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Should you take probiotics with antibiotics?

Medically reviewed by Carmen Pope, BPharm. Last updated on Nov 7, 2022.

Official answer


There is controversy about whether you should routinely take probiotics with antibiotics and the question cannot be answered with a straight yes or no.

Evidence for taking probiotics with antibiotics includes a Cochrane review which reported that children who were given a course of probiotics after antibiotics had less diarrhea. Evidence against taking probiotics with antibiotics includes a 2019 Italian study that reported that the gut microbiome of people given probiotics after antibiotics took six months to return to its normal state compared to only three weeks for those not given any probiotics.

More studies are needed before a definite statement can be made.

What studies support giving probiotics with antibiotics?

A Cochrane review of 23 studies (3938 participants) investigated giving probiotics containing either one or a combination of the following: Bacillus spp., Bifidobacterium spp., Clostridium butyricum, Lactobacilli spp., Lactococcus spp., Leuconostoc cremoris, Saccharomyces spp., or Streptococcus sp.

Results from 22/23 trials that reported on the incidence of antibiotic-associated diarrhea show a significant benefit from probiotics compared to active, placebo, or no treatment control (8% in the probiotic group compared to 19% in the control group). None of the 16 trials (n = 2455) that reported on side events documented any serious side events attributable to probiotics with the most common ones being rash, nausea, gas, flatulence, abdominal bloating, abdominal pain, vomiting, increased phlegm, chest pain, constipation, taste disturbance, and low appetite. The author’s concluded that there was a protective effect of probiotics for preventing antibiotic-associated diarrhea. The relative risk was 0.46 (95% CI 0.35 to 0.61) and the NNT was 10.

The authors considered Lactobacillus rhamnosus or Saccharomyces boulardii at 5 to 40 billion colony forming units/day to be the most appropriate choice. They also commented that although no serious adverse events were observed among the otherwise healthy children in these trials, serious adverse events have been observed in severely debilitated or immuno-compromised children with underlying risk factors (eg, central venous catheter use), and advised that probiotics should be avoided in pediatric populations at risk for adverse events until further research has been conducted.

What studies do not recommend giving probiotics with antibiotics?

Researchers from the Weizmann Institute of Science in Israel and other institutions reported that the gut microbiome took longer to return to normal in those people given an 11-strain probiotic treatment for four weeks following a course of antibiotics. This was despite the probiotics effectively colonizing the gut with healthy bacteria. The trouble was the presence of the new bacteria and yeasts strains prevented the gut microbiome from returning to normal for the full six month study period.

Conversely, the gut microbiome in those given no probiotics returned to normal within three weeks of going off the antibiotics. “ The authors did conclude that this study just examined one type of probiotic, and a different probiotic may be helpful in patients taking different antibiotics. However, they did point out the findings of the study imply that the traditional practice of taking a probiotic after antibiotic may not be beneficial.

More research is needed to determine if other options to strengthen the gut microbiome, such as fermented food products (eg, sauerkraut and kimchi) or fecal transplantation, is beneficial. Studies have shown that autologous fecal transplantation, which involves collecting stool samples before going on antibiotics and freezing them, brought the gut microbiome back to normal within eight days once the stool was returned to the gut following antibiotic treatment. It took 21 days for the gut microbiota in the group that didn’t undergo fecal transplantation to return to perfect health. Currently, however, the only approved indication for autologous fecal transplantation is for people with C. difficile colitis, which is an inflammation of the colon caused by the bacteria Clostridium difficile.

What are the most common side effects of probiotics?

The most common side effects reported with probiotics in clinical trials included:

  • abdominal bloating
  • abdominal pain
  • chest pain
  • constipation
  • flatulence
  • gas
  • increased phlegm
  • low appetite
  • nausea
  • rash
  • taste disturbance
  • vomiting.

What is the gut microbiome?

Our digestive tract is home to trillions of bacteria as well as fungi and viruses – these are known as the gut microbiome.

The makeup of this biome is largely genetically determined; however, it is heavily influenced by several factors such as whether we are born naturally (vaginally) or by cesarean section, if we were breastfed, our use of antibiotics, and our exposure to chemicals, pesticides, and other toxins.

Scientists now know that this microbiome is critical to our overall well-being. Some call it our second brain. Small imbalances can cause significant changes to our mental health and in the appearance of our skin and has been linked to almost every known condition such as Alzheimer’s disease, multiple sclerosis, rheumatoid arthritis, and Type 2 diabetes.

An imbalance may also cause constipation, diarrhea, skin rashes, yeast infections, and a suppressed immune system. Your likelihood of putting on weight also comes down to your microbiome and the influence it has on your response to insulin and thyroid gland function.

What are probiotics?

Probiotics are live bacteria and yeasts that are beneficial for health. They are often referred to as 'good', 'helpful', or 'healthy' bacteria.

Probiotics are available as dietary supplements and can be brought over the counter from a drug store, pharmacy, or health store. Probiotics are also found naturally or added to foods such as dark chocolate, yogurt, miso soup, pickles, sauerkraut, tempeh, or kefir.

What is the rationale behind taking probiotics with antibiotics?

Taking an antibiotic for an infection can kill beneficial bacteria that live in your gut.

Probiotics may be taken orally to restore any imbalance in the normal intestinal or urogenital flora. This is the rationale behind taking probiotics with antibiotics. Severe antibiotic-induced diarrhea can also lead to an infection with Clostridium difficile, also known as C. difficile, a bacteria which can cause dangerous inflammation in your colon (colitis).

Experts have hypothesized that If you suffer from stomach cramping, gas or diarrhea when you take antibiotics, adding a probiotic may help to lessen, or even prevent, these symptoms. The addition of a probiotic will also reintroduce helpful bacteria into your digestive tract that have been killed or had their numbers reduced by the antibiotic.

How should I take probiotics with antibiotics?

If you do decide to take a probiotic with an antibiotic, start it the same day you start the antibiotic, but do not take it at exactly the same time as the antibiotic. Allow at least two hours to elapse after taking your antibiotic before you take your probiotic.

Probiotics are usually taken twice a day on an empty stomach. They should then be continued for at least several weeks after your course of antibiotics has finished, although some people take probiotics daily to not only continue to help digestion but to boost their immune system and enhance the absorption of some nutrients.

If you wish to take probiotic supplements, choose a high-quality probiotic made by a reputable company that contains at least one of the following: Lactobacillus rhamnosus, Saccharomyces boulardii, or Bifidobacterium sp. at 5 to 40 billion colony units/day.

Do prebiotics help return the gut microbiome to normal?

Prebiotics are foods for probiotics and include fiber-rich foods such as fruits, vegetables, cereals.

Mixing prebiotics with probiotics, such as yogurt with fruit and cereal or sauerkraut with a vegetable stir fry could be helpful for your gut, although there is no scientific evidence to support this.

Good prebiotic foods include vegetables such as artichokes, asparagus, garlic, onions, and any green vegetable; fruits such as bananas, berries, and tomatoes; herbs such as chicory or garlic; grains like barley, oat, and wheat; and other fibers such as inulin that may be available on its own or added to foods such as granola bars, cereal, and yogurt.

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  • Suez J, Zmora N, Zilberman-Schapira G, et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018 Sep 6;174(6):1406-1423.e16. doi: 10.1016/j.cell.2018.08.047. PMID: 30193113.
  • Goderska K, Agudo Pena S, Alarcon T. Helicobacter pylori treatment: antibiotics or probiotics. Appl Microbiol Biotechnol. 2018 Jan;102(1):1-7. doi: 10.1007/s00253-017-8535-7. Epub 2017 Oct 26. PMID: 29075827; PMCID: PMC5748437.
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  • Guandalini S. Probiotics for prevention and treatment of diarrhea. J Clin Gastroenterol. 2011 Nov;45 Suppl:S149-53. doi: 10.1097/MCG.0b013e3182257e98. PMID: 21992955.
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