Importance of Gut Microbiome


The Microbiome - Gut - Brain Axis

I want to help you understand the importance of Gut Microbiome and its connection to our brain. I want to address the ways in which your gut microbes, your gut itself, your brain, and your mental health are all interconnected and influence each other. Let’s look at these important relationships, assess the “mood foods” that will help us, and explore stress reducing activities that can help with our gut issues.

Do you know just how much our gut and brain actually interact? Many people live under the illusion that our brains control everything we do, whether consciously or subconsciously, but they are wrong! Our guts also have the power to control many of our bodily functions, and emotional feelings. Have you ever experienced a gut feeling? Many of us will have feelings in our gut from time to time, some that we can’t necessarily explain, but others we perhaps can. In this, we can sense that connection between our emotions, our brains and the gut. A simple example, is the feelings we experience when are we scared and that “knot” in our stomach when we are feeling sad or anxious. These feelings can then affect our appetites (and the number of trips to the loo we need to make!). Many digestive issues are often closely interlinked with our moods. In fact, recent research confirms this connection between the brain and the gut, known as the “axis”, is stronger that we had imagined. With new technology, we have been able to study the gut microbes in a way that was not possible just a few years ago.

So what do we know about our gut?

  • We know that our gut (a.k.a. digestive system) plays an essential role in all aspects of health - including brain health and mental health - because it digests and absorbs nutrients from our food, and gets rid of waste. 

  • Without enough nutrition and essential nutrients, we run the risk of deficiency diseases (but luckily that are not nearly as common now as they were just a few hundred years ago!)

  • When our gut does its job by absorbing what we need - keeping out what we don’t (and what’s harmful) - our gut helps to nourish every single cell in our bodies.

  • Our gut houses our amazing friendly microbes! 

What role do these microbes have?

The gut microbiota is sometimes called a “superorganism”. This gut microbiota (i.e. collections of microbes) are mostly bacteria, but there are also yeasts and viruses in there too. In fact, there are as many microbes that live in our gut as there are non-red blood cell human cells in our entire body! These microbes are friendly because they perform functions that enhance our health:

  • Microbes help break down certain nutrients we can’t use such as fibre, turning them into nutrients we can use e.g. short-chain fatty acids.

  • Our gut microbes crowd out the bad microbes that we ingest which can cause disease, helping us reduce the risk of serious gut infections.

  • They make certain essential vitamins, like vitamins B12, K which are needed for good health.

  • Thanks to new technology developed in the early 2000s that can test hundreds of millions of gut microbiomes (we used to be able to test just a few dozen), research now shows that microbes also have profound effects on other parts of our bodies, including our brain and mental health. In fact, we now know that one person can have 1,000 strains with a total of over 1,000 trillion individual microbes in their gut (but we are still yet to find out what microbes make up an “optimal” gut microbiota!).

How does the gut and microbiome connect with the brain and mental health?

There are lots of interconnections that we’ve seen over the years that point to this axis between microbiome, the gut and the brain. Indeed, there are lots of nutrient deficiency disorders which have brain and mental health connections. Let’s look at some examples. Insufficient amounts of omega-3 fatty acids and certain B-vitamins can be linked with brain and mental health issues. Moreover, there are a higher-than-normal percentage of people with certain bowel diseases who develop mental health symptoms of depression and anxiety as a result of their symptoms. Similar can be said for the psychological side effects after taking antibiotics. Antibiotics are often necessary to treat harmful bacteria, but they don’t only wipe out the bad, they also wipe out our friendly gut microbes too, which can have a psychological effect on us. Meanwhile, stress can also affect our appetite and even change the gut microbiome; and in reverse, studies are starting to show that probiotic supplements may help with stress and some mental health symptoms. The microbiome-gut-brain axis is complex one with complicated connections between nerves, biochemicals, and the immune system itself. However, this axis is fuelling a hotbed of research, and so more details are sure to surface in the near future.

The microbiome-gut-brain axis: The nerve connections

  • Firstly, your gut has lots of nerves and is sometimes called the “second brain”.

  • 200-600 million nerve cells in our bodies together form their own nervous system called the “enteric nervous system”.

  • These nerve cells control the intricate functions necessary for your digestive system to do its job - from the release of digestive enzymes, to movement of food through it, to the blood flow around it that picks up the absorbed nutrients. The gut uses its own brain to function optimally.

  • Second nerve connections between your gut and your brain are through the vagus nerve. This nerve physically connects our gut with our brain and is part of our nervous system that controls the body subconsciously, called the autonomic” nervous system (it works “automatically”).

  • This system is divided into two parts, the sympathetic and parasympathetic: the sympathetic part controls our “fight or flight” reactions, while the parasympathetic part, containing the vagus nerve, controls our “rest and digest” functions.

  • The vagus nerve has recently been shown to send about 80% of  information from your gut up to your brain - and not from your brain down to your gut as we previously thought!

The microbiome-gut-brain axis: The biochemical connections

In addition to physical nerves that surround our gut (enteric nervous system) and the nerve that carries information from our gut and microbiota to our brain (vagus nerve), there are important biochemical connections.


The first type of biochemical that sends information from our gut to our brain are NEUROTRANSMITTERS - transmitters of information between nerve cells which are chemical messengers and allow nerve cells to communicate with each other.


One of the most famous mood-affecting neurotransmitters, SEROTONIN, is made in the gut:

  • Serotonin is sometimes called a “happy” neurotransmitter because it seems to be lower in people with depression.

  • Interestingly, research shows 90% of serotonin is in our gut, not in our brain! Here it plays an essential role, promoting movement of food through the gut (peristalsis).


Another biochemical connection is between our gut microbes and our brains through their metabolites:

  • Our gut microbes need to eat, and in process they produce compounds called metabolites.

  • These include short chain fatty acids from dietary fibre, as well as amino acids from dietary protein and also create essential vitamins B12 and K.

  • All of these microbial compounds travel throughout our bodies and can reach and affect our brains.


A third biochemical connection between our microbiome, gut, and brain is through stress hormones:

  • Our HPA-Axis (Hypothalamic-Pituitary-Adrenal Axis) starts in our brains and uses hormones like cortisol to affect other parts of the body, including the gut.

  • Research shows that stress hormones tell immune cells in our gut to secrete compounds that can cause inflammation and tiny “leaks” in the gut (permeability).

  • In addition to physical nerve connections and biochemical ones the microbiome-gut-brain axis also uses the immune system.

The microbiome-gut-brain axis: The immune and inflammatory connections

Our immune cells travel throughout our body looking for unwelcome invaders like harmful bacteria and viruses. Like most of our neurotransmitters, serotonin is located in our gut together with most of our immune system. We can easily swallow disease-causing microbes which need to be dealt with by our immune system, so it makes lots of sense that most of our immune system are located around our gut. However, if our immune cells become overactive, it can cause autoimmunity and excess inflammation. Autoimmunity is when our immune cells mistake our own cells as harmful ones and then attack them too - which can unsurprisingly affect our moods.

So how can we mentally help our gut?

Mood foods

I believe it really is possible to affect our brain and moods with the foods we eat.

SMILES trial took 67 people who already had depression and ate poor quality foods (eating a lot of sweets, processed meats, and salty snacks; and not very many fruits, vegetables, lean protein, and dietary fibre). They split participants into two groups. One group was given seven nutrition counselling sessions and were asked to eat higher quality foods and fewer poor quality foods. The other group were given “social support” only - they paired up with someone to discuss the news, sports, or even play cards or board games. After 12-weeks people who improved their diet had improvements in some of their symptoms of depression. Researchers concluded that improving dietary quality is a “useful and accessible strategy for addressing depression in both the general population and in clinical settings.”(Jacka et. al, 2017) While this was first study of its kind - had positive results - it would be great to have additional studies to confirm and expand on these results. In the meantime - we can improve our diets by eating more healthful nutrient-dense foods and fewer low quality foods to improve both our mental and physical health.

  • We know that healthy diet is linked with lower risk of mental health issues.

  • Several recent high-quality studies suggest that what we eat is  “modifiable risk factor” for depression and anxiety.

  • Essential components to healthy diet include lots of nutritious and fibre-dense foods.

  • In fact - what we eat is main thing that influences our gut microbes (remember, our microbes like to eat fibre!).

  • Components of healthy diet include fruits and vegetables, whole grains, legumes, nuts, seeds, fish, poultry, lean red meat, eggs and olive oil.

  • Perhaps not surprisingly - foods associated with poorer mental health include processed, sugary, salty, fried, fast, and high-fat foods, as well as sugary drinks.



  • If you have any health conditions or are on medications, please check with your healthcare professional before taking any supplements. 

  • Also, everyone should read labels before purchasing supplements to ensure none of the cautions or warnings apply to them.

There is research specifically looking at probiotics and mental health. “Probiotics” are health-promoting microbes that we can eat, drink, or supplement which are found in products such as yogurt, sauerkraut, kombucha, kefir, miso, kimchi. One review of 10 studies found that there are some mood benefits from probiotic supplementation. Another review looked at seven studies that compared probiotic supplements to placebo in healthy volunteers - researchers concluded that there was a statistically significant improvement in psychological symptoms and perceived stress in people who took the probiotics.

Now that we’ve looked at foods to put in our gut to help our mental health, let’s look at how stress reduction can also help our gut…

As I’ve mentioned, gut issues can affect your stress level and moods and it works the other way around too. If you have gut issues then reducing your stress may help some of them:

  • Irritable Bowel Syndrome (IBS) and Inflammatory bowel diseases (IBD) like Crohn’s and ulcerative colitis are considered to be “biopsychosocial” diseases, which means they’re not just physical issues - stress plays a key role in them as well.

  • In fact, people with IBS have higher-than-normal levels of stress, depression, and anxiety and people who report high levels of stress can go on to develop gut issues.

How does the microbiota-gut-brain axis work for these gut issues? 

  • Stress influences many gastrointestinal functions.

  • These include microbiota and how well food moves through it (motility), secretion of important biochemicals, as well as how tightly the gut cells adhere to each other (permeability).

  • Stress can also stimulate the sympathetic nervous system and the release of stress hormones, as well as inhibiting the vagus nerve and contributing to inflammation. Reducing stress is therefore important for reducing all of these negative effects and trying to improve gut symptoms.

  • Some experts say that most effective treatments for IBS are “mind-body” therapies - hypnotherapy, mindfulness, and cognitive behavioural therapy.

  • Mindfulness also teaches us how to observe one’s current experience, thoughts, and feelings and so ways in which to apply neutral emotional attention to them and help us notice symptoms and sensations in the gut, as well as distinguishing those from thoughts and emotions surrounding those sensations.

If you would like to get in touch about exploring “mind-body” therapies, mindfulness and CBT with me please do contact me and we can discuss therapy options further.

In Summary…

The Microbiome-gut-brain axis consists of nerves, biochemicals, and the immune system - but the interconnections are incredibly varied and vast and there is still so much for us to learn. There is a hotbed of research investing this axis in which studies are trying to get to the bottom of how our “second brain” affects our moods and vice versa. What can we be sure of? There are a number of foods that we can feed our gut with to help our moods and reduce our stress. So be sure to treat your gut and your brain well. The two cannot be separated!


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