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The mighty microbiome

Eve Kalinik provides an overview of the microbiome and looks at the links between the gut and the brain

Microbes might be tiny but their effect on our health and wellbeing is something of epic proportions. These trillions of microscopic organisms and their genetic material, which live in and on us, are collectively referred to as the human microbiome, with the largest community existing in the gut.

It is important to understand and clarify some of the terminology around this subject as it can be a bit confusing. When we talk about the microbiome this refers to microbes and their genes and how they communicate/interact with our human cells. The microbiota is the term that refers solely to the collective population of microbes themselves. The two are used so interchangeably that if you use one or the other it doesn’t really matter, but it is still good to know that they don’t mean the exact same thing.

The gut microbiota is not made up of bacteria alone, although most of the microbes in the gut are from the bacterial kingdom. Living alongside bacteria are fungi, parasites and viruses, and each of us has our own unique set of gut microbes and genes that make up our personal gut microbiome.

Mutually beneficial

We have a truly symbiotic relationship with our gut microbiota. We provide them with a nice cosy home and a buffet of nutrients, such as dietary fibre and polyphenols and they reciprocate in many positive ways. Let’s turn our attention to some of these.

Keeping our natural armour strong

Our gut microbiome teaches and trains our immune system to react appropriately, which starts from the moment we are born. The more exposure that we have to microbes, the more diverse and varied our gut microbiome becomes, which creates an immune system that is better ‘educated’. This is, in part, the reason why the development of atopic allergies and auto-immune diseases has been exponentially increasing – we are becoming almost too ‘clean’ as a result of the overuse of medications like antibiotics, increased elective C-section births and the ubiquitous use of harsh anti-microbial household products. Inadvertently, we are weakening our immune system.

Alongside ‘educating’ our immune system, our gut microbiome protects us against pathogenic microbes that would otherwise make us ill. Moreover, gut immunity is one of the most important parts of our overall immune system, with the immune cells in gut-associated lymphatic tissue (GALT) accounting for 70–80 per cent of total immune cells in the body.

Synthesising super SCFAs

Short-chain fatty acids (SCFAs) are beneficial substances that our gut microbiota generate upon fermenting dietary fibre. SCFAs – specifically butyrate, propionate and acetate – are incredibly important for many processes in the body, including the health of the brain. Butyrate and the other SCFAs provide energy for the cells that line the gut barrier, helping to keep it strong so that the right things are moving in and out of the gut. SCFAs also help in managing inflammation, communicating with the immune system, stimulating the release of hormones in the gut related to appetite, and supporting motility through the gut – they even contribute to the balance of blood sugar levels in order to keep energy levels stable.

Assisting with digestion and absorption

Our gut microbes play a vital role in digesting and helping us absorb nutrients from our food. They produce compounds, such as bile acids and enzymes, that aid the processing and conversion of nutrients. Furthermore, they eat what we can’t digest in the form of dietary fibre.

Making vitamins and amino acids

Vitamin K, biotin, thiamine, folic acid and B12 are made by gut microbes. The latter of these is vital for cognitive health, and deficiency has been associated with conditions such as depression, anxiety and dementia. Our gut microbes are also able to synthesise amino acids, which are the building blocks of protein so that we have a ready supply if our dietary intake of protein runs low.

Creating and stimulating the release of chemical messengers

This includes the action of neurotransmitters such as serotonin, dopamine and GABA, which can exert their influence on emotions and cognitive functioning. Our gut microbiota also has a vital role in producing brain-derived neurotrophic factor (BDNF), crucial for the health of neurons in the brain and something that can be depleted in neuro-degenerative conditions like Parkinson’s disease and Alzheimer’s. Lower levels of BDNF can also negatively impact our physical ability to handle stress.

Detoxing and metabolizing

Gut microbes help us to detoxify toxins from food and the environment, as well as metabolising medications and hormones such as oestrogen.


Psychobiotics refers to supporting the health of the gut microbiota and using probiotic supplementation to directly target and positively enhance brain function. It’s an innovative and ground-breaking new area in the field of neuroscience, pioneered by Irish scientists Professor Ted Dinan and Professor John Cryan at University College Cork.

They researched how the food we eat affects the gut microbiota, and how gut microbes can in turn influence our emotions. The suggestion is that beneficial bacteria ingested from probiotic supplements or fermented foods have the potential to change the output of neurotransmitters and ultimately shape the health of our brain. This could have a major impact on conditions related to cognitive health.

Where this gets even more exciting is the potential to target the microbiome using probiotic therapy to treat depression and other psychiatric illness. Their research indicates that certain microbes have a tendency to supply us with a given neurotransmitter. For instance, lactobacillus bacteria produce more GABA (gamma-amino butyric acid), which has a calming effect, enterococcus strains seem to have a penchant for giving us ‘happy’ serotonin, while bacillus affords us dopamine for movement, motivation and pleasure.

Since evidence of psychobiotic-induced cognitive enhancements in humans is limited and a great deal more research is required, it is very important not to change or stop any medications without the guidance of your GP. It is inspiring, though, to consider a future where we might be able to use prescriptive probiotic treatment to target cognitive conditions. Now that would be smart stuff.

Extracted from Happy Gut, Happy Mind by Eve Kalinik, published by Piatkus.

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