Should You Take Probiotics While on Antibiotics?

Simon Spichak, M.Sc

Written by: Simon Spichak, M.Sc

Updated: November 29th, 2022

And other frequently asked questions about what happens to your gut flora while you’re on antibiotics. 

An invader infiltrates an enemy facility, sabotaging the intricate machinery and throwing a literal wrench in the operations. But we aren’t describing the video game Among Us or the plot of an upcoming James Bond movie. The invaders are bacteria that you can’t see with the naked eye.  

Infection occurs when those bacteria, viruses, or other microbes begin to multiply. As a result of a bacterial infection, your doctor might prescribe you a course of antibiotics to treat the infection.  Antibiotics are a class of drugs that kill off swathes of “bad” bacteria, but what you might not know is that they can also kill the commensal “good” bacteria that compose the gut microbiome, supporting immune and digestive function. Further to this, antibiotics can also cause dysbiosis (gut imbalance). For example, administration of antibiotics can cause diarrhea in about 20 percent of cases[1]

Could ingesting beneficial microbes (aka probiotics) along with the antibiotics buffer these negative effects? Keep reading to find out!  

What are probiotics? 

Probiotics are “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host[2].” Breaking down this definition there are two important components: 

A surplus of recent research shows the promise of probiotics, though the evidence for some digestive conditions is still limited[3]. Fortunately, there is more evidence that certain probiotics can make a difference when it comes to preventing and treating antibiotic-induced diarrhea [4],[5]. Intriguingly, the probiotics don’t even need to make a permanent home in the microbiome to exert their benefits, though in most cases their mechanism of action is unclear. 

Are all probiotics the same? 

Walk into any pharmacy and peruse the probiotics aisle. There are dozens of different labels featuring different strains of bacteria and yeast– some feature one single strain of microbe while others combine half-a-dozen into a capsule. Unfortunately, in Canada probiotics don’t face the same stringent guidelines as other drugs. Many probiotics in the market make wide-ranging claims that aren’t backed up by rigorous science assessing their efficacy and safety[6]

Ensuring you are making an informed choice and taking the right probiotic for the symptoms or condition you wish to treat is important. Referring to the Clinical Guide to Probiotic Products Available in Canada can provide you with probiotic strains and their corresponding brand names that have been reviewed based on scientific evidence.  

For example, if your goal is to prevent antibiotic-associated diarrhea, you will see on the chart that Florastor® features one strain of a beneficial yeast called Saccharomyces boulardii CNCM I-745. Compared to many available products on the market, there has been a substantial amount of research, bolstering their claims. In addition to yeast probiotics, there are a few bacterial probiotic strains that are also effective in preventing antibiotic-associated diarrhea. 

When antibiotics meet the gut microbiome 

While taking a full course of antibiotics is important for getting rid of pathogens, it also damages the commensal “good” gut microbes. One recent review study found that antibiotics cause profound changes in the gut microbiome which can persist for more than four months, though the long-term consequences of these changes is unclear[7].  

Overall, antibiotics reduce the number of different bacteria in the gut which reduces the diversity of the ecosystem[8]. In addition, the total amount of commensal bacteria is reduced after antibiotic treatment[8]. Lower levels of bacterial diversity are also associated with many, though not all, autoimmune disorders[9].  

But there’s another unwanted consequence, pathogenic bacteria could take up some of the empty real estate and in rare cases it can lead to an antibiotic-resistant infection. Scientists are searching for ways to provide more protection to the commensal microbes as well as ways to promote the health of the gut ecosystem.  

If we want to protect the gut microbiome while taking antibiotics, it makes sense to use a probiotic that is resistant to those drugs. Antibiotics can kill bacteria but aren’t as effective for other organisms. As a yeast, S. boulardii CNCM I-745 is the only probiotic resistant to any tested antibiotics, ensuring that it can survive what kills bacterial probiotic strains[10].


Will taking this probiotic along with the antibiotics prevent diarrhea?  

A systematic review looked at 33 rigorous clinical trials conducted in a pediatric population to assess the impact of different types of probiotics[11]S. boulardii at doses between 5 and 40 billion colony-forming units was only one of two probiotics effective in reducing the risk of developing diarrhea by 63 percent.  

Another systematic review found that S. boulardii reduced the risk of antibiotic-associated diarrhea in adults by 37 percent[12].  

One limitation of this research is that many clinical trials did not assess the incidence of side effects.  

How does it work? 

Antibiotics kill off a lot of friendly gut commensals, leaving room for opportunistic pathogenic bacteria to bloom instead.  

S. boulardii CNCM I-745 protects gut commensals through multiple mechanisms[13]. Once inside the gut, the probiotic can prevent the growth of pathogenic bacteria that bloom when gut commensals are killed by antibiotics. S. boulardii uses antibiotic proteins that target these opportunistic bacteria, keeping them at bay and leaving room for commensals to grow back. It also has a beneficial impact on the cells of the intestine, protecting them from bacterial incursions and alerting the immune system to patrol the gut for pathogens.   


Antibiotics are a life-saving intervention. But in more than one in five cases, the antibiotics also lead to diarrhea and profound changes to gut microbial commensals. Afterward, opportunistic bacteria begin to bloom in the gut, leading to diarrhea. Probiotics, beneficial microorganisms with health benefits at specific doses, reduce the risk of developing diarrhea after antibiotic treatment.  

As mentioned, probiotic strains such as S. boulardii CNCM I-745 reduce the risk of developing diarrhea. S. boulardii CNCM I-745 is resistant to antibiotics and itself can fight off opportunistic pathogens. Probiotics also affects the gut, stimulating its immune system to patrol for more of these pathogens. These actions provide support for gut commensals to survive and grow back faster while preventing diarrhea.  


  1. McFarland, L. V. (2008). Antibiotic-associated diarrhea: epidemiology, trends and treatment. 
  2. Hill, C., Guarner, F., Reid, G. et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11, 506–514 (2014). 
  3. McFarland, L. V., Karakan, T., & Karatas, A. (2021). Strain-specific and outcome-specific efficacy of probiotics for the treatment of irritable bowel syndrome: A systematic review and meta-analysis. EClinicalMedicine, 41, 101154. 
  4. Liao, W., Chen, C., Wen, T., & Zhao, Q. (2021). Probiotics for the Prevention of Antibiotic-associated Diarrhea in Adults: A Meta-Analysis of Randomized Placebo-Controlled Trials. Journal of Clinical Gastroenterology, 55(6), 469. 
  5. Altcheh, J., Carosella, M. V., Ceballos, A., D’Andrea, U., Jofre, S. M., Marotta, C., … & McFarland, L. V. (2022). Randomized, direct comparison study of Saccharomyces boulardii CNCM I-745 versus multi-strained Bacillus clausii probiotics for the treatment of pediatric acute gastroenteritis. Medicine, 101(36), e30500. 
  6. Cohen PA. Probiotic Safety—No Guarantees. JAMA Intern Med. 2018;178(12):1577–1578. doi:10.1001/jamainternmed.2018.5403 
  7. Van Zyl, K. N., Matukane, S. R., Hamman, B. L., Whitelaw, A. C., & Newton-Foot, M. (2021). The effect of antibiotics on the human microbiome: a systematic review. International journal of antimicrobial agents, 106502. 
  8. Elvers, K. T., Wilson, V. J., Hammond, A., Duncan, L., Huntley, A. L., Hay, A. D., & Van Der Werf, E. T. (2020). Antibiotic-induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review. BMJ open, 10(9), e035677. 
  9. Ma, Z. S. (2020). Testing the Anna Karenina principle in human microbiome-associated diseases. Iscience, 23(4), 101007. 
  10. Neut, C., Mahieux, S., & Dubreuil, L. J. (2017). Antibiotic susceptibility of probiotic strains: Is it reasonable to combine probiotics with antibiotics?. Medecine et maladies infectieuses, 47(7), 477-483. 
  11. Guo Q, Goldenberg JZ, Humphrey C, El Dib R, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev. 2019 Apr 30;4(4):CD004827. doi: 10.1002/14651858.CD004827.pub5. PMID: 31039287; PMCID: PMC6490796. 
  12. Goodman, C., Keating, G., Georgousopoulou, E., Hespe, C., & Levett, K. (2021). Probiotics for the prevention of antibiotic-associated diarrhoea: a systematic review and meta-analysis. BMJ open, 11(8), e043054. 
  13. Czerucka, D., & Rampal, P. (2019). Diversity of Saccharomyces boulardii CNCM I-745 mechanisms of action against intestinal infections. World Journal of Gastroenterology, 25(18), 2188. 

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