Probiotics and Antibiotics: Evidence-Based Insights

Antibiotics are powerful tools in fighting bacterial infections, but they can also disrupt the delicate balance of the gut microbiome, which is home to trillions of beneficial bacteria that support digestion, immunity, and overall well-being. When this balance is disturbed, issues like antibiotic-associated diarrhoea and increased vulnerability to harmful bacteria may follow. So, can probiotics help protect the gut during and after antibiotic use? And what are the best probiotics to take with antibiotics? This article explores how antibiotics affect the microbiome, how probiotics work to restore gut health, and which probiotic strains are best supported by research for maintaining balance and preventing digestive side effects.

Antibiotics and the gut

Antibiotics are medicines that destroy or inhibit bacterial growth by targeting essential processes like cell wall formation and protein synthesis¹. While highly effective against infections, antibiotics cannot distinguish between harmful and helpful bacteria, so their use often reduces the number and diversity of beneficial microbial species in the gut, sometimes resulting in long-term changes to its balance².

Antibiotics can reduce the number and diversity of beneficial bacteria in the gut³. This disruption, known as dysbiosis, decreases microbiome resilience and may allow harmful microorganisms to flourish, with long-term effects on digestion, immunity, and metabolism⁴. Recovery of microbial diversity after antibiotic use can take weeks or even months and may not always fully restore the original community structure.

This disturbance can lead to side effects such as antibiotic-associated diarrhoea, increased susceptibility to Clostridioides difficile infection, and overall gut dysbiosis, which impairs digestion and immune function^5,6.

Probiotics and antibiotics: how do they interact?

Probiotics are live microorganisms that, when administered in sufficient amounts, confer health benefits to the host, mainly by supporting gut and immune health⁷. After an antibiotic course, probiotics may help restore balance to the intestinal microbiome by colonising the gut and competing with pathogens for space and nutrients, preventing overgrowth of harmful bacteria⁸.

Probiotics support digestive health and overall well-being through several mechanisms:

• Restoring microbiome balance: After disruptions like antibiotic use, probiotics help re-establish healthy levels of “good” bacteria, supporting the restoration of the natural intestinal flora⁹.
• Competitive exclusion of pathogens: Probiotics compete with pathogenic bacteria for nutrients and adhesion sites on mucosal surfaces, making it harder for pathogens to survive and multiply¹⁰.
• Strengthening the gut barrier: Probiotics improve gut health by increasing the production of mucins and tight junction proteins, which reinforce the epithelial barrier and prevent pathogens or toxins from entering the bloodstream¹¹.
• Modulating the immune response: Probiotics actively interact with immune cells, such as dendritic cells and lymphocytes, to modulate both innate and adaptive immunity¹². They also promote the production of anti-inflammatory cytokines and support regulatory T cell development, helping maintain immune tolerance and balance.

The best probiotics to take with antibiotics - what the research shows

• Lactobacillus rhamnosus GG: Multiple randomised controlled trials (RCTs) and meta-analyses show that L. rhamnosus GG significantly reduced the incidence of antibiotic-associated diarrhoea (AAD) in both adults and children, with rates dropping from 28% to 11% in hospitalised patients^13,14. Supplementation during antibiotic therapy has also been associated with a markedly lower risk of Clostridioides difficile infection (CDI), with one study reporting zero cases in the probiotic group compared with 11% in controls¹⁴. Furthermore, supplementation during antibiotic therapy improved dyspepsia after eradication of Helicobacter pylori infection alongside other gastrointestinal symptoms, improving patient comfort and recovery¹⁵.
• Saccharomyces boulardii: Robust RCT evidence supports efficacy in reducing AAD and preventing recurrent CDI when used with or following antibiotic therapy, especially alongside high-dose vancomycin; it was well tolerated in trials^16,17.
• Bifidobacterium lactis: Supplementation with B. lactis (often in combination with other probiotics) during antibiotic therapy has been shown to prevent or improve gastrointestinal symptoms, including diarrhoea, flatulence, abdominal pain, and abnormal stool consistency in both adults and children^18–20. Co-administration with antibiotics helps maintain a more stable gut microbiota composition and faecal SCFA levels, supporting faster recovery of beneficial bacteria and metabolic function after antibiotic use²¹.
• Bacillus coagulans: A high-dose probiotic mix containing B. coagulans significantly reduced the incidence of AAD in adults receiving broad-spectrum antibiotics, with an absolute risk reduction of 16% compared with placebo²².
• Lactobacillus acidophilus: A randomised, placebo-controlled study found that L. acidophilus supplementation was associated with a trend toward reduced AAD incidence and significantly shortened diarrhoea duration, especially in younger adults²³.
• Streptococcus thermophilus: Especially in combination with other probiotics, S. thermophilus has shown benefits during or after antibiotic therapy, including reducing AAD in children and lowering the risk and severity of CDI in adults^24,25.
• Lactobacillus reuteri: Co-administration of L. reuteri with antibiotics has been associated with significantly reduced AAD and complete prevention of CDI in hospitalised adults compared with antibiotics alone¹⁴. In animal models, it also helps restore the balance of gut microbiota disrupted by antibiotics, promotes the growth of beneficial bacteria, and reduces the abundance of pathogens such as Escherichia coli²⁶.

Clinical takeaways for healthcare professionals

Robust evidence supports the use of strain-specific probiotics to reduce risks such as AAD, including CDI, in certain patient groups. Selecting high-quality products is key to maximising safety and efficacy.

Advise patients to take probiotics during and after antibiotic therapy, ideally separating the probiotic dose from antibiotics by at least 2–4 hours to help ensure the survival of beneficial microbes. Set realistic expectations; most patients experience mild benefits, with some reporting a significant reduction in diarrhoea or gut disturbance, while others may see limited improvement. Encourage symptom tracking and inform patients about possible mild transient effects (gas, bloating).

If the patient develops severe diarrhoea, dehydration, or other recurrent symptoms, they should be referred to a specialist. In most cases, evidence-based probiotic supplementation appears safe and well tolerated, and can be a valuable adjunct to antibiotic regimens to support gut health and reduce adverse outcomes.

References

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