Enterococcus faecalis is a bacterium that naturally lives in the human gut, mouth, and female genital tract, where it usually plays a helpful role by supporting digestion and competing with harmful microbes (De Almeida et al., 2018). Some strains are even used as probiotics because they can block pathogens and influence immune function (Fidanza et al., 2021).

However, E. faecalis can also cause illness if it moves outside the gut or if the balance of the microbiome is disturbed, such as after antibiotic use. In these cases, it may cause infections in the urinary tract, wounds, or even the heart (endocarditis) (Cheng et al., 2022). Some strains also carry antibiotic resistance genes, which makes them harder to treat and raises safety concerns when used in foods or supplements.

✔ What it is: A bacterium that naturally lives in the human gut, mouth, and female genital tract.

✔ Role in health: Helps with digestion, competes with harmful microbes, and can support immune function.

✔ Probiotic use: Some strains are used in probiotic products, though safety depends on strain-specific traits.

✔ When harmful: Can cause infections (e.g., urinary tract, wound, or heart infections) if it spreads outside the gut or if the microbiome balance is disturbed.

✔ Antibiotic resistance: Some strains carry resistance genes, making certain infections harder to treat.

✔ Transmission: Can spread through contaminated food, water, surfaces, or person-to-person contact, especially in healthcare settings.

Enterococcus faecalis is a Gram-positive lactic acid bacterium commonly found in the human gastrointestinal tract, where it can play both beneficial and potentially harmful roles. In a healthy gut, E. faecalis contributes to maintaining microbial balance by producing bacteriocins, organic acids, and hydrogen peroxide, which inhibit pathogenic bacteria (De Almeida et al., 2018; Hu et al., 2022). Certain strains have shown probiotic potential, including supporting digestion, modulating immune function, and enhancing gut barrier integrity (Zommiti et al., 2022). These properties make it a valuable member of the microbiome when present in balanced amounts.

However, E. faecalis can become opportunistic, particularly in immunocompromised individuals, where overgrowth or pathogenic strains may contribute to infections or even play a role in colorectal cancer development through genotoxic effects (De Almeida et al., 2018). Its dual nature highlights the importance of maintaining healthy levels. Gut microbiome testing with Epicentre can help identify imbalances, allowing targeted interventions such as dietary adjustments, probiotics, or clinical treatment to support beneficial strains while managing harmful ones.

Unhealthy Enterococcus faecalis levels can cause a wide range of symptoms depending on whether the bacteria are overgrowing or causing an infection. When it becomes too abundant or moves outside the gut, it can cause urinary tract infections, bloodstream infections, or wound infections (Fiore et al., 2019; De Almeida et al., 2018). Gut-related symptoms may include diarrhoea, bloating, abdominal discomfort, and changes in bowel habits, often linked to an imbalance in the gut microbiome (Fiore et al., 2019).

In more severe cases, pathogenic strains of E. faecalis can produce harmful substances like cytolysin and gelatinase, which damage tissues and contribute to conditions such as endocarditis (heart valve infection) and, in rare cases, may play a role in colorectal cancer development by producing DNA-damaging toxins (De Almeida et al., 2018). If left unchecked, these infections can be life-threatening, especially in people with weakened immune systems, highlighting the importance of keeping E. faecalis levels balanced.

Enterococcus faecalis is a common gut bacterium that can be both helpful and harmful depending on its balance in the microbiome. In South Africans, as in other populations, it forms part of the normal gut flora, aiding digestion and helping to protect against harmful bacteria by competing for nutrients and producing antimicrobial substances (de Almeida et al., 2018). However, its ability to survive in harsh conditions and resist certain antibiotics means that when it overgrows or escapes the gut—especially in people with weakened immune systems—it can cause serious infections such as urinary tract infections, bloodstream infections, and wound infections (Krawczyk et al., 2024).

Imbalances in E. faecalis levels can also play a role in chronic health issues. Research suggests that high levels may contribute to gut inflammation, including conditions like inflammatory bowel disease (IBD), by producing enzymes and toxins that damage the gut lining (Borges et al., 2024). In South Africa, where antibiotic use is common and hospital-acquired infections remain a public health concern, the risk of antibiotic-resistant E. faecalis strains is especially relevant. Maintaining a healthy gut microbiome—through diet, probiotic-rich foods, and avoiding unnecessary antibiotics—can help ensure that E. faecalis stays in its beneficial role rather than becoming a health threat.

To maintain healthy levels of Enterococcus faecalis, it’s important to focus on supporting overall gut balance rather than trying to completely eliminate this bacterium. In the right amounts, E. faecalis plays a role in digestion and helps prevent harmful bacteria from taking over (de Almeida et al., 2018).

1. Eat a diverse, fibre-rich diet

A variety of plant-based foods—fruits, vegetables, legumes, whole grains, nuts, and seeds—helps feed beneficial gut bacteria, creating an environment where E. faecalis stays in check and does not overgrow.

2. Include fermented and probiotic-rich foods

Yoghurt, kefir, sauerkraut, kimchi, and other fermented foods help maintain microbial diversity, which naturally regulates E. faecalis populations.

3. Avoid unnecessary antibiotics

Antibiotics can wipe out beneficial bacteria, giving E. faecalis an opportunity to overgrow. Only use antibiotics when prescribed and necessary (Borges et al., 2024).

4. Support your immune system

A healthy immune system keeps potentially harmful bacteria—including E. faecalis—under control. Adequate sleep, regular exercise, and stress management are key.

5. Monitor and test when needed

Regular gut health testing can detect imbalances early. If E. faecalis levels are too high, a healthcare professional can help you make targeted changes to restore balance before health issues develop.