Should I Take Probiotics While On Antibiotics

Probiotics are a bit of a buzzword at the moment. They have been claimed to be able to treat a variety of different conditions including a range of mental and physical health problems.1 Probiotics can be taken in a variety of forms and will contain strains of live bacteria also known as ‘beneficial’ bacteria.2

Antibiotics on the other hand have been proven to be effective at treating a range of infections by killing the bacteria that cause them.3

Some people believe that probiotics should be taken to ‘restore’ ‘good’ bacteria that are killed when taking antibiotics.4,5

So you may be wondering if you should take a probiotic with your course of antibiotics, well it's not as clear-cut as you might think.

The microbiome

The microbiome describes the microbes found in and on humans or animals. In a normal healthy person, these bacteria are generally not harmful and have many beneficial functions. However, the proportions in which bacteria are found can differ between two healthy individuals and are influenced by a range of factors such as your diet.6

The gut microbiome describes the fungi, yeast and bacteria in the gastrointestinal tract. These bacteria perform a range of beneficial functions including playing a role in6, 7, 8

  • immune response 
  • vitamin synthesis 
  • uptake of nutrients
  • harvesting of energy
  • controlling inflammation

What are probiotics?

One of the issues with determining whether probiotics are beneficial to take with antibiotics is that the definition of what constitutes a probiotic may differ depending on who you ask. Generally, it is considered to be a supplement that contains living bacteria that are “beneficial” to the microbiome. They may come in the form of pills, liquids, or fermented foods. However, many products on supermarket shelves may not even contain the amount of bacteria they claim to and few of them may make it to the gut alive.2

My nightly probiotics to help me, barely holding back PostOp issues! Very GRATEFUL for them!.jpg
*Image credit by CC BY 2.0, Link

What is the logic behind taking probiotics and antibiotics together?

Some people suggest that probiotics should be taken alongside antibiotic treatment. The idea behind this is that antibiotics do not just target the ‘bad’ bacteria causing the infection but also the ‘good’, ‘healthy’, bacteria in your gut causing the balance of different microorganisms to become unbalanced (gut dysbiosis). Some bacteria in your gut play important functions in your health and prevent overgrowth of bad bacteria that can lead to infections. So, the logic suggests that by taking a probiotic you are restoring those good bacteria.4,5

Evidence for taking probiotics and antibiotics together?

Saccharomyces and lactobacillus

One study on children looked into the effect of several types of probiotics taken after a course of antibiotics. These include:

  • Lactococcus
  • Lactobacilli
  • Bifidobacterium
  • Bacillus
  • Saccharomyces
  • Leuconostoc cremoris
  • Streptococcus or a combination

Participants either received a probiotic, a placebo or no treatment, it was found that 19% of participants in the control group had antibiotic-associated diarrhoea more than 2x higher than in the antibiotic group (8%). Saccharomyces boulardii (yeast) or Lactobacillus rhamnosus (bacteria) were considered the best choice of probiotic.9 

Lactobacillus plays many important roles in the gut including improving intestinal barrier function and protecting the intestine against harmful bacteria and molecules, it also regulates the immune system, has anti-cancer properties and regulates the metabolism.10 

However, whilst usually healthy children reported no adverse effects, some of the children who were immunocompromised or had a serious illness had some adverse effects, with bacteria and fungi colonizing areas outside the gut. Therefore it is not recommended to use probiotics in children.9


Bifidobacteria are another common bacteria in the gut and have many beneficial qualities such as helping to prevent certain diseases and producing important compounds e.g., folate.11 

A recent 2019 study gave participants a probiotic containing a particular strain of Bifidobacterium longum bacteria with the antibiotic rifaximin to treat symptomatic uncomplicated diverticular disease (SUDD) (a disease that causes abdominal pain, local inflammation, diarrhoea and constipation). The combination of the antibiotic and probiotic led to an improvement in stool consistency and made patients more resistant to gut dysbiosis.4 

Additionally, a rodent study found that several strains of Bifidobacterium longum and Bifidobacterium breve were able to help prevent Bifidobacterium disappearing and improve the diversity of different microbes in the gut.12

Evidence against taking probiotics and antibiotics together?

One study examined the use of a probiotic with several strains of bacteria following the use of antibiotics. Whilst the probiotic successfully colonized the gut with ‘beneficial’ bacteria the presence of these bacteria stopped the gut microbiome from returning to its original state for the duration of the study.13 

However, it was found that the gut microbiome reverted to its previous state within three weeks of ceasing antibiotic treatment, if probiotics were not given. Though this study was done on one probiotic and a single type of antibiotic, further work is required over a broader range of antibiotics and probiotics to confirm that the use of probiotics is not effective.13 

Another recent report also found that probiotic use during antibiotic treatment does not seem to lead to an improvement in the restoration of the gut microbiome after antibiotic therapy. However, there was a low number of studies and patients included in this report.14

Areas for further research

More research needs to be conducted on the potential benefits of fermented foods such as kimchi, sauerkraut and faecal transplants to determine if they may have beneficial effects on the gut microbiome. 

Some research in autologous faecal transplants has shown promise. This procedure involves obtaining stools from you before you have had antibiotics and freezing them. The stool is then defrosted and returned to the colon once the treatment has ended. In one study, they found that performing an autologous faecal transplant returned the microbiome to its normal state in 8 days, this took over twice this long (21 days) in the group who did not receive treatment.13

A similar treatment is currently being used for Clostridium difficile (a bacterial infection in the gut associated with gut dysbiosis) in which a faecal transplant is taken from a healthy donor and put in the patient's colon.15 

Potential side effects of probiotics

If you choose to take probiotics, you must consider the potential downsides, these are:

  • Digestive problems: can cause gas, bloating and constipation, though this usually disappears within a few weeks16
  • Skin problems: in some rare circumstances, you may develop itchiness or a rash if this is the case then you should stop taking that particular probiotic. If the rash is severe you should consult a doctor17
  • Allergic reactions: sometimes probiotics will contain other substances such as lactose or dairy and other foods. Some people may be allergic to these so it is best to check the ingredients before you decide to take them. If you have an allergic reaction, stop taking the probiotic and seek medical care if the reaction is severe18
  • Increased risk of infection: probiotics are considered to be safe in general. However, you may want to be cautious if you have a compromised immune system or a severe illness as there have been some reports of people in these patient groups getting infections from probiotic use. If you fit into these groups and want to take probiotics make sure to discuss this with your doctor first19
  • Bacterial overgrowth: there are different types of bacteria in the small intestine than there are in the large intestine. Small intestine bacterial overgrowth (SIBO) happens when bacteria from the large intestine begin to ‘overgrow’ into the small intestine. This can cause you to have diarrhoea, bloating and gas. It may also cause some short-term memory loss and brain fog.20 It may be more likely if you have IBS or are an older individual AFAB (associated female at birth). If you think you have SIBO consult a doctor21
  • Antibiotic resistance: there is also a risk that some antibiotic resistance genes in your probiotic bacteria may pass on to harmful/infectious bacteria and make them harder to treat.22 So make sure to use a reputable brand of probiotics

How to take probiotics with antibiotics

Make sure that you wait a couple of hours after taking your antibiotic to take your probiotic as antibiotics can kill bacteria found in probiotics such as Bifidobacteria.23,24

Some probiotic supplements should be taken with food and some without food, follow the instructions on the packet to get the best results. You also have the option to consume probiotics in the form of fermented foods like kimchi. Probiotics need to be taken every day to get the best outcome.25

Choose probiotics with 5-40 billion colony-forming units (CFU), they should contain one or more of these types of bacteria4,9

  • Bifidobacterium
  • Saccharomyces boulardii
  • Lactobacillus rhamnosus


  • Antibiotics kill bacteria that cause infection but may also kill ‘beneficial’ bacteria too
  • Probiotics which contain live ‘beneficial’ bacteria are sometimes taken with antibiotics to restore these ‘beneficial’ bacteria
  • Studies have shown that taking probiotics with antibiotics may help prevent diarrhoea after antibiotics
  • However, there is little evidence probiotics restore the beneficial bacteria after taking antibiotics
  • They also have a range of potential side effects including gas, bloating, skin rash and in immunocompromised patients, infection
  • If you choose to take probiotics, use ones with 5-40 billion CFU and take a few hours after your antibiotic


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This content is purely informational and isn’t medical guidance. It shouldn’t replace professional medical counsel. Always consult your physician regarding treatment risks and benefits. See our editorial standards for more details.

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