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09 Apr 2021
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.
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:
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’.
It is widely accepted that the greater the diversity of microbes in the gut, the better.
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.
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.
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.
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.
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.
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:
Other symptoms include:
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.
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’:
Here’s how to nourish and nurture the ‘good guys’:
A lot has been covered in this blog, so here is a short summary of the main points:
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