Probiotics with antibiotics: Let’s follow the evidence

A recent article published in The Washington Post and syndicated throughout North America, by a prominent gastroenterologist, Trisha Pasricha MD, addressed the question, “My doctor prescribed me a course of antibiotics, and my friend told me to pick up a probiotic supplement to protect my microbiome. Should I do it, or am I wasting my money?” 

This same author addressed a similar question in the same forum about a year ago:  “I’ve heard about the benefits of probiotics for years. Should I start taking them?” We disagreed on several points with her response to this question, which evoked our previous blog. Our opinion was that to effectively determine if someone should take a probiotic, clinicians should first evaluate whether the individual is targeting specific symptoms, and if so, look at available evidence, as there are several indications where evidence supports recommending one. Lest anyone accuse us of blanket bias, let’s be completely clear: we are not cheerleaders for indiscriminate use of probiotics. In fact, we recently authored the comprehensive Merenstein et al. 2024 review article (1) looking at whether generally healthy people should routinely take probiotics. Our conclusion in that paper was that there is currently not a sufficiently high level of evidence (Level A) to support recommending probiotics for population-wide, completely healthy individuals. 

Back to this latest question.  In our opinion, the response by Dr. Pasricha again misses some important points and promulgates some misinformation. Dr. Pasricha starts by stating, “There isn’t solid data that probiotic supplements will help, and there’s sobering scientific evidence that they may actually slow your recovery.” She cites a 2023 meta-analysis (2) that she claims demonstrates concurrent probiotic use does not support the microbiome. She also cites a 2018 study (3) that demonstrated a probiotic delayed microbiota recovery, suggesting this is evidence of harm. She concludes that most people should save their money unless they are at high risk for C. difficile. (She is correct about C. difficile; a large 2025 Cochrane review (4) found that probiotics can help prevent C. difficile-associated diarrhea in adults and children.) Instead of probiotic supplements, Dr. Pasricha recommends three dietary strategies to support the gut microbiome: eating a high-fiber diet to fuel the production of short-chain fatty acids, consuming a wide variety of plant-based fibers to promote hallmarks of overall microbial diversity, and incorporating fermented “probiotic foods” such as Greek yogurt or kimchi every day. She concludes by reminding patients to always complete an appropriate course of antibiotics when fighting an active bacterial infection. 

Let’s break down where the science stands, where these recommendations fall short, and why looking at the data matters more than relying on “feel-good” recommendations. 

Evidence that probiotics can help restore microbiome after antibiotics is weak

Although Dr. Pasricha is correct that evidence that probiotics can help restore gut microbiota composition is weak, her argument would be stronger if she cited a comprehensive review of evidence (Szajewska et al. 2024 (5), addressed in this blog) rather than a single 2023 meta-analysis (2), which looked only on maintaining gut microbiome taxonomic composition or alpha- and beta-diversity indices. It  did not address evidence about function, specifically evidence that a certain probiotic can mitigate disruption of short chain fatty acid production by the microbiota (Merenstein et al. 2021) (6). 

Evidence for microbiome support vs. clinical endpoints

The question and answer focus only on gut microbiota composition rather than on the more medically important endpoint of clinical effects. She mentions symptomatic side effects that antibiotics can cause, but she does not present available data for probiotics in mitigating such symptoms. Large Cochrane meta-analyses (here (7), here (4) and here (8)) have found clinical benefits of probiotics for preventing AAD in children and adults. Importantly, probiotics may function using different mechanisms of action and it is possible that restoring microbiome composition may not be essential to mitigate antibiotic-induced symptoms (see here (9) and here (10)).  A reasonable clinical response to the question posed is to point out that microbiome support is a mechanism, and a hypothetical one at that, and perhaps more relevant to the patient is the question about whether a probiotic might provide a clinical benefit.  Dismissing probiotics based on a study that looked purely at DNA sequencing data rather than symptoms is at best a disservice to patients. Clinicians may find this resource useful to clarify the state of clinical vs microbiome evidence and summarise guidelines from clinical societies for this indication. 

Potential for probiotic harm

Dr. Pasricha doesn’t just recommend against probiotics but adds the caveat that probiotics might indeed be harmful. She states, “One small study published in 2018 in Cell (11) found that people who took probiotics after antibiotics took far longer to recover their baseline microbiome compared with those who didn’t take probiotics.” This study is often cited due to the elegant analysis and comprehensive approach. However, the generalizability of the study is strictly limited by its small human sample size (n=8 in the probiotic arm),  its reliance on a single, very aggressive antibiotic regime, and that it tested just a single probiotic preparation. Dr. Pasricha also cites a recent Swedish study of nearly 15,000 people that found even a single course of antibiotics can lead to persistent microbiome changes that last for years. They specifically found one of the antibiotics used in the 2018 Cell study was responsible for long-term alterations. Consequently, over-generalizing findings to suggest that all probiotics (regardless of the strain composition or the antibiotic regimen) may universally delay recovery lacks rigorous pharmacological justification.

Three recommendations

Finally, Dr. Pasricha provides three recommendations, which she presents as more robust approaches to microbiome support than probiotics. While no evidence is provided that they are useful during antibiotic therapy, the reader is led to believe they may be helpful – ‘Skip the probiotic with your antibiotics, and bolster your microbiome with these three strategies instead.’ 

Increase Dietary Fiber. We fully agree that increasing dietary fiber from fruits, vegetables, and whole grains is a sound dietary recommendation. Most people do not meet recommended dietary intakes of fiber and fiber appears to improve parameters of gut health and lowers chronic disease risk under normal conditions. One of us (DM) frequently recommends this to patients. However, making recommendations based on intuition  is very different from making evidence-based recommendations for a specific situation to millions of readers. In the context of this article, recommending a high-fiber diet as a specific remedy to rebuild an antibiotic-perturbed microbiome lacks supporting data, and indeed, no references are provided for this recommendation. 

Consume a wide variety of plant-based fibers. Eating a variety of foods across categories is dietary advice given by many nutrition organizations, and these recommendations are aligned. However, little data support that this action can support a healthy microbiome, let alone an antibiotic-perturbed microbiome. An interesting finding from the Stanford study (12) highlighted by Dr. Pasricha below is “Despite sustained high levels of diverse plant-derived dietary fiber in these participants over 6 weeks, we did not observe a cohort-wide microbiota diversity increase in the high-fiber-diet arm.” This is a reminder that this field is nascent and complex. ‘Common sense’ recommendations may not be supported by data. 

Incorporate fermented “probiotic foods”. If Dr. Pasricha concludes that probiotics are not useful, it is not clear why she finds them worth recommending as probiotic foods. It seems more justified to consider the evidence for probiotics, whether delivered in fermented foods or supplements, on its own merit. While traditional fermented foods can be highly nutritious and excellent additions to a balanced diet, most lack convincing evidence from controlled dietary intervention studies documenting specific health benefits beyond basic nutrition. To be scientifically classified as a probiotic, a product must contain defined, live microorganisms that are characterized by genomic sequencing, and delivered in adequate amounts to confer a scientifically proven health benefit. Most retail yogurts and kefirs contain live starter cultures, but they rarely state the specific strains they contain or guarantee viable counts through the end of the product’s shelf life. And the majority have never been studied. Thus, they are fermented foods, not standardized probiotic interventions.  

Dr. Pasricha supports this recommendation by referencing “a seminal Stanford randomized controlled trial” (Wastyk, et al. 2021) (12) showing that a diet high in fermented foods increased microbial diversity and decreased inflammatory markers. It is a very interesting study, but it has limited generalizability. It was conducted on only 18 healthy individuals – 18! The Cochrane review on probiotics and AAD included 38 trials (13,179 participants). The authors of the Stanford study note the study’s limitations (short duration, no follow up, and no control arm) and surely would hesitate to conclude that their study provides definitive evidence of the benefits of fermented foods. ISAPP has a strong publication record on fermented foods (see this list) and recognizes the potential health benefits. But ISAPP would also acknowledge that the evidence isn’t clear that they protect the microbiome, most importantly when taking an antibiotic, as that is the question at hand. Recommendations should be accompanied by a statement of the level of evidence that supports them. 

Conclusion

This field is a rapidly evolving field driven by many tantalizing hypotheses with too few controlled human trials. Professionals in this field have a duty to separate facts from hypotheses, and to apply the same evidence standard to all interventions being considered. Although as stated above, we are not cheerleaders for probiotics, it is frustrating to us how highly qualified professionals denigrate available randomized controlled trials and meta-analyses for probiotic benefits as insufficient, but then are comfortable recommending fermented foods with little such data. 

Tangentially, we also note that the article concludes, “And remember, once you start a course of antibiotics for an infection, it’s just as important that you finish that full course to ensure the infection is fully eliminated and to stop the development of antibiotic-resistant bacteria.” Readers would benefit from being aware of new evidence that advocates for a much more nuanced approach to long courses of antibiotics. For example, treatment of Streptococcal pharyngitis in the US comprises a strict 10-day course of antibiotics, yet in many parts of Europe, it is being reduced to 5 days. Why? Primarily to protect the microbiome, minimize side effects and – counter to the reason provided above – to fight global emergence of drug-resistant pathogens. A systematic review (13) of 35 studies found a 4% increased odds of adverse events and a 3% increased odds of antimicrobial resistance for each additional day of antibiotic usage.  Thus, the traditional dogma of “always finishing the full course” of antibiotics was once true but not always now and ignores the transition to prescribing shorter courses (for example, see here (14) and here (15), and a review here (16)). Anyone receiving a long course of antibiotics should question their physician about the need for it and many physicians are now telling patients if you are better you can stop before all the pills are completed. 

References

(1) Merenstein DJ, Tancredi DJ, Karl JP, Krist AH, Lenoir-Wijnkoop I, Reid G, Roos S, Szajewska H, Sanders ME. Is There Evidence to Support Probiotic Use for Healthy People? Adv Nutr. 2024;15(8):100265.

(2) Éliás AJ, Barna V, Patoni C, Demeter D, Veres DS, Bunduc S, Erőss B, Hegyi P, Földvári-Nagy L, Lenti K. Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis. BMC Med. 2023;21(1):262.

(3) Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018;174(6):1406-1423.e16.

(4) Esmaeilinezhad Z, Ghosh NR, Walsh CM, Steen JP, Burgman AM, Mertz D, Johnston BC. Probiotics for the prevention of Clostridioides difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2025;9(9):CD006095.

(5) Szajewska H, Scott KP, de Meij T, Forslund-Startceva SK, Knight R, Koren O, Little P, Johnston BC, Łukasik J, Suez J, Tancredi DJ, Sanders ME. Antibiotic-perturbed microbiota and the role of probiotics. Nat Rev Gastroenterol Hepatol. 2025;22(3):155-172.

(6) 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;13(8):2814.

(7) Guo Q, Goldenberg JZ, Humphrey C, El Dib R, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev. 2019;4(4):CD004827.

(8) Goldenberg JZ, Yap C, Lytvyn L, Lo CK, Beardsley J, Mertz D, Johnston BC. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2017;12(12):CD006095.

(9) Mekonnen SA, Merenstein D, Fraser CM, Marco ML. Molecular mechanisms of probiotic prevention of antibiotic-associated diarrhea. Curr Opin Biotechnol. 2020;61:226-234.

(10) Lebeer S, Bron PA, Marco ML, Van Pijkeren JP, O’Connell Motherway M, Hill C, Pot B, Roos S, Klaenhammer T. Identification of probiotic effector molecules: present state and future perspectives. Curr Opin Biotechnol. 2018;49:217-223.

(11) Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018;174(6):1406-1423.e16.

(12) Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14.

(13) Curran J, Lo J, Leung V, Brown K, Schwartz KL, Daneman N, Garber G, Wu JHC, Langford BJ. Estimating daily antibiotic harms: an umbrella review with individual study meta-analysis. Clin Microbiol Infect. 2022;28(4):479-490.

(14) Dinh A, Ropers J, Duran C, Davido B, Deconinck L, Matt M, Senard O, Lagrange A, Makhloufi S, Mellon G, de Lastours V, Bouchand F, Mathieu E, Kahn JE, Rouveix E, Grenet J, Dumoulin J, Chinet T, Pépin M, Delcey V, Diamantis S, Benhamou D, Vitrat V, Dombret MC, Renaud B, Perronne C, Claessens YE, Labarère J, Bedos JP, Aegerter P, Crémieux AC; Pneumonia Short Treatment (PTC) Study Group. Discontinuing β-lactam treatment after 3 days for patients with community-acquired pneumonia in non-critical care wards (PTC): a double-blind, randomised, placebo-controlled, non-inferiority trial. Lancet. 2021;397(10280):1195-1203.

(15) Moragas A, Uguet P, Cots JM, Boada A, Bjerrum L, Llor C. Perception and views about individualising antibiotic duration for respiratory tract infections when patients feel better: a qualitative study with primary care professionals. BMJ Open. 2024;14(2):e080131.

(16) Lee RA, Stripling JT, Spellberg B, Centor RM. Short-course antibiotics for common infections: what do we know and where do we go from here? Clin Microbiol Infect. 2023;29(2):150-159.