What's the downside of probiotics? A balanced look at risks and side effects

October 9, 2025 •

4 min read

While often praised for their benefits to gut health and immunity, an estimated 1 in 1,000,000 people who take probiotics containing Lactobacilli may develop an infection. This sheds light on the crucial and often overlooked question: What's the downside of probiotics?

Quick Summary

Probiotics can cause temporary digestive issues and, in rare instances, carry more serious risks for vulnerable groups. Understanding these potential downsides is key to safe consumption and optimal health outcomes.

Key Points

Temporary Digestive Issues: Minor side effects like bloating, gas, and mild diarrhea are common, especially when starting a new probiotic, but they typically resolve within a few weeks.
Serious Infection Risk: Immunocompromised individuals, premature infants, and the critically ill face a small but serious risk of infection or sepsis due to probiotic bacteria entering the bloodstream.
Potential for Antibiotic Resistance: A rare but theoretical risk exists for the transfer of antibiotic-resistant genes from probiotic bacteria to more harmful pathogens in the gut.
Histamine-Related Side Effects: Some probiotic-rich foods or strains produce histamine, which can cause headaches or allergy-like symptoms in sensitive people with histamine intolerance.
Product Quality Varies: Many supplements are not strictly regulated by the FDA, leading to potential mislabeling or contamination. Choosing reputable brands with third-party testing is crucial.
D-Lactic Acidosis Risk: A very rare metabolic issue, where certain probiotic strains cause an excess buildup of D-lactic acid. This is primarily a concern for individuals with short bowel syndrome.
Strain Specificity is Key: The effects and safety profile of probiotics differ significantly between strains. A positive effect from one strain does not guarantee the same for another.

Common and Temporary Digestive Discomfort

For most healthy people, the most common downsides of probiotics are minor and temporary gastrointestinal symptoms, which occur as the body adjusts to the new microbial population. These side effects typically appear shortly after beginning supplementation and usually resolve within a few weeks.

Bloating and Gas: The introduction of new bacteria and yeasts can increase gas production in the gut as they ferment carbohydrates, leading to temporary bloating and flatulence.
Mild Diarrhea or Constipation: Some people may experience changes in bowel habits, such as soft stools, mild diarrhea, or even temporary constipation. This often resolves as the gut microbiome reaches a new equilibrium.
Stomach Upset: A general feeling of stomach upset or abdominal discomfort is also a possibility, especially with higher doses.

If these symptoms persist beyond a few weeks, it may be a sign that the specific probiotic strain or dosage is not a good fit for your body, and you should consider consulting a healthcare provider.

Serious and Rare Health Risks

While the general population tolerates probiotics well, certain individuals face a higher, albeit still low, risk of more serious complications. Health authorities like the U.S. Food and Drug Administration (FDA) have issued warnings regarding these risks.

Risk of Systemic Infection and Sepsis

For people with compromised immune systems, the bacteria or yeast in probiotics can enter the bloodstream and cause potentially life-threatening infections like sepsis. This is most relevant for vulnerable groups, including:

Premature infants
Critically ill hospital patients
Individuals with severely weakened immune systems (e.g., due to chemotherapy or HIV)
Those with central venous catheters
Patients with badly damaged or "leaky" gastrointestinal tracts

Antibiotic Resistance Transfer

A theoretical risk exists that antibiotic-resistant genes present in probiotic bacteria could transfer to pathogenic bacteria in the gut, potentially creating new, more dangerous antibiotic-resistant pathogens. While rare and not fully understood, this concern highlights the importance of choosing probiotics from reputable manufacturers that rigorously test their products.

Strain-Specific Side Effects and Individual Sensitivity

Not all probiotics are created equal. The effects can be highly specific to the genus, species, and strain, and individual biochemistry plays a significant role in response.

Histamine Intolerance

Certain probiotic-rich foods (like some yogurts and fermented cheeses) and specific strains (Lactobacillus buchneri, Lactobacillus helveticus) produce biogenic amines, including histamine. Individuals with histamine intolerance lack sufficient enzymes to break down this excess histamine, which can lead to headaches, skin rashes, or allergy-like symptoms.

Small Intestinal Bacterial Overgrowth (SIBO)

Probiotics are not always recommended for individuals with Small Intestinal Bacterial Overgrowth (SIBO). Some studies have linked probiotic use to symptoms like brain fogginess and worsened digestive issues in SIBO patients, which improved after stopping the supplements and receiving antibiotics.

Product Quality and Contamination Concerns

Because many probiotics are sold as dietary supplements, they are not regulated by the FDA with the same stringency as prescription medications. This can lead to inconsistencies in product quality, including:

Contamination: A product may contain undeclared microorganisms or harmful contaminants that pose serious health risks.
Mislabeling: The product may contain different strains or a lower number of live Colony Forming Units (CFUs) than stated on the label.
Uncertain Efficacy: The specific strains and dosages used in a supplement may not have robust scientific evidence to support the claimed health benefits.

Navigating the Downsides: A Comparison of Risks


Aspect	Common, Temporary Side Effects	Rare, Serious Risks
Symptom Examples	Bloating, gas, diarrhea, constipation	Systemic infection, sepsis, endocarditis, SIBO exacerbation
Likelihood	Occasional, especially at the start of treatment	Very low, particularly in healthy individuals
Affected Population	Most people, but typically resolves quickly	Critically ill, immunocompromised, premature infants, recent surgery patients
Cause	Gut microbiome adjusting to new bacteria; initial increased gas production	Bacterial or yeast translocation into the bloodstream; presence of underlying health issues

How to Minimize the Risks of Probiotics

To safely incorporate probiotics into your diet, consider the following steps:

Consult a Healthcare Provider: Before starting any new supplement, especially if you have underlying health conditions, are pregnant, or are considering giving it to an infant, speak with a doctor.
Start with a Low Dose: Begin with a smaller dosage and gradually increase it to the recommended amount. This allows your body to adjust and minimizes temporary digestive upset.
Choose Reputable Brands: Look for probiotics from trusted companies that provide transparent labeling and conduct independent, third-party testing for purity and potency.
Check Ingredients Carefully: Read the label for potential allergens like dairy, soy, or gluten if you have sensitivities. If you have a histamine intolerance, avoid fermented foods or supplements with known histamine-producing strains.
Take Probiotics at the Right Time: If taking antibiotics, space out your probiotic dose by at least 2-3 hours to ensure the live cultures are not destroyed.
Listen to Your Body: If side effects are persistent or severe, stop taking the probiotic and seek medical advice.

Conclusion: Weighing the Risks and Benefits

For the vast majority of healthy individuals, the potential downsides of probiotics are minor, temporary, and manageable, often resolving within a few weeks of starting. However, for vulnerable populations such as the immunocompromised, premature infants, and those with severe illnesses, the risk of serious infection, though rare, is a critical consideration. The efficacy and safety profile are also highly dependent on the specific strain, dosage, and product quality.

Ultimately, understanding the full spectrum of potential effects—from temporary bloating to rare systemic infections—is essential for making an informed decision about whether probiotics are right for you. A balanced perspective that acknowledges the potential risks, alongside the possible benefits, is the best approach to incorporating probiotics into a nutritional diet. This empowers individuals to make informed choices with the guidance of a healthcare professional. For more information, the National Center for Complementary and Integrative Health is a reliable resource.

Frequently Asked Questions

The most common side effects are temporary digestive issues like gas, bloating, and mild abdominal discomfort, which usually subside within a few weeks as your body adjusts.

Individuals who are immunocompromised, critically ill, have had recent surgery, or are premature infants should be highly cautious and consult a doctor, as they are at a higher risk of infection.

Yes, especially with antibiotics. Live-bacteria probiotics should be taken at least 2-3 hours before or after antibiotics to prevent the antibiotic from killing the beneficial bacteria.

Yes, though rare, allergic reactions can occur. Some supplements contain allergens like dairy or soy. Certain strains can also produce histamine, causing allergy-like symptoms in sensitive individuals.

This is a theoretical risk where antibiotic resistance genes from probiotic strains could transfer to pathogenic bacteria in the gut. While rare, buying from reputable sources can help mitigate this concern.

Initially, yes. When introducing new bacteria to your gut, it can increase gas production and cause temporary bloating. This should resolve as your microbiome adapts.

If side effects like bloating, gas, or diarrhea continue for more than a few weeks, or if you experience more serious symptoms, you should stop taking the probiotic and seek medical advice.