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Short chain fatty acids and the gut-brain axis: A step-by-step guide

‘Short chain fatty acids’, ‘gut-brain axis’.. These are all words we have heard before; but how much is really understood about these terms?

Let us break it down for you… 

The symbiotic accumulation of various bacteria, fungi and viruses along our gastrointestinal tract is what we call our ‘microbiome’. 

The gastrointestinal microbiome has a bi-directional communication with the neurological system. Thus, the name ‘gut-brain axis’.

 This connection and communication are achieved by various pathways of input including:

  • The Vagus nerve; forming a physically connective tie between the brain and gastrointestinal lining
  • The Hypothalamic-Pituitary-Adrenal axis (or our central response system) that dictates behaviours of the gastrointestinal system by influencing various hormones, feedback systems and nerve signalling between the digestive and neurological divisions
  • Immune system activation; whereby immune cells (both gut-resident and brain resident) will co-respond to stressors, inflammation or imbalance
  • Short chain fatty acid-specific neuroactive properties

Today, we are going to expand on the influence that short chain fatty acids (SCFA) have on our gut-brain axis as a result of digestive activity and microbiome composition.

Firstly; what are short chain fatty acids, and where do they come from?

SCFA’s are small, monocarboxylic acids with a 6-carbon chain length. They are produced during the digestive process of anaerobic gut bacteria (just one bacterial component of the microbiome) metabolising indigestible polysaccharides (e.g. dietary fibre and resistant starches) in the large intestine.

These magnificent metabolites have been detected in locations of the body such as human cerebrospinal fluid, (the protective fluid surrounding the spinal cord; and we simply cannot live without a spinal cord!), therefore it is fair to say that SCFA’s are a pretty big deal. 

There are three particular SCFA’s that have been investigated for their beneficial influences on the gut-brain axis:


Butyrate (or butyric acid) has been identified as a component of dairy – especially butter. But it is majorly produced as a by-product of digesting the following prebiotic-rich food groups:

Rolled oats, rice and potatoes that have been cooked and cooled (resistant starches), legumes (galacto-oligosaccharides), beans, peas and lentils with their skins on, underripe banana (or green banana powder), wholegrains and prebiotic fibres (asparagus, broccoli stems, apples and other celluloses).

Butyrate is the main source of energy and fuel for our colonocytes; the cells of our gut lining. In return, energised colonocytes help to provide an oxygen-free environment that helps our microbes thrive!

With the absence of butyrate, weakened colonocytes can result in heightened intestinal permeability or ‘leaky gut’. In the incidence of leaky gut; bacterial products have passage into circulatory pathways, causing systemic inflammation and even bacterial translocation into the blood-brain barrier.


Microbial-derived sources of acetate are obtained from the fermentation process of dietary galacto-oligosaccharides (foods such as beans, dairy products, cashews & pistachios, freekeh and soy) and inulin (foods & herbs such as asparagus, chicory, dandelion root, Jerusalem artichokes, garlic & leeks). 

Acetate has been directly linked to influence levels of neurotransmitters including glutamate (a message-relaying neurotransmitter) and gamma-aminobutyric acid (GABA) – heavily involved in the process of inhibiting neuronal/nerve cell activity. 

Acetate has also been identified as an important energy source for glial cells and reducing appetite through influences on neuropeptides that favour appetite suppression!


Our third SCFA, propionate, is produced in the gut as a result of dietary digestion of cabbage, carrots, resistant starches, cereal grains, wholegrains & inulin! 

Concentrations are identified as highest in the circulation; and propionate has been identified as an important SCFA involved in regulating the expression of tryptophan 5-hydroxylase; an enzyme involved in the synthesis of serotonin!

Remember that microbiome diversity & client-specific dietary requirements will ultimately influence the digestive capacity of your gut and the ability to produce these magnificent SCFA metabolites.

Start by including small amounts of SCFA-building food groups into the diet each day!

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