Gut Instinct: The importance of the gut and how it can affect your mood - INutrition - Nutrition Cork
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Gut Instinct: The importance of the gut and how it can affect your mood

Gut Instinct: The importance of the gut and how it can affect your mood

Ever feel that when you’re faced with a challenging situation, you get butterflies in your tummy? Have you experienced a gut-wrenching feeling?
When your gut tells you something, do you listen? It’s almost instinctual isn’t it? A physical manifestation of the connection between our brain and our bellies.
Let me tell you it is no coincidence that you link your instincts to what your gut says and in this article I hope to brief you on how your gut, that tube starting with your mouth ending in at your anus is an integral part of your overall health. I want to explore the bugs that reside in our guts, how they affect us, what affects them and how we can keep our microbes healthy and as a consequence, keep ourselves healthy.
You may be surprised to learn about the wide-reaching effects the gut can have in your body and mind. With the science telling us we’re more bacterial cells than human cells, it really makes you wonder who’s controlling whom!


The bugs within us

All the external surfaces of the body are colonised by different microbes that far outnumber our own cells. In fact, 90% of our cells are our microbiota, the collective word for the microbes found in our gut (1). We have been living with these bacteria, yeasts and other microbes since the beginning of time. Bacteria live on all corners of the globe including in glaciers, deep ocean trenches and they even float through the air in every inhalation you take. Take a deep breath and think about that for a sec…


So, how do they affects us?

You would imagine that microbes could have the potential to cause harm to the host but the majority of gut bacteria are non-pathogenic (cause no harm) and actually cohabit with our own cells in a symbiotic relationship.

We are still finding out the true reach of the functions of the microbiota but some of the main roles they have are:

  1. Providing immune support
  2. Influencing the immune system
  3. Aiding digestion
  4. Influencing drug metabolism
  5. Maintaining the structure of the gut barrier
  6. Produce byproducts that are beneficial to our bodies like short chain fatty acids that nourish our gut cells as well as B vitamins and vitamin K (2).

The microbiota plays a crucial role in overall health (3). We provide the bacteria with a warm safe place to live with a good supply of food and they offer us protection, digestion and nutrition. In other words: they need us and we need them.

Researchers have been studying bacteria for hundreds of years but only recently has the scientific evidence supported the claims that the trillions of bacteria living in our gut can influence our brains too. Emerging research is backing up this theory of diet affecting mood and studies have been conducted here in Ireland to explore the relationship between our guts and how we feel.

Professor Ted Dinan of the  Department of Psychiatry and APC Microbiome Institute in UCC says “What we have discovered is that the microbiota influences our emotions to a very significant extent” (4). The gut and brain are linked by a number of different means and the gut has even been coined the “second brain”. This is because it has its own neural network that is vital for digestion and motility and also to communicate with other systems in the body. The vagus nerve directly connects the brain and gut and it is a bi-directional system. Microbes are potentially able to regulate the brain through this vagus nerve through a number of mechanisms (5).  

How do we affect them?

Method of birth: Children born by C-section have a microbiome that is different to those born naturally and this can have long-term consequences for the health of this adult as this method of birth may influence obesity and the development of immune diseases (6, 7).

Antibiotics: and other medication can have wide ranging impacts on the gut, wiping out both good and bad bacteria throughout the gastrointestinal tract. Antibiotics can reduce overall diversity (8) and, as we’re beginning to realise, it is this diversity that is key to good health.

Diet: An interesting study by Jacka et al in the American Journal of Psychiatry highlights that “depressive illness is influenced by genetic, hormonal, immunological, biochemical, and neurodegenerative factors. Diet modulates each of these factors and, as a result, has a plausible impact on the development and course of this illness” (9).

Also chronic stress and chronic infections have a big impact on both our physical and mental health (10).


So what can we do to promote a health microbiome and thus a healthy mood?

Quite a bit in fact and number one starts with diet.

  1. Having a diet with both probiotics (beneficial microbes) and prebiotics (the fertiliser for the probiotics) can enhance the diversity of the gut, change the microbiota composition and also reduce stress related behaviour (11). Including foods like kefir, kimchi, sauerkraut, natural yoghurt or taking a supplement can help to populate the good microbes in the gut.
  2. Avoid processed sugar and refined oils that can damage the microbiome (12) and replace them with good fats from fatty fish, a great source of omega 3s that are also good for the brain (12).  
  3. Manage stress in a way that’s meaningful to you. Be it meditation, spending time in nature or watching a funny film, carve out some time for yourself to spend in an enjoyable way.  
  4. If you have to take antibiotics, which is necessary in certain situations, consider taking a probiotic supplement to re-inoculate your gut with the beneficial microbes to help prevent pathogenic bacteria taking hold.



All this attention paid to our gut microbes requires an adjustment in our thinking—we grew up believing that bacteria were bad things that should be killed at any cost. We now know that this is not true, and scientific research today is still learning about the ways these microbes are necessary to a healthy life.

The more research that is done, the more the microbiota seems to be implicated in health and disease.  Whatever disease you’re suffering, it is clear to see that gut health has an impact on both mental and physical wellbeing.

It is certainly a big part of my protocol for anyone who comes to see me and we’re starting to realise, looking after the gut means looking after the rest of the body. Disease and brain related disorders are very complicated and multi-faceted but focusing in on the gut is an excellent place to start and reacquaint yourself with your ancient friends who’ve been passed down to you from generation to generation. I encourage you to look after your own microbiota as that old phrase may hold some truth: “No guts, no glory”.



  1. Bailey, M., Dowd, S., Galley, J., Hufnagle, A., Allen, R. and Lyte, M. (2011). Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor-induced immunomodulation. Brain, Behavior, and Immunity, [online] 25(3), pp.397-407. Available at:
  2. Jandhyala, S. (2015). Role of the normal gut microbiota. World Journal of Gastroenterology, 21(29), p.8787.
  3. Clarke, G., Stilling, R., Kennedy, P., Stanton, C., Cryan, J. and Dinan, T. (2014). Minireview: Gut Microbiota: The Neglected Endocrine Organ. Molecular Endocrinology, 28(8), pp.1221-1238.
  4. The Irish Times. (2018). UCC scientists to develop ‘psychobiotic’ to treat depression. [online] Available at:
  5. Foster, J., Rinaman, L. and Cryan, J. (2017). Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of Stress, [online] 7, pp.124-136. Available at:
  6. Dinan, T., Stanton, C. and Cryan, J. (2013). Psychobiotics: A Novel Class of Psychotropic. Biological Psychiatry, 74(10), pp.720-726.
  7. R.E. Ley, P.J. Turnbaugh, S. Klein, J.I. Gordon Microbial ecology: human gut microbes associated with obesity, Nature, 444 (7122) (2006), pp. 1022-1023
  8. Jernberg, C., Lofmark, S., Edlund, C. and Jansson, J. (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology, [online] 156(11), pp.3216-3223. Available at:
  9. Jacka, F., Pasco, J., Mykletun, A., Williams, L., Hodge, A., O’Reilly, S., Nicholson, G., Kotowicz, M. and Berk, M. (2010). Association of Western and Traditional Diets With Depression and Anxiety in Women. American Journal of Psychiatry, [online] 167(3), pp.305-311. Available at:
  10. Dinan, T., Stanton, C. and Cryan, J. (2013). Psychobiotics: A Novel Class of Psychotropic. Biological Psychiatry, 74(10), pp.720-726.
  11. Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X., Kubo, C. and Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. The Journal of Physiology, [online] 558(1), pp.263-275. Available at:
  12. Innis, S. (2008). Dietary omega 3 fatty acids and the developing brain. Brain Research, [online] 1237, pp.35-43. Available at:


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