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The link between the gut and our mental health

The link between the gut and our mental health

The link between the gut and our mental health

The rate of mental health issues in Australia is increasing. The National Survey of Mental Health and Wellbeing conducted in 2007 found that an estimated 1 in 5 (20%) Australians aged 16–85 experienced a mental disorder in the previous 12 months (ABS 2008). 1

With such a high proportion of our communities reporting mental health issues, more emphasis should be placed on understanding the root causes of why so many people are suffering from depression, anxiety, bipolar disorder and a host of other disorders.

The Functional Medicine approach is to understand these causes and treat the problem, not the symptoms.

We believe, and evidence overwhelmingly demonstrates, that good nutrition as well as balancing your biochemistry and gut microbiome is key to supporting good mental health.

Consuming a balanced diet, supplement where your diet is lacking and avoid the foods that cause inflammation will go a long way to repairing your gut, the relationship between the gut and the brain and alleviating mental health conditions.

The Gut-Brain Axis

A lack of essential nutrients is known to contribute to the onset of poor mental health in people suffering from anxiety and depression, bipolar disorder, schizophrenia and ADHD.

What is this relationship between the gut and the brain?

The gut-brain axis refers to the link between your brain and your gut: the conversation that occurs between the two.

Your central nervous system (CNS) consists of your brain and your spinal cord and controls your thoughts and emotions, breathing, heart rate, body temperature and the release of some hormones.

Your enteric nervous system (ENS), also known as your “second brain,” consists of 200-600 million neurons that move throughout your digestive system.

The ENS and CNS work together although the ENS regulates some gastrointestinal functions independently, such as moving food through your gut and bowel movements. Your ENS also controls the release of some neurotransmitters, including gamma-aminobutyric acid (GABA) and serotonin.2

How does this affect your mental health?

Research demonstrates that gut microbes produce a variety of compounds that modulate brain function, including:

  • Neurotransmitters such as gamma aminobutyric acid (GABA), serotonin, norepinephrine, and dopamine. Serotonin is a neurotransmitter that helps regulate sleep and appetite, mediate moods and inhibit pain. Approximately 95% of serotonin is produced in the gastrointestinal tract and as your gastrointestinal tract is lined with a hundred million nerve cells, it means that you don’t just digest food, but it also impacts your emotions and mental health.
  • Short-chain fatty acids, including butyrate and propionate
  • Indoles, compounds derived from the amino acid tryptophan that have anxiety-promoting properties
  • Bile acids
  • Choline metabolites
  • Lactate
  • Vitamins including biotin and B12

These compounds interact with your brain to moderate emotional behaviour in the following ways:

  • Activating the vagus nerve, which carries an extensive range of signals from digestive system and organs to the brain and vice versa.
  • Stimulating the immune system in the gut and then circulating immune cells in the blood.
  • They are directly absorbed into the bloodstream and interact with other organs, including the brain. 3

Gut infections and leaky gut

The walls of our digestive tract provide a barrier between what we eat and the rest of our body and an unhealthy gut microbiome can lead to increased levels of inflammation 4. Inflammatory foods such as gluten and sugar can lead to leaky gut, which means that your gut lining becomes permeable, making it difficult to digest and absorb nutrients.

This then leads to nutrient deficiencies, such as B12, and gut infections such as small intestinal bacterial overgrowth (SIBO) and Candida overgrowth. The bacteria and yeast then produce toxins which suppress serotonin production and release chemicals that mimic neurotransmitters.

These chemicals cause brain fog, poor memory, depression, anxiety and mood changes 5.

How can you change your diet to improve your mental health?

Moving away from a modern, highly processed diet that is full of sugar to a Mediterranean or Paleo diet may help bolster mental wellness for management of daily life stresses, anxiety, and grief. Regularly scheduled meals may also prevent mental health issues 6.

A balanced diet includes:

  • vegetables
  • whole fruits
  • healthy fats
  • lean proteins
  • nuts and seeds
  • full fat dairy
  • eggs
  • whole grains if tolerated

Together, the nutrients your body will gain from these foods will support your brain to be healthy.

Collagen-boosting foods

Foods such as salmon and bone broth can help protect your intestinal wall and improve digestion.

High fibre foods

Food that contain high amounts of fibre include broccoli, brussels sprouts, oats, peas, avocados, pears, bananas and berries.

Omega-3 fatty acids

Food such as salmon, mackerel, and flax seeds are high in omega-3 fatty acids and may support mental health by maintaining the fluidity of neuronal cell membranes, thus facilitating seamless, healthy neurotransmission 7.

Probiotics and pre-biotics

Probiotics contain good live bacteria and yeasts that naturally live in your body. We usually think of bacteria as something bad that makes you sick but there are also good bacteria that helps get rid of extra bad bacteria, restoring balance in your body. Probiotic supplements are a great way to add good bacteria to your body. You can also get probiotics from food.

Probiotic foods include the following:

  • sauerkraut
  • kefir
  • kimchi
  • kombucha
  • apple cider vinegar
  • kvass
  • high-quality yogurt

Prebiotics are dietary fibre that feed the good bacteria in your gut, leading to a healthier gut. You can obtain prebiotics from supplements, and you can also consume food that is rich in prebiotics.

Prebiotic-rich foods include the following:

  • jicama
  • asparagus
  • chicory root
  • dandelion greens
  • onions
  • Jerusalem artichoke
  • garlic
  • leeks
  • bananas
  • barley
  • oats
  • apples

Essential nutrients to boost mental health

There are several essential nutrients that are vital to restoring a healthy link between your gut and brain.

These include:


Through the methylation process, folate supports the synthesis of three neurotransmitters involved in mood, behaviour, and sleep – dopamine, serotonin, and norepinephrine.  Folate is the collective term, there are different forms of folate, folic acid, folinic acid and methyl folate, forms that should be used are either folinic acid or methyl folate rather than the synthetic folic acid.  Folic acid will cause problems for those with MTHFR gene variations.

This process also breaks down the amino acid homocysteine, which is often elevated in patients with anxiety and depression. And it creates a molecule called SAMe, which is believed to have anti-depressive effects 8.

Vitamin B12

Vitamin B12 works together with folate in the synthesis of DNA and red blood cells. It’s also involved in the production of the myelin sheath around the nerves and the conduction of nerve impulses 9.

Vitamin B12 deficiency is common in our population and can be caused by gut dysbiosis, leaky gut and gut inflammation. It is also very common in vegetarians as meat is rich in vitamin B12.

Vitamin B6

Vitamin B6 plays an important role in mood regulation.

This is partly because this vitamin is necessary for creating neurotransmitters that regulate emotions, including serotonin, dopamine and gamma-aminobutyric acid (GABA) 10.

Vitamin B6 is also a key cofactor in the CBS detoxification pathway that creates Glutathione, the body’s master antioxidant.


Choline is an organic, water-soluble compound. It is neither a vitamin nor a mineral, but it is grouped with the vitamin B complex due to its similarities. Supplementing with choline has been found to positively impact cognition, behaviour and control mood swings. Rich sources of choline include beef liver, chicken liver, eggs, fresh cod, salmon, cauliflower, broccoli and soybean oil.

Vitamin C

Vitamin C is an antioxidant and plays an important role in balancing your central nervous system. People with vitamin C deficiency often feel tired or depressed. Some studies have shown that people with low levels of vitamin C have found their mood improved after receiving the vitamin.

Vitamin D

Studies have shown that not having enough vitamin D can bring about depression and that people with depression have higher chances of having a vitamin D deficiency. Low levels of vitamin D as are also associated with schizophrenia and anxiety.


Iron is an essential element for brain functions that can dictate psychological behaviours, low iron levels in the body may put you at risk for a variety of mental health issues such as anxiety and depression 11.


Zinc deficiency can lead to depression, increased anxiety, irritability and emotional instability. Clinical studies have shown that low levels of zinc intake contribute to the symptoms of depression and individuals suffering from depression have a lower serum zinc level 12.

Zinc deficiency has also been studied to cause aggression and antisocial behaviour in young adolescent males, a key nutrient required by males through puberty and beyond.


Magnesium is involved in many functions in the central nervous system and several studies have shown its usefulness in neurological and psychiatric diseases. Magnesium levels have been shown to lower in individuals with several mental disorders, especially depression 13.


Many studies have indicated that low selenium intake is associated with lowered mood status. Intervention studies with selenium with other patient populations reveal that selenium improves mood and diminishes anxiety 14.

Brazil nuts, seafoods and organ meats are the richest sources of selenium.  Selenium is one of the key nutrients of the thyroid along with iodine, zinc and tyrosine.

Advanced Functional Testing

Various Advanced Functional testing can gibe us a lot of data about a patient and understand the underlying imbalances that are contributing to the presenting symptoms.

An Advanced Stool test is crucial in ascertaining the integrity of the gut, what bacteria’s are present or in low levels and how the intestinal barrier is functioning.  It also gives us key digestive markers, short chain fatty acids, inflammatory markers plus much more.

The organic Acids test provides us over 70 different metabolic and bacterial markers.  It assesses neurotransmitters, bacterial markers that often don’t show up in the stool test, mitochondrial energy markers, oxalates, key B vitamins and their pathways, methylation markers and much more.

Finally, a comprehensive blood panel assessing 40+ different specific markers that I have developed over time to tie everything together, assess key markers such as insulin, B12, vitamin D, Thyroid, inflammation and the overall blood biochemistry.

How we can help

At Advanced Functional Medicine, we can support you to optimise your health both physically and mentally.

You may require testing and the implementation of an elimination diet so that our Functional Medicine Health Practitioners will be able to ascertain if you have any food sensitivities, vitamin deficiencies or gut dysbiosis that is affecting your mental health.

We use a targeted, individualised approach to help build your digestive health and balance your biochemistry with a nutrient rich diet and supplementation to restore balance and improve your mental health naturally.

The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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