Gut microbiome and the gut brain axis blog image of a young healthy woman wearing gym leggings and sports top holding a yoga mat.

Supporting the gut-brain axis

This article is written by nutritional therapist, health coach and author, Stephanie Moore. With a degree in nutritional medicine and a Masters degree in counselling and psychotherapy, plus a long history as a multi-disciplinary physical therapist, Stephanie combines all three skill sets to help people with many kinds of health issues, both physical and psychological. 

The incredible world of the gut microbiome, the trillions of beneficial bacteria and other microorganisms that live in our gut, has been a hot topic for several years now. Incredibly, between 2013 – 2017 there were over 12,900 scientific publications on the gut microbiome, representing over 80% of the total publications on human health since 1977.1

Despite this intensive focus on the human gut microbiome, there is wide acknowledgement that there is still much to learn.  One of the most recent findings and maybe most fascinating aspects of the gut microbiome is how it communicates with other microbiomes around the body, helping to regulate multiple systems. Not only has microbial cross communication been found to exist between the gut and the mouth, nose, lungs, vaginal canal and skin, so too between the gut and the brain. This is known as the gut-brain axis (GBA).

The gut microbiome and the gut-brain axis

The complex communication network of the GBA involves the central nervous system of the brain and spinal cord; the autonomic nervous system, the peripheral aspects of the nervous system; the enteric nervous system, which is the network of neurons and neurotransmitters within the digestive tract and also the hypothalamic, pituitary, adrenal axis, or HPA axis, which regulates our sympathetic and parasympathetic activation.  The specific mechanisms by which these complex communication systems function is still not fully understood, but increasingly the role of the gut microbiome is being extrapolated as a major part of the gut-brain crosstalk.

Depending on the state of our gut microbiome, that crosstalk can be fluent, supportive and calming or disruptive, irritating and destabilising. Our gut to brain communication is also one of the major systems managing our brain inflammation, a route cause of so much brain imbalance.

Gut-brain axis and the vagus nerve

A key aspect to good gut-brain communication is the vagus nerve, the longest cranial nerve in the body, which passes from the brain stem around the mouth, throat, lungs, heart and entire digestive tract.

The vagus nerve facilitates much of the nerve signalling being sent to and from the gut and brain2 and without good vagal tone, i.e., the vagus nerve not working well, digestive disfunction, from reflux to bloating, disrupted stomach acid management to poor hunger signalling, can all occur.

A healthy gut microbiome is not only utilising the vagus nerve as a communication portal to and from the brain, the health and function of the vagus nerve itself relies upon a healthy microbiome to function well.3

This bi-directional communication super-highway is an area of sharp focus in relation to mental health, stress resilience and neurological well-being as well as gastro-intestinal regulation.

With approximately 80% of the GBA communication going up from the gut to the brain, providing the irrefutable link between the gut-brain connection, the function and health of the brain is, thankfully, no longer being looked at in isolation to the rest of the body.

This opens up a whole conversation around the many dietary and lifestyle interventions that can be employed to support brain health via good gut health, and this is something that many practitioners within the health and wellness field can support clients with relatively easily.

The gut microbiome & emerging specialisms

The discovery of the profound influence the gut microbes, and diet in general, have on the brain has led to a fascinating development in the field of psychiatric health: Nutritional Psychiatry, also now being termed Metabolic Psychiatry. This nascent field of medicine takes an integrative view on mental health by looking at how the metabolites of the gut microbes influence the balance of brain chemistry and mood regulation.

Assistant Professor of Psychiatry at Harvard Medical School, Dr Chris Palmer, recently published his book, Brain Energy, where he cites many studies and explains that the complex mechanisms that lead to poor brain function and specifically mental health conditions are a result of impaired mitochondrial function in the brain, leading to a deficit in brain energy and therefore brain function.4

Dr Palmer considers diet and lifestyle factors to be an imperative first approach to optimising mitochondrial health, which then allows for more energy and function to be generated in the cells. As brain cells are the most mitochondrially dense within the human body, where a single neuron is thought to contain thousands of mitochondria,5 this makes a lot of sense.

As a result, there is much discussion on how to best support the health and function of the brain through optimising diet and gut health.

What is so exciting about this emerging paradigm is that we as nutritional therapists have many protocols to offer clients that are easy and accessible, yet can have a profoundly positive impact on both gut and brain function.

Be it brain fog, anxiety and depression6, poor memory recall and diminished concentration, to headaches, progressive neurological diseases, ADHD and even possibly, autistic spectrum disorders7,8, there is low to no risk and so much to be achieved through working with clients on their gut microbial health to support their GBA function.

Post-biotics and short chain fatty acids (SCFAs)

One of the key mechanisms is the production of post-biotics, the range short chain fatty acids (SCFAs) produced by multiple healthy gut microbes that confer significant benefit locally, to the intestines and systemically.

One of the most studied of these SCFAs, butyric acid, is fundamental to both a healthy colon and to the maintenance of healthy brain chemical balance and neuronal repair and renewal.9

Butyric acid is the main fuel source for the cells that line the colon, the colonocytes, supporting healthy mucosal lining and helping to maintain the integrity of the gut wall. Butyric acid can also pass up to the brain via the vagus nerve, where it increases the production of brain derived neurotrophic factor (BDNF), so-called, Miracle Grow for the brain. BDNF reduces proinflammatory cytokines and increases anti-inflammatory cytokines in the brain while also supporting neuroplasticity.10

Post-biotic production is dependent on the health of the microbiome, which again highlights the imperative that day to day we need to be encouraging focus on gut health. Good gut health results in all body benefit.

Put simply:  When we put in supportive gut foods and we reduce the gut-toxic foods, the gut microbiome rewards us by producing compounds that heal and balance the body and brain for optimal health.

The sequence of events goes like this:

Eat gut friendly foods = a vast range of happy, diverse, commensal gut microbes = by-products from the gut microbes that improve digestion, immune function and brain health.

Put another way:

Prebiotics (fibre, resistant starch, polyphenols) … Fuel our Probiotic Gut Microbes …. which then produce Post-Biotic Short Chain Fatty acids, that have many all-body benefits.

So, what does this mean in practice? It starts with optimising the health and function of the digestive system from top to bottom:

  • The importance of chewing food thoroughly to activate the digestive signalling pathways and supporting HCL acid and enzyme production where needed
  • The use breathing and other techniques to activate the vagus nerve, which is so essential for digestive regulation and for the gut-brain communication to take place
  • Leaving at least 3 hours between meals to allow the migrating motor complex to activate and sweep through the small intestine to keep debris from accumulating and stagnating
  • Hydration for good bowel function and, of course,
  • The essential aspects of a healthy diet to provide nutrients for the brain and also appropriate nourishment for the gut microbes themselves to thrive.

Gut microbiome – feed your microbes!

When addressing what to eat for a healthy microbiome, there is still no absolute consensus on what makes the perfect gut-friendly diet, but there are a few areas where most experts agree. I like to break this down simply as the 3Fs:

Fibre: our gut microbes feed on fibre. Every meal you eat should contain a range of fibre-rich foods. We get fibre from plant foods so aim to get in to your regular diet lots of different vegetables (onions, garlic, leeks, rocket, broccoli and cabbage are especially good gut foods); a little daily fruit (especially berries and kiwi); a range of raw nuts & seeds, ideally pre-soaked, and lots of different beans and lentils.

Pale green banana plus cooked and cooled potatoes provide resistant starch, a particularly potent fuel for the gut microbes.

Supplemental prebiotic / resistant starch powders are very useful to help significantly increase daily pre-biotic fibre intake.

Fermented Foods: these contain living beneficial bacteria that support our own gut microbes. From live natural yogurt, dairy and water kefir, kombucha, sauerkraut, kimchi and live apple cider vinegar, including a small amount of fermented food or drink every day can keep the gut microbiome diverse and active. Again, variety is key. Little amounts regularly can make a big difference plus selective use of probiotic supplements where appropriate / necessary.

Probiotic Supplements: The science of probiotics is fast-moving and ever evolving. Quality is king. Gone are the days that probiotics all had to be kept in the fridge. If live bacteria are so vulnerable that they die-off at room temperature, they will certainly not survive the heat and pH of the stomach. As the science in the production of probiotic supplements has evolved, formulations and encapsulation technology has been able to ensure safe passage through the GI tract until the probiotics reach the colon.

Use of a probiotic supplement is a convenient and highly effective way to introduce new strains to the gut microbiome. The 2 main genus (families) of microbes that live in the human gut are Bifidobacterium and Lactobacillus.

Within these 2 groups are many sub-groups or species, some of the most studied and verified as beneficial are Lactobacillus rhamnosus, Lactobacillus plantarum and Lactobacillus breve, Bifidobacterium longum and Bifidobacterium breve. Bifidobacterium and Lactobacillus species ferment carbohydrates and specific fibres in our food into the short chain fatty acids such a butyric acid.

Fasting: nothing extreme, simply allowing the digestive tract to rest from having a constant stream of food going through it, can help freshen up your gut microbes and the mucus lining of the gut. Aiming for 12 hours every night as an absolute is safe for everyone, and for some people, the fasting window can be extended up to 14 – 16 hours a couple of days a week.

The importance of polyphenol rich foods is also becoming clear. Bitter, peppery tasting and richly coloured foods and drinks such as chicory, radicchio, watercress, raw cacao, peppery extra virgin olive oil, Matcha green tea, berries, cranberries, pomegranate and flax seeds all contain various polyphenols known to fuel keystone gut microbes, such as Akkermansia Muciniphila, which supports other gut microbes and helps maintain a healthy mucin layer in the gut.11

Lifestyle and the impact on our gut microbiome

The positive influences on the gut microbiome go beyond avoiding foods that are disruptive and increasing those that are supportive. Lifestyle matters too.

  • Poor sleep and chronic stress are known to have a negative impact on the gut microbes.12,13
  • Spending large amounts of time indoors, especially in a very sterile environment where strong cleaning / sterilising agents are used, can inhibit proliferation of diverse strains.14
  • Conversely, getting outside in nature, gardening, breathing in through the nose as you walk through the woods – these things support diversity.15
  • Exercise is known to be positive if done in moderation. Excessive exercise can be pro-inflammatory, promoting excess stress hormones and can, therefore be detrimental.16
  • Spending more time in a parasympathetic rest, digest and restore state through the practice of meditation, breathing techniques and moments of gratitude, plus gargling, singing, humming and cold-water exposure are all thought to improve vagal tone and thus positively support the gut-brain axis.

With so many ways in which to support the GBA, this is an enormously empowering area of natural health and well-being that we can all benefit from prioritising.

Stephanie Moore
MA(Hons) BA(Hons) BSc(Nut.Med) mBANT regGRCCT mCNHC

Stephanie is a self-employed natural health therapist, clinical , author and health coach. With a degree in nutritional medicine and a Masters degree in counselling and psychotherapy, plus a long history as a multi-disciplinary physical therapist, she combines all three skill sets to help people with many kinds of health issues, both physical and psychological.

Stephanie has been using Cytoplan products since 1990 and has worked in the natural health field for over 30 years offering a comprehensive assessment of patients’ health issues to provide detailed, personalised health programmes  addressing the individual’s health concerns.

Stephanie is often featured in the media as a health expert and she published her first, best-selling book in 2017 (‘Why Eating Less & Exercising More Makes You Fat!’). She has also co-authored a new book on super foods with doctor of biochemistry and health campaigner, Dr James DiNicolantonio, and is now working on a new book (‘Eat Your Brain Happy’) following her recent training in Nutritional Neuroscience, focusing on the critical role of food, sleep, exercise and other factors known to directly influence the health of the brain.

With many thanks to Stephanie for writing this blog. If you have questions regarding the topics that have been raised, or any other health matters, please contact our team of Nutritional Therapists:
01684 310099

For further reading, you might also like: Probiotics for women: what are the health benefits?

References for gut microbiome and gut-brain axis 


Last updated on 8th December 2022 by cytoffice


8 thoughts on “Supporting the gut-brain axis

  1. Wonderful article – thank you. I had my pituitary gland plus stem removed 52 years ago and have suffered with digestive problems for the last 15 years, plus depression recently and this makes so much sense. I have followed the brain/gut axis information progress and do a lot of what you say already but obviously I can do a lot more. Visit a neural integrationist monthly who has worked wonders (extremely well informed on the HPA axis) but this article is quite the best, easily understood and informative – as well as condensed, that I have read. Thank you

    1. Hello Anna, thank you for your kind comments. We are thrilled that you found it so helpful and will be sure to pass your comments on to Stephanie.

  2. My twice a day Nazitidene tablet for reflux is not completely helping,I wake up with a dry throat almost rough in fact. My sleep is not great and exercise is minimal due to serious knee problems,what would you recommend that could help me.?

    1. Hi Jennie, we would love to get a little more information to be able to offer you some personalised advice. Please drop an email over to our team of nutritional therapists at and we will come back to you shortly.

    2. Great article, helping me to to more information which I can easily understand is just what I need.
      I have been keeping at bay MS but this has quite rapidly deteriorated since vaccinations & Covid.
      Sleep has been awful for decades but when I do sleep well it’s amazing how different every part of me feels.
      I keep a fairly good diet. Live in a wonderful clean environment in NW Scotland but a lack of light I believe is a problem.
      There’s so much advice now it’s hard to pick through it all so I appreciate this article & would love anything further you can add
      I’m also coeliac but manage this v well

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