Taking probiotics while taking antibiotics is a reasonable choice for most healthy people, and the benefit is real but modest. In a 2025 Cochrane review of 38 trials, probiotics with antibiotics cut C. difficile diarrhea from 3.2% to 1.6%, and across 40 trials they cut antibiotic-associated diarrhea from 27.4% to 23%[1].
Timing matters more than most advice admits. Probiotics worked better when started within 2 days of the first antibiotic dose[2], and trials usually continued them for 7 to 14 days after the course ended[3]. No study has tested how far apart to space the two, so the popular "2 hours apart" rule is a precaution, not a proven number[3]. This guide covers the trial results, a simple schedule, the strains with data, and why the yeast Saccharomyces boulardii plays by different rules.
Get medical help promptly if diarrhea during or after antibiotics comes with fever, stomach tenderness or pain, nausea or loss of appetite[4]. These can signal C. diff infection, which needs a stool test and specific treatment, not a probiotic[4].
Is there any point in taking probiotics while on antibiotics?
Yes, for preventing diarrhea, with moderate- to low-certainty evidence[1][5]. Probiotics and antibiotics together lower the risk of antibiotic-associated diarrhea in both adults and children, and lower the risk of C. diff diarrhea. The table shows the size of the effect in the largest reviews.
| Outcome | Without probiotic | With probiotic | Source |
|---|---|---|---|
| C. diff diarrhea, adults and children (38 trials, 13,179 people) | 3.2% | 1.6% | Cochrane 2025[1] |
| Antibiotic-associated diarrhea, adults and children (40 trials) | 27.4% | 23% | Cochrane 2025[1] |
| Antibiotic-associated diarrhea, children (33 trials, 6,352 children) | 19% | 8% | Cochrane 2019[5] |
| Antibiotic-associated diarrhea, adults (42 trials, 11,305 adults) | baseline | 37% lower risk | BMJ Open 2021[6] |
| Any adverse event (37 trials) | 12.2% | 10.9% | Cochrane 2025[1] |
Put another way, about 65 people need to take a probiotic for one case of C. diff diarrhea to be prevented[1]. For diarrhea in children the number is 9, or 6 with high-dose products[5]. The Cochrane authors also noted that 28 of the trials had ties to probiotic companies[1].
Not every antibiotic side effect responds. In a randomized trial of 278 women on short antibiotic courses, oral or vaginal lactobacillus did not prevent post-antibiotic vaginal yeast infections, and the trial stopped early for lack of effect[7]. Our guide to probiotics for BV and yeast infections covers what has been tested since.
What stomach problems can antibiotics cause?
Antibiotic-associated diarrhea affects about 17% of people taking antibiotics, and C. diff diarrhea about 4%; oral and intravenous antibiotics can both cause them[3]. Antibiotics kill helpful "good bacteria" in the gut along with the infection, which lets C. diff (formerly Clostridium difficile) grow[4].
People are up to 10 times more likely to get C. diff infection during an antibiotic course and in the month after it[4]. Our guide to diarrhea from antibiotics covers why it happens and how long it lasts.
Who benefits most
The benefit depends on your starting risk. In the AGA's analysis, trials where more than 5% of untreated patients developed C. diff showed a large risk reduction (RR 0.30), while trials with a baseline risk under 3% showed no clear benefit[8]. The adult diarrhea meta-analysis found the same pattern[6].
Higher-risk groups include people 65 or older, people in hospitals or nursing homes, people with weakened immune systems, and anyone who has had C. diff before[4].
Why don't doctors prescribe probiotics with antibiotics?
Because the guidelines disagree. The American Gastroenterological Association gives a conditional recommendation for probiotics to prevent C. diff in adults on antibiotics, based on low-quality evidence; the American College of Gastroenterology recommends against them[3][9]. European pediatric gastroenterologists strongly recommend selected probiotics to prevent antibiotic-associated diarrhea in children[3].
The doubts come from the evidence itself. The AGA panel downgraded its certainty to low because only 2 of 39 trials had low risk of bias across all domains and several were unpublished[8]. Reviewers also caution that the trial results may not apply to people whose baseline risk is low[9].
ISAPP suggests an informed discussion that weighs the antibiotic class, course length, cost, age, other illnesses, and any past antibiotic diarrhea or C. diff[3]. Probiotics added to Helicobacter pylori treatment carry a separate, weak guideline recommendation[3]. For strains that shorten diarrhea once it starts, see probiotics for diarrhea.
When is the best time to take probiotics with antibiotics?
Start on day 1 or 2 of the antibiotic course, not after it ends. A meta-regression of 19 trials in hospitalized adults found that each day of delay made probiotics less effective against C. diff[2]. Started within 2 days, they cut the risk by about two thirds (RR 0.32); started later, the reduction was smaller and not statistically clear (RR 0.70)[2].
How long to continue is less settled. Trials that showed benefit started dosing as soon as practical, before or within 1 to 2 days of the first antibiotic dose. Continuing for 7 to 14 days after the last dose was a commonly tested pattern[3]. Time of day within that window has not been compared in trials; our guide on when to take probiotics covers meals and morning versus night.
Should you take probiotics at the same time as antibiotics?
Not in the same swallow if your probiotic is bacterial, but the exact gap is a guess. In lab testing, strains from marketed bacterial probiotics were susceptible to most commonly prescribed oral antibiotics[10]. ISAPP notes that no study has compared dosing schedules, so the best interval is unknown[3]. Taking a bacterial probiotic midway between antibiotic doses is a reasonable precaution, even though it is untested.
Penicillin-type drugs may matter for some strains. Lacticaseibacillus rhamnosus GG is sensitive to penicillin, which reviewers flagged as a reason it might be less effective during amoxicillin with clavulanate (Augmentin)[11]. Yet trials of L. rhamnosus GG still cut antibiotic-associated diarrhea from 22.4% to 12.3%[12].
Why S. boulardii is different
Saccharomyces boulardii is a yeast, and like all yeasts it is naturally resistant to antibiotics[13][10]. That means spacing does not matter for it.
In 21 trials with 4,780 people, it cut antibiotic-associated diarrhea from 18.7% to 8.5%, in both children and adults[14]. It reaches a steady level in the gut within about 3 days and is cleared 3 to 5 days after the last dose[13]. Our Florastor review covers one product built on this yeast.
What kind of probiotic do you need while taking antibiotics?
Choose a product that names a strain tested with antibiotics, because results do not transfer from one strain to another[3]. In adults, the benefit came mainly from certain Lactobacillus and Bifidobacterium species, not from every product tested[6].
| Strain or combination | What trials found | Notes |
|---|---|---|
| Saccharomyces boulardii | Diarrhea 18.7% to 8.5%[14]; may reduce C. diff (RR 0.41)[8] | Yeast; antibiotics do not kill it |
| L. rhamnosus GG | Diarrhea 22.4% to 12.3%; clear in children, not significant in adults[12] | Penicillin-sensitive[11] |
| L. acidophilus CL1285 + L. casei LBC80R | May reduce C. diff (RR 0.22)[8] | Low-certainty evidence |
| L. acidophilus + L. delbrueckii subsp. bulgaricus + B. bifidum | May reduce C. diff (RR 0.35)[8] | Low-certainty evidence |
| The same three plus S. salivarius subsp. thermophilus | May reduce C. diff (RR 0.28)[8] | Low-certainty evidence |
| B. animalis subsp. lactis BB-12 yogurt | Faster return of acetate and diversity after amoxicillin with clavulanate[15] | Microbiome outcomes, not diarrhea |
Dose matters too. In children, products with at least 5 billion CFU a day prevented more diarrhea than lower doses[5], and in adults a higher dose of the same probiotic beat a lower one[6]. ISAPP cautions that higher is not automatically better outside the doses tested[3].
Good probiotics when taking antibiotics are the probiotic supplements whose label names one of the strains above at a tested dose[8]. Our CFU guide and list of the best probiotics help match labels to trials, and the Culturelle review covers an L. rhamnosus GG product. The combinations above use Lactobacillus acidophilus and Bifidobacterium bifidum.
A simple schedule
This schedule follows the patterns used in successful trials[2][3]. It does not replace your prescriber's instructions.
| When | Bacterial probiotic (for example L. rhamnosus GG) | S. boulardii |
|---|---|---|
| Day 1 or 2 of the antibiotic | Start, midway between antibiotic doses | Start; no spacing needed |
| During the course | Daily, kept apart from each antibiotic dose | Daily, at any convenient time |
| After the last antibiotic dose | Continue 7 to 14 days | Continue 7 to 14 days |
| A dose taken together by mistake | Carry on; skip nothing | Not an issue |
Do probiotics help your microbiome recover after antibiotics?
Not in any proven way, and one study suggests caution. In 12 healthy men given a 4-day course of three strong antibiotics, the gut bacteria returned close to baseline within about 1.5 months. Even so, 9 common species were still undetectable in most of them after 6 months[16]. Bifidobacterium species and butyrate producers were among the early losses[16].
In a small study in mice and people, a multi-strain probiotic taken after antibiotics delayed gut mucosal microbiome reconstitution, the return of the person's own gut bacteria. A transplant of their own stored stool restored it within days[17]. A 2023 meta-analysis found that probiotics taken during antibiotics did not change gut diversity scores, and both groups drifted back toward baseline after 3 to 8 weeks[18]. In a trial of 62 healthy people, BB-12 yogurt, a fermented food with a named strain, let fecal acetate levels recover by day 30, while they stayed low in the control group[15].
An ISAPP expert panel concluded that no data causally link the clinical benefits of probiotics to protecting or restoring the microbiome[19]. In practice, take a probiotic to lower diarrhea and C. diff risk, not to rebuild your gut microbiota or as a general gut health fix. For diet steps after a course, see our gut restoration protocol.
Which people should not take probiotics with antibiotics?
Most healthy people can take them; the Cochrane review found short-term use was likely not linked to harm in people who were not immunocompromised[1]. ISAPP advises caution in four groups[3]:
- people with a weakened immune system;
- people who are severely ill;
- premature infants;
- people with an indwelling intravenous catheter.
The reason is rare bloodstream infection: almost 100 cases of yeast fungemia from S. boulardii have been reported, linked to central venous lines or to the yeast crossing a damaged gut wall[13]. Serious events have also been reported in severely ill or immunocompromised children with central lines[5].
Other theoretical risks include excessive immune stimulation and transfer of resistance genes[20]. Our page on probiotic side effects covers the common, mild ones.
When to see a doctor
Call your prescriber or a clinician if, during or after antibiotics, you have[4]:
- diarrhea with fever, stomach tenderness or pain;
- diarrhea with nausea or loss of appetite;
- signs of dehydration;
- any diarrhea and a past C. diff infection.
Do not stop the antibiotic on your own. A clinician may stop or switch it if that is safe, and C. diff is treated with specific antibiotics such as vancomycin or fidaxomicin[4].
This article is for general educational purposes and is not medical advice. Probiotics do not treat infections or replace a stool test for C. diff. Do not stop or change a prescribed antibiotic. Talk to a qualified healthcare professional before starting a probiotic, particularly if you are pregnant, immunocompromised, have a central line, are taking prescription medication, or are giving it to an infant or a seriously ill child.
Frequently Asked Questions
What is the dark side of probiotics?
Most side effects in antibiotic trials are mild, such as gas, bloating, nausea or soft stools, and a 2025 Cochrane review found adverse events were no more common than with placebo. The real risks are rare but serious: bloodstream infections in people who are severely ill, immunocompromised or have a central venous catheter, and, in one small study, slower return of the person's own gut bacteria when a multi-strain probiotic was taken after antibiotics.
What should you not mix with probiotics?
The main clash is timing a bacterial probiotic right on top of an antibiotic dose, because in lab tests most bacterial probiotic strains were susceptible to common oral antibiotics. Saccharomyces boulardii is a yeast, so antibiotics do not kill it, but ask a pharmacist before combining a yeast probiotic with antifungal medicine. If you take immunosuppressants or have a central line, check with your clinician before any probiotic.
Should I take a probiotic with Macrobid?
We found no trial that tested probiotics specifically with Macrobid (nitrofurantoin), so there is no drug-specific answer. The general evidence for probiotics alongside antibiotics comes from trials of many different antibiotics. If you want one, a yeast-based Saccharomyces boulardii avoids the question of the antibiotic killing it; with a bacterial strain, keep it a few hours from the antibiotic dose. Ask your pharmacist, and never change how you take the antibiotic.
Can probiotics prevent yeast infections while on antibiotics?
The best trial says probably not. In a randomized trial of 278 women taking short courses of antibiotics, oral or vaginal lactobacillus did not reduce post-antibiotic vaginal yeast infections compared with placebo, and the trial stopped early for lack of effect. About 23% of the women developed symptoms. See our guide to probiotics for BV and yeast infections for what has been tested since.
What helps upset stomach from antibiotics?
For diarrhea, the strongest evidence is for starting a probiotic early in the course: trials of S. boulardii cut antibiotic-associated diarrhea from about 19% to 9%. Do not stop the antibiotic on your own. Call the prescriber if diarrhea is frequent, watery or comes with fever, belly pain or tenderness, because those can signal C. diff, which needs a stool test and its own treatment.
Do probiotics colonize the gut?
Mostly not for long. Saccharomyces boulardii reaches a steady level in the gut within about three days and is cleared three to five days after you stop. ISAPP notes that the microbes that increase in the gut during probiotic use are generally not the probiotic species themselves. One exception: after antibiotics, one study found probiotic strains colonized the human gut lining more easily than usual.
I accidentally took my probiotic with my antibiotic. Is that a problem?
No. ISAPP states there is no evidence that probiotics make antibiotics less effective, because antibiotics already work against the huge number of microbes living in the gut. The only cost is that some of that probiotic dose may be killed. Take the next antibiotic dose on schedule and space the following probiotic dose if you are using a bacterial strain.
How long does it take your gut to recover after antibiotics?
In healthy adults given a 4-day course of three strong antibiotics, the gut bacteria returned close to baseline within about 1.5 months, although 9 common species were still missing in most people at 6 months. CDC notes that antibiotic effects on the gut can last several months. Our gut restoration protocol covers the diet steps that support recovery.
References
- Esmaeilinezhad Z, Ghosh NR, Walsh CM, et al.. Probiotics for the prevention of Clostridioides difficile-associated diarrhea in adults and children. Cochrane Database of Systematic Reviews. 2025;9(9):CD006095. doi:10.1002/14651858.CD006095.pub5 ↩
- Shen NT, Maw A, Tmanova LL, et al.. Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis. Gastroenterology. 2017;152(8):1889-1900.e9. doi:10.1053/j.gastro.2017.02.003 ↩
- International Scientific Association for Probiotics and Prebiotics. Probiotic use alongside antibiotics: A guide to clinical FAQs. ISAPP Clinician Resource. 2024. Available at: https://isappscience.org/wp-content/uploads/2024/12/ISAPP-Clinician-resource-probiotic-use-alongside-antibiotics.pdf ↩
- Centers for Disease Control and Prevention. About C. diff. CDC. 2026. Available at: https://www.cdc.gov/c-diff/about/index.html ↩
- Guo Q, Goldenberg JZ, Humphrey C, El Dib R, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database of Systematic Reviews. 2019;4(4):CD004827. doi:10.1002/14651858.CD004827.pub5 ↩
- 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;11(8):e043054. doi:10.1136/bmjopen-2020-043054 ↩
- Pirotta M, Gunn J, Chondros P, et al.. Effect of lactobacillus in preventing post-antibiotic vulvovaginal candidiasis: a randomised controlled trial. BMJ. 2004;329(7465):548. doi:10.1136/bmj.38210.494977.DE ↩
- Preidis GA, Weizman AV, Kashyap PC, Morgan RL. AGA Technical Review on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology. 2020;159(2):708-738.e4. doi:10.1053/j.gastro.2020.05.060 ↩
- Marlicz W, Rydzewska G. Should physicians prescribe probiotics alongside antibiotics? A practical perspective. Gastroenterology Review. 2025;20(1):1-4. doi:10.5114/pg.2025.148588 ↩
- Neut C, Mahieux S, Dubreuil LJ. Antibiotic susceptibility of probiotic strains: Is it reasonable to combine probiotics with antibiotics?. Médecine et Maladies Infectieuses. 2017;47(7):477-483. doi:10.1016/j.medmal.2017.07.001 ↩
- Mantegazza C, Molinari P, D'Auria E, Sonnino M, Morelli L, Zuccotti GV. Probiotics and antibiotic-associated diarrhea in children: A review and new evidence on Lactobacillus rhamnosus GG during and after antibiotic treatment. Pharmacological Research. 2018;128:63-72. doi:10.1016/j.phrs.2017.08.001 ↩
- Szajewska H, Kołodziej M. Systematic review with meta-analysis: Lactobacillus rhamnosus GG in the prevention of antibiotic-associated diarrhoea in children and adults. Alimentary Pharmacology & Therapeutics. 2015;42(10):1149-1157. doi:10.1111/apt.13404 ↩
- Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therapeutic Advances in Gastroenterology. 2012;5(2):111-125. doi:10.1177/1756283X11428502 ↩
- Szajewska H, Kołodziej M. Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea. Alimentary Pharmacology & Therapeutics. 2015;42(7):793-801. doi:10.1111/apt.13344 ↩
- Merenstein D, Fraser CM, Roberts RF, et al.. Bifidobacterium animalis subsp. lactis BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome. Nutrients. 2021;13(8):2814. doi:10.3390/nu13082814 ↩
- Palleja A, Mikkelsen KH, Forslund SK, et al.. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 2018;3(11):1255-1265. doi:10.1038/s41564-018-0257-9 ↩
- Suez J, Zmora N, Zilberman-Schapira G, et al.. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018;174(6):1406-1423.e16. doi:10.1016/j.cell.2018.08.047 ↩
- Éliás AJ, Barna V, Patoni C, et al.. Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis. BMC Medicine. 2023;21(1):262. doi:10.1186/s12916-023-02961-0 ↩
- Szajewska H, Scott KP, de Meij T, et al.. Antibiotic-perturbed microbiota and the role of probiotics. Nature Reviews Gastroenterology & Hepatology. 2025;22(3):155-172. doi:10.1038/s41575-024-01023-x ↩
- Doron S, Snydman DR. Risk and safety of probiotics. Clinical Infectious Diseases. 2015;60(Suppl 2):S129-S134. doi:10.1093/cid/civ085 ↩