Probiotics For SIBO
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Best Probiotic When Taking Antibiotics
How to Protect and Rebuild Your Gut Microbiome After Antibiotics
Antibiotics have saved countless lives, but their use comes with a hidden cost: disruption of the gut microbiome. This complex ecosystem of bacteria, fungi, and other microorganisms not only helps digest food but also plays a critical role in immunity, metabolism, and even brain function. When antibiotics—especially broad-spectrum ones—are taken, they wipe out harmful bacteria but also unintentionally damage beneficial species, leaving the gut vulnerable to imbalance. In this blog we will discuss the best probiotic when taking antibiotics, as well as the benefit of postbiotics and prebiotics.
The Hidden Impact of Antibiotics on Your Gut
More than a third of patients taking antibiotics develop antibiotic associated diarrhoea (source)
Research shows that antibiotics reduce both the abundance and diversity of gut microbes, while also increasing oxygen levels in the gut. This shift makes it easier for opportunistic pathogens to take hold, such as Clostridioides difficile (C. diff), Escherichia coli, or fungal species like Candida albicans.
Recovery is often slow: while some diversity may return within weeks, certain species may take months to reappear—or never return at all. This phenomenon, called antibiotic-induced dysbiosis, has ripple effects throughout the body, influencing metabolism, immunity, and even mood and cognition. Early-life exposure is particularly concerning, as it may alter developmental pathways with long-term consequences. So thinking about the best probiotic when taking antibiotics is not just an intellectual endeavour, it is crucial for damage limitation and long term gut health.
Why Standard Probiotics Don’t Always Help
It might seem logical to simply take probiotics after antibiotics, but the science paints a more nuanced picture. Many commercial probiotic strains are not native to the human gut. A large trial found that multi-strain probiotic supplements can actually delay the return of natural microbiota compared to doing nothing at all (Szajewska, 2024).
The Best Probiotic When Taking Antibiotics
This partly depends on why you are taking them.
In clinical trials involving individuals undergoing antibiotic treatment for Helicobacter pylori infection, participants were given Lactobacillus acidophilus Rosell-52, Lactobacillus rhamnosus Rosell-11 and Bifidobacterium lactis Lafti B94 alongside antibiotics. All three strains were proven to survive alongside the medication, enhance the efficacy of treatment and reduce side effects like diarrhoea, loss of appetite and pain.
The recommended use for a supplement containing this probiotic combination is as follows:
- Take one capsule daily with breakfast, at the same time as your antibiotic medication.
- Take daily until the antibiotic course is finished, and ideally for one week after.
- Continue until the pack is completed and add a second pack if the antibiotic treatment lasts more than one week.
These strains of bacteria can be found in the product called For Those On Antibiotics.
As another example those taking antibiotics for a vaginal health issue might also like to consider taking probiotic strains which are well researched for intimate health, such as Lactobacillus reuteri RC-14® and Lactobacillus rhamnosus GR-1®. These strains are often used alongside antibiotics for vaginal infections but are best taken 2 hours away from the medication.
These are found in Intimate Flora For Women.
If neither of these examples fit your reason for taking antibiotics then we can consider the below two probiotics, both well researched within the context of antibiotic use.
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Saccharomyces boulardii CNCM I-745, a probiotic yeast, reduces antibiotic-associated diarrhoea and helps restore short-chain fatty acid production.
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Lactobacillus Rhamnossus GG is also well studied to reduce the risk of antibiotic associated diarrhoea. It also reduces the risk of non-beneficial organisms overgrowing by ‘taking up space’ and competing for nutrients.
Evidence-Based Ways to Protect Your Gut
If you must take antibiotics, here are strategies—supported by recent research—to support your microbiome during and after treatment:
1. Eat a Whole-Food, Fiber-Rich Diet
Nutritional choices strongly influence microbiome recovery. A diet rich in vegetables, fruits, whole grains, legumes, fish, and healthy fats helps beneficial bacteria rebound. Prebiotic foods like garlic, onions, leeks, and bananas feed key microbes, though tolerance may vary while your gut is still healing. Avoid sugar and alcohol, which can worsen dysbiosis.
2. Support Butyrate Levels
Antibiotics deplete butyrate-producing bacteria. Butyrate is essential for colon health, keeping gut oxygen low and inflammation in check. Supplementation with tributyrin (a stable butyrate form) may help maintain gut barrier function during recovery.
PHGG, a type of prebiotic increases butyrate producing bacteria and improves the efficacy of antibiotics when uses to treat SIBO. It also attenuates antibiotic induced gut lining damage and inflammation.
3. Consider Targeted Probiotics
Where possible taking an evidence based probiotic is important. We have already given the examples of H. Pylori and vaginal infections. The below two probiotics help when antibiotics are used for more things like a gut infection or SIBO.
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S. boulardii CNCM I-745 is well-studied for preventing diarrhoea and supporting microbiome balance (Sokol et al., 2024).
- Lactobacillus Rhamnossus GG is also well studied to reduce the risk of antibiotic associated diarrhoea. It also reduces the risk of non-beneficial organisms overgrowing by ‘taking up space’ and competing for nutrients.
4. Manage Stress and Lifestyle Factors
Stress disrupts gut motility, increases permeability, and worsens dysbiosis. Practices like mindfulness, yoga, and good sleep hygiene are simple but powerful tools for gut resilience. Exercise, when moderate, also promotes microbial diversity.
When To Take Probiotics With Antibiotics?
Start on the day that you start the antibiotics (or before if possible), and take the probiotics 2+ hours away from your antibiotics. It also actually depends on the strain of the bacteria you are using. You’ll be safe with the typical recommendation of 2+ hours away from the antibiotic.
How Long To Take Probiotics After Antibiotics?
There is currently no consensus on how long to take probiotics for after antibiotics but many advise for approximately one month. It will be, arguably, more important to focus on your diet and lifestyle as ways to mitigate the damage of the antibiotics (as discussed above).
How Long Does Recovery Take?
Recovery varies by antibiotic type, dose, and individual health. Some people see partial recovery in weeks, while others may take months. Emerging evidence shows that without intervention, some microbial species may not return at all. Supporting your microbiome during this period—through diet, targeted supplements, and lifestyle—can make a substantial difference.
Takeaway
Antibiotics remain essential in modern medicine, but they can leave a lasting imprint on the gut microbiome. Protecting and restoring your gut health requires more than a generic probiotic. Instead, a holistic approach—including diet, targeted probiotic strains like S. boulardii, butyrate support, and lifestyle strategies—offers the best path to recovery.
By being intentional about gut health and thinking about the best probtiotic when taking antibiotics, you can safeguard not just digestive health, but also immunity, metabolism, and overall well-being.
References
Agamennone et al., (2018) A practical guide for probiotics applied to the case of antibiotic-associated diarrhoea in The Netherlands (click here).
Szajewska et al., (2015) Systematic review with meta-analysis: Lactobacillus rhamnossus GG in the prevention of antibiotic-associated diarrhoea in children and adults (click here)
Spatz et al., (2023) Saccharomyces boulardii CNCM I-745 supplementation during and after antibiotic treatment positively influences the bacterial gut microbiota (click here)
Waitzberg et al., (2024) Can the Evidence-Based Use of Probiotics (Notably Saccharomyces boulardii CNCM I-745 and Lactobacillus rhamnossus GG) Mitigate the Clinical Effects of Antibiotic-Associated Dysbiosis? (click here)
Liu et al., (2024) Partially hydrolyzed guar gum attenuates broad-spectrum antibiotic-induced gut microbiota disruption associated with intestinal inflammation and barrier damage in mice (click here)
