In part I of the A No Grainer gut health series we were introduced to the gut and learned about the importance of our gut walls. We also learned that leaky gut is a condition that can lead to a host of other ailments. This article covers the gut microbiome and the importance of the bacteria that live inside us. 

Gut flora and the gut microbiome

Microbiota are clusters of microorganisms that live in many different parts of our body. We have skin microbiota, oral microbiota, vaginal microbiota (important for new born babies) and of course gut microbiota. As humans we share many of the same types of microbial colonies, but there are also significant differences, which render us biologically individual (bioindividual).

The gut is a particularly concentrated area of microbiota and these clusters of microorganisms are often referred to as your gut flora. The microorganisms include eukaryotes, archaea, bacteria and viruses. (1)

We have a symbiotic relationship with these microbes meaning they rely on us to survive and we rely on them for good health. The role of the gut and its microbiota is so important for the body that it is now considered to be an ‘organ’. (2, 3, 4)

While the adult gut is a highly populated area of microbes babies are actually born sterile and the colonisation of their gut begins straight after birth. This means we have the ability to influence the health and long-term wellness of our children right from birth. We will discuss this in more detail later.

The gut microbiome


100 trillion

It’s a number that no one can fully comprehend… 

This is estimated to be the number of microorganisms that live in our gut microbiome. (5 Bacteria in our gut have long been thought to exist at a ratio of 10:1 to the number of cells in the entire human body! However, recent research published in the journal Cell suggests that this number might not be as high as was first thought. (6)  Regardless the impact of our microbes is significant.

Our gut acts as a host for the diverse colonies of bacteria that live inside us, and it is these microbes that influence our human differences or bioindividuality. It is estimated that one third of our gut microbiota is common amongst humans and the rest differs from person to person!

To paraphrase Dr Justin Sonneburg, PhD. Department of Microbiology and Immunology Stanford University:

“Humans simply elaborate vessels for the propagation of microbes.” (7)

The gut microbiome is home to more than 1,000 different species of bacteria that between them have over 3 million genes. This is 150 times the number of genes in our entire body. The total content of our gut bacteria is thought to weight as much as 2kg!  (8)

I know that was a lot of numbers to digest, but hopefully you now have an inkling of just how many microbes live inside your gut!

Amongst the 1,000+ strains of bacterial species that inhabit our gut, many are beneficial to our bodies or at the very least innocuous. These kinds of bacteria are essential for the following:

  • Aiding the digestive process, breaking down your food that the stomach and small intestine have not fully digested.
  • Removing waste from the body.
  • Protecting us from illness and infection by preventing the permeation of ‘bad’ bacteria.
  • Assisting the production of vitamins such as B & K and thiamine.
  • Regulating mood and mental wellbeing: approximately 90% of serotonin (your happy neurotransmitter) is produced by gut bacteria.
  • Maintaining the mucosal intestinal lining and thus the integrity of the gut walls.
  • Keeping foreign specimens out of the bloodstream, which is a critical for strong immunity.

So-called ‘bad’ bacteria are referred to as pathogenic and can cause infection and illness. To protect ourselves from pathogens and to ensure our body can perform its functions correctly, it is important to maintain the right balance of these ‘good’ and ‘bad’ bacteria. However, an overgrowth of a certain bacteria can easily occur when the different colonies become disturbed as a result of medication, poor diet and other factors that we will look at later. A slight disruption can result in the ‘good’ colonies no longer being able to regulate the size of the ‘bad’ colonies, which cascade into a cycle of unbalanced gut flora or dysbacteriosis.

Microbial imbalances  

Dysbacteriosis (unbalanced gut flora) can quickly spiral as the damaged ‘good’ colonies in our gut microbiome are overrun by the ‘bad’, meaning the good colonies cannot limit this growth. As the good colonies are overrun they lose their ability to perform other roles such as digestion, waste removal and protection against pathogens. Additionally, as the bad colonies multiply they also create waste by-products. If the growth goes unaddressed the issue becomes twofold: more waste is produced, and the good bacteria become less efficient at waste management. As a result the entire body struggles to cope with the increased waste removal requirements.

the bacteria in our gut microbiome

If the colonies continue to grow without intervention the beneficial colonies become ineffective and we lose our ability to properly digest food and remove waste, and our immunity is lowered. The symptoms of microbial imbalances therefore range far beyond disrupted digestion. Constipation or loose bowels are certainly an indication of dysbacteriosis, however many other conditions that may seem completely unrelated are also being traced back to gut flora imbalances. In fact they can manifest in ways completely unrelated to the gut, such as in mood and behavioural disorders and autoimmunity. (9)

Below I detail some of examples gut conditions that are the result of a disrupted microbiome.

Small Intestinal Bacterial Overgrowth (SIBO)

SIBO is the overgrowth of normal bacteria in the small intestine. This condition differs to dysbacteriosis, which is an overgrowth of ‘bad’ bacteria in the large intestine.  Instead SIBO is when the bacteria in the small intestine become more like the bacteria that should be limited to the large intestine (colon).

The body is normally able to prevent the onset of SIBO because our stomach acid breaks down food and we have antibodies in our intestinal fluid. We also have a valve (ileocecal valve) between our small and large intestine, which allows substances to pass through from the small intestine, but not back towards it.(10) However, when one of these functions isn’t working correctly SIBO can develop. Therefore low stomach acid, irritable bowel syndrome (IBS), coeliac disease and bowel surgery are risk factors for SIBO. Additionally, heavy alcohol consumption and the contraceptive pill have been associated with SIBO as they can disrupt your gut flora.

If untreated SIBO can damage the integrity of the gut wall, which in turn inhibits functions such as digestion and nutrient absorption. Symptoms are wide ranging and difficult to treat because the overgrowing bacteria are fed by the same things as the regular bacteria. Additionally the imbalance of bacteria can further affect our digestive abilities. If you suspect this might be something that you might be affected by I would advise that you do some more research and consult a medical practitioner or naturopath. Dr Allison Siebecker’s site has some useful information and would be a good place to start.


As well as diverse bacteria our microbiome is also home to yeasts. Candida is one of these yeasts that is normal in the gut and exists in a competitive environment with our good bacteria. This competition is healthy and normal, and these two microorganisms work synergistically to regulate each other. However, if something happens to reduce the number of good bacteria in the gut, Candida can easily take over. Candida yeast feeds off sugar so many of the foods we consume from refined sugars and bread, to fruit and vegetables, can further promote its growth.

Once Candida has taken over it wants to stay alive. To do this it needs sugars therefore crazy sugar cravings are a common symptom of Candida overgrowth. It’s a pretty vicious cycle, the more sugar you consume the more you feed the Candida. The more the Candida grows, the more sugar you crave.

Another particularly unpleasant symptom of Candia overgrowth is thrush. For women who have experienced this, you will know that it is not much fun. For vaginal thrush symptoms you can easily get an oral or pessary treatment from your pharmacy, but being aware of some dietary interventions can also be useful.

Candida can be difficult to treat, but there are protocols that exist and have proved helpful for many people. You have to actively starve the yeast so it can be a fairly long process that requires commitment.  As a precaution it is a good idea to limit your consumption of sugary foods and other things like grains that are nutritionally depleted carbohydrate sources.

If you are concerned about Candida overgrowth I think Christa Orrecio’s protocol is balanced and helpful.

I hope this post has provided you with a basic understanding of the gut microbiome and the importance of a healthy bacterial balance for overall wellbeing. In part III of the gut health series we will look at the many conditions that are influenced by our guts – there are way more than you probably think!

Pin It on Pinterest

Share This
%d bloggers like this: