How do I support my gut health when on antibiotics?

R.Parnell (ANutr, MSc)

Antibiotics are essential for treating bacterial infections, but they also disrupt the delicate balance of your gut microbiome. Many people notice bloating, loose stools, or other digestive changes during or after a course of antibiotics.

Taking evidence backed probiotics alongside antibiotics can be a helpful approach to protect your gut health and help your microbiome recover.

 

How antibiotics affect the gut

Your gut is home to trillions of bacteria that support digestion, immunity, and overall health. Antibiotics don’t just eliminate harmful bacteria they also affect beneficial species such as Lactobacillus and Bifidobacterium, reducing microbial diversity and allowing less desirable microbes to overgrow¹.

This imbalance, known as dysbiosis can:

• Lead to antibiotic-associated diarrhoea (AAD)
• Cause bloating, constipation, or abdominal discomfort
• Increase susceptibility to opportunistic infections, including Clostridioides difficile¹

While your gut microbiome can eventually recover, this process can take several months without support².

 

How probiotics help during antibiotic use

Probiotics, live microorganisms that support gut health, can help protect the microbiome during antibiotic treatment. They don’t permanently colonise the gut, but they can help stabilise the microbial environment, support the gut barrier, and reduce the growth of harmful bacteria as your microbiome recovers³.

Clinical research shows that specific probiotic strains can reduce the risk of antibiotic-associated diarrhoea⁴ and support microbial diversity during and after treatment³.

 

Best probiotic strains to supplement with antibiotics

Not all probiotic strains are equally effective during antibiotic therapy. The strongest evidence supports a few key strains:

• Lactobacillus rhamnosus GG (LGG) - one of the most studied for preventing antibiotic-associated diarrhoea⁵.
• Saccharomyces boulardii - a yeast probiotic naturally resistant to antibiotics, shown to reduce the risk of AAD and C. difficile infection⁶.
• Bifidobacterium lactis BB-12 - helps maintain bowel regularity and gut microbiome stability during antibiotic use⁷.

 

How and when to take probiotics

• Take your probiotic a few hours apart from your antibiotic dose (for example, antibiotics with breakfast and your probiotic with lunch or dinner) to help reduce the chance of interference.
• Start early - ideally on the same day you begin your antibiotic course.
• Keep taking for at least 1–2 weeks after finishing antibiotics to support your gut microbiota as it recovers.

 

What to look for in a probiotic supplement:

• Clinically studied strains - clearly identified by their strain codes.
• A daily dose aligned with clinical research, often around 10⁹ CFU (colony forming units) per strain.
• A shelf-stable, well-labelled product, showing the strains and CFU count clearly on the packaging.

 

Other gut-supporting habits

Probiotics work best alongside gut-friendly habits that nourish beneficial bacteria:

• Eat fibre-rich foods like oats, fruit, and vegetables once digestion settles, these provide prebiotic fuel for good bacteria.
• Stay hydrated, especially if you experience diarrhoea.
• Limit refined sugar and alcohol, which can promote the growth of less beneficial bacteria.
• Get adequate rest and manage stress, as the gut–brain axis plays a major role in recovery.

 

Summary

Antibiotics can disrupt the balance of your gut microbiome, but probiotics and healthy habits can help protect and restore it.

Strains such as Lactobacillus rhamnosus GG, Bifidobacterium lactis BB-12, and Saccharomyces boulardii have been shown to reduce antibiotic-associated diarrhoea and support faster recovery. Taking probiotics throughout your antibiotic course and for a short period after could help you avoid unwanted antibiotic associated side effects and reduce the risk of long-term disruption to your gut microbiome.

 

References

1. Patangia DV, Anthony Ryan C, Dempsey E, Paul Ross R, Stanton C. Impact of antibiotics on the human microbiome and consequences for host health. Microbiologyopen. 2022 Feb;11(1):e1260. doi: 10.1002/mbo3.1260. PMID: 35212478; PMCID: PMC8756738.

2. Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018 Nov;3(11):1255-1265. doi: 10.1038/s41564-018-0257-9. Epub 2018 Oct 22. PMID: 30349083.

3. Fernández-Alonso M, Aguirre Camorlinga A, Messiah SE, Marroquin E. Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review. J Med Microbiol. 2022 Nov;71(11). doi: 10.1099/jmm.0.001625. PMID: 36382780.

4. Goodman C, Keating G, Georgousopoulou E, Hespe C, Levett K. Probiotics for the prevention of antibiotic-associated diarrhoea: a systematic review and meta-analysis. BMJ Open. 2021 Aug 12;11(8):e043054. doi: 10.1136/bmjopen-2020-043054. PMID: 34385227; PMCID: PMC8362734.

5. Szajewska H, Kołodziej M. Systematic review with meta-analysis: Lactobacillus rhamnosus GG in the prevention of antibiotic-associated diarrhoea in children and adults. Aliment Pharmacol Ther. 2015 Nov;42(10):1149-57. doi: 10.1111/apt.13404. Epub 2015 Sep 13. PMID: 26365389.

6. Szajewska H, Kołodziej M. Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Aliment Pharmacol Ther. 2015 Oct;42(7):793-801. doi: 10.1111/apt.13344. Epub 2015 Jul 27. PMID: 26216624.

7. Merenstein D, Fraser CM, Roberts RF, Liu T, Grant-Beurmann S, Tan TP, Smith KH, Cronin T, Martin OA, Sanders ME, Lucan SC, Kane MA. Bifidobacterium animalis subsp. lactis BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome. Nutrients. 2021 Aug 17;13(8):2814. doi: 10.3390/nu13082814. PMID: 34444974; PMCID: PMC8398419.