Should You Take Probiotics Now After Your Course of Antibiotics?

Have you just taken antibiotics and are wondering how to get your friendly gut micro-organisms back? Wondering if you should take probiotics? Antibiotics are a hugely important medical treatment that save millions of lives a year, but what are the effects on your gut microbiota and do they matter? Read to on to find out if you should take probiotics now after your course of antibiotics.

What Are the Effects of Taking an Antibiotic on Your Gut?

Firstly, before we look at the evidence about probiotics after antibiotics, it’s important discuss what effects antibiotics have on the microbiota. Evidence from 129 studies combined (meta-analysis) found that antibiotics have a profound effect gut microbiota (micro-organisms that live in the gut and play an important role in general health) (Zimmermann & Curtis, 2019). Effects differed between antibiotics, but those that had the most persistent effects were ciprofloxacin (one year), clindamycin (two years) and clarithromycin plus metronidazole (four years) (Zimmermann & Curtis, 2019).

Another study found that the microbiota of healthy adults were resilient to short term broad spectrum antibiotics, but that even 180 days post treatment, 9 common species had not recovered (Palleja et al., 2018). Understanding how to mitigate these effects, may enable us to reduce collateral damage of the gut microbiota.

Studies on mice have also confirmed a decrease in the gut microbiota after antibiotics, that rebounded after stopping, but was augmented by close proximity to other mice who weren’t treated with antibiotics (Lichtman et al., 2016).

Should You Take Probiotics Now After Your Course of Antibiotics

Probiotics and Antibiotic Associated Diarrhoea

When antibiotics reduce the microbiota, this provides an opportunity for less beneficial and pathogenic bacteria to establish themselves instead. Sometimes this can lead to antibiotic associated diarrhoea. A specific type of diarrhoea caused by a particularly nasty bacteria (Clostridium difficile) accounts for 25% of diarrhoea after a course of antibiotics. It can be particularly severe, so studies have investigated if this can be prevented by probiotics. A Cochrane Review of the data (meta-analysis combining multiple studies) looked at 31 trials, totalling 8672 participants and found that probiotics reduced the risk of Clostridium difficile associated diarrhoea (Goldenberg et al., 2017). Although this effect was greatest where the risk was higher, safety in immunocompromised patients isn’t well documented (Goldenberg et al., 2017).

Should You Take Probiotics After Your Course of Antibiotics to Replace Your Friendly Gut Micro-organisms?

If antibiotics impact your microbiota, should take probiotics after your course of antibiotics to replace them? Previous evidence from analysis of studies combined (meta-analysis) has suggested that probiotics can help with infections and antibiotic-associated diarrhoea. Taking probiotics after antibiotic treatment has become increasingly common.

However, two recently reported studies in Cell has called this evidence into question. One study investigated the recovery of gut microbiota after antibiotic treatment and found that probiotics might actually interfere rather than help (Suez et al., 2018). The probiotics rapidly colonised the gut but prevented the normal microbiota from repopulating for up to 5 months. But these effects seemed very individualised, with some people becoming colonised by the probiotics, while other’s guts rejecting them altogether (Zmora et al., 2018).

Although rather unappealing, the group who received their own-pre antibiotic treated faeces transplanted (autologous faecal transplant) back into their gut after the antibiotic therapy, recovered their microbiota the quickest (Suez et al., 2018). Faecal transplant is not a new phenomenon, with reports of people using it to treat food poisoning in China, as early as the 4th Century!

While the logic behind probiotics might seem sound, there is still much research to be done before we understand the complexity of the microbiota and effects of probiotics.

Probiotics and Gastroenteritis

In the United States children account for up to 1.7 million hospital visits per year with gastroenteritis (Freedman et al., 2018). A randomised double-blinded trial of 886 children with gastroenteritis compared a 5 day course of probiotic (Lactobacillus rhamnosus R001 and L.  helveticus R0052) or placebo. No significant difference was observed between the two groups (Freedman et al., 2018). Another similar study with 931 children, used a probiotic containing Lactobacillus rhamnosus GG, and again did not find this was associated with a better outcome compared with placebo (Schnadower et al., 2018).

Why Does Your Microbiota Matter?

Disturbances of the microbiota have the potential to affect the development of several autoimmune, inflammatory and allergic diseases (Kummeling et al., 2007). Asthma has been linked with childhood antibiotics (Kummeling et al., 2007). Long term risk of inflammatory bowel disease and effects on metabolic profiles leading to obesity have been observed post antibiotic disturbances to the gut microbiota (Neuman, Forsythe, Uzan, Avni, & Koren, 2018).

Can Probiotics Reduce the Need for Antibiotics?

A meta-analysis combined 17 randomised controlled trials of children treated with a placebo or probiotics (Lactoballius or Bifidobacterium) and found that probiotics were associated with a reduced risk of common acute infections such as acute respiratory tract, gut and ear infections (King, Tancredi, of, 2019, n.d.). More research is needed to understand these findings further.

What are the Side Effects of Probiotics?

What are the risks of taking probiotics? Although probiotics are freely available to purchase without prescription or full regulation, there are risks associated with them. Hospitalised patients are increasingly are increasingly being treated with probiotics, but there are now reports of patients in intensive care becoming seriously ill with the same strain of bacteria found in the probiotics (Yelin et al., 2019). While for most people who have a healthy immune system, this risk is low, it highlights the need for greater understanding about possible risks and benefits.

Should You Take Probiotics Now After Your Course of Antibiotics

Should you take probiotics now after your course of antibiotics? At the moment the evidence just isn’t there to support this for all people.

Practical Tips on How to Help Your Gut Health

While currently the best way to restore your gut health is an autologous faecal transplant, optimising your diet to support your gut health, might also help:

  • Eat a variety of fruit and vegetables
  • Eat at least 30g of fibre per day
  • Eat fermented food and drink such as kefir, tempeh, miso, kimchi, and sauerkraut
  • Avoid trans fats and sweeteners

If you enjoyed this article you may like to read about how stress and nutrition impact each other, with practical tips to help.


Freedman, S. B., et al. Multicenter Trial of a Combination Probiotic for Children with Gastroenteritis. 2018. New England Journal of Medicine, 379(21), 2015–2026.

Goldenberg, J. Z., et al. Probiotics for the prevention of Clostridium difficile‐associated diarrhea in adults and children. 2017. Cochrane Database of Systematic Reviews, 382(12), 1249.

King, S., et al. Does probiotic consumption reduce antibiotic utilization for common acute infections? A systematic review and meta-analysis. 2019.

Kummeling, I., et al Early Life Exposure to Antibiotics and the Subsequent Development of Eczema, Wheeze, and Allergic Sensitization in the First 2 Years of Life: The KOALA Birth Cohort Study. 2017. Pediatrics, 119(1), e225–e231.

Lichtman, J. S., et al. Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases. 2016. Cell Reports, 14(5), 1049–1061.

Neuman, H., Forsythe, P., Uzan, A., Avni, O., & Koren, O. (2018). Antibiotics in early life: dysbiosis and the damage done. FEMS Microbiology Reviews, 42(4), 489–499.

Palleja, A., Mikkelsen, K. H., Forslund, S. K., Kashani, A., Allin, K. H., Nielsen, T., et al. (2018). Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology, 3(11), 1255–1265.

Schnadower, D., Tarr, P. I., Casper, T. C., Gorelick, M. H., Dean, J. M., O’Connell, K. J., et al. (2018). Lactobacillus rhamnosusGG versus Placebo for Acute Gastroenteritis in Children. New England Journal of Medicine, 379(21), 2002–2014.

Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., et al. (2018). Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell, 174(6), 1406–1423.e16.

Yelin, I., Flett, K. B., Merakou, C., Mehrotra, P., Stam, J., Snesrud, E., et al. (2019). Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients. Nature Medicine, 25(11), 1728–1732.

Zimmermann, P., & Curtis, N. (2019). The effect of antibiotics on the composition of the intestinal microbiota – a systematic review. The Journal of Infection, 79(6), 471–489.

Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., et al. (2018). Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell, 174(6), 1388–1405.e21.

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