-associated diarrhea (AAD). In fact, 5–35% of people who take antibiotics experience AAD, depending on the type of antibiotic. 

AAD commonly results from a rapid increase in numbers of Clostridium difficile bacteria. While AAD is often more of a nuisance, it can sometimes be severe enough that you need hospital treatment. 

It’s important to remember that not all antibiotics affect your gut microbiome in the same way. The type of antibiotic you take, how long you take it, and the dosage will all play a part. 

Probiotics after antibiotics

You can find probiotics in live yogurts, some cheeses, and fermented foods like kimchi, kombucha, and sauerkraut. 

Recently, there’s been an upsurge in companies selling probiotics in supplements — as pills, powders, and drinks. 

Many people are interested in whether probiotics can help support gut health during and after a round of antibiotics. So, over the last few years, a number of clinical trials have explored this.

Frustratingly, much of this research has produced findings that are confusing and difficult to translate into actionable advice. 

For example, a 2018 clinical trial found that certain probiotic strains were effective at colonizing the gut after antibiotics.

However, it took longer for the microbiomes of people taking the probiotics to return to normal, compared with the people who didn’t take the probiotics. 

The same research team conducted another experiment. This time, they found that the probiotics took hold and began to multiply in some people but not others. 

This variability in how people respond might be because our gut microbiomes are unique. ZOE’s own research has shown that identical twins — who share the same DNA — share only 34% of the same microbes. 

Meanwhile, many studies on probiotics after antibiotics look at specific population groups. This, too, makes it hard to come up with a general consensus.

Still, a 2017 meta-analysis found that probiotics may reduce the risk of AAD by 51% without an increase in side effects. 

And a large-scale meta-analysis in BMJ Open backed up these findings. The authors pooled data from 42 studies, including more than 11,000 adult participants. 

The researchers concluded that giving probiotics with antibiotics reduced the risk of AAD by 37%, compared with a placebo or an alternative treatment. But only certain species of probiotics — mostly strains of Lactobacilli and Bifidobacteria — were effective. 

So, it looks like there may be a role for probiotics in reducing the risk of getting AAD, but the jury is still out about which strains and dosages are the most effective. 

Improving gut health

In the last 10 years, interest in the gut microbiome has exploded. Scientists have discovered that having a diverse microbiome, with many beneficial bacteria, is linked to a stronger immune system, a lower risk of chronic diseases, and improved mood. 

So, it’s a good idea to look after your gut, even if you’re not taking antibiotics.

Here are our top tips for supporting your gut health:

Pack your plate with plants

Research has shown that the more fiber-rich foods you eat, the more diverse your microbiome is.

Our good bugs particularly enjoy foods like whole grains, vegetables, nuts, seeds, beans, and pulses. Look for ways to add plants to every plate.

Find time to relax

Scientists believe that stress can negatively affect the gut microbiome. Increased stress is also linked to a reduction in the number of beneficial bugs like Lactobacilli

Techniques like deep breathing may help induce feelings of calm — though researchers still need to explore whether stress-reduction techniques can benefit gut health directly. 

Move your body

Being active is another way to improve microbial diversity.

For instance, a recent observational study found that the microbiomes of active women have more of the “good” bugs Faecalibacterium prausnitzii, Roseburia hominis, and Akkermansia muciniphila than those of women who weren’t active.

These bacteria are associated with better health outcomes. 

If you’d like to learn which bugs live in your gut, ZOE’s at-home test can tell you. We can also show how your body responds to different foods and help you tailor your diet to suit your health goals.

You can start by taking our free quiz.

Feast on fermented foods

Kimchi, kefir, kombucha, live yogurt, artisanal cheese, and sauerkraut not only taste tangy and delicious but are also packed with probiotics.

Prof. Christopher Gardner, a member of the ZOE Scientific Advisory Board, recently led a groundbreaking study. His team found that eating a diet rich in fermented foods increased the number of “good” gut bugs and lowered inflammation. 

Eat the rainbow

Brightly colored plants are full of polyphenols, which our “good” gut bugs devour with glee.

Berries, nuts, seeds, extra virgin olive oil, and dark chocolate all contain high levels of these antioxidant and anti-inflammatory compounds. 


Antibiotics are an important weapon in the fight against certain diseases. Their antimicrobial properties are highly effective at killing harmful bacteria. 

However, they can also disrupt the delicate balance of microbes that live in our guts. This can lead to an upset stomach and, in some cases, severe diarrhea. 

Probiotics are live bacteria that may help increase the diversity and abundance of “good” bugs in your gut.

Research suggests that certain strains of probiotics — particularly Lactobacilli and Bifidobacteria can help reduce the risk of this type of diarrhea in some people. 

But there are many other ways to support your gut health. 

Eating a fiber-rich diet full of colorful plants and fermented foods can help keep your gut bugs happy. 

Also, getting regular exercise can help reduce stress and increase the number of beneficial bacteria in your microbiome: It’s a win-win.


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