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What are the side effects of taking probiotics?

 Introduction to Probiotics

Probiotics have been shown over and over again to have many health benefits. In an open label study, FitBiomics found that our Nella Gut Health Probiotic (3 species of Lactobacillus sourced from elite athletes) provided benefits in digestion, improved sleep, and increased energy.1 However, while they provide benefits when used long term, experiencing side effects when first starting to take probiotics is very common and completely normal. In fact, in our same open label study, while 94% of people experienced at least one benefit over two weeks, 44% experienced at least one mild side effect.

To understand why these side effects, happen and why they are so common, it is first important to understand what probiotics are. Probiotics are live microorganisms, usually bacteria but some yeast, which have provided health benefits to the host when consumed either in food or as a dietary supplement. The most common types of probiotics belong to the Lactobacillus and Bifidobacterium genera, but other common types include Streptococcus, Enterococcus, Bacillus, and Saccharomyces (this is yeast, not a bacterium, but it is still a probiotic). The best evidence for beneficial probiotic effects is in prevention and treatment of episodes of diarrhea and constipation, but some studies have shown improvements in symptoms and biomarkers associated with a wide variety of conditions from hypertension and obesity to allergies, diabetes, and depression (to name a few).2 Probiotics are generally thought to work through the production of antimicrobial substances that help keep opportunistic pathogens at bay, competition with those same pathogens for nutrients and adhesion to the gut epithelial wall, modulating the immune system of the host to promote immune homeostasis, and inhibition of toxin production by other bacteria in the gut.3

The Side Effects of Taking Probiotics

The good news is that you cannot overdose on probiotics. Unless who are severely immunocompromised with a compromised gut barrier, probiotics will never kill you. In fact, serious side effects like infection caused by probiotics containing Lactobacillus are so rare, they occur in less than 1 in 1 million people, similar to the likelihood of getting hit by lightning.4 If you take a yeast-based probiotic, the risk is even lower, less than 1 in 5 million.5,6 As probiotics have become more commonly used, the incidence of these infections has not significantly increased either.6

Typically, the side effects that people experience are mild, and they tend to subside after continuing to take the probiotic for a few weeks.7,8 In general, these side effects include gas, bloating, and diarrhea, though the specific symptoms you experience will depend on the type of probiotic you take (S. boulardii tends to cause constipation and thirst)7 as well as the initial state of your gut microbiome and your diet.

Rarely, these symptoms persist for more than a few weeks or more serious symptoms may appear. In these cases, you should discontinue use of the probiotic and contact your doctor. Some of these more serious symptoms include rashes and skin itchiness. This is usually a sign that you may be having an allergic reaction to a component of the probiotic, and you should check the probiotic ingredients for any gluten, soy, eggs, or dairy-based ingredients). However, these symptoms may also be a result of a sensitivity to biogenic amines like histamine. These biogenic amines alter how blood flows through the nervous system and can cause both allergy like symptoms and more general symptoms like headaches.9–11 The most serious potential side effect of probiotic use are the systemic infections mentioned above. These tend to occur when the probiotic escapes the gut into the bloodstream and continues to grow and divide throughout the body. This will never happen in a healthy person with an intact immune system but is a significant concern for people with compromised gut epithelia and immune system like patients undergoing certain types of chemotherapy. Furthermore, people who have recently had certain types of gastrointestinal surgery might be at a greater risk for small intestinal bowel overgrowth (SIBO). For example, people with Short Bowel Syndrome are at a much greater risk for developing D-lactic acidosis (a condition caused by overproduction of D-lactate by bacteria like Lactobacillus) and experiencing altered mental status and other central nervous symptoms like inability to walk and speak correctly.

The most common side effects (gas, bloating, changes in bowel movements) can generally be linked to changes in the gut microbiome that occur when you take a probiotic. Small changes in the gut community can result in huge changes in gut function, which is how probiotics provide such huge health benefits, but these changes require time for your body to adapt to them. As your body adapts, your diet, microbiome, intestinal transit, and sensory functions in the gut all play a part in the symptoms you experience.12

Your diet can affect what types of side effects are experienced when trying a new probiotic. Changes to the gut microbiome change how your body digests some fibers and carbohydrates. If these fibers aren’t digested properly and not fermented by the gut bacteria as usual, they draw water into the gut from the rest of the body. Depending on how fast this occurs and for how long, this can cause borborygmi (abdominal sounds), pain, and diarrhea. However, even if these fibers are fermented, the changes to the gut community can change how they are fermented and what byproducts are produced, which can cause side effects as well. This is because the altered community produces a different composition of gases during fermentation than usual. Even if the volume of gas does not change (the average person produces 700ml of gas per day, enough to almost fill a bottle of wine), the composition of the gas produced can vary. Changes in the relative amount of methane, hydrogen, and carbon dioxide alters how the body responds to gut contents, changing intestinal transit and visceral sensation.12 This gas can cause flatulence, bloating, feelings of abdominal pain, and irregular bowel movements. Changes to transit time can also result in constipation, larger stools, and feelings of fullness.

How To Minimize Side Effects and Maximize Benefits

There are a few things you can do to decrease the likelihood of experiencing these types of side effects, while gaining as many of the benefits of probiotics as you can. First of all, if you have a weakened immune system, recently had surgery or critical illness, or have a history of D-lactic acidosis or sensitivity to histamines, talk to your doctor before taking probiotics. And while probiotics are safe, make sure to speak to a pediatrician before starting your infant or young child on probiotics. Secondly, do not take probiotics if you are concurrently prescribed oral antibiotics. The antibiotics will likely kill the probiotic before you get to experience its benefits. Other medications may interfere with probiotic function, and changes to the microbiome may also change how you respond to any existing medications you are on. Any changes to medication efficacy (both good and bad) should be reported to your doctor. Your diet can also affect how well your probiotics work. Research has shown that probiotics tend to work best when taken with or up to 30min before a meal.13 Having food in the gut helps the probiotic survive the acidic conditions of the stomach. The type of food may matter as well. Fresh fruit, milk products, and complex carbohydrates like oatmeal provide the probiotic bacteria with food right off the bat, which helps them survive in the gut and provide their health benefits more quickly.14 Furthermore, if you tend to be sensitive to histamine containing foods, it might be helpful to try and maintain a low histamine diet to lower the concentration of biogenic amines in your gut as you get used to new probiotics. Furthermore, a low FODMAP diet may help with some side effects. By decreasing the concentration of fermentable sugars and fibers in your gut (like lactose, fructose, sorbitol, etc.), you can minimize the changes in gas production that occur as your gut microbiome changes to adjust to the probiotic. Finally, if nothing else works, trying a different probiotic or a different dose of the same probiotic could help with these side effects.


While the side effects experienced when trying a new probiotic can be frustrating at times, they are common and a normal result of the changes going on in your body as it adjusts to a new gut microbial community. As long as these side effects do not last more than a couple of weeks or alter your lifestyle too drastically, they are generally not concerning. Hopefully, with the suggestions included here, you can minimize these side effects and get the benefits of your probiotics more quickly.


  1. Performance Benefits of Nella Probiotics; Beta Test Data Analysis. NELLA Probiotic by FitBiomicshttps://nella.fitbiomics.com/blogs/news/performance-benefits-probiotics.
  2. Rondanelli, M. et al. Using probiotics in clinical practice: Where are we now? A review of existing meta-analyses. Gut Microbes 8, 521–543 (2017).
  3. Markowiak, P. & Śliżewska, K. Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients9, (2017).
  4. Lightning Strike Victim Data | Lightning | CDC. https://www.cdc.gov/disasters/lightning/victimdata.html.
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  6. Borriello, S. P. et al. Safety of Probiotics That Contain Lactobacilli or Bifidobacteria. Clinical Infectious Diseases 36, 775–780 (2003).
  7. Williams, N. T. Probiotics. American Journal of Health-System Pharmacy 67, 449–458 (2010).
  8. Doron, S. & Snydman, D. R. Risk and Safety of Probiotics. Clin Infect Dis 60, S129–S134 (2015).
  9. Kj, B. et al. Effects of dietary amines on the gut and its vasculature. The British journal of nutrition 101, (2009).
  10. Vt, M. & B, V. Diet and Headache: Part 1. Headache 56, (2016).
  11. Y, G., I, A., E, K. & F, Ö. Biogenic amines formation in Streptococcus thermophilus isolated from home-made natural yogurt. Food chemistry 138, (2013).
  12. Lacy, B. E., Gabbard, S. L. & Crowell, M. D. Pathophysiology, Evaluation, and Treatment of Bloating. Gastroenterol Hepatol (N Y) 7, 729–739 (2011).
  13. Tompkins, T. A., Mainville, I. & Arcand, Y. The impact of meals on a probiotic during transit through a model of the human upper gastrointestinal tract. Benef Microbes 2, 295–303 (2011).
  14. Corcoran, B. M., Stanton, C., Fitzgerald, G. F. & Ross, R. P. Survival of Probiotic Lactobacilli in Acidic Environments Is Enhanced in the Presence of Metabolizable Sugars. Appl Environ Microbiol 71, 3060–3067 (2005).


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