Gut Dysbiosis: Symptoms, causes, treatments and prevention


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Gut Dysbiosis: Symptoms, causes, treatments and prevention


Gut dysbiosis refers to any kind of disruption to the balance of microorganisms within the gut which has a negative effect on your health. Gut dysbiosis is a very broad term that includes many different changes to the gut microbiota which each have their own cause and effects on health.

The gut microbiome

When microorganisms were first discovered, they were considered to be the cause of disease and nothing more. Since that time, we have discovered that a healthy human is home to trillions of microorganisms and have recognised the complexities of the microbial world: a mixture of microorganisms which are beneficial and harmful, and those that lie somewhere in between.

We now know that the community of microorganisms living in our gut, known as the gut microbiota, can impact our health and influence the function of many of our vital organs and body systems. These microorganisms perform a variety of important biological functions in the gut with both local and far reaching effects. It is now widely accepted by modern science that the influence of the gut microbiome extends far beyond our digestive tract with effects on our immune system, skin health, bone health and more (1).

Its effects on our health depends on the balance that exists between the more beneficial microorganisms in the gut and those with the potential to cause harm. All sorts of microorganisms which offer a range of different benefits and potential threats live within the gut. When kept in balance, they each play an important role and work together to create the conditions for a healthy gut and body (2). Competition for resources and other interactions between microorganisms in the gut helps to keep those with the potential to cause harm at a lower level and create a well-balanced gut microbiota that supports health. We are also responsible for providing the right conditions within the gut to support microbial balance; for example, eating a well-balanced and fibre-rich diet feeds different kinds of microorganisms and supports a diverse and balanced gut microbiota (3).

What is gut dysbiosis?

Gut dysbiosis refers to any kind of disruption to the balance of microorganisms within the gut which has a negative effect on your health. Gut dysbiosis is a very broad term that includes many different changes to the gut microbiota which each have their own cause and effects on health. Broadly speaking, it can include the loss of specific beneficial microorganisms (such as bifidobacteria), the overgrowth of particular unfavourable microorganisms (such as methane-producing microorganisms), or the loss of overall diversity (2). These are the three general classifications of dysbiosis, and will often occur at the same time or as a result of another. For example, when specific protective microorganisms are lost, it can disturb the balance that exists between competing microorganisms. This lack of competition can create an opportunity for microorganisms with the potential to cause harm to overgrow. While strictly speaking the ‘gut’ refers to the large intestine, small intestinal bacterial overgrowth (SIBO) is an increasingly recognised form of dysbiosis which occurs in the small intestine and is often included in discussions of gut dysbiosis (4). Just as a balance of microorganisms within the gut contributes to human health, gut dysbiosis contributes to disease due to inflammatory and other effects that it triggers within the gut and the body (3).

What causes gut dysbiosis?

A number of external influences can disrupt the diversity and composition of the gut microbiota. Some factors can cause widespread reductions across all types of microorganisms, while others can change the environment in more subtle ways and either allow for unfavourable microorganisms to grow or prevent beneficial microorganisms from thriving.

Antibiotics and dysbiosis

One of the most well-known causes of gut dysbiosis is the use of antibiotics. Antibiotics are designed to kill bacteria, and many commonly prescribed antibiotics are broad spectrum which means they act against the bacteria causing the infection as well as those bacteria that are a natural part of the gut microbiome. Antibiotics can significantly reduce the richness and diversity of bacteria living in the gut in the short term and may also lead to the permanent loss of specific types of microorganisms in the long term (4).

While studies show that the gut microbiota generally returns to normal after 1-2 months following antibiotics, some people have been shown to be missing several groups of bacteria even after 6 months (5). While these subtle changes don’t necessarily cause any immediately apparent symptoms, the loss of important beneficial microorganisms from the gut may be responsible for the growing number of diseases associated with increased antibiotic use (6).

Diet and gut dysbiosis

The makeup of your gut microbiota is heavily influenced by your diet. The foods and food habits we generally consider to contribute to poor overall health are the same that contribute to gut dysbiosis. A high intake of saturated and trans-fat, sugar and other refined carbohydrates, and other processed foods can increase the risk of gut dysbiosis. Fibre is one of the most important foods for gut microorganisms. Diets low in fibre significantly reduce microbial diversity and may even reduce the numbers of certain groups of microorganisms to the point of no return (3).

Other links to gut dysbiosis

Being born via caesarean section and formula feeding can change the kinds of microorganisms that first colonise the gut during early life, particularly reducing the level of important bifidobacteria. Other factors such as the use of certain chemicals in household cleaning products, cigarette smoking, alcohol consumption, certain medications (such as ibuprofen and proton-pump inhibitors), inflammation caused by other diseases and physical or psychological stress can contribute to changes in the composition and quantity of microorganisms in the gut (4, 8).

Often, a single factor is not sufficient to induce dysbiosis as many microorganisms within the gut have an ability to adapt to changes in their environment. However, the combined actions of several factors over time can impact specific groups of microorganisms to a tipping point and create changes that lead to symptoms and/or disease (8).

Immune system and gut dysbiosis

Immunocompromised people are also at an increased risk for gut dysbiosis. The immune system plays an important role in regulating the types of microorganisms which can live in the gut and deterring the growth of microorganisms which carry the most risk of infection. It also prevents microorganisms in the gut from causing systemic infections. Impaired immune function, such as in those undergoing chemotherapy or undergoing systemic corticosteroid treatment, increases the risk of gut dysbiosis and of this turning into serious gastrointestinal infections which are rarely seen in healthy individuals, such as intestinal fungal overgrowth (4).

What are common symptoms of gut dysbiosis?

Gut dysbiosis can lead to common digestive symptoms such as abdominal pain, bloating, flatulence, diarrhoea and constipation (4). However, not all instances of gut dysbiosis will present in the same way or cause any digestive symptoms at all.

For example, gut dysbiosis from antibiotic use can cause temporary diarrhoea. This is a consequence of the antibiotic’s reduction of protective gut bacteria allowing for harmful infectious microorganisms which cause diarrhoea, such as Clostridium difficile, to overgrow (9). On the other hand, the overgrowth of a particular group of microorganisms known as methanogens, such as Methanobrevibacter smithii, can have the opposite effect and cause constipation (4). SIBO typically presents with a range of digestive complaints typically associated with gut dysbiosis, including abdominal pain, bloating, gas, diarrhoea and irregular bowel movements (4).

Sometimes, gut dysbiosis may go unnoticed due to the relative lack of gastrointestinal symptoms. Reduced diversity in the gut microbiota may not be enough to trigger digestive complaints, but could be having a more long-term effect on overall health (5). Gut dysbiosis can be an underlying contributor to other health conditions and their symptoms, and it has been associated with a growing number of chronic diseases including irritable bowel syndrome, autoimmune diseases such as ulcerative colitis, metabolic disorders such as obesity and diabetes, cardiovascular disease, depression and anxiety, and allergies such as asthma and eczema (2, 6). For example, a reduction in gut bifidobacteria at a young age has been associated with a significantly increased risk of developing allergies and obesity in later life (7). Gut dysbiosis may contribute to the development of these diseases as in this example, or make existing diseases worse by increasing inflammation. In some cases, gut dysbiosis may be a consequence of the disease rather than the cause and more research is needed to understand these relationships (4).

How does gut dysbiosis contribute to disease?

There are many different ways in which gut dysbiosis can contribute to the development of disease in the digestive system and in other parts of the body (2).

Specific microorganisms within the gut are responsible for generating health-promoting substances or ‘metabolites’, and the loss of these microorganisms can contribute to disease development. For example, butyrate is a substance with a multitude of health benefits. The loss of butyrate-producing bacteria such as Faecalibacterium prausnitzii has been implicated in the development of a number of diseases, including inflammatory bowel disease (2). On the other hand, the overgrowth of other microorganisms can produce substances which contribute to disease. The overgrowth of sulphate-reducing bacteria is an example of this, as they produce hydrogen sulphide which is a toxic molecule that has also been associated with inflammatory bowel disease (2).

In states of gut dysbiosis, the reduced production of beneficial metabolites and/or the over-production of potentially harmful metabolites can weaken the health of intestinal cells lining the digestive tract and trigger a phenomenon known as leaky gut (2). Leaky gut allows gut microorganisms to inappropriately pass through our intestinal lining, which are then intercepted by immune cells. The immune response to microorganisms from an unhealthy gut can create inflammation which affects the gut and travels to the rest of the body via chemical messengers circulating in the blood (6). Chronically raised inflammation stemming from the gut is thought to impact the health of many different organ systems, and contribute to the increasing prevalence of chronic disease such as obesity and type II diabetes (6).

Are there gut dysbiosis treatments?

The treatment and management of gut dysbiosis is determined by the nature of the gut dysbiosis. As gut dysbiosis is a broad term that encompasses many different changes to the gut microbiome, treatment will be determined by what is going on in each individual. It will also depend on the seriousness of the condition, and the type of health professional you are working with. For example, in the case of less common but more serious gastrointestinal infections, such as by Clostridium difficile following antibiotic use, immediate medical attention and treatment is required.

The concept and the effect of gut dysbiosis outside of its more serious manifestations, such as C. difficile infections, is less recognised by medical practitioners. If you are experiencing symptoms that may lead you to suspect gut dysbiosis, it is recommended that you see a doctor who can help you to investigate your symptoms and rule out serious underlying medical conditions. However, they may not be able to test for more general instances of gut dysbiosis or assess the complete balance of microorganisms within your gut. Recently, SIBO has become increasingly recognised in the medical community and may be tested by some doctors. Antibiotics are often prescribed for this, which has a varying degree of success (10).

Naturopaths and nutritionists are often sought out when it is suspected that gut dysbiosis may be the underlying cause of or a contributor to poor health. Many naturopaths and nutritionists will use a ‘weed and feed’ approach to address gut dysbiosis, often after performing a microbiome stool analysis and a series of other tests to understand the balance of microorganisms in your intestines. When a specific microorganism or group of microorganisms have overgrown, such as in SIBO or intestinal methanogen overgrowth, the most common treatments are antibiotics (if being treated by a medical doctor) or other antimicrobial agents, such as antimicrobial herbs, that aim to reduce their numbers. After offending microorganisms have been adequately controlled or when important beneficial communities are lacking from the gut, strategies are used to support the growth of beneficial microorganisms and re-establish a healthy balanced gut microbiota that will prevent future gut dysbiosis. This may include the use of prebiotic and probiotic supplementation and dietary and lifestyle modifications (see below).

When a serious infection has been excluded, many gut microbiota experts are beginning to encourage an approach that focuses more on feeding and supporting the beneficial microorganisms in the gut rather than targeting those microorganisms which have overgrown directly. Increasing beneficial communities can help to competitively inhibit those microorganisms and, over time, restore balance to the gut microbiota. The support for this approach is in large part due to the unknown consequences of using broad-spectrum antibiotic or antimicrobial therapy, even those which claim to be “natural”, on the rest of the gut microbiota. Research into alternative antimicrobial therapies that selectively target specific groups of microorganisms is growing and may be used alongside this feeding-focused approach.

Is there a gut dysbiosis diet?

Making changes to the diet is one of the most important parts of addressing gut dysbiosis. The foods you choose to eat can either feed beneficial communities or microorganisms that have the potential to negatively affect your health. Eating a high-fibre diet rich in minerals and vitamins with high-quality protein and avoiding excessive consumption of saturated and trans-fat, sugar, and other processed foods has a protective effect against gut dysbiosis (3).

Diets can also be tailored to support specific forms of gut dysbiosis. Different plant fibres will feed different communities of microorganisms in the gut. Using specific prebiotic fibre supplements or eating more foods that contain these fibres can be used to support the growth of specific beneficial communities which may be diminished within your gut. For example, legumes and the prebiotic fibres inulin and galactooligosaccharides can increase the growth of Faecalibacterium prausnitzii which is an important butyrate-producer and often associated with health. On the other hand, you may need to avoid specific foods or supplements that are encouraging the overgrowth of microorganisms that are having a negative health effect. For example, foods rich in sulphur (e.g. cruciferous vegetables, eggs and animal protein) may need to be reduced if testing reveals an overgrowth of sulphate-reducing bacteria that produce hydrogen sulphide (11).

Are there ways to prevent gut dysbiosis?

Maintaining a diet rich in plant foods, which provides important prebiotic fibres and other dietary components that feed beneficial microorganisms in the gut, is the best way to help support a healthy balanced gut microbiota (2). Prebiotic fibre supplements may help to bolster your diet and provide extra support to your gut microbiota. Avoiding those factors which are known to disrupt the gut microbiota is also important, such as excessive alcohol consumption and cigarette smoking.

When antibiotics are needed, using probiotics may also help to prevent gut dysbiosis and unwanted side effects. Probiotics are beneficial microorganisms which can be supplemented to help to protect or restore balance to the gut microbiota while they are present in the digestive tract. However, not all probiotics offer the same benefits and their effects depend entirely on the specific strains being used. One of the best probiotic strains for supporting a healthy balanced gut microbiota during and after antibiotic use is Lactobacillus rhamnosus GG. This strain reduces the risk of antibiotic-associated diarrhoea in children and adults by 51%, which is supported by the highest level of scientific evidence (12). During antibiotic treatment, L. rhamnosus GG helps to prevent gut dysbiosis by competing against and preventing the overgrowth of potentially harmful microorganisms in the gut.

Specific probiotic strains can help to improve the diversity and health of your gut microbiota. Probiotics introduce more beneficial microorganisms into the gut and, while they don’t become permanent residents of your gut and will only remain in the gut for as long as you take them for, they can act like renovators which improve the gut environment and create a more friendly and inviting home for your own beneficial microorganisms to grow in (13).

Interestingly, research has shown that the environment you are living in can also help to prevent gut dysbiosis. Growing up on a farm and growing up with pets in the first year of life, specifically dogs, exposes individuals to a range of different microorganisms that they wouldn’t otherwise encounter. Therefore, exposure to nature is beneficial for our gut microbiome diversity and has even been shown to reduce the risk of allergies (14).


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