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What is the ‘Microbiome’? And how does it Influence our Health?

Did you know there is a huge community of microorganisms (bacteria, viruses, fungi and archaea) that live in and on our body – outnumbering our cells by 10:1 and our genes by 100:1?

The name given to these microbial organisms is ‘The Human Microbiome’.
Scientists have been researching this over the last twenty years and have discovered these microorganisms are essential for our health and wellbeing.

What is the Human Microbiome?

The community of microorganisms that live in and on our body is called the Human Microbiome. This includes trillions of bacteria, fungi, viruses and archaea that have co-evolved with us (humans) over millions of years.

We are hosts to many different species of microorganisms all living together in communities. They communicate with one another and indirectly with us.

It is estimated we can harbour from two hundred to more than a thousand different species within our body. Bacteria are the most abundant of these microorganisms.

We have an Intimate Connection with our Microbiome

Our microbiome connects and communicates with us intimately. They send signals and messages to each other and influence the expression of our genes. They are able to evolve quickly, swap genes, multiply and adapt to changing circumstances within us.

They have access to every part of us, as they circulate throughout our body, ending up in different organ systems and influencing their function depending on the species type and where they live in our body.

We have a ‘symbiotic’ relationship with them and regard them as ‘our friends’ – we need them as much as they need us for survival. And just like any friendship, it works both ways – if we look after them, they will look after us!

Where do our Microbiome organisms live?

Each part of our body provides a different environment for Microbiome organisms. Different species of microbes have adapted to specific habitats, depending on where they live.

The largest and most important microbial habitat is in our gut. The lining of our large intestine (colon) has the highest number of different species of organisms in our body.

Others are found within various tissues, fluids, glands and mucous membranes – including our internal organs as well as our external reproductive organs, our skin, mouth, nose, eyes and even in the lining of our blood vessels… they are everywhere!

What are the functions of our Microbiome?

Our microbiome has specific jobs to do depending on their species and where they live.

Some microorganism species living in the lining of the gut (e.g. Bifidobacteria, Lactobacillus, Akkermansia, Faecalibacterium) will ensure the cells lining the gut are healthy enough to provide a good barrier to prevent pathogenic (disease-causing) organisms from entering the digestive tract and causing infection, gastrointestinal disorders, immune dysregulation as well as nervous system, metabolic and reproductive system disorders.

Hypocrites, the father of medicine, quoted: ‘All disease begins in the Gut’.
Now, more than two thousand years later, this famous quote has been proven to be correct (according to rapidly increasing amounts of scientific literature).
In fact, this has led to the more nuanced quote in modern-day scientific circles: ‘All Health and Disease begin in the Gut’.

All in all, our microbiome is vital for the healthy functioning of our Digestive system; Nervous system; Immune system; Reproductive system and Metabolic system.

Variety is the Spice of Life!

Because we humans are such complex beings, we need a large variety of different species of microorganisms in order to carry out a variety of different tasks.

As I mentioned before, our large community of microorganisms (bacteria, fungi, viruses and archaea) living symbiotically with us are all important for our health. I know it sounds strange to think that it’s considered ‘healthy’ to have bugs such as bacteria, let alone fungi and viruses living in and on us, but researchers have discovered (and are continually discovering) reasons for their presence.

Because each species has different functions, the more variety of different friendly microorganisms we have, the more diverse our microbiome and the healthier we are.

In this regard ‘variety is the spice of life!’

Our Microbiome – Friend or Foe?

Our microbiome is made up of both friend (commensal) and foe (opportunistic) bugs. We actually need both in their right numbers to keep things balanced and stable.

If our commensals are low in number and variety, our opportunistic bugs will take advantage of the situation, grow in numbers and cause an imbalance in the environmental ecology. This is called ‘dysbiosis’.

How does Dysbiosis affect our Health?

An imbalance between the types of organisms present in our natural microbiome is thought to contribute to a wide range of chronic diseases.

There is much ongoing scientific research and published papers discussing how dysbiosis and intestinal permeability (leaky gut) are often the drivers of inflammation and hence chronic disease.

Some examples of dysbiosis-driven chronic diseases include cardiovascular disease, obesity, diabetes, depression, anxiety and other mental health conditions, inflammatory bowel disease, irritable bowel syndrome (IBS), ulcerative colitis, Crohn’s disease, allergic disorders, skin diseases such as eczema, acne, autoimmune diseases such as rheumatoid arthritis, and also neurological diseases such as Parkinson’s disease, ADHD, autism and Alzheimer’s disease.

What does our Microbiome feed on?

We need to keep our friendly organisms strong, healthy and in good numbers. Like all living creatures, our microbiome needs to be nourished to live and function properly.

When we eat, all the nutrients get absorbed into our bloodstream via the small intestine. The left-overs – whatever we aren’t able to digest which is mostly fibre, end up in the large intestine where most of our microorganisms reside.

The job of our friendly ‘commensal’ organisms is to munch on this (human indigestible) fibre and produce metabolites called ‘Short Chain Fatty Acids’. These are very important substances that prevent inflammation and are used to keep the gut lining and our mucus membranes healthy and disease-free which as I’ve explained, prevents inflammation and chronic diseases.
These metabolites are also used to make essential vitamins especially all the vitamin B’s, including folic acid.

Nutritional psychiatry research has shown that the bacteria in our gut make many of the calming neurochemicals in our brain, such as serotonin, GABA, dopamine, adrenalin and noradrenalin. In fact, 95% of all our serotonin (the feel-good hormone) is produced by our microbiome.
There is two-way communication between our microbiota and our brain – this is called the ‘Gut-Brain Connection’. This communication may occur directly through these neurochemicals or via the Vagus Nerve.
So, when we address gut health, we can often help to eliminate or ease anxiety and other mental health disorders, and vice versa – i.e. when treating anxiety, we often end up improving gut health.

Alcohol, smoking, recreational drugs, certain medications, antibiotics, antimicrobials, processed foods (including sugar – real and artificial), flavours and colours will starve or kill our commensals. So we end up feeding and increasing the numbers of opportunistic ones instead.

These opportunistic organisms devour all that processed stuff and produce ‘Lipopolysaccharides’. These substances get into our bloodstream, travel all over our body causing havoc! They bring about inflammation and interfere with our immunity, fertility, mental health, digestion and our hormones.

Where does our Microbiome originate?

It all starts with our mothers!

Right from the beginning of life, the foetus is exposed to small amounts of the mother’s unique microbiome through the amniotic fluid, the umbilical cord blood, as well as the placenta.
From birth, the microbiome will influence the development of the baby’s immune system.

If this process is disrupted, there is an increased risk of developing many inflammatory and allergic conditions including allergies, food intolerances, asthma, eczema and autoimmune diseases.

What’s the best way to look after our Microbiome?

We need to keep our friendly organisms strong, healthy and in good numbers. Like all living creatures, our microbiome needs to be nourished to live and function properly.

To keep your microbiome healthy and nourished:

  • Eat real, unprocessed foods – organic, seasonal variety is best.
  • Eat a variety of foods that provide a diverse range of essential microorganisms (Probiotics) e.g. fermented foods such as yoghurt, kefir, kimchi, sauerkraut, kombucha and tempeh.
  • Consume plenty of diverse fibre from fruits, veggies, beans, legumes, nuts, seeds, berries and whole grains (Prebiotics). These provide nourishment for the good micro-organisms to grow and reproduce.
  • Look after your oral health – brush and floss your teeth every day.
  • Aim to get a good quality 7-8 hours of sleep every night.
  • Connect with nature and soil microbes – gardening, hiking, having a pet animal.
  • Keep physically active – do exercise daily.
  • Socialise and become community involved.
  • Reduce stress – yoga, meditation etc.

Naturopath and Microbiome Analyst

As a  Naturopath and Microbiome Analyst, I place a huge importance on the microbiome health of all my patients.

This is especially the case for those who have been diagnosed with mental health issues and chronic diseases such as cardiovascular disease, obesity, autoimmune diseases, allergies, neurological diseases, gastrointestinal disorders, as well as hormonal imbalances and fertility-related issues.

I will design a naturopathic programme to suit each person individually – personalising my prescription according to their needs.

I always discuss diet, oral health, exercise, stress reduction and sleep, as these are very important features known to impact health and wellbeing.

Sometimes I might prescribe specific prebiotic fibres to help increase the abundance of certain friendly organisms – if I’m led to believe, through microbiome analysis, that they are in low numbers.

And in certain circumstances, if I think it’s appropriate, I may prescribe a specific probiotic strain alongside this. But I only prescribe those strains that have been researched in well-designed clinical trials to provide a particular health benefit for the specific condition I am treating.

I hope my explanation has helped you understand the vital role that a healthy microbiome plays in health and vitality!

Joanne Lipinski – Integrative Naturopath Melbourne