Are there any negative side effects to probiotics? A comprehensive review

October 9, 2025 •

4 min read

Probiotics, which are live microorganisms intended to provide health benefits, have been used in fermented foods for thousands of years. While widely considered safe, many wonder: Are there any negative side effects to probiotics? The answer depends largely on an individual's health status, with risks ranging from mild digestive upset to serious infections in vulnerable populations.

Quick Summary

Probiotics can cause temporary side effects such as gas, bloating, and digestive discomfort, especially when starting a new supplement. For high-risk individuals, including the critically ill and immunocompromised, serious adverse effects like systemic infections or sepsis are possible, requiring caution and medical consultation. Potential reactions to amines in fermented foods or allergens in supplements also occur.

Key Points

Mild digestive issues are common: Temporary gas, bloating, or changes in bowel movements can occur as the gut adjusts to new probiotics.
Risk is higher for immunocompromised individuals: Patients who are critically ill, have weakened immune systems, or are premature infants face a rare but serious risk of infection from probiotics.
Allergies can be triggered: Some probiotic supplements may contain allergens like dairy or soy, while certain strains or fermented foods can produce histamine, causing allergy-like symptoms or headaches.
Start with a low dose: To minimize initial digestive side effects, gradually increasing the dosage allows your body to adjust more comfortably.
Consult a healthcare professional: Before taking probiotics, especially if you are in a high-risk group or have underlying health issues, it is essential to discuss it with a doctor.
Not all probiotics are created equal: As a dietary supplement, products are not heavily regulated by the FDA, making brand reputation and quality crucial for minimizing risks.
Watch for persistent symptoms: If mild digestive discomfort lasts for more than a few weeks or if you experience severe symptoms, stop taking the probiotic and seek medical advice.

Common, Mild Digestive Side Effects

For the majority of healthy individuals, the most frequently reported negative side effects of probiotics are mild and temporary digestive issues. These symptoms often arise as the gut microbiota adjusts to the new influx of beneficial bacteria and typically resolve within a few weeks of consistent use.

Gas and Bloating: As new probiotic strains begin to ferment carbohydrates in the intestine, an increase in gas production (hydrogen, methane, carbon dioxide) can lead to temporary feelings of gas and bloating.
Abdominal Discomfort: Mild cramping or general abdominal discomfort can accompany the initial changes in gut flora.
Changes in Bowel Habits: Some individuals may experience temporary constipation, thirst, or diarrhea as their system recalibrates.

To mitigate these initial effects, experts suggest starting with a lower dose of probiotics and gradually increasing it, allowing the body time to acclimate. Staying well-hydrated can also help alleviate some of the discomfort.

Rare, Serious Risks in Vulnerable Individuals

While probiotics are generally safe for the healthy population, they can pose a significant risk for those with weakened immune systems or serious underlying medical conditions. In these rare cases, the live bacteria or yeast in probiotics can enter the bloodstream and cause severe infections.

Populations at High Risk

Critically Ill Patients: Individuals in intensive care units (ICUs) or with prolonged hospitalizations are at higher risk of systemic infections like sepsis from probiotic translocation.
Immunocompromised Individuals: Patients with compromised immune systems due to conditions like HIV/AIDS, cancer (especially during chemotherapy), organ transplantation, or immunosuppressant drugs should exercise extreme caution.
Premature Infants: The U.S. Food and Drug Administration (FDA) has issued warnings regarding the use of probiotics in preterm infants due to reports of fatal infections and sepsis.
Post-Surgical Patients: Patients who have undergone recent surgeries, particularly involving the venous system, also face an elevated risk of infection.

Allergic and Histamine Reactions

Beyond gut-related issues, certain probiotics can trigger other adverse reactions, especially in sensitive people.

Headaches from Amines: Some probiotic-rich fermented foods like sauerkraut and kimchi naturally contain biogenic amines, such as histamine and tyramine. In individuals sensitive to these substances, consumption can trigger headaches or migraines. Some probiotic strains used in supplements can also produce histamine in the digestive tract, causing allergy-like symptoms like flushing, itching, or a runny nose. People with a histamine intolerance may need to avoid specific strains or opt for supplements over fermented foods.
Allergen Content in Supplements: It is crucial to read labels carefully, as many probiotic supplements contain common allergens such as dairy, soy, or eggs. People with allergies or lactose intolerance should choose products explicitly labeled as free from these ingredients. Yeast-based probiotics should also be avoided by those with yeast allergies.

Other Adverse Considerations

Antibiotic Resistance Transfer: Though rare, there is a theoretical risk that some probiotic strains could transfer antibiotic resistance genes to other bacteria in the gut, making future infections more difficult to treat. Reputable probiotic companies typically test for this risk, but unregulated supplements may be less trustworthy.
Metabolic Effects: Rare cases have reported unfavorable metabolic changes or unexpected weight fluctuations, though the mechanisms are not well understood.

Comparison of Probiotic Risks


Feature	Healthy Individuals	Immunocompromised/Critically Ill	Preterm Infants
Common Side Effects	Mild, temporary digestive issues (gas, bloating, discomfort).	Not applicable, as baseline risk is higher.	May experience digestive issues.
Serious Side Effects	Extremely low risk of systemic infection; generally considered safe.	Elevated risk of sepsis, bacteremia, or fungal infections; requires extreme caution.	Elevated risk of severe or fatal infections, including sepsis.
Allergic Reactions	Possible reactions to supplement ingredients (e.g., dairy, soy) or histamine in fermented foods.	Reactions to ingredients can still occur, and systemic infection risk outweighs other concerns.	Possible reactions to ingredients in supplements.
Recommendation	Safe to try, starting with a low dose; consult a doctor if side effects persist.	Do not take without strict medical supervision; often not recommended.	Should only be administered under medical guidance due to FDA warnings.

Conclusion

While probiotics can offer notable health benefits for many, including aiding digestion and bolstering the immune system, it is crucial to recognize that they are not without potential negative side effects. For healthy individuals, these effects are typically mild, temporary, and involve minor digestive discomfort. However, the risks become much more significant for those with compromised immune systems, critical illnesses, or premature infants, where life-threatening systemic infections are a real, albeit rare, danger. Always consult a healthcare provider before starting a probiotic regimen, especially if you have pre-existing health conditions, to ensure the potential benefits outweigh the risks. A personalized approach, informed by a medical professional, is the safest way to incorporate probiotics.

Note: Probiotics are not regulated by the FDA in the same way as drugs, so quality and contents can vary. Seeking reputable brands and professional advice is highly recommended.

For more information:

National Center for Complementary and Integrative Health: Probiotics

Frequently Asked Questions

Yes, it is common to experience temporary side effects like gas and bloating when you first start taking a probiotic supplement, as your gut adjusts to the new influx of bacteria.

People with weakened immune systems, those who are critically ill, and premature infants should avoid probiotics unless under strict medical supervision, as they face a higher risk of serious infections.

Yes, some probiotic-rich fermented foods and certain strains can produce biogenic amines, such as histamine, which may trigger headaches or migraines in sensitive individuals.

Mild digestive side effects like bloating and gas usually subside within a few weeks as your body gets used to the probiotic.

In rare cases and primarily in immunocompromised or critically ill individuals, the live microorganisms in probiotics can cause systemic infections or sepsis.

If you experience severe or persistent side effects, such as a fever, severe abdominal pain, or a rash, you should stop taking the probiotic and consult a healthcare provider immediately.

Yes, some people can have an allergic reaction to ingredients within a probiotic supplement, such as dairy or soy. It is important to read the label carefully if you have known allergies.

Giving probiotics to infants, especially preterm or low-birth-weight babies, carries risks of severe infection. Always consult a pediatrician before administering any probiotic to an infant.

While probiotics are often used to manage antibiotic-associated diarrhea, there is a rare risk of resistance gene transfer. Choosing reputable brands and discussing use with a doctor is recommended.