What is Dysbiosis?

Kathy Wheddon Nutritional Therapist DipION

Humans have trillions of bacteria and other microbes living within their digestive tract. Amongst these microbes are many ‘good guys’ (also known as probiotics) alongside lesser amounts of ‘bad guys’ (pathogens). There is also a third group known as commensals, which are neither particularly detrimental nor beneficial to us (their host). The collective name for this vast microbial colony is the microbiome, and the health of the microbiome plays a surprisingly large role in our overall health and well-being.

Everybody, even those with no obvious signs of ill health, has a certain amount of pathogens in the gut, including species of pathogenic yeasts, such as Candida albicans. Health professionals can read more about Candida dysbiosis on our sister site, Probiotic Professionals.

So long as there are enough beneficial microbes to prevent the pathogens from over-growing, they do not pose us a problem. It is when there is a shift in the composition of the microbiome towards a higher proportion of pathogenic versus probiotic microbes that problems arise. This situation is referred to as ‘dysbiosis’. 

If the composition of our gut microbiome is not optimal, then neither will our health be. But, defining ‘optimal’ when discussing the microbiome is not that easy.

What does a healthy gut microbiome look like?

The short answer is that we are not completely sure, as no two microbiomes are the same. There is a huge degree of diversity from one individual to another, even in healthy people. In fact it is thought that our microbiome is as unique to us as our fingerprint, which makes it difficult to categorise a microbiome as ‘healthy’ or otherwise. Often they are just different.

Scientists have, however, identified many features that they think could be common to a healthy microbiome. These include:

The most prevalent organisms found1

Two studies 2,3 have shown that healthy gut microbiomes (as assessed by bacterial gene sequencing) are consistently dominated by bacteria from two specific phyla (level of classification)—Bacteroidetes and Firmicutes.

This initially sounds like a great starting point for being able to assess the health of an individual’s gut microbiome, however, it should be noted that within these two phyla there exist many, many different types of bacteria.

Therefore, even within just these two phyla, there is still an almost endless amount of different bacterial combinations that could be considered ‘healthy’.

Levels of microbial diversity2

It is widely accepted that the greater the diversity of microbes in the gut, the better.

Levels of stability3 of our resident flora

It is generally accepted that a healthy gut microbiome is relatively stable; in other words, the number and types of bacteria present remain consistent.

Thanks to the advent of gene-sequencing techniques, research has now been carried out4,5 that has implied the existence of a set of microbial genes that are common to all individuals. Despite huge variations between two individuals’ microbiomes (even between twins!), it seems that there could also be a ‘core microbiome’. This ‘core’ is thought to total approximately 40% of the microbiome.

One study6 suggests that a core healthy microbiome is one that includes specific microbial ‘family’ combinations that together promote a stable host ecology. This core microbiome, it is thought, needs to be able to fulfil several key functions, including ‘housekeeping’ functions necessary for all microbial life, such as transcription and translation (the processes involved when bacteria create proteins) and energy production3. Additionally, the core microbiome will also carry out more specialized processes specific to gut microbes. These include adhesion to host cell surfaces; the production of compounds used in interactions between microbes and our bodies (including essential vitamins, such as vitamin K); and the production of other essential molecules, such as amino acids (which make up proteins)7.

Therefore, a healthy gut microbiome consists of a mix of microbial species that can carry out specific sets of functions. These microbial functions are either enhanced or diminished by long-term external influences such as diet8.

Rather than trying to define the exact species that create a ‘healthy’ microbiome, this approach defines health as how the whole population functions together, and whether these key processes are able to be carried out.

Factors that cause dysbiosis

A lot of sugar can have a detrimental effect on the gut microbiota

Anything that shifts the healthy balance of the microbiome is a factor for dysbiosis. Many external influences have a detrimental impact on the gut microbiome, including:


Taking a course of antibiotics is well known to diminish the good bacteria living in our gastrointestinal tract, as well as reducing the pathogens. Recovery of the bacteria after treatment has been shown to be ‘highly variable’ amongst different species. Some species may be lost forever, weakening the community’s future ability to exclude pathogens9. However, others are able to return to differing extents. It is, of course, necessary to take antibiotics sometimes, and there are many ways to replenish gut bacteria levels, which we will discuss later.


Certain medications are known to cause dysbiosis, including NSAIDs, the contraceptive pill, HRT and steroid medications.

High sugar diet

Lots of sugar in the diet has been shown in research to have a detrimental effect on the gut microbiota. This is because it feeds yeasts and pathogenic species of bacteria10. Additionally, a 2020 study discussed the possible negative effects of ‘novel’ sugars, such as chemically derived sweeteners, sugar alcohols and glycosides. The study11 suggested that bad bacteria seem better able to adapt to these sugars, particularly chemically derived food stuffs such as sweeteners.

Low fibre diets 

Fibre is the preferred food source for many different strains of probiotic bacteria living in the gut. Our increasingly fibre-poor diets challenge the health of the microbiome, and one study showed that this can have ‘lasting’ negative effects12.


Our gut microbiota is sensitive to fluctuations in hormones, including sex hormones, thyroid hormones and adrenal hormones. This is one reason why women sometimes suffer from gut-related symptoms such as constipation before their menstrual period, or during pregnancy.


Increases the levels of adrenal hormones circulating in the blood, and for this reason long-term stress is known to have a detrimental impact on various aspects of gut health.  Research suggests that stress and the impact of stress hormones alters the permeability of the intestine (making it ‘leaky’), increases inflammation, and significantly changes the types of microbes found in the gut13.

Foreign travel 

When we travel, we often come into contact with different microbes to those that we are used to, in both the local food and water. There are multiple pathogens that have been identified to be associated with traveller’s diarrhoea (TD), such as E. coli, members of the Shigella and Campylobacter species, and Norovirus14. However, it is not only foreign pathogens that can lead to dysbiosis. Doctors at the Weizmann Institute in Israel found that our gut microbes have a distinct circadian pattern. The research showed that when the host was asleep the microbiome was different to when the host was awake. It found that the microbiome performs different functions, depending on the host’s state of consciousness; focusing on repair and growth when we sleep, and switching to more detoxifying activities when we are awake. When we travel, and our sleeping and eating times are altered this greatly affects the microbiome, causing dysbiosis and the onset of digestive symptoms15.

Dysbiosis signs and symptoms

When the gut microbiome has been affected by any of these factors listed above, it upsets the balance of the gut and symptoms of dysbiosis can arise. Symptoms can be limited to the gut, or they can have knock-on effects to other parts of the body. 

Probiotic strains of bacteria produce beneficial metabolites, such as vitamins, whereas pathogens produce toxins. When there is gut dysbiosis the body has to work harder to maintain homeostasis (balance). The organs of elimination (liver, kidneys, skin) are required to break down and eliminate the toxins released by these pathogens, and they can become over-burdened. Signs of poor detoxification can often be seen on the skin, with the appearance of skin conditions such as eczema, acne, and psoriasis. For more information, read our article on the gut microbiome and skin health.

Emotional health may also suffer as a result of dysbiosis. ‘Psychobiotics’ are an area of science looking specifically at the impact of the gut microbiome on our mood and mental health. Many studies show a clear link between gut health and emotional health, and the microbiome is now known to play a significant role in our ability to synthesize certain hormones and neurotransmitters implicated in mood. Find out more about the gut-brain axis and probiotics.

More recently links have been found between gut dysbiosis and certain metabolic conditions, such as type 2 diabetes, metabolic syndrome and even obesity18.

Specific gut-related symptoms of dysbiosis include:

  • Bloating
  • Excess wind/flatulence
  • Abdominal pain
  • Diarrhoea
  • Constipation
  • Inflammatory bowel diseases16
  • Irritable bowel syndrome17
  • Acid reflux/GERD
  • Halitosis
  • Food intolerances/sensitivities

Other symptoms include:

  • Low mood/anxiety
  • Difficulties sleeping
  • Joint pain
  • ‘Foggy’ thinking/poor concentration
  • Skin complaints
  • Sugar cravings
  • Allergies18
  • Metabolic syndrome18
  • Obesity18
  • Fatigue

Correcting dysbiosis

So, how can we overcome dysbiosis, and recover from the myriad of possible symptoms that might arise as a result of it? Is it possible to address dysbiosis naturally? You’ll be glad to hear that the solution is relatively straight-forward. We just need to nurture and feed our friendly bacteria.

tummy ache
Symptoms of dysbiosis can include constipation.

Rebalancing the gut often requires a dual-pronged approach, as we need to work to eradicate the pathogenic over-growth, whilst encouraging the proliferation of healthy, probiotic microbes.

Let’s look first at how to eradicate the ‘bad guys’:

  • This might require some diagnostic work, in the form of stool testing. Your GP can organise this for you, or if you prefer to take a more holistic approach to your wellbeing then you could work with a nutritional therapist or medical herbalist, who can also arrange a home-test kit for you.
  • Dependent on your individual preferences, an effective anti-microbial protocol may involve either antibiotics from your GP, or nutritional/herbal remedies from a qualified natural health practitioner.
    There are many nutritional supplements with excellent anti-microbial properties, including: allicin (found in garlic), citricidal (found in grapefruit seed extract), oregano, colloidal silver, berberine (from grape seeds), olive leaf extract, and the probiotic yeast Saccharomyces boulardii. Saccharomyces boulardii has demonstrated its anti-microbial effects in many clinical trials. It prevents pathogens from adhering to the gut wall, and also binds toxins19. Health Professionals can read more about Saccharomyces boulardii on the Probiotics Database.
  • Eliminate certain foods from the diet which are known to preferentially feed pathogenic species of bacteria and yeasts, such as sugar11, sweeteners11 and refined carbohydrates.

Here’s how to nourish and nurture the ‘good guys’:

  • Include traditional fermented foods in the diet. Foods such as live yoghurt, kimchi, kombucha, sauerkraut, apple cider vinegar and kefir have been a part of traditional diets for hundreds of years. They contain naturally occurring probiotic bacteria, which support the microbiome.
  • Consume different sources of prebiotic fibre, by including a wide range of fresh fruit and vegetables in your daily diet.
  • Take a well-researched, high-quality probiotic supplement every day. Different strains of probiotic bacteria produce acids and other by-products, which improve the intestinal environment, and favour the further growth of healthy species of bacteria. In this way we can ‘tip the balance’ back in favour of beneficial organisms and a healthier microbiota. You should always choose a probiotics supplement that has clinical research for your main symptoms. So, if bloating is your particular dysbiosis symptom, the best probiotics for dysbiosis in your case would contain strains that are well researched for bloating.


A lot has been covered in this blog, so here is a short summary of the main points:

  • We rely heavily on the gut microbiome to keep us healthy.
  • The microbiome always contains pathogens, but they are usually kept under control by the friendly strains of bacteria.
  • When there is a shift towards greater levels of pathogens and proportionately less probiotic bacteria, this is known as dysbiosis.
  • Causes of intestinal dysbiosis include antibiotics, medications, stress, travel and poor diet.
  • Symptoms of dysbiosis can include gut-based symptoms, such as bloating and constipation, but also more general symptoms such as poor concentration, low immunity and even metabolic syndrome.
  • Correcting dysbiosis can be done by reducing pathogens in the gut with either antibiotics, anti-microbial herbs/nutrients or the probiotic Saccharomyces boulardii. It’s also important to then replenish the levels of friendly bacteria through improved diet and probiotic supplements.

You might also be interested in the following articles:

Gut Health - All You Need To Know

All About The Microbiome

Bloating - All You Need to Know


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