Staphylococcus aureus is a type of bacterium that can live on the skin, in the nose, and—less commonly—in the gut. In the gut microbiome, it is usually present in small amounts or not at all, as the digestive tract’s balance of “good” bacteria tends to keep it under control (Schneeberger et al., 2022). However, under certain conditions—such as after antibiotic use, a weakened immune system, or significant changes in gut bacteria—S. aureus can grow in higher numbers and become harmful (Jiménez-Truque & Saye, 2020).

When S. aureus becomes too abundant in the gut, it can produce toxins and cause inflammation. This overgrowth is linked to gut infections, food poisoning, and even the spread of bacteria to other parts of the body, potentially leading to serious conditions like bloodstream infections or sepsis (Tong et al., 2015; Acton et al., 2020). Some strains are methicillin-resistant (MRSA), meaning they are harder to treat with common antibiotics. While it is not always harmful, its presence in the gut needs careful monitoring—especially in people with other health issues—because it can quickly shift from being harmless to a serious health concern (Schneeberger et al., 2022).

✔ Type of bacteria: Gram-positive, round-shaped (coccus) bacterium.

✔ Where it’s found: Commonly on skin, in the nose, and occasionally in the gut.

✔ Normal role in the gut: Rare or present in very small amounts; usually kept in check by other gut bacteria.

✔ When it becomes harmful: Overgrowth can occur after antibiotics, immune suppression, or disruption of normal gut flora.

✔ Potential health issues: Food poisoning, gut infections, skin infections, bloodstream infections, and sepsis.

✔ Dangerous strains: Some are methicillin-resistant (MRSA), making them harder to treat.

✔ Transmission: Spread through direct contact, contaminated food, or surfaces.

✔ Why it matters in the gut microbiome: It can switch from harmless to harmful quickly, producing toxins and causing inflammation.

While Staphylococcus aureus (S. aureus) is better known as a potential cause of infections, in rare and carefully balanced cases it may contribute indirectly to gut health by interacting with the immune system and microbial community.

In very low levels, S. aureus can act as a “training partner” for the immune system — helping your body recognise and respond quickly to harmful bacteria and toxins (Ibarra et al., 2020). This mild stimulation can strengthen immune readiness, a concept similar to how exposure to harmless bacteria early in life can promote balanced immune development (Nakatsuji et al., 2021). Additionally, if S. aureus is kept under control by healthy gut flora, it may coexist without causing harm, contributing to overall microbial diversity, which is important for gut resilience (Magryś et al., 2022).

However, the line between helpful and harmful is thin — if the balance tips, S. aureus can quickly switch to producing toxins and causing inflammation. That’s why its potential benefits only apply when it is present in very small numbers, within a healthy and diverse gut microbiome.

Unhealthy levels of Staphylococcus aureus (S. aureus) in the gut can lead to a range of symptoms, driven mainly by its ability to produce toxins, trigger inflammation, and disrupt the balance of the gut microbiome. Signs that S. aureus may be causing problems include:

✔ Frequent or persistent diarrhoea: caused by toxins irritating the gut lining (Nakatsuji et al., 2021).

✔ Abdominal pain or cramping: due to inflammation or infection of the gut wall (Ibarra et al., 2020).

✔ Nausea and vomiting: linked to toxin production, which can affect the stomach and small intestine.

✔ Fever or chills: indicating the infection may be spreading beyond the gut.

✔ Skin infections or boils: S. aureus can travel from the gut to other areas of the body.

✔ Signs of systemic infection: such as fatigue, weakness, or low blood pressure, which may indicate bacteraemia (Magryś et al., 2022).

Because S. aureus can quickly shift from harmless to harmful when the immune system is weakened or the gut microbiome is disturbed, these symptoms should be taken seriously — especially if multiple signs appear together or symptoms are severe. Early testing and medical guidance are key to preventing complications.

Even in South Africa’s wealthiest communities, where people typically have better access to healthcare, good nutrition, and modern sanitation, Staphylococcus aureus — including methicillin-resistant strains (MRSA) — can still impact gut health. Wealth does not fully protect against this bacterium because its presence in the gut is often linked to factors that occur across all socioeconomic groups, such as hospital visits, antibiotic use, travel, or dietary imbalances (Kosiewicz et al., 2021; Steenkamp et al., 2008).

In healthy, diverse gut microbiomes, S. aureus is usually kept in check. However, lifestyle habits common in affluent communities — like frequent international travel, elective medical procedures, or high antibiotic exposure for minor illnesses — can disrupt gut bacteria and give S. aureus an opportunity to colonise more strongly (Kinnevey et al., 2021). Even without causing obvious infection, gut carriage may contribute to low-grade inflammation, increase the risk of recurrent infections elsewhere in the body, or transfer antibiotic resistance genes to other gut microbes (Askarian et al., 2018).

For people in high-income areas, the risk often lies in silent colonisation — meaning they may feel well but still carry the bacteria in their gut, which can seed infections during surgery, immune suppression, or travel-related stomach illness. This makes routine gut health monitoring, careful antibiotic use, and proactive infection control measures just as important in wealthy communities as in lower-income ones (Kosiewicz et al., 2021).

To maintain healthy levels of Staphylococcus aureus in your gut, the goal is to keep your gut microbiome diverse and resilient so this bacterium stays in check without causing harm. Here’s how:

1. Support a balanced gut microbiome

Eat a fibre-rich diet from whole plant foods (fruits, vegetables, legumes, whole grains) to feed beneficial bacteria, which can help prevent S. aureus from overgrowing (Kosiewicz et al., 2021).

Include fermented foods like yoghurt, kefir, kimchi, and sauerkraut, which provide probiotics that can help maintain balance (Askarian et al., 2018).

2. Avoid unnecessary antibiotic use

Only take antibiotics when prescribed and necessary, as they can wipe out protective bacteria, giving S. aureus more opportunity to grow (Kinnevey et al., 2021).

If you must take antibiotics, pair them with probiotic-rich foods or supplements to help restore gut balance (Kosiewicz et al., 2021).

3. Practise good hygiene and infection control

Wash hands regularly, especially after hospital visits, travel, or contact with people who have infections.

Keep wounds clean and covered to reduce the risk of S. aureus spreading between the skin and gut.

4. Strengthen your immune system

Exercise regularly, manage stress, and get enough sleep — all of which improve immune defences, making it harder for S. aureus to cause problems (Askarian et al., 2018).

5. Test and monitor

If you’ve had recurrent infections, digestive issues, or are at higher risk (e.g., hospitalisation, surgery, immune suppression), consider gut microbiome testing. This can help identify S. aureus levels early and allow for targeted interventions (Kosiewicz et al., 2021).