The Negative Side of Probiotics: Risks, Side Effects, and Who Should Avoid Them

December 29, 2025 •

4 min read

According to the National Center for Complementary and Integrative Health, while probiotics have a history of safe use, detailed safety studies are lacking, and the risk of harmful effects is greater for people with severe illnesses or compromised immune systems. This highlights the importance of understanding the potential negative side of probiotics beyond the marketed benefits.

Quick Summary

This guide covers the potential negative aspects of probiotics, detailing common side effects like bloating and gas, as well as rarer risks such as infections and antibiotic resistance transfer. It also identifies at-risk populations and provides guidance on safely navigating probiotic use.

Key Points

Digestive Discomfort: Common side effects include temporary gas, bloating, and changes in bowel movements, which typically resolve within a few weeks as the body adjusts.
Infection Risk for Vulnerable Groups: Severely ill or immunocompromised individuals face a heightened risk of infection from probiotics, with reported cases of sepsis in high-risk patients.
Antibiotic Resistance Transfer: A rare but possible negative side of probiotics is the transfer of antibiotic-resistant genes from probiotic bacteria to other microbes in the gut.
Histamine Sensitivity: Certain probiotic strains can produce biogenic amines like histamine, which can trigger headaches and allergic-like symptoms in sensitive individuals.
Product Quality Concerns: The unregulated nature of probiotic supplements means they can be mislabeled or contaminated, posing potential health risks.
Managing Side Effects: To minimize negative effects, start with a low dosage, take probiotics with food, or switch to a different strain if symptoms persist.
Consult a Doctor: High-risk individuals and those experiencing severe side effects should consult a healthcare provider before starting or continuing probiotic supplements.

Common Negative Side Effects of Probiotics

For many healthy individuals, the introduction of probiotics is uneventful. However, a significant portion of users, especially those new to supplementation, experience temporary digestive discomfort as their gut flora adjusts. These side effects are typically mild and often disappear within a few weeks of consistent use.

Digestive Discomfort

The most frequently reported negative side of probiotics involves the digestive system.

Bloating and Gas: When probiotics are introduced, they can alter fermentation processes in the intestines. This leads to increased gas production, a natural byproduct of bacterial metabolism, which can cause bloating, flatulence, and stomach rumbling.
Constipation and Diarrhea: While probiotics are often used to treat these very conditions, they can sometimes cause temporary changes in bowel habits. Some yeast-based probiotics, for instance, have been linked to constipation, while others can cause loose stools as the gut microbiome shifts.

Headaches and Histamine Reactions

Certain probiotic supplements, particularly those containing specific strains of bacteria, can increase the production of biogenic amines, such as histamine. For individuals with histamine sensitivity, this can trigger side effects.

Triggering headaches: Elevated levels of biogenic amines can affect blood flow to the central nervous system, which may result in headaches or migraines in sensitive individuals.
Allergic-like symptoms: Histamine intolerance can manifest with allergic-like symptoms, including nasal congestion and skin flushing.

Serious Risks and Considerations for At-Risk Groups

While uncommon, more severe negative consequences can arise from probiotic use, particularly for those with compromised health.

Risk of Infection

For severely ill or immunocompromised individuals, the live microorganisms in probiotics pose a small but significant risk of causing systemic infections. In rare cases, this can lead to life-threatening conditions like sepsis.

Who is at risk: This is a major concern for patients with a weakened immune system due to medication (e.g., chemotherapy), serious illnesses, or recent surgery. Premature infants have also been identified as a particularly vulnerable group.
How it happens: If the probiotic bacteria cross the compromised gut barrier and enter the bloodstream, they can cause an infection. In 2023, the FDA issued a warning to healthcare providers regarding the risk of severe infections in premature infants given probiotics.

Antibiotic Resistance Transfer

Some probiotic bacteria naturally possess genes that make them resistant to certain antibiotics. There is a theoretical concern that these genes could be transferred to other, potentially harmful bacteria within the digestive tract, rendering them resistant to treatment. While the likelihood of this occurring is considered low, it is a risk that requires ongoing research and consideration.

Supplement Contamination and Mislabeling

Unlike pharmaceuticals, probiotics are largely unregulated in the United States when sold as dietary supplements. This lax oversight has led to instances where products are mislabeled, containing different strains or quantities than advertised. In some cases, harmful contaminants have been found, posing a health risk.

How to Mitigate Negative Side Effects

Fortunately, for most healthy people, the discomfort from probiotics can be managed effectively with a few simple strategies.

Comparison of Probiotic Management Strategies


Strategy	Description	Best For	What to Expect	When to Consult a Doctor
Starting with a low dose	Introduce a small amount of probiotics and gradually increase over a few weeks.	New users or those with sensitive digestive systems.	Mild, temporary gas and bloating that subsides.	If symptoms are severe or don't improve after a few weeks.
Taking with food	Consume probiotics alongside a meal, as food can act as a buffer.	Individuals with stomach sensitivity or who experience nausea.	Reduced likelihood of initial digestive upset.	If nausea or pain persists.
Switching strains	Try a different probiotic product with alternative bacterial strains.	Those with persistent side effects or histamine sensitivity.	Side effects may change or disappear entirely, especially with a low-histamine strain.	If new strains cause different or worse symptoms.
Monitoring and journaling	Keep a record of dosage, symptoms, and dietary changes.	All users, especially those trying to pinpoint triggers.	Better awareness of your body's specific response to different strains and doses.	If you notice severe or recurring negative patterns.

Choosing Quality Products

To minimize risks, select products from reputable brands known for their transparency and third-party testing. Looking for quality seals can provide assurance that the product contains what it claims and is free of contaminants. It is also important to carefully check for common allergens like dairy, soy, or eggs, which may be present in some supplements.

Conclusion

While the market is flooded with claims of universal benefits, the negative side of probiotics is a real and important consideration. The majority of healthy users experience only mild, transient digestive issues like gas and bloating, which can be managed with a measured approach. However, for vulnerable populations—including the immunocompromised, the severely ill, and premature infants—the risks of serious infection and other complications outweigh the potential benefits. Additionally, concerns regarding antibiotic resistance transfer and the varying quality of unregulated supplements highlight the need for informed decisions and caution. Before starting any probiotic regimen, it is best to consult a healthcare professional to ensure it is appropriate for your individual health status. For most people, a diet rich in probiotic-containing foods may offer a safer, more natural approach to supporting gut health. For more detailed information on probiotic safety, consult reputable resources such as the National Center for Complementary and Integrative Health.

Frequently Asked Questions

Yes, it is common to experience temporary gas, bloating, and other digestive discomforts when first taking probiotics. These symptoms typically occur as your gut microbiome adjusts to the new bacteria and often subside within a few weeks.

People with severely compromised immune systems, premature infants, and those with critical illnesses or recovering from major surgery should avoid probiotics due to the increased risk of infection.

While rare, probiotics can cause serious infections, such as sepsis, in high-risk individuals if the bacteria cross a compromised gut barrier and enter the bloodstream. This risk is very low for healthy individuals.

Yes, some probiotic strains and fermented foods contain high levels of biogenic amines, such as histamine, which can trigger headaches or migraines in people with a sensitivity to these compounds.

Yes, some probiotic supplements may contain common allergens like dairy, soy, or eggs. Individuals with allergies should always read product labels carefully and, if necessary, choose hypoallergenic options.

There is a theoretical concern that antibiotic-resistant genes could transfer from probiotic bacteria to other bacteria in the gut. This risk is considered low but is a subject of ongoing research, especially in high-risk patients.

Keeping a journal of your symptoms and dietary changes can help you identify if a probiotic is causing negative effects. Common signs include persistent bloating, gas, stomach pain, or headaches. If symptoms are severe or do not resolve, consult a healthcare provider.