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Yes, Probiotics Can Have Side Effects. Here’s What You Need to Know.

Evidence Based

iHerb has strict sourcing guidelines and draws from peer-reviewed studies, academic research institutions, medical journals, and reputable media sites. This badge indicates that a list of studies, resources, and statistics can be found in the references section at the bottom of the page.

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Key Takeaways

  • Probiotics may cause temporary digestive changes: Gas, bloating or changes in bowel habits are among the effects some people notice when starting probiotics.
  • Different probiotic strains can affect the body differently: Formulation, amounts, and strain type may all influence tolerance and response.
  • Adjustment periods can vary: Some people notice changes within days, while others may take longer to adapt to a new probiotic routine.
  • Storage and product quality may influence effectiveness: Refrigeration requirements, expiration dates, and strain stability can vary between products.
  • Persistent or severe symptoms should be evaluated: Ongoing digestive discomfort or adverse reactions may warrant discussion with a healthcare provider.

Probiotics can be a useful ally when you’re trying to improve your gut health – and they usually don’t cause any problems. But some people experience side effects or worsening symptoms when taking probiotic supplements.

Why is that? Not every supplement is right for every gut. There are many different types and strains of probiotics, and some strains might cause disruption instead of restoring balance.

Here’s what you need to know about probiotics side effects so that you can make smart supplement choices, avoid symptoms, and feel your best.

Common Probiotics Side Effects

Most probiotics supplements contain combinations of beneficial bacteria and yeasts from various sources. Fermented foods like sauerkraut, kimchi, and yogurt also contain probiotics, which play a role in the fermentation process.

When you ingest probiotics from either of these sources, they interact with your body’s own microbiome–the trillions of microbes that colonize your body, specifically your gut. These interactions are often beneficial but can occasionally cause:

  • Digestive discomfort
  • Bloating
  • Gas
  • Constipation
  • Thirst

Fermented foods may also be allergy or headache triggers for people who are sensitive to amines, such as histamine. Certain strains of probiotics can increase histamine in the gut, which could lead to symptoms of an allergic reaction. However, this correlation hasn’t been proven.

Sometimes supplement ingredients, not the probiotics themselves, are to blame for side effects. Lactose, soy, dairy, gluten, and other common allergens can trigger digestive symptoms or rashes, which is why it’s important to always read labels before buying!

Can Probiotic Side Effects Be Dangerous?

Healthy people should be able to take probiotics without any severe reactions or long-term problems. Side effects like bloating often resolve within a week or two of starting a supplement as the body adjusts to the new microbial strains.

However, healthcare experts recommend avoiding probiotic supplements if you:

  • Have a weakened or suppressed immune system
  • Are you suffering from or recovering from a serious illness
  • Suffer from small intestine bacterial overgrowth (SIBO)

Weakened immunity increases the risk of getting sick from probiotics. Instead of creating balance, the microbes may cause issues when the immune system isn’t working optimally. A doctor can advise on whether a low dose may be safe in these circumstances or if probiotics should be avoided altogether.

How to Minimize Side Effects From Probiotics

The smartest way to keep the risk of symptoms at a minimum when taking probiotics is to start small. More isn’t always better! Most people don’t need megadoses of microbes to get benefits.

What’s the best amount? Supplement potency is measured in colony-forming units (CFUs), which are usually listed on the front of the package or bottle. Doses between 10 billion and 20 billion CFUs are common for adults, although amounts as low as 1 billion can still provide support.

But the number of microbes isn’t the only thing that matters. Strain types are also important. Many strains have been studied and cited for their unique effects. If you’re trying to address a specific condition, supplements containing strains known to reduce the associated symptoms or address the underlying cause may be the most beneficial. Be sure to speak with your healthcare provider.

Take probiotics on an empty stomach and with plenty of water for best results. Follow the product manufacturer’s instructions or the advice of a qualified healthcare professional.

Additional Cautions to Consider

Before taking any probiotic supplement, you want to be sure the strains you want are actually in the bottle. Probiotics often don’t need FDA (Food and Drug Administration) approval to get on shelves, so low-quality products may not actually contain what they claim—and may incorporate additives or contaminants that could cause their own side effects. To avoid this, choose products from companies known for safety and quality.

Note that some newer probiotic supplements and strain types haven’t been studied or tested as much as strains that have been on the market for longer. Further research may show that these probiotics have their own range of benefits, but for now, it’s best to proceed with caution if you’re not sure how your body will react.

Taking Probiotics Safely

You might have to try several different probiotic supplements before finding one that offers the benefits you want without side effects. (Some companies offer to do the work for you by creating personalized probiotics based on the results of a gut test, but this is still a fairly new concept without a great deal of scientific support.)

If side effects from a probiotic last longer than a couple of weeks, stop taking the supplement. Wait for symptoms to resolve before switching to a different product. If the side effects are serious or get worse, discontinue all probiotics and talk with your doctor. 

References: 

  1. Harvard Health Publishing. (2020). Should you take probiotics? Evaluating the benefits, risks, and clinical evidence. Harvard Medical School Staying Healthy Guidelines.
  2. Health Editorial Board. (2023). Can you overdose on probiotics? Understanding colony-forming units and gut safety limits. Health Digestive Health Library.
  3. Insider Medical Review. (2022). Can you overdose on probiotics? Symptoms of excessive microflora consumption. Insider Health Science Series.
  4. McDonough, M. (2021). Probiotics side effects: What happens when good bacteria cause temporary gas, bloating, or headaches. Healthline Nutrition Guide.
  5. Wilkins, T., & Sequoia, J. (2017). Probiotics for gastrointestinal conditions: A summary of the evidence. American Family Physician, 96(3), 170–178.

DISCLAIMER: These statements have not been approved by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent disease.