How can single celled organisms rumbling around in your stomach possibly be connected with all the world’s auto-immune conditions as well as autism, ADHD, stress, anxiety and depression?

Those single celled organisms, mostly referred to as gut bacteria, perform extraordinary tasks of which we are blissfully unaware. They also wreak havoc on our entire bodily system when they are not treated with respect and fed the food that they need!

Gut microbiome may not have been in our language ten years ago, but it certainly is today.

  • many people know that they have poor digestion of some sort, potentially with diagnosed leaky gut, Crohn’s Disease or Irritable Bowel Syndrome
  • many people also have a relatively mild ailment, but may not know it’s an auto-immune condition – food allergies, eczema, psoriasis, asthma, alopecia are all ‘mild’ versions of auto-immune disease
  • some will know that they have one or more debilitating auto-immune conditions – Coeliac, Multiple Sclerosis, Rheumatoid Arthritis, Lupus, Diabetes
  • many children suffer differing levels of Asperger, Autism, ADHD, or poor concentration and severe mood swings
  • many children and adults suffer from stress, anxiety or depression
  • Other people have some form of chronic inflammation creating illness, pain or discomfort

At some level, an imbalance in the gut will be connected with ALL of these conditions

My goal in this article is to explain, in simple terms, how and why a decline in gut health occurs, what the consequences are, and some suggestions for reversing health conditions or stopping them from occurring.

What is your gut microbiome?

Your gut microbiota consists of fungi, bacteria and other single cell organisms. Like all things in nature, when these organisms are in balance, they perform extraordinary tasks of which we are blissfully unaware. This includes:

  • Digesting our meals – breaking down food and beverage particles for the body to (a) absorb the nutrients it wants and (b) excrete the rest
  • Ruling our immune system
  • Ruling our metabolism
  • Protecting us against disease
  • Shaping which parts of our DNA manifest and which remain dormant

We mostly only become aware of our body and its functions when some sort of imbalance occurs, and it starts giving us signals of discomfort.

What we may not realise is that an imbalance in the gut is the source of most mild or serious chronic ill health, even though it may have manifest as something that appears to be completely unrelated to our digestive system!

Ninety percent (90%) of all cells and all genetic bacteria in our bodies is our gut flora. The body is really just a habitat for these mass of microbes inside us. Our chromosomes have about 22,000 genes in them. But we have 3.3 million microbial genes that we use to conduct most of our biochemical functions. Rather than our bodies being a collection of organs (heart, brain, lungs) all connected by vascular tissue, we are instead an ecology which only stays stable and healthy with proper balance. Once the ecology has been destroyed there will be a trickle-down effect on the rest of the garden.

What creates an imbalance in gut bacteria?

The mass of microbes that live inside our gut is a highly organised microbial world of trillions of varieties of bacteria, fungi, protozoa, worms and other creatures all living together. In a healthy person, all these creatures live in harmony with each other, feed each other and control each other. However, we frequently interfere with that world. For example, when we take antibiotics, this kills some of the bacteria in that microbial world and creates an imbalance. Once this imbalance is generated, then pathogenic microbes start proliferating and overgrowing. As the imbalance continues, other healthy microbes in the food chain die as well, allowing the pathogens to dominate further rather than be kept under control. As a result, the whole ecosystem goes wrong. Sometimes, if the imbalance in your gut is extreme, then even good food can become toxic. This creates extreme frustration for people who are trying to correct their diet but still suffering serious digestive issues.

Does the gut affect the immune system?

If we accept that our immune system needs to be strong in order to sustain good health, then it is important to understand what governs our immune system. Eighty percent (80%) of the immune system is set up in the gut itself. That 80% also dictates how the rest of the body’s immune system will function. Messages that you get and build up in your gut are the messages that are sent out to all the other organs and tissues in the body, including the brain. The gut also has its own nervous system, called the ‘enteric nervous system’ that lines your intestinal tract. This gut nervous system functions independently of your spinal cord and your brain, gathering and distributing its own messages. When gut health is very poor, the immune system functions in overdrive and inadvertently delivers false messages in an attempt to resolve the issue, instead exacerbating current symptoms.

How is the gut wall relevant?

It is the integrity of the gut wall that is at issue here.

The mucosa is the innermost layer of the gastrointestinal tract. It comes into direct contact with digested food. Most bacteria in our body reside in this mucosal layer which only stays stable and healthy with proper balance. The breakdown of this mucosal layer is where it all starts. What follows is a range of different chronic health conditions. The way disease manifests in your body will be different between individuals, but they all have the same origin and the breakdown of the same system – the digestive system resulting in the breakdown of the gut wall. Once part of the ecology is destroyed there will be a trickle-down effect on the rest of the body.

As already mentioned, this mucosal layer is where most of the microbes live. It is also where our key immune tissue functions and immune communication occurs. Part of this mucosal layer is the inner cellular lining which is the last barrier between the outside and inside of the body. It is called the epithelial layer and it is only one cell thick! The mucosal layer acts as the defence for this one cell lining. The intestinal tract is considered the ‘outside’ of the body because it comes into contact with outside influences that are ingested.

Overgrowth of bad bacteria in the body creates dysbiosis or imbalance. This can occur through lifestyle, antibiotic use, chemicals in processed foods and many modern food choices. This dysbiosis leads to a weakened digestive system due to the destruction of healthy bacteria resulting in the over-growth of pathogenic bacteria. It also leads to a breakdown of the mucosal layer.

At this point, the body starts to recruit immune cells to try to protect the mucosa. When the body tries to ‘right a wrong’ its natural immune response is to draw on inflammation to counter the attack. In isolated incidences (acute inflammation), this works well, and the body returns to balance after the inflammation has destroyed the pathogens. Constant onslaught, as exists today for many people, means that the inflammation becomes chronic or permanent, rather than occasional. This inflammation causes the thin inner-cellular lining to open up which allows all the substances ‘outside’ the body in the digestive tract to leak through the weak mucosa and ‘inside’ the body to the blood stream.

How does this relate to auto-immune conditions?

Connection between our gut and chronic health conditions become easier to understand when we recognise that this mucosal layer, apart from conducting our digestion and most of our immune function, also separates our blood system from the outside world. The blood system is considered the ‘inside’ of the body because it should have no access at all to the outside influences. Once constant inflammation is enacted by the body’s immune system, the single celled epithelial layer of the mucosa becomes compromised. The ‘tight junctions’ that hold those single cells together start to move apart and turn this once protective layer into a sieve, letting through material that does not belong in the blood stream.

The body’s immune cascade that follows is due to three main areas of activity:

  1. First the balance of bacteria and other organisms has been compromised and pathogenic bacteria start to dominate
  2. To mount a response to this imbalance, the immune system activates and calls on inflammation to attempt to destroy the pathogenic activity.
  3. When chronic inflammation sets in, this causes the epithelial layer (the final single celled protective layer that separates the digestive system from the blood system) to weaken. The cells move apart, leaving access from the digestive system into the blood stream.

The movement of unwelcome material from the digestive system into the blood stream includes bacteria and other organisms, partially digested food, and immune cells, none of which belong in the blood stream of a balanced body.

This causes systemic immune activation because the last line of defence has been penetrated. Once leaking gut occurs, then the body starts to react to all its proteins which are the building blocks of the body. Continuing the cascade, this systemic immune activation looks something like this:

  1. The immune system first identifies undigested particles of food and other substances that have passed through the gut wall.
  2. It then develops antibodies against these proteins in order to destroy them (because they do not belong where they have been found in the blood supply).
  3. Proteins in the body and in the foods that we eat are very similar, so it then finds a similar type of protein in your own body and incorrectly attacks it as well.

The part of the body being attacked could be the pancreas creating diabetes, the skin creating eczema or psoriasis, the hair follicles creating alopecia, the lungs creating asthma, the optic nerves creating optic neuritis, and so it goes on.

This is how auto-immune conditions occur. And it all begins with an imbalanced gut flora! Simple, yes?  And also, a little complicated!

What do we do about it?

I often think that the first step to correcting something is to recognise and understand it. I like to make sense of something before I am committed to it as an action. I hope this explanation so far has at least given you some new concepts to think about, and potentially something to follow up with for yourself.

The simple goal of imbalanced gut bacteria, or gut dysbiosis, is to rebalance that bacteria. It does depend on the level of seriousness of your condition as to the sequence of steps to be taken. However, there are common actions for all gut conditions which will form the foundation of improving your health. Any, or all of these, will be helpful.

  1. Go camping or to the beach on the weekends, to destress your body and let you breathe in different healthy microbiome to increase your gut diversity.
  2. Introduce bone broth from organic or pasture-raised animals into your diet. Bone broth is on the top of the inclusion list for all gut health dietary recommendations that I am aware of. It is an immensely healing food that plays a direct role in healing and sealing the gut wall. The only small caveat here is if your gut condition is very poor then short-cooked (two hour) bone stock may be all your body can handle rather than the recommended 5-6 hours for chicken bone broth and 24 – 48 hours for beef, lamb or goat bone broth.
  3. Fermented foods such as natural unsweetened yoghurt, sauerkraut, kombucha and beet kvass have all been pre-digested in the fermentation process and provide a range of healthy bacteria to the gut.
  4. Refer to my expanded list of traditional food preparation techniques for added ideas.
  5. Take a look at the changes we have made to our pantry and fridge in recent years.

These suggestions are embraced by organisations that promote the preparation and consumption of foods as practiced by traditional cultures. You can also read previous blogs titled ‘Simple Steps to Healthy Eating’ and ‘Bone Broth – the Healing Powerhouse’.

These food practices were also used by many families in our western societies prior to the expansion of the industrial food system after WWII, probably the way that your grandmother used to cook.  We are so lucky that people are starting to record these practices in modern recipes to allow us to reintroduce them into our lives!

What about brain function?

In this article I have focused on auto-immune conditions and an explanation behind their occurrence. In the introduction, I also mentioned some conditions of brain function such as Autism, Asperger, ADHD, anxiety and depression. Although there is not space to include further detailed explanation, what I have already explained so far about gut health is also true for these conditions. The added complexity is the breakdown of the blood-brain barrier. The endothelial lining of this wall is also only a single cell thick.

The decline in the gut lining, allowing toxins into the blood stream, can eventually also destroy the blood-brain barrier and toxins then accumulate, upsetting the function of the neurotransmitters in the brain.  In addition, aluminium, mercury and formaldehyde, are known to be neurotoxic chemicals and are often associated with poor functioning neurotransmitters. Sometimes they bypass the gut wall altogether when they are injected straight into the blood stream such as with vaccinations. Glyphosate is also present in the industrial food system. It directly breaks down the gut wall and quickly makes its way through the blood-brain barrier.

A healthy body copes much better with these neurotoxins as it is able to undergo some natural detoxification when the body recognises the assault. So even if you don’t undergo a specific detox program for any of these toxic conditions, you may find that adopting the approaches above will still strengthen your body enough to begin that detoxing naturally.

Where can I obtain further information?

Please send your comments or queries from this article through the blog reply at the bottom of this post. I will attempt to guide you to more specific information that may be of assistance to your individual enquiry.

Also, I regularly give presentations on a variety of topics, such as ‘Gut Health Made Simple’ and ‘Foods That Heal’. If you would like me to speak to a local group, please contact me and I will be happy to discuss this with you.

I wish you well with your improved health! In the meantime, remember … ‘Let nature be the doctor’.


Dr Natasha Campbell McBride – podcasts

Keiran Krishnan, microbiologist – podcasts

Dr Zac Bush – podcasts