Gut brain connection and how it affects your mood

Gut-Brain Connection and How it Affects Your Mood

It’s not all in your head. Medication and therapy aren’t the only solutions to mental health conditions. Recent gut-brain research has found that mental health is not only a ‘mental’ issue.

It’s also determined by your gut and microbiome.

Excitingly, gut-brain science is booming. The connection is undeniable. Countless scientific papers are being published daily. Often pointing to the success of natural diet and lifestyle solutions.  A welcome prospect for those struggling with mental illness.

People all over the world are healing!

We will discuss some of those healing strategies in more detail. With a focus on diet, lifestyle and finding the right support.

Gut brain connection and how it affects your mood

And to be clear. Positive thinking, therapy, counselling and relaxation tools all have their place. And can be an important part of the healing journey.

However, science is demonstrating part of the long term solution lies in the simplicity of natural healing.  Healing your gut, your liver and building your microbiome for better brain health.

Brain fog, anxiety, depression and other (now common) mental health conditions can improve. By focusing on your gut health, you can support your healing journey to brain wellbeing.

Here we will discuss:

  • How your gut-brain connection governs your brain health
  • Why looking after your microbiome drives your mental wellbeing
  • Mental conditions associated with gut health
  • Ways to improve and support your gut health for mental health

Your Incredible Gut-Brain Connection

The connection between your digestive system and your brain has many names:

  • Microbiota-gut-brain axis
  • Brain-gut-microbiome axis
  • Microbiome-gut-brain connection
Gut brain connection and how it affects your mood

Here we will call it the gut-brain axis or GBA for short.

But each of these names describes the gut-brain connection. Between your gut, it’s microbiome and your central nervous system (CNS – and your brain).

This two-way communication highway, every moment, is working to maintain balance and health. For you.

Gut brain connection and how it affects your mood

Feeling low, unable to think clearly or other minor neurological symptoms are hints. Your body’s clues that you have an imbalance somewhere in your system.

You may already know your gut acts as a second brain being home to hundreds of millions of neurons. Popular media often points to our common use of faecal (poo) related terms.  Often used to describe emotional states.

Like “feeling crappy”.

Gut brain connection and how it affects your mood

Unconsciously we assumed a connection between our mood and toilet habits.

And there’s definitely truth in it. Your Enteric Nervous System (remember“rest and digest”) is home to  500 million neurons. In and around your gut.

And while this number is staggering, it’s only 0.5% of your body’s total neuron estimate. With your brain comprising perhaps 100 billion! And a lowly 100 million in your spinal column.

Gut brain connection and how it affects your mood

Comparisons aside, your body’s nerve cells are always talking to each other. Providing invaluable real-time feedback.

About the innumerable interactions. Whether biochemical feedback loops or cell (and microbe) signalling, something is always happening. Every moment of your life.

Science is still figuring out how it precisely works together. But there is also a lot we do know, some of which we will talk about next.

How does the signalling mechanisms between the gut microbiota and brain actually work?

How Your Gut-Brain Connection Works

Current evidence suggests 2 main connection mechanisms. About how the microbiome uses to influence our brain and central nervous system (CNS):

  • Neuroimmune signalling pathways (immune and CNS connection)
  • Neuroendocrine signalling pathways (hormone and CNS connection)

Both of these mechanisms often involve the vagus nerve. And both need several microbial metabolites. Including short-chain fatty acids (SCFA), secondary bile acids (2BAs) and tryptophan (Trp).

These molecules then stimulate signals. Via interactions with specialised cells in the mucosal epithelial lining.

  • Enteroendrocrine cells (EECs). Specialised hormone releasing cells in your gut wall. There are at least 12 different types of EECs. Some processes EECs regulate include glucose levels, food intake and stomach emptying.
  • Enterochromaffin cells (ECCs). Account for <1% of all intestinal epithelial cells types. These powerhouses produce >90% of your body’s serotonin (the happiness hormone). And are thought to affect intestinal motility, secretion, nausea and hypersensitivity.
Gut brain connection and how it affects your mood

Another GBA mechanism for SCFAs and other metabolites may be through direct transport. This means across the intestinal barrier and even the blood-brain barrier!

Interestingly, the microbiome can also activate CNS signalling. By producing neuroactive molecules; such as dopamine, norepinephrine, gamma-aminobutyric acid and 5-HT (serotonin).

We’ll talk more about each of these pathways as we go. But first let’s explore the vagus nerve.

Gut brain connection and how it affects your mood

The Vagus Nerve

The vagus nerve, also known as cranial nerve X, is an extremely long nerve. It runs from your brainstem to your colon.

It has many functions including:

  • Internal organ sensory information signals. From the neck, chest and abdomen including your gut.
  • Carries information from the heart. Including sensors that detect oxygen levels in the blood and blood pressure.
  • Controls muscles critical in swallowing and speaking.
  • Plays a significant role in the parasympathetic nervous system. Including “rest and digest” enteric nervous system functions and slowing of heart rate.
  • Carries pain, touch and temperature information. From the throat, ear and meninges (brain membrane).
  • Plays a minor role in taste sensations. From the root of the tongue and epiglottis (the dangly thing at the back of your throat).

As you can see, the vagus nerve plays a critical role in the gut and digestive process. Top to bottom, from taste and swallowing through to digestion and excretion.

Understandably, if the vagus nerve is damaged these many functions are negatively affected.

As a side note, the soothing affect of infant sucking occurs when pressure is applied to the soft palate. This acts to stimulate the vagus nerve and oxytocin production. Oxytocin has also been found to modulate serotonin release (remember our ECCs!).

In a nutshell…

The vagus nerve acts as an information highway, both to and from the gut.

It carries information from specialised cells, microbial metabolites and other organ systems.

And also influences many critical functions. Including digestion and associated intestinal epithelial immune and hormone signalling pathways.

Gut brain connection and how it affects your mood

Intestinal Epithelial Lining – Your Intestinal Barrier

Your intestinal lining is a single cell layer thick. With its protective immunity boosting IgA rich mucus layer, it is all that stands between you and your food (and poo). And it’s integrity is foundational to your gut and overall health.

We’ve previously covered the importance of a healthy gut lining, here we will briefly discuss it’s pivotal function.

Read more:

  1. How to Improve Gut Health Naturally: The Ultimate Guide
  2. The Gut-Immune System Connection
  3. Do You Have Leaky Gut (Plus Warning Signs to Look For)

Your gut lining acts as a gate-keeper.

Daily you expose it to all the food and drinks you consume (and microbial hitchhikers). And it’s the job of your intestinal barrier and associated cells to figure out who is welcome and who is not.

You millions of gut lining neurons constantly relay information to your vagus nerve. And through all your ENS nerve cells too. All working to maintain a healthy and happy state of wellbeing.

However, it’s important to understand what can affect it all. Gut microbes, stress and inflammation can change your gut lining permeability. And the amount of information passing through our delicate intestinal barrier.

This means the amount of information reaching the brain from the gut is highly variable. And dependent on you.

Stress causes epithelial defects (leaky gut) by two known mechanisms:

  • Direct influence on epithelial permeability
  • Alterations in intestinal mucosal layer

Both lead to increased transit. Of gut microbes and metabolites through the gut lining.

Gut brain connection and how it affects your mood

Escherichia coli (E.coli) is an important example.  It’s membrane lipopolysaccharide (LPS) promotes gut inflammation. It resides on the membrane of E.coli and other Gram-negative bacterial cell walls.

Receptors in the gut lining can also moderate inflammation, antimicrobials and immune tolerance.

Specific cells types act as triggers. They can release antibacterial factors. And microbes even help to maintain gut integrity. Supporting the tight-junctions crucial to holding the intestinal barrier together.

Your intestinal barrier is a key player in the gut-brain connection.

The Blood-Brain Barrier (BBB)

The intestinal lining is the natural barrier to signalling within the gut. And part of the gut-brain axis. So too is the blood-brain barrier, or BBB, but for the brain.

It regulates molecular traffic. Between your blood and your cerebrospinal fluid (CSF). CSF is the critical fluid surrounding your brain and spinal cord.

The BBB too is highly influenced by stress, gut microbes and inflammation. All affecting the amount of information passing through.

Gut brain connection and how it affects your mood

Gut microbes can influence this permeability. Because the BBB has tight-junctions like your gut.

Gut brain connection and how it affects your mood

Science shows mice born without microbiomes, “germ-free”, have more permeable (or open) barriers. Both brain and gut.

This permeability decreases (closes) with introduction of SCFA-producing bacteria. So SCFAs are thought to be critical in BBB development and maintenance.

We will discuss SCFAs and the microbes that produce them in more detail later.

What is important to understand here?

The connection between your microbiome, gut and your brain.

It’s undeniable.

To help with this understanding, let’s introduce the gut signalling mechanisms. Those your body uses to communicate with your brain.

Gut Signalling Mechanisms

We spoke about some of the mechanisms used in gut-brain signalling. Here we will go into a little more detail.

But first a quick note.

The GBA signalling mechanisms have names that may be a little complex at first. Because of this will explore them slowly. To help you further understand exactly how your gut and brain can talk to each other.

And because it’s fascinating!

  • Neuroendocrine and Enteroendocrine Signalling Pathways

These are important pathways. Where gut microbes communicate with the endocrine cells in the gut. There are at least 12 types and numerous subtypes of gut endocrine cells.  One of these we covered briefly above, enteroendocrine cells (EECs).

EECs contain and release greater than 20 types of molecules used in signalling. These molecules enter circulation and influence specific CNS centres. Like those involved in ingestive behaviour. Or even directly in the gut (or liver) to generate brain signals!

Gut brain connection and how it affects your mood
  • Short chain fatty acids (SCFAs) are major signalling molecules via EECs (and ECCs – see below).

SCFAs are microbial fermentation products from resistant-starch. They serve as important sources of energy. They stimulate colonic blood flow and the cells responsible for secretion of factors. Like those which induce satiety (feeling full) and behaviour.

Specifically, acetate, butyrate and propionate (common microbially derived SCFAs)  regulate food intake and digestion. Via specialised receptors on EECs in the gut.

Gut brain connection and how it affects your mood
  • Enterochromaffin Cell (ECCs) Signalling

ECCs are a great example of two-way gut-brain communication.

A molecule called 5-HT, (5-hydroxytriptamine – you may know it as the neurotransmitter serotonin) is produced and stored by ECCs in the gut. They stockpile more than 90% of the body’s serotonin!

Serotonin regulates many functions:

  • Gut motility and secretion
  • Mood
  • Pain responses
  • Behaviour and cognitive function
  • Even platelet function

Incredibly, SCFAs and secondary bile acids (derived from spore-forming bacteria in the gut) regulate a large fraction of ECC serotonin synthesis and release.

The essential amino acid tryptophan (Trp) is the precursor to serotonin. And many other important neuroendocrine signalling metabolites. Humans do not produce Trp making it one of the so-called ‘essential’ amino acids needed in human diets.

Trp is used in the synthesis of serotonin. Gut microbes contribute to the availability of Trp in the blood in yet to be confirmed pathways. However, Lactobacillus reuteri has been associated with Trp regulation.

Some common gut colonising bacteria can even produce serotonin. Like Streptococcus and Enterococcus sp. Escherichia coli is also known to produce serotonin and also dopamine and norepinephrine. All important mood regulators.

Gut brain connection and how it affects your mood
  • Neuroimmune Signalling

The gut microbiome and the immune system connection has been researched extensively.

There is much information around the direct link between gut microbes and immune response in CNS illnesses. Some of this we will cover shortly.

An interesting example is multiple sclerosis (MS). A demyelination disease of the nerves. It causes functional problems and stops cell to cell signalling. This impairs motor function.

Imbalance or changes to gut microbiota are connected to MS. Offering potential for treatment and management of this debilitating illness.

Microbes are also implicated in inflammation, autoimmunity and immune cell trafficking. And by many sources.

In particular Bacteroides fragilis (B.fragilis) can protect against demyelinating disease. As seen in experimental autoimmune encephalomyelitis (EAE). This is a common bacteria naturally found in the human gut.

Gut brain connection and how it affects your mood
  • Direct Neural Signalling

Microbe to nerve cell signalling can occur. B.fragilis has been implicated in direct activation of intestinal neurons. So too has Lactobacillus rhamnosus in polysaccharide A laboratory studies.

This shows that some microbes can directly affect neuronal responses. Without needing cell mediated responses or other intervention.

There are also microbial metabolites which can affect neurons and their signalling. We won’t cover these here.

Gut brain connection and how it affects your mood

Other Neurotransmitters Produced in Your Gut

  •  GABA

Gamma-amino butyric acid, or GABA, is the main CNS inhibitory neurotransmitter.  GABA is the body’s natural relaxant.

When GABA interacts with GABA-receptors in neurons it acts to inhibit their action. And blocks nerve impulses. A suppressing effect is created. To oppose the excitatory effect of its precursor glutamate another amino acid.

Interestingly, GABA is also produced by some gut bacteria.

Bacteroides, Parabacteroides, Eubacterium, Bifidobacterium and Escherichia sp all express GABA producing pathways. Lactobacillus rhamnonsus also produces GABA.

  • Acetylcholine

Another Lactobacillus sp, Lactobacillus plantarum, which is found is sauerkraut, produces acetylcholine.

Acetylcholine is an abundant neurotransmitter found in the body. It is known to be crucial in muscle contraction, memory, attention and cognition. Those suffering from Alzheimer’s disease show severe depletion of acetylcholine.

  • Melatonin

Melatonin is produced by the ECCs in the gut. L-tryptophan is a precursor for melatonin. Reinforcing the importance of this essential amino acid.

Melatonin is also produced in the pineal gland. It drives our circadian rhythm and sleep-wake cycles once released into the bloodstream. Digestion and food intake are also regulated by this important endocrine hormone.

Enterobacter aerogenes (E.aerogenes) is a bacteria which colonises the human gut. It responds to melatonin and exhibits circadian growth patterns. Meaning t’s growth pattern change when exposed to melatonin. This supports the notion that non-algal microorganisms exhibit bacterial biological clocks.

Similarly, the human microbiome exhibits diurnal changes. In both expression and abundance corresponding to feeding times and circadian cycles. Hence why shift-workers and frequent flyers are more likely to suffer with dysbiosis. And associated disease states.

The microbiome can recover with reinstated circadian and feeding cycles. Showcasing the incredible ability of the microbiome to heal.

And we all know the importance of sleep for mental health.

Gut brain connection and how it affects your mood

Mental Health and Your Gut

There are many conditions linked with both gut and mental health. Here we will briefly discuss only a few of the most common.

Inflammation and gut health are key in mental illness and associated disease states. Mental health is not only in your brain. If you believe you or anyone you know is suffering from these conditions seek help.

Gut brain connection and how it affects your mood
  • Depression & Anxiety: Your Brain (and Gut) on Fire

Anxiety and depression often present together. And often with other gut conditions. Such as irritable bowel syndrome (we talk about this more shortly).

Feelings of helplessness, extreme irrational fears, and inability to cope with daily life are typical of depression and anxiety. Inflammation is a common trait for those suffering with depression.

Inflammation can alter brain signalling patterns and many other functions. Inflammatory conditions show an increased risk of depression. Conditions such as diabetes, multiple sclerosis and asthma.

Excitingly, evidence is mounting around specific microbial changes in common mental health conditions. Like depression.

There are an increasing number of studies showing positive results. Specifically in modifying the intestinal microbiome with probiotic supplements to ease anxiety symptoms. 

  • Autism Spectrum Disorder (ASD): A Rising Concern

Autism is a rapidly rising condition. It is currently predominantly seen in children. Typical symptoms include; difficulty in social situations, communication and repetitive behaviours.

But so too significant gut symptoms.

Children with ASD are at a higher risk for general gastrointestinal complaints. Such as diarrohea, constipation and abdominal pain. The term ‘autistic enterocolitis’ has been coined to describe these debilitating symptoms.

Anxiety and sensory symptoms are also common in this complex and multifaceted condition. And while the cause is still unknown there is mounting evidence. Implicating the gut microbiome. And it’s role in normal development and function of the nervous system.

Microbiota transfer therapy (MTT) and faecal microbial transplant treatments can alleviate ASD symptoms.  Bacterial diversity and relative abundance can change. In particular, common gut bacteria Prevotella and Bifidobacteria were seen to increase post treatment.

Research such as this offers hope to families living with ASD. The once thought ‘neurological’ disease is a far more complex gut-brain connection syndrome.

  • IBS: Gut and Brain Irritation

Irritable bowel syndrome (IBS) is what’s termed a function intestinal disorder. Where the function of the intestines are affected. Approximately 10 – 20% of the population worldwide suffer with IBS.

Typical IBS symptoms are varied. But may include:

  • Abdominal pain
  • Bloating
  • Straining
  • Muscle aches
  • Urgency
  • Generally altered bowel habits

Most sufferers also report decreased quality of life.

A strong link exists between IBS and mental health. Both depression and anxiety are common in those with IBS.

A number of studies report IBS patients as having significantly different microbiome communities. Compared with normal healthy patients. Some even show different brain volumes. Suggesting a link between brain structure and microbiome structure.

This is an area that more research is needed. The exact cause is unknown. However some natural treatments show promising results. Such as those combining diet modification, pre and probiotics and lifestyle changes.

Gut brain connection and how it affects your mood

Power of the Microbiome

What this all shows us, is how the microbiome has a massive effect on our brains. It influences everything we thought was ‘all in our heads’. From mood and behaviour to classical mental illnesses.

Ultimately, your thousands of gut microbial species form a complex ecology. Feeding both each other and us. With nutrients, vitamins, neurotransmitters and metabolites critical for our wellbeing.

To this end there is a new field of science, called ‘psychobiotics’. It’s investigating how powerful our gut bacteria can be. Especially in influencing common mental conditions like depression and anxiety.

So with the microbiome playing such a huge role in our mental (and general) health it makes sense to look after it.

Are you keen to understand your gut microbes better?

If so, a non-invasive home microbiome test can help. And you will learn exactly which microbes you have supporting your health.

Once you know what’s going on in your gut, there are a number of simple changes you can make. To positively influence you gut and mental health.

How to Improve Your Gut-Brain Health

Fix Your Gut First

Most gut healing advice follows the advice of a familiar phrase. ‘In case of emergency, put your own oxygen mask on first’.

Similarly, you need to fix your gut lining first.

Tighten those incredible ‘tight junctions’. Stem the flow of inflammation causing food and microbes. Stop the sneaking through your gut lining.

Healing (and sealing) your gut lining you can reduce the inflammatory cytokine cascade. A natural immune process wreaking havoc on your gut and brain.

And followed by seeding your gut with beneficial microbes.  This is a powerful combination to start your journey back to health.

Step 1: Heal & Seal – Nourish and Nurture Your Gut with Diet

Reduce inflammation and support your brain health. Healing and sealing your gut is absolutely vital.

Some easy first steps include the points listed below. However a personalised consult with a qualified holistic practitioner may help. Support is key.

Eat whole foods. Cut out processed and packaged food-like-substances. They are laden with artificial sweeteners and chemically derived flavours, colours and preservatives. 

These compounds are known to negatively affect the microbiome. And do not provide the nutrient building blocks needed for a healthy gut. In addition to being nutrient-poor they are also often difficult to digest. And they are loaded with hidden sugars feeding yeasts like Candida, a common culprit in leaky gut.

  • Increase your liquids Estimates may vary but it’s commonly recognised that our bodies are 70 – 80% water with digestion requiring up to 9L. Eating foods with higher water content can assist your digestive action and allow your gut to heal.
  • Drinking more water is a simple and effective healing tool – Another easy way to increase your liquids is to gently cook your food with abundant water. Methods such as boiling and steaming provide much needed hydration to your food. And are an easy-to-digest alternative to raw foods which can be tough on a damaged gut.
  • Supplement for healing – There are many easy to find supplements that support your liver to detox and your gut to heal. Some of these include: L-glutamine, arabinogalactin, slippery elm, colostrum DGL licorice root and quercetin. But as always, it’s helpful to work with a qualified practitioner when looking to choose supportive supplements.
Gut brain connection and how it affects your mood

Step 2: Seed – Build a Better Microbiome

Balance is key. What do we really mean by balance?

Microbiologists describe microbiota balance as being a combination of these factors:

  • Species richness This is a term describing the number of species in your gut. Species richness describes the dynamic balance keeping trouble-makers in lower numbers.

Think: Too many crows in your neighbourhood. The different types of birds you see are all species and the number of each type of bird determines richness.

  • Diversity Diversity is the vast array of different types of microbiome inhabitants. It’s a multicultural microbial community if it were. And describes their abundance relative to each other. Beneficial vs non-beneficial microbes.

Think: How many more (and different) types of birds you see in a native bush or forest habitat compared with the urban – crow infested – environment. Native populations are more diverse.

Essentially, you want lots of different types of microbes. And lots of the beneficial health-supporting species, a rich and diverse ecology.

How? There are many easy and natural methods. To boost or build a better microbiome, we will discuss a few simple steps here:

  • Eat fermented foods – Naturally fermented (and non-pasteurised) sauerkraut, miso, kimchi etc, contribute to gut flora diversity. Eating these foods everyday is a great way to seed beneficial gut microbes.

    And it needn’t be expensive. You can easily make sauerkraut at home. If you are new to fermented foods it’s best to start small. You can add a teaspoon of the fermenting liquid to your meals at first (you won’t even taste it!) and build up to 1-2 tablespoons or more. Just check-in on how you feel. And trust your gut.

  • Fill up on fibre – Fibre feeds the beneficial bacteria in your gut. Eating more fibre is an absolute must, non-negotiable step in gut seeding. You need to eat foods that feed all those good bugs you’re eating, or they will starve.

    Good sources of fibre include many vegetables. Like leafy greens, asparagus, carrots, artichokes, radishes and more. Healthful fibre, including resistant starch, is often termed a prebiotic. And though you can now find prebiotic supplements, enjoying your fibre in whole foods is always best.

  • Take a good probiotic – Probiotic supplements are not all created equal. Finding a high-quality probiotic is key. These often include multiple strains and a high number of colony forming units (CFUs). This means you will get more species richness and higher diversity.

    You’ll receive a good dose of bacterial strains proven to be gut supportive. Some of those we’ve already discussed are brain health-supportive. Check the label for L.plantarum (acetylcholine producing) and Bifidobacteria (GABA).
Gut brain connection and how it affects your mood

Step 3: Thrive: – Build a Healthier Lifestyle

Building a lifestyle that supports your gut and mental health is so important.

Stress has been shown to affect the community structure of the microbiome for over 40 years. Relatively brief exposures to stress can change the microbiome significantly. In as little as 2 hours.

Similarly, stress while pregnant can alter infant outcomes including microbiome profiles.

Reducing your exposure to psychological and emotional stress is essential.  Physical stress also hinders your healing journey. Look out for stressors such as exposure to pesticides, chemicals and electromagnetic stress.

Getting outside in nature is also paramount. Enjoying your family and friends provides innumerable benefits. Including much needed support and a healthy change for your microbiome.

There are many ways to heal your gut and your brain. And they all start with acknowledging it’s not all in your head.

Gut brain connection and how it affects your mood


The gut brain axis is a very real and innately powerful connection affecting us all everyday. The influence your microbiome has on your mental health is fascinating. And an undeniable supportive relationship.

Many gut bacteria produce neurotransmitters responsible for neurological communication. They are fundamental to many brain functions.

And so too, many mental health conditions have gut health ties. There is ample evidence supporting this connection. But it’s a rapidly evolving field and new studies are being published daily.

So while it’s helpful to keep up with the science, there are fundamentals you need to know. You can make a difference to your brain and gut health everyday with amazing results.

Simply changing to a whole food, fibre rich and healing diet has numerous health benefits. And may assist with positive mental health.

You may also feel the need to find the right support or take a microbiome test. Both are powerful tools to use on your healing journey.

And remember it’s not all in your head. You can fix your head but helping your gut.

Gut brain connection and how it affects your mood
Gut brain connection and how it affects your mood

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