Who Should Not Take Prebiotics and Probiotics?

December 12, 2025 •

2 min read

While generally considered safe for healthy adults, research shows that prebiotics and probiotics can pose serious risks for certain individuals. It is crucial to understand who should not take prebiotics and probiotics and when to consult a healthcare provider before adding these supplements to your routine.

Quick Summary

This guide outlines specific health conditions and situations where prebiotics and probiotics should be avoided or used with extreme caution to prevent adverse health events. It details the risks for vulnerable populations, including people with compromised immunity, severe illnesses, and certain gastrointestinal disorders.

Key Points

Immunocompromised Individuals: People with weakened immune systems from conditions like HIV/AIDS, cancer, or organ transplants face a higher risk of serious infection from probiotic bacteria.
Critically Ill Patients: Those in intensive care units (ICU) or recovering from major surgery should avoid probiotics due to the risk of bacteremia or sepsis.
Severe Acute Pancreatitis: Probiotics are contraindicated for patients with severe acute pancreatitis due to a documented increase in mortality risk.
Small Intestinal Bacterial Overgrowth (SIBO): Individuals with SIBO should be cautious with both prebiotics and probiotics, as they can exacerbate symptoms like bloating and gas. Specific guidance from a doctor is necessary.
Inflammatory Bowel Disease (IBD) : The use of probiotic supplements for IBD (Crohn's and ulcerative colitis) is not recommended, particularly during active inflammation, due to insufficient evidence and potential risk.
Allergy and Sensitivity: People with severe allergies should check for potential allergens in supplement ingredients. Some fermented foods or specific probiotic strains can also trigger reactions.
Potential Antibiotic Interaction: In some cases, probiotic supplements may contain bacteria that could transfer antibiotic-resistant genes to other gut flora, a concern that warrants caution.

Understanding Prebiotics and Probiotics

Probiotics are live microorganisms that, when consumed in adequate amounts, can provide health benefits by improving the balance of the gut microbiota. They are found in fermented foods like yogurt and kimchi, as well as in dietary supplements. Prebiotics, on the other hand, are non-digestible fibers that act as food for the beneficial bacteria in your gut. They are present in foods like garlic, onions, and asparagus. While often beneficial, their use is not universal and can be dangerous for certain individuals.

Vulnerable Populations Who Should Avoid Probiotics

Immunocompromised Individuals

Individuals with weakened immune systems due to conditions or treatments are at a higher risk of infection from the bacteria in probiotic supplements. This includes patients undergoing chemotherapy or those with HIV/AIDS or who are organ transplant recipients. Critically ill patients and premature infants also face risks.

Individuals with Certain Gastrointestinal Disorders

Certain gut conditions can be worsened by or do not benefit from probiotics. This includes Small Intestinal Bacterial Overgrowth (SIBO) where adding more bacteria can potentially worsen symptoms. Prebiotics can also worsen SIBO symptoms. Probiotics are not generally recommended for people with IBD.

Comparison of Risks for General and High-Risk Populations


Feature	Healthy Individuals	Immunocompromised/High-Risk Individuals
Primary Risk	Mild, temporary digestive discomfort (gas, bloating) as the body adjusts.	Serious infections, including sepsis and bacteremia, due to compromised immunity.
Underlying Condition	Generally no serious health issues affecting the immune system.	Conditions like cancer, HIV/AIDS, or recent major surgery.
Effect on Gut Barrier	Strong intestinal barrier prevents bacteria from entering the bloodstream.	Weakened gut barrier, allowing translocation of bacteria and causing systemic infection.
Standard of Care	Can be taken for general wellness and some mild issues without direct medical oversight.	Must only be taken under the direct supervision and recommendation of a medical professional.
Regulation Status	Over-the-counter supplements are not strictly regulated, so product quality can vary.	Safety and efficacy are more critically assessed, often requiring specific, pharmaceutical-grade formulas and close monitoring.

Additional Considerations and Side Effects

Individuals with severe allergies should check supplement labels for allergens like dairy, soy, or gluten. Rarely, probiotic strains or fermented food components can cause allergic reactions. There is also some research suggesting a concern about the potential for antibiotic-resistant genes in probiotic strains to transfer to harmful gut bacteria. Avoiding prebiotics with certain GI conditions like SIBO is recommended as they can increase gas and bloating. A low-FODMAP diet may be recommended in such cases.

The Need for Professional Guidance

Determining the safety of prebiotics and probiotics requires considering individual health profiles. Those with underlying health conditions, especially compromised immune systems, must consult a doctor. For healthy individuals, obtaining prebiotics from whole foods is generally a safe and effective approach to gut health.

Conclusion

Prebiotics and probiotics are not suitable for everyone. Individuals with severely compromised immune systems, critical illness, premature infants, and those with specific gastrointestinal disorders face significant risks. Always consult a healthcare provider before taking these supplements, especially with existing health conditions.

Frequently Asked Questions

No, if you are on chemotherapy, you should generally not take probiotic supplements without strict medical supervision. Chemotherapy suppresses the immune system, and live bacteria in probiotics could cause a serious infection.

The relationship between SIBO and probiotics is complex. Some conventional thought advises against them as they can worsen overgrowth symptoms. However, newer research shows that specific strains might be beneficial. It is crucial to consult a healthcare provider for personalized guidance.

Critically ill patients, particularly those in the ICU or recovering from major surgery, may have a compromised gut barrier. This increases the risk of probiotic bacteria entering the bloodstream and causing life-threatening infections like sepsis.

Prebiotics are non-digestible fibers that feed gut bacteria. For someone with Small Intestinal Bacterial Overgrowth (SIBO), adding more 'food' for bacteria in the small intestine can increase fermentation, leading to worsening gas, bloating, and discomfort.

Yes, although it is rare. Allergic reactions are typically caused by other ingredients in supplements, such as dairy or soy. However, some individuals may have sensitivities to specific probiotic strains or fermented foods. Always check labels and consult a doctor if you have known allergies.

While some studies have not shown adverse effects, there is a lack of conclusive data regarding the safety and efficacy of many strains during pregnancy. Some doctors advise caution, and pregnant women should always consult their doctor before starting any new supplement.

Worsening symptoms like bloating, gas, or headaches can occur, especially in the first few days as your gut adjusts. If these symptoms persist or worsen, or if you develop any severe reactions, stop taking the supplement and consult your healthcare provider. It may indicate an underlying issue or an unsuitable strain.