What are the negative side effects of taking probiotics? A Look at the Risks

October 5, 2025 •

3 min read

While typically safe for healthy individuals, probiotics can sometimes cause unwanted side effects, which can range from mild digestive discomfort to, in rare cases, serious complications in high-risk patients. Understanding what are the negative side effects of taking probiotics is essential before beginning supplementation, especially for those with underlying health conditions.

Quick Summary

Probiotics can cause temporary digestive issues like gas and bloating. In rare instances, they pose a risk of infection for immunocompromised individuals and may trigger allergic reactions in sensitive people.

Key Points

Initial Discomfort: Temporary gas, bloating, and digestive upset are the most common side effects as the gut adjusts to new bacteria.
Rare Infection Risk: Individuals with compromised immune systems, critical illness, or central venous catheters face a rare but serious risk of systemic infection from probiotics.
Histamine Issues: Certain probiotic strains can produce histamines, which may cause headaches, rashes, or allergic-like symptoms in sensitive individuals.
Vulnerable Populations: Premature infants and critically ill patients should only take probiotics under strict medical supervision due to heightened risks.
Check for Allergens: Some supplements contain common allergens like dairy or soy, which can trigger adverse reactions in intolerant individuals.
Consult a Professional: Discussing probiotic use with a healthcare provider is essential to weigh the benefits against the risks, especially if you have pre-existing conditions.

Understanding the Most Common Side Effects

For most people, probiotics are well-tolerated, and any side effects are mild and temporary. The most frequent issues are linked to the body adjusting to changes in the gut microbiome. These typically subside as the body becomes accustomed to the new microbial balance.

Gastrointestinal Upset

Initial probiotic supplementation can lead to a temporary increase in gas and bloating. Other digestive symptoms that may occur include:

Abdominal pain or cramping
Diarrhea or changes in stool consistency
Increased thirst, especially with yeast-based probiotics

These effects are generally short-lived, resolving within a few weeks of consistent use. If symptoms persist, it is advisable to consult a healthcare provider.

Allergic Reactions and Histamine Intolerance

Though rare, some individuals may experience allergic reactions to probiotics, which can be linked to ingredients in the supplement, such as dairy, soy, or eggs. More specifically, some probiotic strains can increase histamine levels in the digestive tract, potentially causing issues for those with histamine intolerance. This can manifest as:

Headaches or migraines from biogenic amines in fermented foods
Skin rashes or itchiness
Watery eyes or a stuffy nose

If you have a known histamine intolerance or experience these symptoms, consider switching strains or choosing a supplement-based probiotic over fermented foods.

The Critical Concerns: When Probiotics Can Be Dangerous

While the risks are low for healthy individuals, certain populations face more significant dangers from probiotic use. This is primarily due to a compromised immune system or a weakened intestinal barrier that can allow beneficial bacteria to become opportunistic pathogens.

Increased Risk of Infection

In rare cases, the live bacteria or yeast in probiotics can enter the bloodstream and cause serious, systemic infections, such as sepsis. This risk is heightened in individuals who are:

Immunocompromised, such as those with HIV/AIDS, cancer (undergoing chemo/radiotherapy), or certain autoimmune diseases
Critically ill patients in the hospital or ICU
Premature infants, who have particularly vulnerable immune and digestive systems
Individuals with a venous catheter
Those who have recently undergone surgery

It is crucial that these high-risk groups only use probiotics under strict medical supervision.

Potential for Antibiotic Resistance Gene Transfer

Some probiotic bacteria naturally carry antibiotic-resistant genes, which is not harmful on its own. However, there is a theoretical risk that these genes could be transferred to other bacteria in the gut, including harmful ones. While more research is needed, this poses a long-term public health concern regarding the potential for increasing antibiotic resistance.

SIBO and Metabolic Consequences

Excessive probiotic use or specific strains can lead to small intestinal bacterial overgrowth (SIBO), a condition where bacteria from the large intestine colonize the small intestine. This can cause persistent gas, bloating, and even "brain fog" in some people. Additionally, some probiotics can produce D-lactic acid, which can cause D-lactic acidosis in susceptible individuals, especially those with short bowel syndrome.

Comparing Common vs. Severe Probiotic Side Effects


Aspect	Common Side Effects	Severe Side Effects (Rare)
Nature	Temporary and mild	Persistent and potentially life-threatening
Symptom examples	Gas, bloating, diarrhea, stomach discomfort	Systemic infection (sepsis), allergic reaction, D-lactic acidosis
Timeline	Occur during initial weeks, resolve with continued use	Can occur at any point, especially in vulnerable individuals
Resolution	Often self-resolves; may require dosage adjustment	Requires immediate medical attention and discontinuation of probiotics
Affected population	Healthy individuals starting probiotics or new strains	Immunocompromised, premature infants, critically ill patients, specific GI conditions

Conclusion: Navigating Probiotic Use Responsibly

While probiotics offer a range of potential health benefits, it is vital to approach their use with an understanding of the potential negative side effects, particularly for those in high-risk categories. For most healthy adults, adverse effects are minor and temporary, typically consisting of mild digestive discomfort as the body's microbiota adjusts. However, the rare but serious risks of systemic infection, especially for immunocompromised individuals, underscore the importance of medical consultation before beginning a supplement regimen. Always read product labels carefully, consider starting with a low dose, and consult a healthcare provider if you experience persistent or worrying symptoms. Prioritizing safety through informed decision-making ensures that you can maximize the benefits of probiotics while minimizing potential risks.

For more information on the safety and efficacy of probiotics, you can refer to authoritative sources 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 you first start taking probiotics. These symptoms usually subside as your body adjusts to the new microbial balance.

Probiotics should be avoided or taken only under medical supervision by those with weakened immune systems, critically ill patients, premature infants, and people with venous catheters or recent surgery.

Allergic reactions to the probiotic bacteria themselves are rare. However, reactions can occur due to other ingredients in the supplement, such as dairy, soy, or eggs. Individuals with histamine intolerance may also react poorly to certain strains.

Yes, some probiotic-rich foods contain biogenic amines like histamine, which can trigger headaches in sensitive people. In such cases, a supplement might be a better option than fermented foods.

For healthy people, the risk of infection is extremely low. The risk is primarily for high-risk individuals, such as the immunocompromised, where probiotics can rarely cause systemic infections like sepsis if bacteria enter the bloodstream.

Taking probiotics with antibiotics is often recommended to help restore gut flora, but there is a theoretical concern about the transfer of antibiotic resistance genes. It is best to space out the doses and consult a doctor.

Most mild digestive side effects, such as gas and bloating, resolve within a few weeks as your body adapts. If symptoms persist or worsen, you should stop taking the probiotic and seek medical advice.