Taking certain probiotics such as Lactobacillus rhamnosus, L. acidophilus and the probiotic yeast Saccharomyces boulardii can help reduce diarrhoea and certain infections caused by the antibiotics, including C. difficile.
If you are going to have an antibiotic, will taking a probiotic help overcome the side effects and damage to the microbiome. Back in 2013, that was a research-based suggestion from the University of North Carolina (1). The reason was simple. More than a third of patients developed Antiniotic-associated-diarrhoea or AAD. In 17 per cent of cases it was fatal. Why? Because taking an antibiotic was not just linked to diarrhoea,; the antibiotic could damage the gut bacteria that normally prevented infection. AAD was associated with several increased pathogens, including Clostridium difficile, Clostridium perfringens, Klebsiella oxytoca, and Staphylococcus aureus. The recommendation was to take a simultaneous probiotic.
If only it were that simple.
Alarming levels of unnecessary and inappropriate use
In 2016, the CDC in the USA was warning that 30 per cent of antibiotics were unnecessary being prescribed for illnesses (e.g. viruses) that antibiotics cannot treat, with a further 20 per cent being prescribed inappropriately - wrong antibiotic, wrong dose etc.(2).
By 2022, a University of Texas Study (3) was showing that almost 75 per cent of antibiotics prescribed to the over 65s were unnecessary or inappropriate. This statistic was presented at the European Congress of Clinical Microbiology & Infectious Diseases.
What do antibiotics do? Antibiotics kill bacteria (Chris Woollams, the Oxford University Biochemist, calls them 'bugs') to stop them from growing and multiplying. They do not kill viruses, or yeasts, or fungi or archaea, or protists.
The antibiotic matters
First, it depends on what type of antibiotic you are taking. By that I mean that some antibiotics are broad-spectrum. These are used if the Doctor thinks several pathogens may be in play simultaneously, or he/she is unsure which pathogen is causing the infection. Broad spectrum antibiotics thus attack both Gram-positive and Gram-negative bacteria and are quite destructive of the microbiome.
Other antibiotics are narrow-spectrum and used to target a specific pathogen. They might target a Gram-negative bacterium, or a Gram-positive bacterium but never both. They are this far less destructive of the Microbiome.
Gram-positive and Gram-negative refer to a classification of bacteria based on their cell wall structure, determined by the Gram stain test developed by Hans Christian Gram. Gram-negative have a far more complex cell wall and this makes them more resistant to antibiotics.
Broad-spectrum antibiotics include tetracyclines (e.g., doxycycline), fluoroquinolones (e.g., ciprofloxacin), aminoglycosides (e,g, streptomycin:), cephalosporins (e,g. cephalexin) and carbapenems (e.g., meropenem). While these drugs offer versatility and reduced time to effective therapy in uncertain diagnoses, their use is associated with risks such as disruption of normal gut flora, increased potential for antibiotic resistance, and secondary infections like Clostridioides difficile colitis.
Narrow spectrum antibiotics target a much more limited range of bacteria and so have a much lower microbiome damage potential. They have a lower incidence of secondary infections. Examples would include Penicillin G and Vancomycin.
So what happens when you take an antibiotic?
Let’s be clear up front: The Human Microbiome Project in the USA (a 3-year study involving 200 scientists and 40 medical schools had an overall conclusion: “Your gut gets ill first, then you get ill. And you cannot get fully better until your gut gets better”.
What happens when you take an antibiotic? As we explained above, it depends on the antibiotic. Doxycycline can flatten the microbiome members across the board; a narrow spectrum antibiotic like penicillin just attacks certain bacteria. But basically the microbiome will be damaged.
The fear is the AAD, the loss of immunity and the gain of pathogens, and other adverse events such as loose stools, abdominal cramping, nausea, fever, flatulence, increased yeasts, mouth ulcers, sore tongue and taste disturbance. A Cochrane review in 2025 showed that taking probiotics during antibiotics did result in a small reduction of Clostridium difficile infection (4).
Dose is another important factor as is duration. For example, we would not be using Doxycycline every other month for 2 years just because one research study suggests it reduces cancer stem cell numbers.
Timing matters. For example, many Doctors suggest you take a probiotic after the antibiotic treatment is over. However, a meta-analysis shows that you should be using probiotics as early as possible during antibiotic therapy as this has a positive and safe effect on preventing AAD in adults (5)
The bottom line is that meta-analyses of Clinical Studies with patients using multi-strain probiotics during antibiotics show they reduce digestive side effects and prevent AAD, resulting in a 40-60% reduction in these risks, depending on the study. For example, one from Cardiff (6), following 7427 patients concluded that probiotics reduced AAD incidence by 40 per cent, especially multi-strain probiotics. It is suggested that you take the two rivals at least 5 hours apart.
Which probiotic should you take with the antibiotic?
Try probiotics that are antibiotic resistant. This would include yeast strains (antibiotics have no effect on yeasts).
Saccharomyces boulardii is a probiotic yeast and so is not killed by antibiotics. In a 2023 study (7), it enhanced the microbiome during the antibiotic use and, when continued afterwards for another 7 days, it helped the return of a healthy microbiome. In a 2024 ‘real world’ study (8), the effect of S. boulardii in controlling diarrhoea was better than anti-diarrhoeal and/or oral rehydration therapy in real-world clinical practice.
Lactobacillus rhamnosus can reduce antibiotic side effects because they are not completely wiped out by the antibiotics.
Indeed, several Lactobacillus strains, including Lactobacillus acidophilus and L. planatarum have been found to be heteroresistant in a study from the University of Atlanta Medical School (9). Heteroresistant means the members are not all killed off completely by antibiotics although this does depend on the type of antibiotic being used.
A 2023 study showed that Lactobacillus strains were particularly beneficial in restoring the microbiome after antibiotics (10).
We also know that L. reuteri produces reuterin, an antibiotic, reducing AAD and Clostridium difficile levels (11).
Bifidobacterium strains generally exhibit high susceptibility to most antibiotics, with heteroresistance primarily limited to specific classes of antibiotic like aminoglycosides (e.g., streptomycin, gentamicin) and variable resistance to tetracyclines and fusidic acid. However, certain strains actually enhance the antibacterial activity of certain antibiotics against multidrug-resistant pathogens like MRSA and VRE (12). There is some indication that Bifidobacterium lactis may reduce infection and diarrhoea levels because it is resistant to certain antibiotics and exhibits Heteroresistance to others.
Bifidobacterium strains alongside Lactobacillus strains set off the restoration process after the antibiotics finish.
How should you take your probiotic?
20 billion per day seems the appropriate dose with some experts advocating taking pills 2 or 3 times a day if you are taking antibiotics or even having chemo.
But, there are suggestions from some research studies that, apart from the benefits of Latobacillus strains noted above, multi-strain probiotics taken after the antibiotics have finished, may restrict the return of a healthy microbiome. Can this be true?
We asked our own microbiome expert Chris Woollams for his views. “My patients are told very clearly to stop the probiotic, and instead switch to a little raw (unpasteurised) cheese for exactly that reason. We want to repopulate the microbiome naturally and fully without bias to one or ten strains. We use the bacterial coloniser - the Short Chain Fatty Acid Butyrate - for exactly that reason. Then we give the patient raw cheese. This gives the patient trillions of every member of the Lactobacillus and Bifidobacterium families, with Butyrate colonising those members. After antibiotics the bacteria in the microbiome that make the Short Chain Fatty Acids (SCFAs) Propionate, Acetate and Butyrate are almost certainly missing. These two families are what mother gives her baby at birth and they attract ‘like-minded’ bacteria. Essentially, we reboot the patient’s microbiome. It works.”
Go to: Heal Your Gut - give yourself a HUG
References
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Rodgers B, Kirley K, Mounsey A. PURLs: Prescribing an antibiotic? Pair it with probiotics. J Fam Pract. 2013 Mar;62(3):148-50. PMID: 23520586;
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CDC: 1 in 3 antibiotic prescriptions unnecessary. Press release Tuesday May 3rd 2016
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Alarmingly high rates of inappropriate antibiotic prescribing to older and Black patients, finds US study; News Release.
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Probiotics for the prevention of Clostridioides difficile-associated diarrhea in adults and children; Zahra Esmaeilinezhad et al; Cochrane Database Syst Rev, 2025 Sep 11;9(9):CD006095
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Probiotics for the Prevention of Antibiotic-associated Diarrhea in Adults; Wanqian Liao et al; Journal of Clinical Gastroenterology 55(6):p 469-480, July 2021.
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Henry Wanyama et al; Probiotic use reduces the incidence of antibiotic-associated diarrhea among adult patients: a meta-analysis; Prz Gastroenterol. 2025 Mar 16;20(1):5–16.
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Saccharomyces boulardii CNCM I-745 supplementation during and after antibiotic treatment positively influences the bacterial gut microbiota; Madeleine Spatz et al; Front Med (Lausanne). 2023 Aug 4;10:1087715.
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Effectiveness of Saccharomyces boulardii CNCM I-745 in Adult Indian Patients with Diarrhoea: A Real-world, Multicentre, Retrospective, Comparative Study; Bhaskar Bikash Pal et al; Drugs Real World Outcomes, 2024 Jun;11(2):309-316.
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Widespread heteroresistance to antibiotics in Lactobacillus species; Dormarie E Rivera-Rodriguez et al; bioRxiv [Preprint]. 2025 Mar 24:2025.03.24.644958.
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Advances in Lactobacillus Restoration for β-Lactam Antibiotic-Induced Dysbiosis: A System Review in Intestinal Microbiota and Immune Homeostasis; Ying Shi et al; Microorganisms. 2023 Jan 11;11(1):179.
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Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis; Jennifer K. Spinler et al; ASM Journals, Infection and Immunity, Vol. 85, No. 10
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Antimicrobial and Immunomodulatory Effects of Bifidobacterium Strains: A Review’; Hyun Jung Lim, Hea Soon Shin; J Microbiol Biotechnol. 2020 Oct 20;30(12):1793–1800