How To Restore The Gut Microbiome After Antibiotics

Restore The Gut Microbiome After Antibiotics

In this post I discuss how to restore the gut microbiome after antibiotics, looking at the side effects of antibiotics, prevention, the best probiotics and more.

It’s important to appreciate that antibiotics are life-saving drugs and are brilliant at what they do. They have saved millions of lives and are especially important in treating diseases like pneumonia, meningitis, and sepsis. The real concern is that they severely affect the gut microbiome, both in the short term and the long term.

Short-term consequences include diarrhoea and the development of antibiotic-resistant bacteria. (source)

Long-term consequences include the association between antibiotic usage and allergy and obesity (source). There is also data associating antibiotic usage with depression.

A fascinating fact is that although most of us think of Alexander Fleming as the discoverer of antibiotics, researchers have found traces of antimicrobials in skeletons as far back as 350 A.D!

There are different ways to classify antibiotics. One way is as narrow-spectrum or broad-spectrum.

  • 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 beneficial for fighting infections when it’s unclear what type of bacteria is responsible.

They can alternatively be classified as bactericidal or bacteriostatic.

  • Bactericidal antibiotics “kill” bacteria.
  • Bacteriostatic antibiotics “prevent the growth” of bacteria. 

Unfortunately, the true definition is not so simple (but we don’t need to go there!

The problem is that these powerful medicines don’t just kill the ‘bad bug’ but also lots of “good” bugs in the process. 

I once heard this get called a scatter gun approach – taking a broad spectrum antibiotic to kill the infection, but a lot of bystanders at the same time – this creates what we call dysbiosis, an imbalance in the gut microbiome. 

One of the problems with killing lots of bystanders is that room opens up for opportunistic organisms to expand their colony. 

Side Effects of Antibiotics

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

  • Nausea
  • Vomiting
  • Loss of appetite
  • Stomach pain
  • Bloating
  • Diarrhoea
  • Yeast infections
  • Gas
  • Constipation (rarer than constipation, but it can happen)

These ‘bad’ microbes may not just be bacteria but yeasts such as candida albicans. 

One of the most common side effects is antibiotic-associated diarrhoea (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 number of Clostridium difficile bacteria. 

The use of broad-spectrum antibiotics has been observed to have several impacts on gut health, including:

  • Reducing microbial diversity in the gut (source)
  • Reducing protective species such as Bifidobacterium spp. (source)
  • Promoting the colonisation of opportunistic pathogens such as Clostridium difficile that can cause antibiotic-associated diarrhea (source)
  • In infants and young children, antibiotic use has also been linked to an increased risk of asthma and weight gain (source)

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. 

The Evidence 

A 2018 study (source) found that certain strains of probiotics were indeed effective at colonising the gut after antibiotics usage. However, and a critical finding, 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 researchers then conducted another experiment (source). This time, they found that the probiotics colonised the gut in only some participants

Also, in a 2017 meta-analysis (source), this is when researchers took a look at all the evidence to date and made an ‘overall conclusion,’ found that probiotics may reduce the risk of antibiotic-associated diarrhoea by 51% without an increase in side effects. 

Finally, a massive meta-analysis in the British Medical Journal Open (source) backed up the 2017 meta-analysis. The authors of this paper gathered data from 42 studies, meaning there was data from more than 11,000 participants. The researchers concluded giving probiotics with antibiotics lowered the risk of antibiotic-associated diarrhoea by 37%. Again, the key finding was that this was true only for certain species of probiotics — mostly strains of Lactobacilli and Bifidobacteria

The Dose Of Probiotic Matters

Researchers found that only the high dose compared with a low dose of the same probiotic demonstrated benefit, and again, they found that only certain species, mainly from lactobacillus and bifidobacteria, were found to be effective. (source)

What’s Your Risk of Developing Antibiotic-Associated Diarrhoea?

In a systematic review and meta-analysis from The British Medical Journal Open, the researchers explored probiotics for the prevention of antibiotic-associated diarrhoea. One of their findings was that, when they pooled studies, those with a low baseline risk of antibiotic-associated diarrhoea did not show any difference in risk, whereas those with a moderate or high baseline risk demonstrated 39% and 45% risk reduction, respectively. (source)

Prevention Is The Best Option

When we have a healthy gut microbiome, one of the many functions of the resident bacteria is to help protect us against exogenous pathogens, as well as indigenous pathobiont outgrowth (pathobionts are just organisms that, under the right circumstances, can become problematic). This protective function that a healthy microbiome plays is called “colonisation resistance” (source). Colonisation resistance involves different methods to inhibit pathogens, including:

  • Nutrient competition – organisms need certain nutrients to grow.
  • Competitive metabolic interactions – for example, bacteria actually produce antimicrobial compounds.
  • Niche exclusion – meaning the bacteria literally compete with pathogens for space in the gut.
  • Induction of our immune response.
  • Maintaining the thick mucus layer that lines the inner gut to prevent pathogens reaching intestinal cells.
  • Training the immune system to respond to pathogens (source)

When the resident gut bacteria are reduced by antibiotic use, these protective functions will not function as well as they should, allowing pathogenic bacteria and yeasts to take hold.

What’s The Best Probiotic After Antibiotics

The following probiotic strains demonstrated a significant reduction in AAD when compared with a control: L. acidophilus, L. bulgaricus, L. casei, L. paracasei, L. rhamnosus, Lactobacillus spp, S. boulardii, B. animalis ssp Lactis, B. longum, B. licheniformis, B. subtilis and Bacillus clausii (source).

Saccharomyces boulardii, a probiotic yeast, is particularly good at preventing and resolving antibiotic-associated diarrhoea and traveler’s diarrhoea (source). Saccharomyces boulardii has numerous benefits to the gut microbiome and is a staple in many of my ‘gut protocols,’ including SIBO, SIFO, and IBS. For example, it can be beneficial for the microbiome and prevents inflammation.

Lactobacillus acidophilus, a bacteria well known for being in yogurt, is also great for your gut. Studies show that it’s good at treating and preventing infections and reducing the digestive side effects of antibiotics (source). Lactobacillus acidophilus Rhamnosus GG is one of the most researched probiotics in the world, with great evidence behind it for alleviating diarrhoea.

When To Take Probiotics To Reduce The Side Effects Of Antibiotics

It is best to allow for a two-hour gap between taking your antibiotic and taking the probiotic.

How Long Should I Take Probiotics For After Antibiotic Treatment?

In the research, probiotics were taken for the duration of antibiotic therapy plus a further 7 days, or a total of 14 days. 

Research has stated that it would make sense to suggest probiotics should be continued for some period after the cessation of antibiotics (source). Further research is required around this though.

Is It OK to Take Probiotics With Antibiotics At The Same Time?

It depends on the strain of bacteria used in the probiotic.

Lactobacillus acidophilus Rosell-52, Lactobacillus rhamnosus Rosell-11, and Bifidobacterium lactis Lafti B94 can be taken at exactly the same time as antibiotic medication.

These three strains have been proven to survive, even when taken with an antibiotic, and actually enhance the efficacy of the antibiotic, and reduce side effects like diarrhoea, loss of appetite, and pain.

The Best Ways To Restore The Gut Microbiome

Prevention is best, and there are plenty of things we can do to support a healthy and diverse microbiome. A diverse microbiome is described as a resilient microbiome because it is more able to ‘bounce back’ to its original set point after an insult such as antibiotics. How do we create a resilient microbiome?

Stay physically active.

People who are more physically active typically have a more diverse microbiome and a more resilient immune system. As always, context matters here – excessive amounts of exercise will compromise both. What’s excessive – it will vary from person to person depending on their allostatic load. 

Spend time in nature.

Our gut microbiome is partly a representation of the microbiome we live in and around. Research has shown that immersing ourselves in nature does indeed diversify our microbiome.

Eat fermented produce

Eating and drinking things like kefir, sauerkraut, kimchi, and kombucha have been shown to support the diversity of the gut microbiome, and it is thought that doing so will support the immune system too.

Eat polyphenols.

Polyphenols are plant-based compounds that give plants their colour. So ensure you eat a colourful diet with lots of local and in-season fruit and vegetables. Other options include coffee and green tea.

Maintain a healthy circadian rhythm

Gut health is dependent on circadian health – meaning a healthy body clock. We can maintain a healthy body clock through several ways:

  • Get outside in the morning as close to sunrise as possible. 
  • Get outside at solar noon and at sunset, too. 
  • Practice time-restricted feeding – i.e., fast for 12 hours overnight. 
  • Limit blue light exposure from sunset onwards by wearing blue light-blocking glasses, limiting your use of technology, and considering the lighting you use in your home. 
  • Limit/avoid caffeine from midday, and limit/avoid alcohol (at all times!).
  • Have an evening routine to calm the mind and body before sleep. 
  • No phones/technology in the bedroom.


So, it seems the jury is still out a little in regards to probiotics after antibiotics usage. I would highlight two key points:

  • There are definitely probiotics to consider if you experience symptoms after antibiotics, especially diarrhoea. 
  • Don’t leave it too late! Focus on prevention as much as possible, make the necessary changes, and embed them into your lifestyle.


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