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The Microbiome: Hidden Roots of Your Energy, Mood and Digestive Health

The Microbiome: Hidden Roots of Your Energy, Mood and Digestive Health

How your microbiome affaects your energy, mood and digestion

Right now you are unknowingly hosting trillions of bacteria (now you know). These bacteria come in all shapes and sizes, are of a variety of species and even exist in hierarchical structures. Our bacterial tenants make themselves very much at home within us and do their fair share of influencing how we may be feeling, thinking and acting.

Now you are aware of your bacteria, you may start to think of the idea of ‘you’ as a collective you. The reason your bacteria contribute to the idea of self stretches far beyond just their physical presence within you.

Symbiosis is natures idea of ‘you scratch my back, and I’ll scratch yours’ – a harmonious existence where one organism depends on the other. If one organism breaks the reciprocity, the benefits that both experienced fade away.

Because the presence of bacteria within us and their role they play is becoming better understood; we can now start to live with their existence in mind. For many of us, we have lived with the idea of our mind~body constituting us and us alone. It is this lack of awareness beforehand which has played a surprisingly large role in undermining our health.

Right now millions of people are dragging fatigued bodies around. They are a slave to their emotions and let their fluctuations in mood run their lives. Their digestive complications are sabotaging their quality of life, causing a heavy, clogged, bloated feeling which makes waves in other aspects of their lives. YOU may be one of these people. I know I was.

In order to reclaim our vitality, we need to take a look at how our bacteria shape our health and how we can restore the bonds of symbiosis.

The Microbiome

I bet you have lived, until very recently under the impression that the self you recognise as you, is you and you through. The self that you identify with is a body of cells, tissues, organs, water, hormones, thoughts, emotions, desires, dreams, fears….and the rest.

What if there was more to us than meets they eye? What if there was a force at work which is pulling the strings of our health – mentally, physically, emotionally and arguably, spiritually.

We’ve all heard about bacteria; for most, the emphasis was probably the negative ways in which bacteria can affect us. GERMS, beware of the germs! Of course some bacteria can be pathogenic in nature and cause us harm. On the flip side, there are also bacteria which seek a symbiotic existence with us humans, and many other organisms.

The community of bacteria, and their genes constitutes the microbiome. Your micro biome is unique to you and is present throughout your body. The micro biome of greatest significance arguably, is the one thats housed within your digestive system. Its mostly in the large intestine with a few microbes lodging in the small intestine.

Your gut microbiome is home to 10-100 trillion bacteria  – a number which vastly outweighs the number of cells which constitute your body. Such a number of bacteria can weigh up to 1-2KG! Based on the sheer size, weight and diversity of these bacteria, it is no surprise that such an environment plays a great significance in supporting, or undermining our health.

You are born with an indigenous microbiome; it grows in size and diversity as you pass out of the womb, become coated in bacteria and start to build Bifidobacterium and Clostridium through your mothers breast milk . As you are newly aquatinted with the world, nature has assigned your bacteria to protect you from viruses, infection, toxicity and pathogenic bacteria.

The bacteria which constitute your microbiome are unique to you. They comprise different strains of bacteria of different concentrations. Its balance responds to changes from your genes, your diet, and the environment. The factors which differentiate you from someone else.

The balance of bacteria to one another is very important, as is their diversity. The microbiome is a highly sensitive entity – it is so sensitive that its composition can change in response to your diet within as little as one day!  As well as your diet, the micro biome is very receptive to other influences:

  • Stress
  • Environmental Toxicity
  • Antibiotics
  • Medications/Drugs

These can all alter the diversity and balance of your microbiome, which in turn affects its function and the level at which it remains symbiotic with you.

Your bacteria form a hierarchy within the microbiome. This hierarchy ensures homeostasis within the community and is ultimately what maintains symbiosis with us.

Gut Microbiome

Beneficial Bacteria – These are indigenous strains of bacteria which we inherit at birth from our mothers. These include Lactobacillus, Bifidobacterium, Proprionobacteria …. to name a few.

The beneficial bacteria play a regulatory role over other forms of bacteria. They are like the shepherds of a flock – without them, the sheep run wild. The true masters of the microbiome. They also hold a tight relationship between the mucosal lining of the intestines and our immune system, ensuring a harmonious existence for us, and them.

Opportunistic Bacteria – Are a subset of the beneficial bacteria. These bacteria come in various combinations and concentrations, which can be very unique from person to person. A few include Peptococci, Bacteroids, Staphyiococci. Under the rule of beneficial bacteria, these microbes can be supportive in digestion, assimilation and immunity.

Transitional Bacteria – Environmental bacteria that come from our food and drink, which make passage through our bodies. Again, the shepherds keep a watchful eye on these bacteria. Without the shepherds, these bacteria can cause us ill.

Environmental bacteria that we eat, make passage through our bodies. Again, the shepherds keep a watchful eye on these bacteria. Without the shepherds, these bacteria can cause us ill.

A harmonious community of microbes bounce off of one another much like the population of a small village. Every microbe provides a service to the community. Bacteria meet our needs through their co-ordinated and collective action. When one member of the community drops, or doesn’t pull their weight – it is the host that suffers (us).

The supportive function of the microbiome depends very much on the harmony within the community. Our microbes support us in a variety of ways:

  • Provide a physical, chemical and immunologic barrier between the outside world and us
  • Ferment residual food particles into beneficial nutrients
  • Perform digestive action after regular digestion
  • Provide energy for the gut wall, maintaining its structure and function
  • Regulates the action of the immune system
  • Produce chemical messengers that allow our nervous system and brain to communicate
  • Insure against malnutrition
  • Help regulate a healthy metabolism

Digestive Health

Microbiome and digestive health

Without our bacterial friends, the food we eat may as well be passing through a sieve. Beneficial bacteria act as middle men when handling our food, before passing onto our enterocytes (gut cells) for absorption.

The relationship we have with our bacteria is symbiotic. We feed them, and the products of their metabolism get passed on to us. It just so happens that these metabolites are incredibly important and beneficial for us. It does of course depend on what you feed your bacteria, and which strains of bacteria get their mitts on your latest meal. This depends on your unique microbial profile.

A well balanced community of bacteria process the food we eat by way of fermentation. Following the action of the stomach, pancreas, gall bladder and intestines, beneficial bacteria breakdown amino acids and lipids, and ferment carbohydrates and fibre. Bacterial action also produces a spread of the all important B vitamins and Vitamin K. These get used far and wide across the body and its systems. Not only do they produce these valuable nutrients for us – their metabolites facilitate the absorption of vitamins, minerals, fats, proteins, sugars and the water we take in.

If you feed a balanced community of bacteria quality fibre; they ferment this into Short Chain Fatty Acids. These then go on to support the function and integrity of the gut cell wall. This fortifies us against toxins, pathogenic bacteria, viruses and infection.

On the flip side; if your bacterial ecosystem becomes depleted or imbalanced, some nasty by-products occur from bacterial fermentation. In some cases, certain strains of bacteria can multiply and take over fermentation. When the wrong bacteria get their mitts on your food, an endotoxin called Lipopolysaccharide gets produced. LPS can trigger inflammation, and as a result cause damage to the integrity of the gut cell wall.

Depleted beneficial bacteria leave us exposed to nutrient deficiencies. We need sufficient nutrients – our survival currency for powering the brain, immune system, nervous system, and muscle contraction. You name it, nutrients cover it.

The role of beneficial bacteria in digestion is two fold – to breakdown what we have eaten to facilitate absorption, and provide extra sustenance in the form of B Vitamins, Vitamin K amongst others.


Dont beat yourself up

The relationship between food and mood is well established by now. But how does it come to pass that food can affect our mood? Surprisingly, your bacteria are pulling some strings here.

Amongst the nutrients produced by our microbiome are Neurotransmitters. These are the chemical signalling molecules that allow our nervous system to communicate. You may know these as Serotonin, Dopamine, GABA, Aceytlcholine, Adrenaline, Noradrenaline – the big names.

Certain strains of beneficial bacteria are responsible for producing these chemicals – Lactobacillus produces Acetylcholine and GABA, Bifidobacterium – GABA, Escherichia – Noradrenaline, Serotonin and Dopamine, Streptococcus and Enterococcus – Serotonin. 

Neurotransmitters keep us chemically balanced. They ensure we feel good, happy, safe, alert, relaxed, strong, responsive and adaptive. Neurotransmitter dysregulation, shown by neuroimaging have been implicated with a host of mood disorders. It is uncertain however, whether these correlate with the illness or cause it.

Neurotransmitters make their way from the enteric nervous system to the brain where they allow the brain to communicate. When bacterial action is efficient, we are able to harness abundant neurotransmitters from our food. As much as 90% of Serotonin is produced in the gut. This means that our microbes can affect our mentality, our emotions, our thoughts, possibly even our beliefs. Spooky.


Our bacteria are like the butter to the bread of the gut wall. Bacteria cover the lining of the gut cells to protect against nasties. When our bacteria are well balanced and diverse, they ensure a healthy ecosystem which keeps inflammation to a minimum.

With a compromised micro biome, invaders are able to penetrate the layer of butter and start causing damage to the gut wall, the bread – cue inflammation. To make matter worse, when beneficial bacteria become depleted, the opportunistic bacteria run wild producing more inflammatory byproducts (LPS) which causes further inflammation.

Eventually the bread becomes damaged without the butter to protect it. This allows pathogenic bacteria and toxins to enter into the body where they cause further inflammation by way of an immune response.

Recent evidence has shown that inflammation coexists with mood disorders such as anxiety and depression. The brain can become inflamed due to the action of Pro-inflammatory cytokines. These occur as a result of invaders in the body, hitching a ride through the damaged gut wall into the bloodstream and eventually, to the brain. An inflamed brain doesn’t sound good. It is possible that depression, anxiety and other mood disorders are a warning signal for chronic inflammation, which you may not be aware of.


With a compromised microbiome and damaged gut cell wall, your ability to harness valuable nutrients from your food drops. Amino Acids, Fats, Vitamins and Minerals are the life-force your body needs to keep going. Hormones, Neurotransmitters, enzymes and the backbones of cells are all made from Proteins.

Without sufficient absorption, your body cannot communicate properly, is short of the raw materials to fuel metabolic pathways such as energy metabolism, detoxification, neurotransmitter synthesis and is structurally vulnerable – muscle wasting, bone catabolism.

Thats just Proteins – its a similar story for a lot of other nutrients too.

In terms of mood, hormones and neurotransmitters can become imbalanced and/or depleted which effectively creates a game of Chinese whispers – messages sent are different to the messages received. This disruption in communication has been noted in several mood disorders.


As you know already, depleted bacteria leave the gut wall vulnerable to damage, opening it to viruses, toxins and pathogenic bacteria. When the gut wall becomes damaged, it cannot deal with food particles with the same efficiency.

The digestive enzymes that line the surface area of the gut wall which were once plentiful, are now depleted without the bacteria to nourish them. Therefore, food particles are not processed to the same extent. Two food particles to note are Casomorphins and Gluteomorphins. These are Exorphins – Endorphin like molecules that enter the body from the outside world. These come from the proteins in Dairy and Wheat, Casein and Gluten and mimic the action of endorphins. These can bind to receptors in the brain which influence your mood, throwing you off mentally and emotionally. Evidence suggests links between Exorphins and Psychosis, ADHD, Depression, Schizophrenia. That bread and butter sandwich may not seem so innocent now if you have depleted Gut microbes. 

It is amazing what the presence or absence of bacteria can mean for our wellbeing. It really reveals the delicate balance we must live with other organisms and ourselves!


Microbiome and energy

Because our bacteria play such an important role in our digestion, it is no wonder that their efficiency affects our energy. The nutrients we extract from food get put into action as part of metabolic pathways which synthesise our energy currency, ATP (Adensoine Tri – Phosphate).

B Vitamins

The all Important B Vitamins – Thiamin, Niacin, Riboflavin, Folic acid, Pantothenic Acid, Pyridoxine, Cyanocabalamin are all produced from healthy bacterial fermentation. These get used far and wide across the body, including energy synthesis. They are essential components fuelling the pathway which allows us to build energy in the form of ATP, our energy currency.

Our mitochondria are responsible for using the all important B Vitamins to give us that get up and go we need. These are tiny organ systems that lie within cells, known as Organelles. The mitochondria are present throughout Eukaryotic cells (cells with organelles) throughout the body, especially in muscle cells.


If we lack a healthy community of microbes, we can also miss out on the ability to harness sufficient Iron. This nutrient enables us to efficiently transport oxygen throughout the body via the red blood cells in the bloodstream. Oxygen, as you know very well, us humans don’t do very well without.

Oxygen is also used by the mitochondria to produce our ATP. Plentiful Iron allows the haemoglobin of our red blood cells to pick up optimal amounts of Oxygen.

This is the case for many other substances we obtain from food, such as Co-enzyme Q10 which is responsible for the transportation of electrons throughout the mitochondria, a crucial step in ATP production.

Damaged Gut Wall

Our microbiome protects our gut wall from damage and the infiltration of toxins. A ‘Leaky Gut’ from damaged gut cells effectively means our nutrients are passing through a sieve – some nutrients make it, others don’t. Malnutrition often ensues. You could be eating the best quality foods the world over, yet some will pass unabsorbed. When we lack sufficient nutrition, our bodies struggle to keep its systems running optimally, including those that support our vital energy.


Another consequence of a Leaky Gut from depleted microbes is toxicity. Caso and Gluteomorphins cause quite a ruckus in the body. They are improperly broken down due to depleted/imbalanced bacteria and register as invaders by the immune system. They can cause the immune system to attack healthy tissues of the body, known as auto-immunity. In certain individuals, the immune system attacks cells of the thyroid, affecting its function.

Your thyroid links to the action of the mitochondria, and affects the efficiency of energy production. Those with over and under active thyroids commonly experience fatigue. 

Immune System Activity

When environmental toxins, pathogenic bacteria and viruses seep through a leaky gut, they trigger an immune response. These don’t come cheap – they deplete energy and levels of nutrients within the body. If you are cavalier about what you eat, with depleted gut microbes and a leaky gut, immune responses will be going off left right and centre. You bet this will cost you your precious energy.


Amongst the precious nutrients we can lose out on from deficits in bacterial action are the macronutrients – Protein, Fat and Carbohydrate – the essentials for providing us fuel. These comprise the raw materials which we build ATP from. Carbohydrate breaks down to Glucose, as is Protein in times of Carbohydrate scarcity. Fat, when carbohydrate is lacking gets used to fuel ATP production by way of Ketone metabolism as opposed to glucose. You can measure the amount of energy macronutrients supply in calories.


  • The Microbiome is extremely sensitive to changes in diet, environment, drugs, medications and stress.
  • The state of your Microbiome can influence the way you think, feel and act.
  • Your microbes are as much a part of you as the cells in your body.

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