What is the Gut Microbiome?

What is the Gut Microbiome?

So our microbiome is what makes us uniquely individual – not our DNA.

What is the microbiome?  How does it influence who we are and how we feel?

what is the gut microbiome
Pictorial of gut microbiome

Microbiome – collection of microorganisms bacteria, fungi, viruses, protozoa and parasites – not visible with the naked eye but under a microscope there are trillions and trillions of these microbes.  We are covered from top to toe, inside and out.  We have far more microbial cells than we have human cells, about 39 trillion bacteria living in us!

They cover every millimeter of our bodies.  They  are on all external surfaces – Skin, mouth, genitals – but the highest concentration exists in your colon.  We are in fact whats called a Holobiome, a walking talking rain forest, an extremely complex human ecosystem, made up of thousands of different species that have to work together in order to convert the health and benefit of the whole.

The Microbiome is the collection of organisms and all of their genetic elements in relation to the host – that’s us, we are the host. They go to work in your colon and are a critical part of human health.

There has never been a moment in human history that we didn’t have a relationship with microbes.  Your microbes are your best friend.  They are so important to our health, regulating our digestion, metabolism, immunity, balancing out hormones and affecting our brain health.  They can even affect the expression of our genetics.

So the most important thing to human health turns out not to be human!

The Human Genome project that launched in the early to late 90s, to map out our entire human genome, our genes, DNA that’s found in our chromosome.  The idea behind that, was, for every disease state that was known of,  there was probably a gene that was either messed up or mutated and maybe we could use something like gene therapy to address these issues.

The amazing thing that was discovered was that we have very little genetic material considering how sophisticated we are. 

The human chromosome has around 22 to 24 thousand functional genes compared to something like an earthworm that has around 38,000 or a rice plant that has somewhere between 30 to 40 thousand functional genes, making us much less sophisticated in comparison in terms of our genetic material.

Big Question – how is it that we are so sophisticated?  How do we conduct the thousands upon thousands of biochemical reactions that occur every minute of every day?  How is it that we can have consciousness and intelligence to develop new technologies with our miniscule amount of genetic material? The answer Epigentics

Misconception of our Genes

After in depth research genome project, it turns out that our health is not dictated by our genes or our parents or our grandparents genes.  It is actually influenced by Epigenetics.


Is a layer of instructions over our genes and changes the way genes work based on our behaviour, food and the environment and even exercise and movement.  These “labels” act like start/stop or on/off switches, activating and deactivating certain functions.

The interesting thing about Epigenetics is that they change after we are born. Your lifetime exposure changes the epigenetic footprint on your DNA and this affects how your immune system works.

So the question is, can we change our exposure as we get older, so that our immune system gets better and works for longer? The way that we spend time in nature, the way that we eat and our stress levels or levels of joy, all determine our epigenetics, how genes are read and translated is what ultimately really determines our health.

What is the connection to the Microbiome?

We are all unique based on our environment and our cultures, but the beauty of epigenetics is that we can turn on and off genes based on how we live, our lifestyle, thoughts and of course our food.  These all make up the genetic make up and expression of ourselves.

We already know that there are some countries where our “western diseases” are quite rare, and yet as they become socio economically developed, they too start to develop these diseases.  So what is it about our modern lifestyle that adds so much risk to developing obesity, diabetes and autoimmune conditions?

Fergus Shanahan  set out to find a group of people, a human model of modernisation.   People who were of the same genetic make up as “us” but not yet affected by our modern diseases.  He found them in the form of Irish Travelers 1% of the Irish population.  He discovered that their microbiome was much like that which we see in studies of our ancestors and nomads in other parts of the world.

We are a living breathing eco-system

What he found was, when comparing the microbiome to “westernized” individuals, was that they had a very diverse and unique microbiome.  They were not only protected from autoimmune diseases but their microbiome has been mainly influenced by some of the elements of an ancient lifestyle.  

In summary the findings were that their living conditions, large family sizes and early exposure to household pets and other domestic animals, allowed them to retain their ancient microbiome.  This is compared to the rest of society who are losing their microbiome.

Nature has a huge influence on our microbiome, from touching our surroundings to inhaling the air in our environment.  This brings a super important dimension to being outside in nature to bring about a favourable influence on our microbiome.

The Microbial Ecology 

The 2.5-3 million microbial genes in our system are over 120 times more microbial DNA than human DNA.  So this accounts for over 90% of all our biochemical functions, everything that makes us human.

In essence the Human and Microbial genes interact with each other to create functions that we have as a human organism.  So we have harnessed the capacity of microbes to do what our human genes cannot.  This includes breaking down certain molecules and vitamins from plants for example.  So with the help of the unique enzymes of the microbiome, it helps break down our veggies and access the nutrients we would otherwise have difficulty doing so.

Symbiosis with our microbiome means we function as a whole organism.

Our health is never about just one thing, we need to look at the whole picture if we want to improve our health.