Ever had a “gut feeling” about something? It turns out, the connection between our gut and our brain might be stronger than we think.

What is the microbiome?

The microbiome are all the little bacteria that live in and on you, from your mouth and nose, to your bottom, your skin and almost every millimetre of you – inside and outside.

You are made up of approximately 1,000,000,000,000 bacterial cells. Over 40,000 strains have already been identified, and believe it or not, more than 99% of you is made up of microbial genes, with only 1% human genes. The weight of your microbiome is roughly the same as your brain! Your microbiome live inside you, even inside your cells, and they help keep you alive.

Links have been made between your microbiome and a range of non-communicable diseases including obesity, auto-immune disorders,  diabetes, autism, multiple sclerosis, epilepsy, Alzheimer’s and Parkinson’s disease, and even depression and anxiety – our leading modern-day mental health challenges.

John F. Cryan is Professor and Chair of Anatomy and Neuroscience and Principal Investigator at APC Microbiome Ireland, and in his presentation at the 6th IPPA Congress in Melbourne in July, John shared surprising facts and insights about how our thoughts and emotions are connected to our gut and its microbiome.

Where does your microbiome come from?

You acquire your first, frontier microbes during birth. As you were delivered through the birth canal (for those who were), you received this birthday present from your mother in an evolutionary ‘relay race’. These microbes then inform the development of your immune system, gut health, and the programming of many of the systems in your body.1 Many factors in early life have the possibility of impacting this programming. These include how you are born (e.g. being born by c-section bypasses the above process), how you get your nutrients as a child (breast feeding vs bottle), stress, maternal stress, the environment you live in, the hospital environment etc.2

Why is the microbiome so important?

Think of your microbiome as “nature’s security blanket”.

Your microbes are little factories that create all sorts of different chemicals that your body wouldn’t have otherwise. They take compounds from your diet and turn them into really important chemicals that your body needs.

It might be unusual for you to think that what goes on in our brain is affected by what goes on in our gut, yet if we review our language, we often make references to our gut. Examples include “gut instinct” or “gut feelings”, “feeling gutted” when we are disappointed, having “butterflies in the stomach” when we are nervous, or making “gutsy” moves when we are brave. So is there an underlying biology to all of this?

In one experiment that John ran, he and his team bred germ-free mice (that grew up in a bacteria-free bubble) and used these mice to see if bacteria were involved in brain development. When John and his team explored the pre-frontal cortex of these bacteria-free mice, they found more ‘stressed’ neurons in comparison to controls3, and neurons that had an excess of myelin. Myelin is the insulation that allows electrical impulses to transmit quickly and efficiently along the nerve cells. This ‘hyper-myelination’ resulted in elevated stress responses, altered neurodevelopment and changes in anxiety, cognition and social behaviour.4

This study (and many like it over the years) provides clear evidence that the microbiome is critically involved in sculpting brain circuits in early life. Without microbes, brains don’t develop properly.

How does your gut communicate with your brain?

We are only at the beginning of trying to figure this out. Essentially, a conversation is going on all the time between your brain and your gut through the central nervous system. One of the key pathways involves the vagus nerve. Vagus comes from the latin word for ‘wandering’, so this ‘wandering’ nerve sends signals from the brain to all of our organs, and from our organs all the way back to the brain. It is the key circuit recruited during mindfulness training.

In an animal study done by John and colleagues a number of years ago, it was shown that cutting the vagus nerve signal eliminated all the effects of a specific bacteria. So what happens in vagus, doesn’t stay in vagus! It affects our organs in many ways.5 And this is just one pathway. There are many other ways in which your gut sends signals to your brain to modify your behaviour. And if the conversation between your brain and your gut is in any way impaired, there can be outcomes of a variety of neurogenerative diseases and auto-immune diseases.

“If microbes are controlling the brain, then microbes are controlling everything.”  John F Cryan

What is the impact of diet on the microbiome?

A study from John’s colleagues in Cork looked at elderly people who were in good health, versus those who were quite frail, and found that their microbiome compositions were very different.6

They put this down to diet. Those who ate a diverse diet, rich in green vegetables and fish, had a much more diverse microbiome than those who had an ‘everyday routine’ diet (stodgy, white, repetitive foods).

The introduction of processed foods and antibiotics into the food chain, and increases in stress, are causing an extinction of our microbiome – and we are yet to discover long-term consequences of this on our brain health.

What is the relationship between stress and the microbiome?

A small study by John and colleagues involved giving healthy individuals a bacteria (probiotic) for a month. They were then stressed in the lab whilst wearing a brain scanner, and this EEG brain scan showed that those who had been taking the probiotic had a reduced stress reponse and better cognitive performance than those who had not been taking the bacteria. 7

In another study, people were asked to do a task that made them experience social rejection and exclusion, which illicits a stress response in the brain. Interestingly, those on the probiotic did not have this stress response, as measured by a brain scanner.8

Yet in the words of Hans Selye, “it’s not stress that kills us, it is our reaction to it”.  How you view stress will influence how it impacts you. So how can you change your response to stress? If you believe stress is harmful, you are more likely to experience more stress, when adversity occurs. If you think stress is helpful, you are more likely to use positive strategies to handle it, when adversity occurs.

How can you change your microbiome to support brain health?

‘Psychobiotic’ is a term coined by John Cryan and his colleagues in Cork, to describe any way in which you target the microbiome for mental health benefits – and there are many ways to do this.

One interesting way of altering your microbiome is called Faecal Microbiota Transplantation i.e. taking someone else’s poop! Research shows that this process can have a significant impact on the brain.

Studies have in fact used this ‘poop transplant’ process to show a strong link between gut bacteria and depression. The microbiome from depressed individuals has been transplanted into mice, and surprisingly, this resulted in rats with depressive-related symptoms. Exciting research also showed that across a large cohort of individuals (two sets of 1,000 people), quality of life scores and depression were correlated with specific changes in their microbiome. So this tells us that there is something in the microbiome that is mediating effects on depression.

So what other (more palatable) ways can you get closer to a ‘psychobiotic life’?

According to the experts, you can increase your intake of ‘real food’. This includes:

  • Prebiotics – Fibres and vegetables such as artichokes, leeks, onions and garlic.
  • Omega3 Fatty Acids
  • Polyphenols including nuts, seeds, coffee, dark chocolate, red wine, olive oil and berries
  • Yoghurt and fermented milk (Kefir), fermented foods, sauerkraut, kimchee, miso and kombucha
  • Antioxidants

Decrease your intake of:

  • Processed food
  • Emulsifiers
  • Sugar and sweeteners
  • Alcohol

Try to:

  • Exercise
  • Fast occasionally
  • Avoid or manage stress and sleep disturbances (jetlag)
  • Avoid c-sections and support breastfeeding
  • Minimise antibiotic usage
  • Have a pet to increase your microbiome diversity!!

It is worth noting that studies in this area have mixed results, for many reasons, and it is important that we are always reviewing the evidence behind certain claims, and continuing the research journey. Yet this is an exciting area of research because unlike your DNA, there is potential for your microbiome to be modified, to allow you to take control of your health and wellbeing. This could be a completely new way of thinking about, and approaching, mental health challenges. A psychobiotic revolution.

In the words of John Cryan, “a state of gut” will markedly affect your “state of mind”, so “let food (for your microbes) be thy medicine”.

This blog was written using content from John Cryan’s presentation at the 2019 World Congress of Positive Psychology. This is available on the IPPA website to all IPPA members.  


  1. Dinan and Cryan, The Journal of Physiology, 2017
  2. Borre et al. Trends Mol Med 2014
  3. Growing up in a Bubble: Using Germ-Free Animals to Assess the Unfluence of the Gut Microbiota on Brain and Behavior, Luczynksi et al., International Journal of Neuropsychopharmacology, (2016) 19(8): 1-17
  4. Hoban et al., Translational Psychiatry, 2016
  5. Fulling et al. Neuron, March 2019
  6. Claesson et al., Nature, 2012.
  7. Bifidobacterium longum 1714 as a translational psychobiotic:modulation of stress, electrophysiology and neurocognition in healthy volunteers, Allen et al. Translational Psychiatry [2016] 6, e939; doi:10.1038/tp.2016.191; published online 1 November 2016
  8. Bifidobacterium longum 1714TM Strain Modulates Brain Activity of Healthy Volunteers During Social Stress, Wang et al. American Journal of Gastroenterology, April 17, 2019.

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