In this article, we’ll explain how to get rid of bad bacteria in the gut and what steps you can take to support a healthier digestive system. We’ll look at how your environment and lifestyle can influence the balance of bacteria in your gut and what symptoms might suggest that harmful bacteria are causing issues. 

We’ll also cover practical and helpful ways to support gut balance. including diet and lifestyle changes, as well as which foods may help. If you're wondering whether it's possible, or even necessary, to change your gut bacteria quickly, we’ll guide you through what to consider before making any changes.

It’s important to note, ‘bad bacteria’ refers to potentially pathogenic or opportunistic microbes that become harmful when gut balance is disrupted.

Here are the five biggest takeaways from this article about getting rid of bad bacteria in the gut:

• Restoring balance is more important than eliminating bacteria

• Antibiotics can reduce both harmful and helpful bacteria, sometimes allowing resistant strains to take over

• Microbes, some of which live in the gut of many people, include both harmful and beneficial strains

• Foods with natural antimicrobial properties (garlic, oregano, green tea and pomegranate husk) can help manage bacterial imbalances

• Gut dysbiosis can cause symptoms such as bloating, fatigue, skin issues, mood changes and even food intolerances

The balance of bacteria in the gut, known as the gut microbiome, is strongly influenced by what we eat. A diet high in processed foods, saturated fats and added sugars can promote the growth of harmful bacteria and reduce the number of beneficial ones. This imbalance, known as dysbiosis, can lead to inflammation, digestive problems, and even affect the immune system [1].

Many common ingredients in a typical Western diet, including food additives, emulsifiers and high levels of fat can disrupt the gut environment. These substances may weaken the protective lining of the gut and encourage the overgrowth of bacteria that are linked to inflammation and disease.

Even short-term changes in diet can have a noticeable effect on the types and activity of bacteria in the gut. For example, switching to a high-fat or high-sugar diet, even temporarily, can shift the microbial balance in a way that favours potentially harmful strains [2].

The quality, source, and even the amount of water we drink can influence the balance of bacteria in the gut. Research shows that drinking water can introduce specific microbes into the gut, some of which may be harmful, particularly in infants under 12 months of age who are more vulnerable to disruptions in gut health [3].

Different water sources, such as tap, bottled, or filtered water, can carry distinct microbial profiles. These microbes may affect the composition of the gut microbiome depending on the source and quality of the water. For example, variations in the bacterial content of drinking water have been found to influence the types of microbes found in human faecal samples [4].

In fact, drinking water has been identified as an important factor in shaping the gut microbiome overall. The quantity and type of water consumed should be considered when studying or managing gut health, as water-borne microbes can alter microbial diversity or function [5].

On the other hand, not drinking enough water can also be harmful. Studies have found that water restriction disrupts gut homeostasis, leading to an overgrowth of certain bacteria and a reduction in immune cell numbers. This imbalance can affect the body’s ability to fight off infections and maintain a healthy gut environment [6].

The soil in your local environment can influence the types of bacteria that develop in your gut. This connection is due to the close relationship between environmental microbes and the human microbiome. Soil microbes can be introduced into the body through direct contact with the ground, gardening, or even consuming unwashed food [7].

Studies suggest that soil serves as a reservoir of microbial diversity that can affect the gut microbiome when people are exposed to it regularly. Microbes from the soil can enter the body and either support or disrupt the natural balance of bacteria in the gut.

Changes in urbanisation and reduced contact with natural environments may limit our exposure to beneficial soil microbes, potentially increasing the risk of dysbiosis. Evidence suggests that people living in less biodiverse areas, such as cities, may have less diverse gut microbiota compared to those with greater exposure to natural surroundings [8].

Your gut is home to a complex community of bacteria, often referred to as your gut microbiome. This environment relies on a variety of different species working together [9]. When everything is in balance, your gut bacteria help with digestion, support your immune system and even influence your mood.

However, just like a natural environment, things can start to go wrong if the balance is disturbed. Factors such as diet, stress, antibiotic use and even pollution can affect which bacteria thrive and which ones struggle to survive. If helpful bacteria are reduced, harmful ones can take over, causing problems such as bloating, discomfort and poor digestion.

Below are some bacteria that can be considered ‘bad’, depending on context:

Escherichia coli (better known as E. coli) is often thought of as a harmful bacteria, however, whilst some strains can cause serious illness, many types of E. coli are a normal and necessary part of a healthy gut. Certain strains actually play a role in producing vitamin K and supporting the gut’s natural barrier against more dangerous bacteria [10].

Problems tend to arise when pathogenic strains enter the digestive system, usually through contaminated food or water. These strains can produce toxins that damage the lining of the gut, leading to symptoms like stomach cramps, bloody diarrhoea and in severe cases, kidney complications [11]. In severe cases, some strains can lead to death. Young children, older adults, and people with weakened immune systems are particularly at risk [12].

One of the reasons harmful E. coli strains are so dangerous is that they’ve developed ways to survive in the body. Some are able to stick tightly to the cells in your gut lining, where they release toxins and avoid being flushed out [13]. Others can even disrupt your immune system's normal response, making it harder for your body to fight off infection [14].

E. coli’s ability to adapt is also what makes it a valuable tool for bacterial research. Scientists have used non-harmful strains of E. coli to learn more about genetics, antibiotics and how bacteria behave [15]. 

In the gut, non-pathogenic strains often compete with harmful bacteria for space and resources, acting as a natural form of defence [16].

Clostridium is a group of bacteria that naturally live in the gut. While some strains can be harmless, or even helpful, others have the potential to cause illness when they grow out of control. 

Certain species within the Clostridium group play a role in breaking down food and producing compounds vital for gut health. However, when the balance of the gut microbiome is disrupted, harmful strains such as Clostridium difficile (C. diff) can multiply, potentially causing an infection [17].

C. diff is a well-known cause of diarrhoea, particularly in people who have recently taken a course of antibiotics. Antibiotics can disturb the natural balance of the gut, killing off beneficial bacteria and creating space for resistant strains like C. diff to grow [18]. This can result in inflammation of the bowel and symptoms such as abdominal pain, fever and persistent diarrhoea.

It’s important to note that not all Clostridium species are harmful. Some produce short-chain fatty acids, which play a role in maintaining the gut lining and supporting the immune system. A healthy gut tends to include a range of Clostridium species, including beneficial ones that help maintain order among other microbes.

The most effective way to deal with harmful bacteria in the gut isn’t always to try and wipe them out completely; instead, it's about creating the right conditions for your beneficial bacteria to flourish. Research suggests that supporting the growth of good bacteria is often more effective than directly targeting the bad ones, especially since we don't always fully understand what we're getting rid of [19].

While broad-spectrum antibiotics can directly kill bacteria, they can also affect helpful strains. This can lead to a reduction in microbial diversity, making your gut more vulnerable to future imbalances. Trying to eliminate bad bacteria without caution can have unpredictable consequences [20].

Despite this, there are some situations where a more targeted approach may be helpful. For example, if you’ve tested positive for SIBO (Small Intestinal Bacterial Overgrowth), or if stool testing shows high levels of problematic bacteria, yeast or significant bacterial overgrowth, then gentle antimicrobial support may be recommended.

Candida albicans is a type of yeast that lives in most people’s digestive systems without causing any problems. Normally, it’s just one of many microbes that make up the gut microbiome. However, when the balance is disrupted, Candida can take the opportunity to multiply, leading to what’s known as an overgrowth [21].

Research suggests that Candida albicans is one of the species that can quickly move in when other microbes have been wiped out or weakened [22]. For example, a study found that over 40% of children who had taken antibiotics within the previous three weeks had signs of Candida overgrowth, compared to just over 20% of those who hadn’t taken antibiotics [23]. This supports the idea that antibiotic use can leave behind a vacuum in the gut, creating the perfect environment for Candida to thrive.

An overgrowth of Candida has been linked with a range of symptoms, including bloating, indigestion, nausea, diarrhoea, and excess gas [24]. It has also been associated with long-term conditions such as Crohn’s disease, ulcerative colitis and chronic fatigue syndrome [25]. 

Most mainstream doctors currently only consider Candida a concern in people with severely weakened immune systems, such as those undergoing chemotherapy or with advanced HIV. On the other hand, some nutritional therapists may consider Candida overgrowth as a possible contributor to symptoms [26].

Gut dysbiosis is the term used when the natural balance of bacteria and other microbes in your digestive system is disrupted. It usually means that there’s a drop in the diversity of your gut bacteria. Some types may decrease or disappear entirely, while others take the opportunity to grow in their place [27].

Researchers define dysbiosis as a “decrease in microbial diversity which promotes the expansion of specific bacterial taxa” [28]. While this shift might not cause obvious symptoms at first, it can affect how your gut functions and may lead to a range of health concerns.

Studies have linked gut dysbiosis to several conditions, including [29]:

• Inflammatory bowel disease

• Irritable bowel syndrome (IBS)

• Coeliac disease

• Allergies

• Asthma

• Metabolic syndrome

• Cardiovascular disease

• Obesity

Many experts believe that aspects of modern Western lifestyles (such as processed diets, high stress levels and frequent use of antibiotics) are contributing to a loss of microbial diversity [30]. 

Fortunately, gut dysbiosis isn't necessarily permanent. With the right support, such as a diet rich in fibre, fermented foods and careful use of antibiotics, it’s possible to restore a healthier balance over time [31].

Over the last two decades, our understanding of the gut microbiome has grown rapidly. One of the most consistent findings across the research is that diversity is crucial for a healthy gut. A mix of bacteria covering many different species and strains seems to give your microbiome the resilience it needs to protect you from disease and support overall well-being.

When diversity starts to fall, problems can arise. An unbalanced microbiome, known as dysbiosis, occurs when certain families of bacteria are lost and others multiply in their place. While science has not yet defined what an ‘ideal’ microbiome looks like, evidence so far suggests that variety is almost always better.

Although your microbiome is unique, shaped by your genetics, lifestyle, diet, and environment, researchers have found that certain types of bacteria are regularly linked with better health. These include Lactobacillus and Bifidobacteria.

Higher levels of these microbes are associated with lower risks of chronic disease and seem to have a gatekeeping role in maintaining gut balance.

While research is ongoing, one thing is clear. Maintaining a rich, diverse microbiome could be one of the most important things you do for your health.

Lactobacillus is one of the most well-known groups of bacteria found in the gut. These friendly microbes help support digestion, protect against harmful bacteria and play a role in immune health. Unfortunately, their numbers can decline when we’re unwell, and they also naturally reduce as we age.

Supporting your Lactobacillus population isn’t just about taking probiotics. In fact, one of the most effective ways to help them thrive is by feeding them the right foods.

You can boost your intake of these prebiotics through foods such as:

• Soy

• Apples

• Bananas

• Onions

• Garlic

• Asparagus

• Artichokes

Some probiotic foods that contain Lactobacillus include:

• Yoghurt

• Kimchi

• Pickles

Including more of these foods in your diet may help maintain healthy Lactobacillus levels, particularly when you are ill or stressed.

Bifidobacteria, often shortened to Bifido, are another group of beneficial bacteria found in a healthy gut. These microbes are particularly known for supporting digestion, modulating the immune system and helping to maintain the integrity of the gut lining.

One study found that supplementing with a Bifidobacteria probiotic for just 45 days led to a reduction in both body mass index (BMI) and cholesterol levels in people with metabolic syndrome, suggesting these bacteria may have a role in supporting metabolic health [32].

To keep your Bifido population thriving, a high-fibre, whole-food diet is one of the best approaches. Some good food options include:

• Bananas

• Nuts

• Onions

• Garlic

• Oats

• Blueberries

• Apples

When most people hear E. coli, they think of food poisoning, but not all strains are harmful. Some E. coli strains live peacefully in our gut and may even support digestion and immune function. One of the best-known beneficial strains is E. coli Nissle, which has been used as a therapy for certain gut conditions. However, beyond this strain, research into the helpful types of E. coli is still in its early stages [33].

If you’re looking to improve your gut health naturally, it might seem like getting rid of ‘bad’ bacteria is the best solution. However, the gut is home to a wide variety of microorganisms, and maintaining balance is more important than eliminating specific microbes.

In fact, trying to wipe out bacteria in the gut can often do more harm than good. Most gut issues, such as bloating or discomfort, are linked to imbalances in the microbiome, rather than the presence of a harmful strain.

Not all bacteria in the gut are harmful. In fact, many of the bacterial families that are sometimes seen as ‘bad’ can play a vital role in keeping the digestive system working properly.

For example, certain strains of E. coli are commonly thought of as dangerous, but many types of E. coli are actually a natural part of the human gut flora and contribute to a healthy intestinal environment [34]. 

Similarly, the Clostridium genus includes some well-known pathogens, however, it also contains species that are essential for digesting fibre and producing important short-chain fatty acids like butyrate [35].

When it comes to managing gut health, it’s important to understand that you can’t simply target and remove individual strains of bacteria without affecting the rest of the microbiome. The gut is a complex and connected system, where different species often work together or influence one another. 

Attempting to wipe out a single strain can disrupt this balance and lead to unintended consequences, including reduced microbial diversity or the overgrowth of other unwanted microbes [36].

In fact, studies show that even after strong antibiotic treatments, some strains persist while others are completely wiped out. The effects can vary widely from person to person and may lead to long-term changes in the gut microbiota [37]. This is why most experts now recommend focusing on promoting balance and diversity rather than trying to eliminate specific bacteria.

An imbalance of bacteria in the stomach and gut can lead to a variety of symptoms. These symptoms often affect the digestive system, but can also impact other areas of health, including mood and energy levels. Common symptoms of excess or harmful bacteria in the stomach include:

An overgrowth of certain bacteria can produce methane and hydrogen, leading to a build-up of gas and a feeling of fullness or bloating after meals [38].

This may feel like general stomach pain, pressure, or sharp pains and is often linked to an imbalance in gut bacteria irritating the lining of the gut.

Some harmful bacteria can cause the gut to work too quickly, leading to watery stools and urgent bowel movements. It is important to note that sudden or ongoing diarrhoea can be caused by pathogenic bacteria, and will require treatment.

Dysbiosis may slow down digestion and contribute to infrequent or difficult bowel movements.

Poor gut health can interfere with nutrient absorption, which may lead to tiredness and feelings of low energy [39].

Imbalances in gut bacteria may affect how your body processes certain foods, particularly those containing fibre, lactose, or FODMAPs (Fermentable Oligo-, Di-, Mono-saccharides and Polyols, short-chain carbohydrates that are poorly absorbed in the small intestine).

Harmful bacteria in the digestive tract can also contribute to unpleasant breath odours.

Conditions like acne, eczema or rosacea have been linked to gut imbalances in some people.

Small Intestinal Bacterial Overgrowth (SIBO) is a condition where excessive amounts of bacteria grow in the small intestine, an area of the digestive system that normally contains relatively low levels of microbes. This can disrupt digestion, damage the gut lining and cause a range of uncomfortable symptoms.

Unlike the large intestine, which is designed to host a diverse microbial population, the small intestine plays a different role. It’s primarily responsible for nutrient absorption, and when too many bacteria are present, they can interfere with this process. The bacteria begin to ferment carbohydrates too early in the digestive process, leading to the production of gas and other by-products that irritate the gut [40].

Common symptoms of SIBO include:

• Bloating and a feeling of fullness, especially after eating

• Excess gas (flatulence and burping)

• Abdominal pain or discomfort

• Diarrhoea, constipation, or alternating between both

• Nutrient deficiencies (such as vitamin B12 or iron)

• Unexplained weight loss

• Fatigue

• Brain fog

The large intestine is home to the majority of your gut microbiome. In a healthy state, this ecosystem is diverse and balanced, allowing beneficial bacteria to thrive and keep potentially harmful ones in check.

However, when this balance is disrupted, the effects can be great. Dysbiosis usually means there’s a reduction in beneficial bacteria, an overgrowth of potentially harmful ones, or a general lack of diversity in the gut. This imbalance can lead to a range of digestive symptoms such as:

• Bloating

• Constipation

• Diarrhoea

• Gas

• Abdominal discomfort

The impact of dysbiosis doesn’t stop at the gut. It can also cause symptoms elsewhere in the body, including:

• Bad breath

• Nausea or an upset stomach

• Fatigue

• Brain fog or difficulty concentrating

• Anxiety and depression

• Skin issues such as rashes or redness

• Chest pain or unexplained aches

• Urinary or intimate itching and discomfort

While studies are ongoing exploring the exact relationships between dysbiosis and disease, there is growing evidence linking an imbalanced gut microbiome to a number of chronic health conditions, including:

• Irritable bowel syndrome (IBS)

• Inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis

• Coeliac disease

• Type 2 diabetes

• Obesity and metabolic syndrome

• Liver disease

• Heart disease

• Eczema and other skin disorders

• Polycystic ovary syndrome (PCOS)

• Neurological conditions, including dementia and Parkinson’s disease

• Bowel cancer

Certain foods have natural antimicrobial properties and may help reduce the presence of harmful bacteria in the gut, while also supporting the growth of beneficial bacteria. It's important to note that the goal should be balance, rather than wiping out bacteria completely. If you're trying to discourage the overgrowth of potentially harmful microbes, the following foods may help:

Garlic is widely recognised for its antibacterial and antifungal properties, making it a popular natural remedy for gut health. The key active compound in garlic, allicin, is released when garlic is crushed or chopped. Allicin has been shown to have a powerful antimicrobial effect, targeting a wide range of harmful microorganisms, including certain strains of bacteria found in the gut.

Research has found that garlic may help reduce populations of potentially harmful bacteria without significantly disrupting the balance of beneficial microbes. This makes it a valuable food for supporting a healthy gut microbiome while managing bacterial overgrowths [41].

Oregano has notable antimicrobial properties. Its essential oils, particularly carvacrol and thymol, have been shown to help inhibit the growth of various harmful bacteria, including some that are resistant to antibiotics.

Research suggests that oregano oil can be effective in disrupting bacterial cell membranes, reducing the ability of harmful microbes to survive and reproduce in the gut [42]. This makes oregano a potentially helpful natural option for supporting gut health and managing bacterial imbalances.

Ginger is a well-known for its natural anti-inflammatory and antimicrobial properties that may help reduce harmful bacteria in the gut. Research has shown that ginger can actively inhibit the growth of several strains of pathogenic bacteria [43].

Its antibacterial effects are thought to be largely due to compounds like gingerol and shogaol, which help protect the gut lining and support a healthier balance of gut microbes. These compounds not only fight harmful bacteria but may also encourage the growth of beneficial bacteria, helping to restore balance in the gut microbiome.

Ginger may support gut health by reducing inflammation, easing symptoms like bloating and nausea, and improving digestion [44].

Turmeric, particularly its active compound curcumin, has been shown to have powerful antimicrobial and anti-inflammatory properties that may help reduce harmful bacteria in the gut. Studies suggest that turmeric can suppress the growth of certain pathogenic bacteria while supporting a more balanced and diverse gut microbiota [45].

Curcumin appears to influence gut health in several ways. It may help strengthen the gut barrier, reduce inflammation in the digestive tract and modify the composition of the gut microbiome by increasing levels of beneficial bacteria such as Bifidobacteria and Lactobacilli [46].

Cinnamon is known for its natural antimicrobial properties, which may help reduce harmful bacteria in the gut. Research shows that compounds found in cinnamon have antibacterial effects against a variety of pathogens [47].

As well as its ability to inhibit the growth of bad bacteria, cinnamon may also support overall gut health by helping to maintain a healthy balance of the gut microbiota. One study found that cinnamon extract can influence the diversity and structure of the gut microbial community, potentially supporting beneficial bacteria while suppressing harmful strains [48].

Cloves contain powerful compounds which have been shown to exhibit strong antimicrobial and anti-inflammatory properties. These natural substances can help reduce harmful bacteria in the gut by disrupting bacterial cell walls and inhibiting their growth [49].

Studies also suggest that clove extract may play a role in restoring microbial balance in the digestive system, particularly after periods of inflammation or imbalance caused by a poor diet or infection. Clove compounds help regulate gut microbial composition and support the growth of beneficial bacteria while reducing the presence of potentially harmful ones [50].

Green tea is well known for its antioxidant properties, but it also has antimicrobial effects that may support gut health. One of its key active compounds, epigallocatechin gallate (EGCG), has been found to help inhibit the growth of harmful bacteria in the digestive system.

Studies have shown that the polyphenols in green tea can reduce levels of specific pathogenic bacteria without significantly disturbing beneficial bacteria like Lactobacillus and Bifidobacterium [51].

Apple cider vinegar (often shortened to ACV) has gained popularity for its potential benefits in supporting gut health and reducing harmful bacteria in the digestive tract. Its natural acidity, mainly from acetic acid, creates an environment that can inhibit the growth of certain pathogenic microbes while promoting the growth of beneficial bacteria [52].

Research shows that acetic acid may help suppress the growth of harmful gut bacteria and encourage a healthier balance of the gut microbiome when consumed in moderation [53]. ACV also appears to have a positive impact on blood sugar levels and lipid profiles, both of which are linked to overall metabolic and gut health [54].

It’s generally not possible, or advisable, to take action quickly. Attempting to eliminate bad bacteria rapidly can disrupt this balance, sometimes making symptoms worse or leading to other health problems.

Gut issues linked to harmful bacteria, such as small intestinal bacterial overgrowth (SIBO) or dysbiosis, usually require a careful, gradual approach. Here are some reasons why you should be careful when it comes to altering your gut bacteria.

Bacteria can develop resistance to treatments quite quickly, which is a significant challenge in managing gut health. When exposed to antibiotics or antimicrobial agents, some bacteria can adapt by changing their genetic makeup. 

This not only reduces the effectiveness of the medication but can also lead to the growth of resistant strains that are harder to control. It’s one of the reasons why antibiotics should be used carefully and only when necessary, following medical advice.

This highlights the importance of a balanced approach to managing gut bacteria, aiming to support a healthy microbiome rather than simply trying to eradicate harmful bacteria quickly [55] [56].

You could inadvertently kill other helpful bacteria in the process of trying to eliminate bad bacteria quickly. Using broad-spectrum antibiotics or strong antimicrobial agents without careful management can disrupt this balance, reducing microbial diversity and potentially leading to further digestive issues or other health problems [57].

This is why treatments aimed at addressing harmful bacteria in the gut should be targeted and guided by healthcare professionals to minimise unintended harm to the helpful microbes that keep the gut ecosystem healthy.

Some bacteria are good at hiding in biofilms, which makes them much harder to eliminate. Biofilms are protective layers that bacteria produce to shield themselves from the immune system and antibiotics. Within these biofilms, bacteria can survive harsh conditions and resist treatments that might otherwise kill them [58].

This ability to “hide” means that simply trying to kill bad bacteria with antimicrobials or antibiotics may not be enough. Effective treatment often requires breaking down these biofilms first, allowing medications or the immune system to reach and eliminate the bacteria more effectively.

Trying to kill bad bacteria too quickly or aggressively in your gut can actually cause more harm than good. Rapidly eliminating bacteria can disrupt the delicate balance of your gut microbiome. This can lead to worsened dysbiosis, where not only harmful bacteria but also beneficial microbes are reduced, leaving your gut more vulnerable to more imbalances and digestive issues [59].

No, it is not always a good idea to try to kill bad bacteria in your gut. The gut microbiome is a complex community of many different bacteria, some of which may be considered ‘bad’. Simply eliminating these bacteria can disrupt this balance and may lead to further digestive problems or other health issues.

There are a number of ways you can spot dysbiosis in your gut, including:

There are several signs that may indicate dysbiosis in your gut, and one of the more reliable ways to spot it is through a comprehensive stool test. These tests, like the one provided by Vivere, can identify problematic bacterial overgrowths or imbalances in your gut flora.

Results of stool tests can help healthcare professionals understand whether your symptoms are linked to dysbiosis and what kind of intervention might help. For example, if there's an overgrowth of specific bacteria known to cause gastrointestinal symptoms, a tailored treatment plan can be developed, including dietary changes, targeted antimicrobials, or probiotics [60].

Improving gut health isn’t about eliminating all 'bad' bacteria, but rather creating the right environment for beneficial microbes to thrive. The gut is home to a wide range of bacteria, some of which can become problematic if the balance is disrupted by factors like diet, stress, or antibiotics. Instead of aiming to wipe out harmful strains, the most effective approach involves supporting microbial diversity through a fibre-rich diet, fermented foods and careful use of antimicrobial agents when needed. 

While certain foods and natural compounds can help discourage overgrowth of unhelpful bacteria, maintaining balance and variety in the gut microbiome is key. Looking after your gut health is a long-term process.

Vivere helps you take control of your health with personalised insights from state-of-the-art gut microbiome testing, nutritional guidance, science-backed supplements and expert support. Sign up today and start living better, for longer.

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