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The Microbiome – Our Last Human Organ – From the Womb to Adulthood

The Gut-Brain Axis: Connecting brain and gut health

Until 2007 or so, we did not know the level to which our gut and brain work together as a unit. Some people thought that our brains controlled everything we did, consciously and subconsciously but we now know this is not true!  We now know that the bacteria in your gut can be a real deal breaker.  Our wellbeing is ultimately tied to the microbes that surround us internally and externally and we now have evidence suggesting the mother’s diet when pregnant, shapes the baby gut microbiota, which is tied to the diversity of their gut microbes. 

In a study published in Gut Microbes it was concluded that what a mother eats while pregnant shapes the composition of their baby’s gut microbial community.   In fact, the first 1,000 days of life is a crucial period in a baby’s life where the foundations of health can be set, and the gut microbiota plays a main role.  It is during pregnancy, in birth, and breastfeeding where the mother passes on the gut microbiota to their infants, which begins the gut colonization and contributes to the diversification of the gut microbiota.  When this colonization is disrupted, this can lead to increased risks of a range of conditions later in life.  Not to place worry or throw on the mom guilt in hindsight, as there is much that can be done to improve gut health and work with these issues.

This study followed 86 pregnant women on both their diet and babies over an 18-month period.  Those women whose diets contained high amounts of dietary fiber, omega 3 fatty acids, and polyphenols found a greater presence of Ruminoccocus which is a gut bacterium that produces butyrate and is a biomarker of gut health with associations to anti-inflammatory properties.  The second group who ate a high intake of carbohydrates, saturated fatty acids, and animal protein, showed greater amounts of Prevotella, an oral bacterium tied to increased risk of disease and pregnancy complications.  The children born to mothers who ate the first diet, appeared to have a healthier gut microbiome and less developmental issues than the diet of high carbs, saturated fatty acids, and animal protein.    It is now becoming widely recognized by public health doctors and primary care physicians that initial bacteria colonization of the gastrointestinal tract, and good nutrition from pre-conception until the second year of life, has a big impact on health through infancy, childhood, and adulthood.  

Many of us already sense the gut brain connection when we feel emotions or ‘butterflies” in our gut. Or how about, when we’re scared, and feel a “knot” in our stomach.  Feeling sad or anxious can affect both our appetite and the number of trips to the washroom. Not to mention, many digestive issues trickle over to mood issues.

Research is now viewing the microbiome as its own organ, due to its many roles in overall health, not just the gut-brain connection also known as the ‘second brain.” This microbiome-gut-brain axis is stronger and different than we had imagined.  New technology has allowed us to study the gut microbes even better than a few years back.

Let’s chat about how your gut microbes, your gut itself, your brain, and your mental health are all interconnected and influence each other! Plus, shall we dive into some “mood foods,” as well as stress relieving activities that can help with gut issues.

The gut and microbiome

We are aware that our gut (a.k.a. digestive system) plays an essential role in all health aspects – including brain health and mental health. This is because it digests and absorbs nutrients from our food and gets rid of waste. Without adequate nutrition and all essential nutrients, we get deficiency diseases (that are not nearly as common now as they were just a few hundred years ago). When our gut does its job absorbing what we need and keeping out what we don’t it helps to nourish every single cell in our bodies.

 Our gut also houses our powerful friendly microbes! The gut microbiota (collection of microbes) are mostly bacteria, but there are also yeasts and viruses included within. Fun Fact: there are as many microbes that live in our gut as there are (non-red blood cell) human cells in our entire body! The gut microbiota is sometimes called a “superorganism!”  Another fun fact:   Did you know you carry more microbes on yourself than there are people on earth?  That’s right – I’m talking about more than 100 trillion of them.

Here’s why these microbes are friendly.  They perform functions that enhance our health:

●     Help break down certain nutrients we can’t use (e.g. fibre) and turn them into nutrients we can use (e.g. short-chain fatty acids);

●     Crowd out bad microbes we ingest that can cause disease, which reduces the risk of serious gut infections;

●     Make some essential vitamins, like vitamins B12 and K that are needed for good health; and,

●     New research shows the profound effect on microbes on other parts of our bodies – like our brain and mental health.

The microbiome is the collection of the genes contained within the microbiota.  Technology developed in the early 2000’s has allowed testing of hundreds of millions of gut microbiomes, where we used to be able to test just a few dozen. We now know that one person can have 1,000 strains with a total of over 1,000 trillion individual microbes in their gut.

FUN FACT: Researchers don’t yet know what microbes make up an “optimal” gut microbiota.

The microbiome-gut-brain axis: What we’ve seen to date

There are several interconnections we’ve observed over the years that showcase this microbiome-gut-brain axis.

Firstly, our gut’s main job is to digest and absorb nutrients from our food and get rid of waste. We are aware there are nutrient deficiency disorders which have brain and mental health connections. For one, insufficient amounts of omega-3 fatty acids and certain B-vitamins are linked with brain and mental health issues.

Secondly, many digestive issues seem to be associated with some mental health issues. A higher-than-normal percentage of people with certain bowel diseases develop mental health symptoms of depression and anxiety.

Another observation is through these friendly gut microbes.  Several people report psychological side effects after taking antibiotics. While antibiotics are often necessary to treat harmful bacteria, along with wiping out the bad bacteria, they also wipe out our friendly gut microbes too.

Let’s not forget the effect of stress on our gut.  While stress can affect our appetite, it can even change the gut microbiome. Research now shows that altered gut microbes are associated with mental health symptoms.

Studies are starting to show that probiotic supplements may help with stress and some mental health symptoms.

As you can see, there are several ways our guts and brains affect each other. But How is it that these microbiota-gut-brain connections actually work?

The microbiome-gut-brain axis is complex. It involves connections between nerves, biochemicals, and the immune system itself. And this is what we know now – but this area of research is exploding, and more details will surface in the near future.

Let’s discuss each one separately.

The microbiome-gut-brain axis: Nerve connections

In terms of nerves themselves, there are a few ways the microbiome and gut connect with the brain.

Your gut a lot of nerves and is often called the “second brain.” These 200-600 million nerve cells together form their own nervous system called the “enteric nervous system.” These nerve cells control the complex functions necessary for digestion activities – from 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.

The second nerve connection between your gut and your brain is through the vagus nerve. This nerve physically connects our gut with our brain.

The vagus nerve is part of the nervous system and controls the body subconsciously. This system is divided into two parts: sympathetic and parasympathetic. The sympathetic part controls our “fight or flight” reactions. The parasympathetic part, containing the vagus nerve, controls our “rest and digest” functions. Which makes sense, as it links the digestive system to the brain.

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

The information travelling to the brain through the vagus nerve is from the gut as well as its microbiota.

The microbiome-gut-brain axis: The biochemical connections

In addition to the physical nerves that surround our gut (enteric nervous system) and the nerve that carries info from our gut and microbiota to our brain (vagus nerve), we have biochemical connections. The first type of biochemical sending information from our gut to our brain are neurotransmitters.

“Neurotransmitters” are just that – transmitters of information between nerve cells. The chemical messengers that allow nerve cells to communicate with each other. One of the most famous mood-affecting neurotransmitters, serotonin, is made in the gut. Serotonin is known as the “happy” neurotransmitter because it seems to be lower in people with depression. Research shows that 90% of serotonin is in the gut, not in the brain! It also plays an essential role, promoting the 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 the process, they produce compounds (i.e. metabolites). These are short chain fatty acids from dietary fibre, as well as amino acids from dietary protein. As noted earlier, they also create the essential vitamins B12 and K. All of these microbial compounds travel throughout our bodies and can reach and affect our brains.

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

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

Our immune cells travel throughout our body looking for invaders like harmful bacteria and viruses. Just like most of our neurotransmitter serotonin is located in our gut, most of our immune system is there too. This is because our mouths are a huge portal for the outside world to get into our bodies. We can easily swallow disease-causing microbes which are dealt with by our immune system. So, it makes sense that most of our immune system is located around our gut.

When our immune cells start working to attack invaders, they can cause inflammation.

If our immune cells become overactive, this can cause autoimmunity and excess inflammation. Autoimmunity is when our immune cells mistake our own cells as harmful ones, then attack them. This can also affect our moods.

All three of the connections, nerve, biochemical, and immune system, are part of the complex microbiome-gut-brain axis!

From what we know, let’s discuss what we can put in our gut to feed our moods, what we can do mentally to help our gut.

Mood foods

Our brain and mood are affected by the foods we eat. In fact, a new area of research is called “nutritional psychiatry.”

What do we already know?

We know a healthy diet is linked with a lower risk of mental health issues. Several recent high-quality studies suggest that what we eat is a “modifiable risk factor” for depression and anxiety. This means that what we eat affects our risk of mental health issues, and we can control what we eat.

The essential components to a healthy diet include nutritious and fibre-dense foods. In fact, what we eat is the main thing that influences our gut microbes (remember, our microbes like to eat fibre!). Components of a healthy diet include:

●     Fruits and vegetables  

●     Whole grains, legumes, nuts, and seeds;

●     Fish, poultry, lean red meat, eggs; and

●     Olive oil, Avocado oil, hemp oil, sesame seed oil, coconut 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.

A recent randomized clinical study shows that what we eat can help improve symptoms of people who already experience depression!

The SMILES trial took 67 people who already had depression and ate poor quality foods. This means they ate a lot of sweets, processed meats, and salty snacks; and not very many fruits, vegetables, lean protein, and dietary fibre.

They split the participants into two groups. One group was given seven nutrition counselling sessions and were asked to eat more higher quality foods and fewer poor quality foods. The other group was given “social support” only – they paired up with someone to discuss the news, sports, or even play cards or board games.

After 12-weeks the people who improved their diet had improvements in some of their symptoms of depression!

The 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)

What about probiotics?

There is research specifically looking at probiotics and mental health. “Probiotics” are health-promoting microbes that we can eat, drink, or supplement with.  Also found in foods like yogurt, sauerkraut, kombucha, kefir, miso, and kimchi.

Few studies have looked at the mood effects of people who take probiotic supplements.

One review looked at seven studies that compared probiotic supplements to placebo in healthy volunteers. The researchers concluded that there was a statistically significant improvement in psychological symptoms and perceived stress in people who took the probiotics.

This research is promising, but still preliminary.

PRO TIP: If you have any health conditions, or are on medications, please check with your healthcare professional before taking any supplements. Also, everyone should read the labels before purchasing a supplement to ensure that none of the cautions or warnings apply to them, and to ensure they’re taking it as per the directions for use on the label.

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 help our gut.

Reduce stress for your gut

As we’ve mentioned, gut issues can affect your stress level and moods, but 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. This means that they’re not just physical issues, but 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.

All of these can worsen gut symptoms by increasing the number and severity of flare ups.

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

Stress influences many gastrointestinal functions. These include the microbiota, 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 inhibit the vagus nerve and contribute to inflammation. So, reducing stress is a strategy to reduce all of these negative effects and try to improve gut symptoms.

Some experts say that the most effective treatments for IBS are “mind-body” therapies. Mind-body therapies include hypnotherapy, mindfulness, and cognitive behavioural therapy. Individual counselling or participating in support groups can also help.

Gut-directed hypnotherapy, for example, induces a state of relaxation while verbally suggesting improvements and coping skills. Mindfulness teaches how to observe one’s current experience, thoughts, and feelings, and to learn to apply neutral emotional attention to them. Mindfulness can help people to notice symptoms and sensations in the gut and distinguish those from the thoughts and emotions surrounding those sensations.

A review of 12 studies found that mind-body approaches were effective in helping some IBS symptoms. These were improvements in both mental health symptoms, and quality of life for gut symptoms.

The researchers recommend more studies in this area.


There is ongoing heavy research digging into the wide interconnections between our gut and our brain. The microbiome-gut-brain axis consists of nerves, biochemicals, and the immune system.

There are a number of foods that we can feed our gut that can help our moods, and reduce our stress which has a significant impact on several digestive diseases.

The microbiota-gut-brain axis is an active area of research now. Make sure you don’t overlook the impact of how you treat your gut!


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