When should I not take probiotics? A comprehensive safety guide

November 15, 2025 •

3 min read

While generally safe for healthy individuals, rare but serious infections have been linked to probiotic use in vulnerable populations, including immunocompromised people and preterm infants. Knowing when to avoid probiotics is crucial for preventing severe complications and ensuring proper gut health.

Quick Summary

Probiotics, while often beneficial, pose risks for certain high-risk groups, including immunocompromised patients, the critically ill, and premature infants. Severe infections, antibiotic resistance transfer, and minor digestive side effects are potential concerns, necessitating caution and medical consultation before use.

Key Points

Immunocompromised Individuals: Avoid probiotics due to heightened risk of life-threatening systemic infections like sepsis.
Preterm Infants: Do not give probiotics to premature infants due to documented cases of fatal infections and FDA warnings.
Post-Surgery Patients: Consult a doctor before taking probiotics after major surgery due to risks like bacteremia or bowel ischemia.
Pre-existing Allergies: Be aware of potential adverse reactions from certain probiotic strains or supplement ingredients if you have allergies or histamine intolerance.
Minor Side Effects: Persistent digestive discomfort like bloating or gas in healthy people should prompt consultation.
Lack of Regulation: Be aware that the supplement industry lacks strict FDA regulation, impacting product quality and safety for vulnerable groups.

Who Needs to Exercise Caution with Probiotics?

Probiotics are beneficial bacteria and yeasts that are widely available and marketed for improving gut health and supporting the immune system. However, they are not universally safe, and certain individuals should avoid them, especially in supplement form, unless under direct medical supervision.

The Immunocompromised and Critically Ill

Individuals with a weakened immune system due to medical conditions or treatment are at significant risk.

Risk of systemic infection: Probiotic bacteria or fungi can enter the bloodstream and cause opportunistic infections like sepsis or fungemia in immunocompromised patients. A healthy immune system would normally clear these microbes, but a weakened one may not, leading to life-threatening complications. {Link: Drugs.com https://www.drugs.com/npp/probiotics.html}. The PROPATRIA trial indicated increased mortality in critically ill patients with severe acute pancreatitis given probiotics. Patients on immunosuppressants after an organ transplant face a heightened risk of infection.

Preterm Infants

Preterm infants, particularly those with very low birth weight, are a vulnerable population where probiotic use is risky. The FDA has warned healthcare providers about the risk of invasive, potentially fatal disease in preterm infants given probiotics. Cases of fatal sepsis have been linked to probiotic strains in this group. Their immature gut barriers and underdeveloped immune systems make them susceptible.

Patients Recovering from Major Surgery

Postoperative patients, especially after major abdominal surgery, should be cautious. Compromised gut barrier integrity can increase the risk of bacteria entering the bloodstream. Case reports of infection like bacteremia and endocarditis have been reported in surgical patients using probiotics. The PROPATRIA trial suggested high-dose probiotics might increase gut oxygen demand, potentially causing bowel ischemia in critically ill patients, a risk relevant to complex surgical cases.

Individuals with Existing Allergies or Sensitivities

Individuals with allergies or sensitivities should be aware of potential issues. Certain strains can produce histamine, potentially triggering headaches or allergy-like symptoms. Fermented foods with probiotics are rich in biogenic amines, which can cause headaches in susceptible people. Contamination with allergens like dairy, soy, or eggs can also occur during manufacturing.

Potential Complications of Probiotic Use

Other potential complications include:

Antibiotic resistance transfer: A rare theoretical risk exists where probiotic bacteria might transfer antibiotic-resistant genes to harmful bacteria.
Excessive immune stimulation: For individuals with autoimmune diseases, probiotics could theoretically cause excessive immune stimulation.
Gut-related side effects: Temporary gas, bloating, or stomach discomfort can occur when starting probiotics, usually subsiding. Persistent symptoms warrant consulting a healthcare provider.
Brain fogginess: An association between probiotics and brain fogginess has been noted in some individuals with SIBO.

Comparison of Probiotic Risks: Healthy vs. High-Risk Individuals


Feature	Healthy Individuals	High-Risk Individuals (e.g., Immunocompromised, Preterm Infants)
Likelihood of Serious Infection	Extremely low due to a healthy immune system.	High; systemic infections like sepsis can occur if microbes enter the bloodstream.
Common Side Effects	Mild and temporary digestive issues as the gut adjusts.	Gastrointestinal issues may be more persistent or severe. Infection risk is paramount.
Allergic Reactions	Low risk, but possible from certain strains or ingredients.	Heightened risk due to compromised immunity and potential for cross-contamination.
Risk of Antibiotic Resistance Transfer	Theoretical and low risk.	Potential risk exists, particularly with overuse of supplements.
Professional Oversight	Often taken without medical guidance.	Medical consultation is essential and use should be under strict supervision.

Conclusion

While generally safe for healthy adults, probiotics pose risks for certain individuals. High-risk groups, including the immunocompromised, premature infants, and those recovering from major surgery, should avoid probiotics unless medically instructed and monitored due to the risk of serious infection. Healthy individuals should be aware of potential side effects and consider dietary sources as a safer alternative. The decision to take probiotics requires considering individual health status and risks. Consulting a healthcare professional before starting any new supplement is always recommended, especially for those with existing health conditions. For information on product safety and regulations, refer to the FDA's warnings.

Frequently Asked Questions

You should not take probiotics after major surgery unless explicitly approved by your doctor. Surgery can compromise the intestinal barrier, and probiotics introduce a risk of systemic infection, especially for critically ill patients.

The risks include potentially fatal systemic infections, such as sepsis, because premature infants have immature gut barriers and weak immune systems. The FDA has issued strong warnings advising against this practice.

Individuals with autoimmune diseases should be extremely cautious and consult their doctor before taking probiotics. Their already overactive immune system could be excessively stimulated by the supplement, leading to potential complications.

Yes, probiotics can interact with medications. For example, antibiotics can kill the beneficial bacteria in probiotics, so they should be taken at different times of the day. If you are on immunosuppressants, you should avoid probiotics.

If initial, temporary side effects like bloating or gas persist for more than a few weeks, you should stop taking the probiotic. Consult your healthcare provider, who may recommend a different strain or dose, or investigate for an underlying condition.

For most healthy people, the risk of infection is very low. However, in individuals with compromised immune systems, the risk is significantly higher. Cases of sepsis and other serious infections have been reported in vulnerable populations.

For healthy individuals, consuming a balanced diet rich in prebiotic fiber and probiotic-rich foods like yogurt, kefir, and sauerkraut is often sufficient and safer than supplements. You may not need a supplement unless a doctor recommends it for a specific condition.