Probiotics After Antibiotics: What to Take and When (2026)

Q: Which probiotic should I take with antibiotics?

S. boulardii CNCM I-745 (Florastor) is the first choice because it is a yeast, unaffected by antibiotics, and has the strongest evidence for preventing antibiotic-associated diarrhoea. L. rhamnosus GG (Culturelle) is the best bacterial option and should be separated from antibiotic doses by 2-3 hours.

Q: How long should I take probiotics after antibiotics?

Most clinical guidelines recommend continuing probiotics for at least 2-4 weeks after the antibiotic course ends to allow gut microbiome restoration. Some microbiome research suggests full restoration takes 30-60 days after short antibiotic courses.

Q: When should I take probiotics relative to antibiotics?

S. boulardii can be taken at any time including simultaneously with antibiotics (as a yeast, it is unaffected). Bacterial probiotics (LGG, L. acidophilus, etc.) should be taken 2-3 hours apart from antibiotic doses to avoid the antibiotic killing the probiotic before it reaches the colon.

Updated June 2026 · Sources: Szajewska & Kolodziej 2015, Palleja 2018, Cleveland Clinic, NIH ODS

Quick summary: the evidence-backed protocol

Start S. boulardii CNCM I-745 (Florastor) on Day 1 of your antibiotic course. 250-500 mg twice daily. No separation needed - it is a yeast.
Add L. rhamnosus GG (Culturelle) if you want bacterial probiotic support. Take 2-3 hours from your antibiotic dose.
Continue both for 2-4 weeks after the antibiotic course ends.
Eat prebiotic-rich foods throughout: oats, legumes, cooked and cooled potatoes, garlic (if tolerated). Avoid high-sugar diet which depletes Bifidobacterium.

How Antibiotics Affect the Gut Microbiome

Antibiotics are designed to kill bacteria. They do not distinguish beneficial resident gut bacteria from the pathogen being treated. A standard 7-day course of broad-spectrum antibiotics (amoxicillin, ciprofloxacin, clindamycin) can:

Reduce total gut bacterial diversity by 30-60%
Reduce Bifidobacterium and Lactobacillus counts by 2-3 log units (99-99.9% reduction)
Create overgrowth niches for Clostridium, Candida, and antibiotic-resistant bacteria
Impair short-chain fatty acid (SCFA) production, reducing butyrate-mediated colon cell protection

Recovery time: a 2018 study (Palleja et al., Nature Microbiology 2018) followed healthy adults given a short broad-spectrum antibiotic course and found the gut microbiota recovered to near-baseline within about 1.5 months, but several common species were still missing at 6 months. Recovery is substantial but not always complete. Antibiotic-associated diarrhoea (AAD) affects 5-35% of patients taking antibiotics; this incidence varies significantly by antibiotic type, with clindamycin having the highest AAD rate.

Evidence-Graded Probiotic Recommendations

S. boulardii CNCM I-745 (Florastor) - First Choice

Strong Evidence

The standout option. A 2015 meta-analysis (Szajewska & Kolodziej, Aliment Pharmacol Ther 2015) of 21 RCTs (4,780 patients) found S. boulardii roughly halves the risk of AAD (RR 0.47, 95% CI 0.38-0.57), cutting it from about 19% to 9% (NNT 10), with benefit in both children and adults. The critical advantage: S. boulardii is a yeast and is completely unaffected by antibiotics. You can - and should - take it simultaneously with your antibiotic.

Dose: 250-500 mg twice daily (Florastor capsules). Timing: Can be taken at the same time as antibiotics. Duration: Start Day 1 of antibiotics; continue for 2-4 weeks after course ends.

Cite: Szajewska & Kolodziej, Aliment Pharmacol Ther 2015;42(7):793-801; McFarland, World J Gastroenterol 2010

L. rhamnosus GG (Culturelle) - Second Choice

Strong Evidence

The best bacterial option. Multiple RCTs show LGG reduces AAD risk compared to placebo, with effect size smaller than S. boulardii but clinically meaningful. The key limitation: LGG is a bacterium and is sensitive to most antibiotics. Separate LGG from antibiotic doses by at least 2-3 hours to allow the probiotic to transit through the GI tract before the antibiotic depletes it.

Dose: 10 billion CFU once daily (Culturelle). Timing: 2-3 hours after antibiotic dose. Duration: Throughout antibiotic course + 2 weeks after.

Cite: Szajewska & Kolodziej, Aliment Pharmacol Ther 2015;42(10):1149-57

S. boulardii + LGG Combined

Emerging Evidence

Some clinicians recommend both simultaneously for high-risk cases (clindamycin or fluoroquinolone antibiotics, elderly patients, history of C. diff). The combination provides both the direct anti-infective mechanism of S. boulardii and the mucosal barrier-restoring effect of LGG. No large RCT has tested the combination directly; the recommendation is extrapolated from individual strain evidence.

C. difficile Prevention: Higher-Risk Antibiotics

Clostridium difficile (C. diff) is the most serious complication of antibiotic-associated microbiome disruption. C. diff produces toxins A and B that cause colitis; in severe cases, it can be life-threatening. Antibiotic-associated C. diff most commonly follows clindamycin, fluoroquinolones (ciprofloxacin, levofloxacin), and broad-spectrum cephalosporins and penicillins.

S. boulardii CNCM I-745 has specific anti-C. diff evidence: it secretes a 54 kDa protease that cleaves both C. diff toxin A receptor binding domain and toxin B. This mechanism is unique to S. boulardii. Multiple RCTs and clinical guidelines (Cleveland Clinic, ESCMID) support its use as adjunct prophylaxis during high-risk antibiotic courses.

If you have had C. diff infection previously, the recurrence risk with a subsequent antibiotic course is 20-25%. S. boulardii is the most evidence-supported adjunct in this recurrence-prevention scenario. Discuss with your prescribing clinician.

Dietary Support During and After Antibiotics

Probiotics work best alongside a diet that supports microbiome recovery. Key dietary strategies:

Prebiotic-rich foods: Oats, barley, legumes (lentils, chickpeas), garlic and onion (if tolerated), asparagus, green bananas. These feed the recovering Bifidobacterium and Lactobacillus populations.
Cooked and cooled starches: Cold potato, cold rice, and cold pasta have higher resistant starch content and provide excellent prebiotic substrate.
Live-culture fermented foods: Yogurt (live cultures), kefir, kimchi, sauerkraut. Increase their frequency during antibiotic recovery.
Reduce refined sugar and ultra-processed food: High sugar diets selectively feed Candida and displace Bifidobacterium. This is particularly important during and after antibiotics.
Avoid excess alcohol: Alcohol disrupts the mucosal barrier and suppresses Bifidobacterium growth. Minimise during recovery.

When Symptoms Require Medical Attention

Antibiotic-associated diarrhoea (AAD) is common and often self-limiting. C. difficile colitis requires medical treatment (metronidazole or vancomycin). Seek urgent medical care if you develop:

Watery diarrhoea more than 3 times per day
Blood or mucus in stool
Fever above 38.5C (101.3F)
Severe abdominal cramping or tenderness
Symptoms persisting for more than 3 days after antibiotic course ends

Frequently Asked Questions

Which probiotic should I take with antibiotics?+

S. boulardii CNCM I-745 (Florastor) is the first choice - it is a yeast, unaffected by antibiotics, with the strongest AAD prevention evidence (Szajewska & Kolodziej 2015, RR 0.47). L. rhamnosus GG (Culturelle) is the best bacterial option, taken 2-3 hours from the antibiotic dose.

How long should I take probiotics after antibiotics?+

Minimum 2-4 weeks after the antibiotic course ends. Microbiome research suggests full restoration takes 30-60 days. Continue prebiotic-rich foods for 4-8 weeks.

When should I take probiotics relative to antibiotics?+

S. boulardii: any time, including simultaneously. Bacterial probiotics (LGG, etc.): 2-3 hours after antibiotic dose. Never mix the probiotic capsule with the antibiotic in the same glass of water.

Do I need probiotics after a short antibiotic course?+

A 3-day antibiotic course (e.g. for UTI) causes less microbiome disruption than a 10-14 day course. If you have no history of AAD or C. diff and tolerate antibiotics well, S. boulardii is still reasonable but less critical. For courses of 7+ days with high-risk antibiotics (clindamycin, fluoroquinolones), the evidence for S. boulardii is compelling.

Can I eat yogurt during antibiotics instead of taking a supplement?+

Yogurt with live cultures (L. acidophilus, B. lactis) can help but delivers lower CFU counts than supplements and is sensitive to the antibiotic. It is a useful dietary adjunct but not a replacement for S. boulardii supplementation for AAD prevention in clinical evidence.