Are there negatives to taking a probiotic? The Risks and Side Effects

October 5, 2025 •

5 min read

While millions of people use probiotics for gut health, many are unaware of the potential drawbacks that exist, particularly for certain populations. Are there negatives to taking a probiotic that you should consider before starting a new supplement?

Quick Summary

Probiotics, while generally safe, can cause side effects like gas and bloating. Individuals with compromised immune systems, severe illnesses, or certain allergies face more serious risks, necessitating professional medical advice before use.

Key Points

Mild Side Effects: Common initial side effects include temporary gas, bloating, nausea, and changes in bowel movements as the body adjusts.
Serious Infection Risk: Individuals who are immunocompromised, critically ill, or premature infants face a rare but serious risk of infection from probiotics.
Allergies and Intolerances: Probiotic supplements may contain undisclosed allergens like dairy or soy, and certain strains can produce histamines that trigger headaches in sensitive individuals.
Limited Regulation: The FDA does not regulate dietary probiotic supplements, meaning product quality and potency can be inconsistent and labels may be inaccurate.
The 'More is Not Better' Rule: Taking a single probiotic strain long-term can potentially reduce overall gut microbiome diversity, and high CFU counts don't always equate to higher effectiveness.
Strain Matters: The effectiveness of a probiotic depends on the specific, clinically tested strain, not just the brand or dose.
Professional Guidance is Key: Consulting a healthcare provider is especially important for those with health conditions or for navigating the many options available.

Common Digestive Side Effects

For most healthy individuals, probiotics are well-tolerated. However, it is common to experience temporary digestive discomfort as your body adjusts to the new microorganisms. These effects typically subside within a few weeks and are not a cause for serious concern. The most commonly reported side effects are:

Gas and bloating: The introduction of new bacteria can cause an initial increase in gas production, leading to a bloated sensation.
Nausea: Some individuals may feel slightly queasy when first starting a new probiotic supplement.
Diarrhea or constipation: Probiotics are often used to address these very issues, but a change in the gut's bacterial balance can sometimes have the opposite, albeit temporary, effect.
Increased thirst: Some people, particularly those taking yeast-based probiotics like Saccharomyces boulardii, may experience temporary increased thirst.

Considerations for those with pre-existing digestive conditions

For some people with specific gut conditions, probiotic side effects can be more intense. Individuals with Irritable Bowel Syndrome (IBS) or Inflammatory Bowel Disease (IBD) have reported worsening abdominal pain and other symptoms when taking certain probiotics. Furthermore, some studies indicate a link between probiotic use and Small Intestine Bacterial Overgrowth (SIBO), which can cause gas, bloating, and even neurological issues like brain fog. It is important for anyone with these conditions to work with a healthcare provider to determine if probiotics are appropriate.

Serious Risks for Vulnerable Populations

While rare in healthy people, the most significant negatives to taking a probiotic are the serious risks posed to vulnerable individuals. For these high-risk groups, the benefits almost never outweigh the potential for harm.

Immunocompromised Individuals: People with weakened immune systems due to conditions like HIV/AIDS, cancer (especially during chemotherapy or radiation), or organ transplants are at a higher risk of developing a systemic infection (bacteremia or fungemia) from the live organisms in probiotics. In rare cases, the probiotic bacteria can escape the gut and enter the bloodstream, leading to severe, even fatal, infection.
Premature Infants and Critically Ill Patients: Severe or fatal infections have been reported in critically ill hospital patients and premature infants who were given probiotics. The FDA has issued warnings to healthcare providers about this risk.
Patients with Severe Acute Pancreatitis: A 2008 study found an increased risk of mortality in patients with severe acute pancreatitis who were given probiotics, a finding that has led to a contraindication for this patient group.

Product-Specific Concerns and Allergies

Beyond the risks posed by the live organisms themselves, several issues related to the products and their ingredients can cause negative effects.

Lack of Regulation and Variable Quality

Probiotic supplements are not strictly regulated by the Food and Drug Administration (FDA) in the United States. This means that manufacturers do not have to prove the safety, efficacy, or even the accuracy of their products before they are sold to the public. This lack of oversight can lead to several problems:

Inaccurate Labels: Some products may not contain the strains or colony-forming units (CFU) promised on the label.
Contamination: In rare cases, products have been found to contain contaminants or other microorganisms not listed on the label, which can pose serious health risks.

Allergic Reactions and Histamine Intolerance

Many people take probiotics to improve digestive health, but ingredients in the supplements or the metabolic byproducts of the bacteria can cause adverse reactions. Certain probiotic strains, especially in fermented foods like sauerkraut and kefir, can produce biogenic amines like histamine. In individuals with histamine intolerance, this can trigger reactions like headaches or migraines. Furthermore, many supplements contain allergens like dairy, soy, or gluten from the manufacturing process. It is crucial for those with allergies to check labels and, if necessary, verify with the manufacturer to ensure the product is free of these triggers.

Comparison: Probiotic Supplements vs. Fermented Foods

When considering probiotics, it is important to distinguish between those found naturally in fermented foods and those in dietary supplements. Their safety profiles and effectiveness differ significantly.


Feature	Probiotic Supplements	Fermented Foods
Regulation	Varies by manufacturer, not strictly regulated by FDA in the US.	Generally considered safe (GRAS), regulated as food products.
Strain Specificity	Allows for targeted strains and CFU counts based on clinical studies.	Strain content and viability can vary greatly; often not specified or clinically proven.
High-Risk Use	Small but serious risk of systemic infection for vulnerable individuals.	Very low risk of infection; concerns are mainly related to contamination from improper preparation.
Allergen Risk	May contain hidden allergens from manufacturing. Labels must be checked carefully.	Allergen risk is specific to the food source (e.g., dairy in yogurt, soy in miso).
Overall Risk	Higher potential for negative side effects, especially in high-risk groups.	Considered safe for most healthy individuals, with minimal risk.

The “More is Better” Fallacy

Many supplement brands advertise high CFU counts and a wide variety of strains, but this does not necessarily translate to a better or more effective product. In fact, some evidence suggests that taking one specific strain over a long period could crowd out other beneficial species and decrease the overall diversity of the gut microbiome, which is generally associated with good health. The effectiveness of a probiotic is highly dependent on the specific strain or blend and whether it has been clinically studied for a particular health goal.

Conclusion: Weighing the Risks and Seeking Guidance

While often marketed as a universal wellness solution, the potential negatives to taking a probiotic are real and should be carefully considered. For the average, healthy adult, the side effects are typically mild and temporary, largely limited to digestive issues like gas and bloating as the body adjusts. However, for vulnerable populations such as the immunocompromised, premature infants, or critically ill patients, probiotics pose a small but potentially life-threatening risk of serious infection. Given the variable quality of unregulated dietary supplements and the importance of strain specificity, a one-size-fits-all approach is ineffective and potentially unwise. Before starting any probiotic regimen, it is crucial to consult a healthcare professional, who can help weigh the risks against the potential benefits and guide you toward a safe and effective choice for your specific health needs. You can also often get sufficient probiotic bacteria from naturally fermented foods, which carry a lower risk profile.

Frequently Asked Questions

The most common initial side effects of probiotics are mild and temporary digestive issues, such as gas, bloating, and changes in bowel movements. These symptoms usually resolve within a few weeks as your body adjusts.

Individuals who are immunocompromised (e.g., due to chemotherapy or HIV), critically ill, or premature infants should avoid taking probiotics unless under strict medical supervision, as there is a serious risk of infection.

Yes, in some sensitive individuals. Certain probiotic foods and supplements contain biogenic amines like histamine, which can trigger headaches or migraines in those with histamine intolerance.

Due to the lack of strict regulation for dietary supplements, there is a small risk of product contamination. Some products have been found to contain microorganisms not listed on the label, which can pose health risks, especially for vulnerable individuals.

Fermented foods like yogurt and kefir are generally considered safe for healthy people, though they may not offer clinically proven benefits. Probiotic supplements carry a higher potential for risk, particularly concerning inconsistent quality and potential contamination.

While allergic reactions to the bacterial strains themselves are rare, many probiotic supplements may contain common allergens like dairy, soy, or gluten from the manufacturing process. It is important to check the product label for allergen information.

Theoretically, probiotic bacteria could transfer antibiotic-resistant genes to harmful bacteria in the gut, making antibiotic treatment less effective. While this theoretical concern has not been widely observed, it remains a consideration for some experts.