The Interaction Between Antibiotics and Probiotics

May 19, 2025Annie Davies

Impact on Gut Health

Antibiotics are crucial in treating bacterial infections, but they can have significant unintended effects on the gut microbiome by disrupting beneficial bacteria. This disruption often leads to gastrointestinal issues and may compromise overall gut health. Probiotic supplementation during and after antibiotic use is a strategy often employed to mitigate these negative effects and restore the gut’s balance.

How Antibiotics Affect Gut Bacteria

While antibiotics effectively target harmful pathogens, they can also reduce the populations of beneficial bacteria in the gut. Broad-spectrum antibiotics, in particular, can cause significant disruptions in the balance of gut flora, including reductions in important bacterial species such as lactobacillus and Bifidobacterium. Research shows that antibiotics can decrease bacterial diversity and richness, with some strains taking weeks or even months to fully recover. A study published in Nature found that antibiotics like ciprofloxacin reduced the diversity of the gut microbiome by up to 40%. While some bacterial strains quickly return to normal, others remain disrupted long after the course of antibiotics is finished.

Probiotics and Their Benefits

Probiotics are live microorganisms that can help restore the balance of gut bacteria, particularly following antibiotic treatment. Certain strains, such as Lactobacillus rhamnosus GG and Saccharomyces boulardii, have been shown to reduce antibiotic-associated diarrhoea (AAD) by replenishing beneficial bacteria and enhancing gut barrier function.
Studies indicate that probiotic supplementation can lower the risk of AAD by up to 42%, as shown in a review published in the Journal of Clinical Gastroenterology. These beneficial bacteria help reduce inflammation, support immune function, and compete with harmful pathogens.

Timing of Probiotic Supplementation

The timing of probiotic supplementation during antibiotic therapy is critical to its effectiveness. Taking probiotics too closely with antibiotics may result in reduced efficacy, as the antibiotics may destroy the probiotic organisms. Studies suggest that taking probiotics 2-3 hours after an antibiotic dose is optimal, allowing the probiotics to pass through the digestive tract without interference.

Continuing probiotic supplementation for at least 1-2 weeks post-antibiotic treatment helps restore the gut microbiome to a healthier state. Some research suggests that probiotic supplementation for up to 30 days post-antibiotic therapy can provide greater benefits in reestablishing bacterial diversity.

Best Probiotic Strains and Duration

Saccharomyces Boulardii: A probiotic yeast resistant to antibiotics, ideal for concurrent use with antibiotic therapy.

  • Buy Saccharomyces Boulardii HERE

Lactobacillus Rhamnosus GG: This strain has been proven to prevent AAD and promote gut health.

  • Buy Lactobacillus Rhamnosus HERE

Bifidobacterium Bifidum: Effective in promoting gut flora colonisation and restoring bacterial diversity post-antibiotics.

  • Buy Bifidobacterium HERE

Conclusion

Antibiotics, while essential for treating infections, disrupt the gut microbiome by depleting beneficial bacteria. Probiotic supplementation can help mitigate these effects by replenishing good bacteria, preventing side effects like diarrhoea, and promoting a faster recovery of the gut ecosystem. The best time to take probiotics is a few hours after an antibiotic dose, and continuing supplementation for at least two weeks post-therapy ensures optimal gut recovery.

Further testing at Body Fabulous

GI360 Stool Test: If you are experiencing post-antibiotic symotoms (such as diarrhoea, bloating, gas. etc) and are interested in assessing the effect this may have had on your gut health, our GI360 stool test includes an overall assessment of your gut microbiome, parasites, harmful bacteria and more.

Book a General Advice Call: Speak with our clinical team who can advise on the right testing to help you identify the right tests or supplements based on your symptoms

 

References

1. Shankar, P. R. et al. "Antibiotics and gut microbiota." Gut Microbes 11.3 (2020): 541-555.
2. Perez-Cobas, A. E. et al. "Gut microbiome recovery after antibiotics." mBio 8.5 (2017):
e00896-17.
3. Sanders, M. E. et al. "Probiotics and prebiotics in intestinal health." Nature Reviews
Gastroenterology & Hepatology 16.11 (2019): 635-647.
4. Dethlefsen, L., et al. "The pervasive effects of an antibiotic on the human gut microbiota." Nature 466 (2010): 334-338.
5. McFarland, L. V. "Antibiotic-associated diarrhoea: epidemiology, trends, and treatment."
Gastroenterology Clinics 39.2 (2010): 275-290.
6. Hempel, S. et al. "Probiotics for the prevention and treatment of antibiotic-associated
diarrhoea." JAMA 307.18 (2012): 1959-1969.
7. Dinleyici, E. C. et al. "Lactobacillus rhamnosus GG for the prevention of antibiotic-associated diarrhoea." Journal of Clinical Gastroenterology 50 (2016): 469-477.
8. McFarland, L. V., et al. "Timing of probiotic administration relative to antibiotics affects
outcomes." Frontiers in Microbiology 8 (2017): 1317.
9. Szajewska, H., et al. "Probiotics in the prevention of antibiotic-associated diarrhoea."
Alimentary Pharmacology & Therapeutics 25.8 (2007): 843-854.
10. Ouwehand, A. C. et al. "Probiotic strains and their properties." Beneficial Microbes 1.1
(2010): 39-53.
11. McFarland, L. V., "Saccharomyces boulardii in gastrointestinal related disorders." Clinical Gastroenterology (2015).

 

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