Is Enterococcus faecium safe in probiotics?

December 10, 2025 •

4 min read

While the Enterococcus genus includes both beneficial commensals and dangerous pathogenic species, regulatory bodies have established stringent guidelines to ensure that only specific, non-virulent E. faecium strains are used in commercial probiotic products. This dual nature requires a careful, strain-specific approach to safety.

Quick Summary

The safety of Enterococcus faecium in probiotics is highly dependent on the specific strain, with commercial versions undergoing strict safety assessments to lack pathogenic traits and antibiotic resistance genes.

Key Points

Strain-Specificity is Key: The safety of E. faecium is entirely dependent on the specific strain, as the species includes both harmless gut commensals and dangerous hospital pathogens.
Rigorous Safety Screening: Commercial probiotic strains of E. faecium are subjected to extensive testing to ensure they lack genes for virulence and transferable antibiotic resistance.
Risks for Vulnerable Patients: While safe for most, critically ill or immunocompromised individuals face a theoretical, low risk of systemic infection from live probiotics, including E. faecium.
Horizontal Gene Transfer Concerns: The primary risk of E. faecium is its potential for genetic exchange, which could theoretically transfer antibiotic resistance genes to other bacteria, though probiotic strains are screened to avoid this.
Benefits of Safe Strains: Properly vetted strains of E. faecium have demonstrated health benefits, such as supporting gut barrier function, modulating immunity, and inhibiting harmful bacteria.
Distinguish Clinical vs. Probiotic: It is essential to differentiate between the harmful, multi-drug resistant E. faecium strains found in hospitals and the beneficial strains found in safe, commercial probiotic products.

The Dual Nature of Enterococcus

The genus Enterococcus is a fascinating yet complex group of bacteria found widely in the environment and the gastrointestinal tracts of humans and animals. However, this genus contains a troubling dichotomy: while some species are harmless and offer probiotic benefits, others have emerged as notorious opportunistic pathogens, particularly in hospital settings. Enterococcus faecium is one such species that sits on this fence, making it crucial to distinguish between safe, commercial probiotic strains and their harmful clinical counterparts.

Why Pathogenic Strains are a Concern

Pathogenic strains of E. faecium are a significant cause of hospital-acquired infections, such as urinary tract infections (UTIs), bacteremia (bacteria in the bloodstream), and endocarditis. Their ability to cause illness is often linked to the acquisition of virulence factors and, most critically, widespread antibiotic resistance. Vancomycin-resistant Enterococcus (VRE) is a well-known example of a highly resistant, hospital-associated pathogen that poses a serious threat to patient health. The potential for genetic material transfer, including antibiotic resistance genes, between different Enterococcus strains is a major safety concern.

The Rigorous Screening Process for Probiotic Strains

To address safety concerns, specific E. faecium strains intended for use in probiotics must undergo extensive evaluation, far exceeding the general safety reputation of the genus. Regulatory bodies, like those that guide European food safety, have established clear criteria for approval. These tests ensure that commercial strains are free from harmful characteristics.

Here is a list of the rigorous criteria used to evaluate potential probiotic strains:

Absence of Virulence Genes: The strains are specifically screened to ensure they do not carry genes known to encode toxins, adhesins, or other factors associated with pathogenicity.
Antibiotic Susceptibility: Probiotic strains must not possess transferable antibiotic resistance genes. This prevents the spread of resistance to other bacteria, a phenomenon known as horizontal gene transfer.
Genomic Analysis: Advanced whole-genome sequencing is used to compare a candidate strain's genetic makeup against known pathogenic isolates, confirming it belongs to a safe lineage.
Functional Assessment: In addition to genetic screening, tests are performed to confirm the absence of harmful activities like excessive immune stimulation, especially in vulnerable individuals.
Clinical Efficacy and Safety: Many strains, like E. faecium CRL 183, have their safety and benefits documented through in vivo and clinical studies.

Benefits Associated with Safe E. faecium Strains

For healthy individuals, properly screened E. faecium probiotic strains can offer several health benefits. Research, including animal studies and some human trials, indicates a positive effect on gut health and immune function. These benefits are distinct from the risks posed by pathogenic strains.

Supports Gut Barrier Function: Some strains can help fortify the gut mucosal barrier, improving its integrity and protecting against pathogens.
Enhances Nutrient Absorption: In animal studies, certain E. faecium strains have improved feed efficiency and nutrient utilization.
Stimulates Immune Response: Studies suggest that safe strains can modulate the immune system, inducing an anti-inflammatory response and improving overall immune function.
Inhibits Pathogens: Certain probiotic E. faecium strains, such as CRL 183, produce antibacterial compounds (bacteriocins) that can inhibit the growth of harmful bacteria like Staphylococcus aureus and Salmonella.

Comparison of Probiotic and Clinical Enterococcus faecium


Feature	Probiotic E. faecium	Clinical E. faecium (e.g., VRE)
Source	Carefully selected and screened; food, animal, or human origin.	Isolated from hospital-acquired infections in immunocompromised patients.
Antibiotic Resistance	Screened to be susceptible to common antibiotics; must not carry transferable resistance genes.	Frequently resistant to multiple antibiotics, including vancomycin.
Virulence	Must lack virulence factors and genes that promote infection.	Carries multiple virulence genes and is a major cause of opportunistic infections.
Risk to Healthy Individuals	Generally considered safe, with side effects being rare and mild (e.g., gas, bloating).	Poses a significant infectious risk, especially in healthcare settings.
Risk to Vulnerable Patients	Caution advised for immunocompromised or critically ill patients.	Highest risk to immunocompromised, elderly, or critically ill individuals.

Special Considerations for Vulnerable Populations

While the risk of infection from probiotic E. faecium is extremely low for healthy individuals, people who are immunocompromised, critically ill, or who have impaired intestinal barriers should exercise caution. Some case reports link probiotics in general to systemic infections in high-risk individuals. The Norwegian Scientific Committee for Food Safety, for example, has concluded that probiotics should not be used in critically ill patients, including those with severe pancreatitis or other conditions that compromise gut integrity. This is not a risk specific to E. faecium, but a general concern for all live probiotics in certain medical contexts.

Conclusion: Safety is Strain-Dependent

The question of whether Enterococcus faecium is safe in probiotics has a definitive answer: yes, for specific, well-screened strains used in commercial products by healthy individuals. The safety relies heavily on the manufacturer's due diligence in selecting a strain that lacks antibiotic resistance genes and virulence factors. However, the existence of virulent and drug-resistant clinical strains means that not all bacteria of this species are benign. Consumers should ensure they are using products with well-documented, specific strains. Vulnerable populations, such as the critically ill or immunocompromised, should consult a healthcare professional before taking any probiotic to assess potential risks. For additional context on probiotic safety, one can refer to the National Institutes of Health.

Frequently Asked Questions

Concerns arise because the Enterococcus genus includes some species that are opportunistic pathogens, particularly in hospital settings, where they can cause serious, drug-resistant infections. The key is to distinguish between safe probiotic strains and these dangerous variants.

Probiotic strains are specifically selected and rigorously screened by manufacturers and regulatory bodies. This process ensures they do not contain genes for virulence or transferable antibiotic resistance, minimizing risks for the consumer.

While the screened probiotic strains do not possess these genes, the theoretical risk of horizontal gene transfer (acquiring genes from other bacteria in the gut) is a major reason for the strict safety screening process.

VRE are pathogenic strains of Enterococcus found primarily in hospital environments and are highly resistant to antibiotics. Safe probiotic E. faecium strains are explicitly screened to be susceptible to vancomycin and other key antibiotics.

People who are immunocompromised, critically ill, or who have compromised intestinal barriers should consult a healthcare provider before use. While generally safe for healthy individuals, risks are higher for these vulnerable groups.

Benefits can include supporting a healthy gut barrier, modulating the immune system, producing antimicrobial compounds, and inhibiting the growth of certain harmful bacteria.

No. Safety is completely strain-dependent. Manufacturers must clearly state the specific strain (e.g., SF68) and provide evidence of its safety and efficacy. Choosing a product from a reputable company is key.

For healthy individuals, minor gastrointestinal side effects like gas, bloating, or mild cramping are possible, as with any probiotic. Serious adverse effects are extremely rare.