I read two online articles on the use of probiotics to help maintain balance of gut bacteria when undergoing antibiotic treatment:

I was looking for "weight of the evidence" on whether eating probiotics (pills, yogurt, kimchi, kefir) actually maintains good gut bacteria when one goes on antibiotic treatment.

The four cited articles that seemed focus on this are:

There seems to be weak evidence that it helps with diarrhea, and weaker evidence that it helps with the gut flora overall (notwithstanding the phrase "reasonable evidence" used in the Wikipedia article). However, it doesn't hurt.

Is this a reasonable summary of the current knowledge?

NOTE: This differs from another article in that I'm asking not for suggestions or anecdotes, but an assessment of current information.


2 Answers 2


Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Published: September 6, 2018 DOI:https://doi.org/10.1016/j.cell.2018.08.047

Abstract: Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa but only mildly improved colonization in mice. Compared to spontaneous post-antibiotic recovery, probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In vitro,Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection without compromising microbiome recolonization in the antibiotics-perturbed host.

My conclusions from reading this abstract: it includes human study. It is not directed specifically to C. diff. It discusses recolonization of the gut microbiome and that recolonization might be necessary for probiotics to be effective for ulcerative colitis.

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    I wonder what "antibiotic perturbation" means. Probiotics' delaying of recover is contrary to the current belief (as muddy the substantiation of that belief is),and it isn't clear from the sentence whether that was only observed in mice ("...probiotics induced a markedly delayed ..."). Same for the punch line "...post-antibiotic probiotic benefits may be offset by a compromised gut mucosal recovery...". Commented Apr 15, 2019 at 12:09
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    Found interpretations of the technical language here and hear, but I believe that my questions above still stand. Commented Apr 15, 2019 at 12:19
  • Yes, I agree with you that your q still stands. It is an area with a lot of complexity leading to different conclusions. This included human subjects and had a particular focus. I thought it would add some context for what is going on in the GI. Also, the authors do not dismiss probiotics.
    – bparn
    Commented Apr 19, 2019 at 14:13


There seems to be moderate evidence that probiotic supplements can reduce the risk of antibiotic-associated diarrhea.

The use of probiotics to prevent Clostridium difficile diarrhea associated with antibiotic use (Cochrane.org, 2017)

Based on this systematic review and meta-analysis of 31 randomized controlled trials including 8672 patients, moderate certainty evidence suggests that probiotics are effective for preventing CDAD [C. difficile-associated diarrhea after antibiotic use].

Comparative efficacy and tolerability of probiotics for antibiotic-associated diarrhea: Systematic review with network meta-analysis (PubMed, 2018)

LGG [Lactobacillus rhamnosus GG ] is probably the best option to consider when AAD is indicated. L. casei appears to be the most efficacious choice when associated with severe C. difficile-related cases.

A practical guide for probiotics applied to the case of antibiotic-associated diarrhea in The Netherlands (BMC Gastroenterology, 2018)

After systematic review of available literature, they conclude that:

...there is sufficient evidence to make a recommendation for the use of specific probiotic products for the prevention of antibiotic associated diarrhea. In particular, we provide a three-star recommendation for preparations with...the probiotic strain Lactobacillus rhamnosus GG.

Probiotics for the Prevention of Antibiotic-Associated Diarrhea in Outpatients—A Systematic Review and Meta-Analysis (MDPI, 2017)

...the overall quality of the included studies was moderate...The results suggests that probiotic use may be beneficial in the prevention of AAD among outpatients.

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis (Gatroenterology, 2017)

...we found evidence that administration of probiotics closer to the first dose of antibiotic reduces the risk of CDI by >50% in hospitalized adults.


There seems to be insufficient evidence to claim that commercially available probiotic capsules or foods, such as yogurt, kefir, cheese, sauerkraut, kombucha and kimchi, help in overall health. Even if they "help with the gut flora overall," this dos not already mean they are beneficial for health.

What do Cochrane systematic reviews say about probiotics as preventive interventions? (PubMed, 2107)

Despite the marketing and the benefits associated with probiotics, there is little scientific evidence supporting the use of probiotics. None of the reviews provided any high-quality evidence for prevention of illnesses through use of probiotics.

Probiotics in prevention of antibiotic associated diarrhoea: meta-analysis (theBMJ, 2002)

Commercially available strains are being marketed in capsules and yoghurt based drinks, but their potential benefit needs further investigation. It would be wrong to credit the proved benefits of one strain to an untested but closely related strain.

  • With regard to evidence for combatting diarrhea, my question posits that it was "weak", while your evidence indicates "moderate". Given all the information on this page at the time of this comment, I now suspect that the use of supplements is contraindicated. My primary reason is bparn's answer. Commented Apr 18, 2019 at 3:52
  • With regard to restoring gut flora, the first article seems to be about overall health and seems to somewhat align with my posit that there is very weak evidence; it says there's no evidence. However, I'm not sure if it deals specifically with restoration of overall gut flora after antibiotic treatment. The second article seems to focus on diarrhea. Commented Apr 18, 2019 at 3:52
  • Thanks for providing your thoughts. Commented Apr 18, 2019 at 3:53

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