What is Dysbiosis?

Kathy Wheddon Nutritional Therapist DipION

What is dysbiosis and what are the symptoms?

Simply put, the word ‘dysbiosis’ is the term given to an imbalance in the gut microbiome. We’re all becoming aware of the importance of good gut health, but how do you know when things are out of balance, and if so, what do you do about it? Read on to find out everything you need to know about gut dysbiosis, and how probiotics might help.

In this article we look at:

What does a healthy gut microbiome look like?

The short answer is that we are not yet sure, as no two microbiomes are the same. There is a huge degree of diversity from one individual to another, even in the absence of any obvious ill health or disease. 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.

Humans have trillions of bacteria and other microbes living within their digestive tract. These populations of microbes can be divided into three types: the ‘good guys’ (also known as probiotics) which offer benefits to their host, the ‘bad guys’ (pathogens), which can be harmful in large numbers, and ‘commensals’, which are benign, offering neither benefit nor harm to their host. The collective name for these colonies is the gut microbiome, and the health of the microbiome plays a surprisingly large role in our overall health and well-being. Find out more about the microbiome in Dr. Kate’s informative article.

It’s normal to have a mix of all three types of microbes in the gut, and even those with no obvious signs of ill health at all will still play host to pathogens. Pathogens may also include viruses, parasites, and yeasts, such as Candida albicans. Health professionals can read more about Candida overgrowth on the Professionals site.

However, as long as there are enough beneficial microbes to keep pathogen populations in check, they do not pose us any great problem. It is when there is a shift in the composition of the gut microbiome towards a higher proportion of pathogenic versus probiotic microbes that problems arise. This situation is referred to as ‘dysbiosis’.  

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

1. The types of bacteria found in a healthy gut1 

Two studies 2,3 have shown that healthy gut microbiomes (as assessed by bacterial gene sequencing) are consistently dominated by bacteria from two phyla (classes of bacteria): Bacteroidetes and Firmicutes. However, these phyla are huge, so it still leaves a multitude of different combinations of bacteria (belonging to these two groups) which could be considered a ‘healthy’ microbiome. (Read more about Firmicutes and their impact on our metabolism)

2. The number of different microbial ‘families’ inhabiting the gut2

It is widely accepted that the greater the diversity of probiotic microbes in the gut, the better. They have some common characteristics, like discouraging pathogens, but all probiotics fulfil slightly different functions. Therefore having a good variety of bacterial ‘families’ means that we might benefit from a broader spectrum of benefits.

3. Stable populations of microbes

It is generally accepted that a healthy gut microbiome is relatively stable. Reducing exposure to factors that can disrupt the delicate balance of gut microflora, such as antibiotics18, is essential to maintain this stable environment.

What causes dysbiosis?

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

Anything that shifts the health of the microbiome in such a way that it becomes less able to keep us healthy, is a factor for dysbiosis. Many external influences and lifestyle factors have a detrimental impact on the gut microbiome, including:

1. Antibiotics

Taking a course of antibiotics is well known to reduce the numbers of beneficial bacteria living in the gut, at the same time as reducing the pathogens that the drugs are being taken for. Whereas some species of friendly bacteria recover to some degree after antibiotic treatment ends, other species may be lost forever. The loss of friendly bacteria weakens the community’s future ability to exclude pathogens9 and prevent infections.

2. Certain medications

Certain medications are known to cause dysbiosis, by damaging the delicate gut lining and affecting the gut microbiome. Such medications include: NSAID’s, the contraceptive pill, HRT and steroid medications

3. High sugar diet

High sugar diet has been shown in studies to have a detrimental effect on the gut microbiota, by preferentially feeding yeasts and pathogenic species of bacteria, above beneficial strains of bacteria10. Additionally, a 2020 study discussed the possible negative effects of ‘novel’ or new types of sugars, such as chemically derived sweeteners and sugar alcohols on the gut flora. The study11 summarised that pathogens appear to have a greater ability to use and adapt to these new sugars than friendly bacteria species do. This could lead to further proliferation of ‘bad’ strains of bacteria in the gut, as we seek lower calorie, but often man-made alternatives to natural sugars.

4. 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 has ‘lasting’ negative effects12.

5. Hormones

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

6. Stress

Stress 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, can make our gut ‘leaky’ or more permeable than it should be. Stress also alters immune activity in the gut and causes changes to the bacterial population that lives there13.

7. Age

Although not truly a lifestyle factor, our age can also have an impact on the microbiome. As the microbiome develops in an infants early years, we see significant changes. It then starts to stabilise before changing again significantly through pregnancy, menopause and as we enter old age. Read more about the microbiome in childhood years.

8. 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), including: E coli, Shigella species, Campylobacter species and Norovirus14.

However, it is not only pathogens encountered in foreign destinations that can lead to dysbiosis when we travel. When we sleep may also be a factor. Doctors at the Weizmann Institute in Israel conducted fascinating research which showed that the activities of our gut bacteria follow a distinct circadian pattern. The research results showed that when the ‘host’ was asleep the microbiome was different to when the host was awake. This could explain why foreign travel, and the resulting change to our sleeping and eating times can greatly affect the microbiome, and cause digestive symptoms15.

What are the symptoms of dysbiosis?

When the gut microbiome is out of balance, symptoms of dysbiosis can arise. These symptoms may be felt principally in the digestive tract as digestive disturbances, but there may also be knock-on effects in other parts of the body, such as the immune system and organs of elimination, for example.

Probiotics produce beneficial metabolites, such as Vitamin K and short chain fatty acids, which can be used by the body, whereas pathogens produce toxins. When we have greater quantities of undesirable microbes in the gut, the organs of elimination (liver, kidneys, skin) must work harder to breakdown and then eliminate their toxins. Signs of poor detoxification can often be seen on the skin, with the appearance of skin conditions such as eczema, acne, psoriasis.

Emotional health may also suffer due to the impact of dysbiosis. ‘Psychobiotics’ is 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. Read more about the gut-brain axis and probiotics.

More recently links have been found between gut dysbiosis and certain metabolic conditions, including: Type 2 Diabetes, Metabolic syndrome and even obesity18. Inflammation caused by an imbalanced microbiota is thought to play a causative role in metabolic ‘dis-regulation’. In the case of obesity it has been observed that certain types of bacteria allow for a greater ‘harvest’ of energy from the foods that we eat, whilst also altering levels of available short-chain-fatty-acids in the gut. Read more about gut bacteria and obesity here.

Gut-related symptoms, 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
  • Allergies16
  • Metabolic syndrome16
  • Obesity18
  • Fatigue

How do I address dysbiosis?

So, how can we overcome dysbiosis, and recover from the myriad of possible symptoms that might arise as a result of it? 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.

Healing gut dysbiosis 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’:

Stool testing

It can be useful to know which pathogens are present in your gut, and how many there are. 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. Read more about stool testing.


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,


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.


The probiotic yeast; Saccharomyces boulardii is one of the best probiotics for dysbiosis, and has demonstrated its anti-microbial effects in many clinical trials. It works in several ways, including preventing pathogens from adhering to the gut wall, and also binding their toxins17 You can find this strain in Optibac Saccharomyces boulardii.

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

Fermented foods

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.


Include different sources of prebiotic fibre in your daily diet, by including a wide range of fresh fruit and vegetables, pulses and whole grains.


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.

Several probiotic strains, including the strain Lactobacillus acidophilus NCFM ® have been studied and shown in clinical trials19 to help restore and stabilise the gut microbiota following antibiotic therapy.

You should always choose a probiotic 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.

For those lucky few that do not show any signs of an unhappy gut, taking a high-quality probiotic every day still has great benefit, as it helps to prevent any future issues.                                                                            


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

  • We rely on the health of 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, include gut-based symptoms, such as bloating and constipation, but also body-wide symptoms such as poor concentration, low immunity, and even metabolic syndrome.
  • Correcting dysbiosis can be done by eradicating pathogens from the gut with either antibiotics, anti-microbial herbs/nutrients or the probiotic Saccharomyces boulardii. Coupled with replenishing the levels of friendly bacteria through improved diet and probiotic supplements.

Health Professionals can read more about Saccharomyces boulardii and Lactobacillus acidophilus NCFM ® over at the Probiotics Database).


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