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Can you trust your gut?

Aisling FitzGibbon

A tale of two brains

In the unseen world of our digestive system resides our second brain, whose intelligence is as remarkable than the first. For optimal health our two brains need to work in tandem. Our second brain, found in the enteric nervous system, resides in tissue lining the oesophagus, stomach, small intestine and colon and is home to a vast network of neurotransmitters and neurons.

The two brains are linked via the Vagus nerve, (a cranial nerve that extends from the brainstem to the abdomen via the heart, oesophagus and lung) with a two-way communication system. This bi-directional system means that the way we think can influence our gut and the condition of our gut can influence the way we think and feel. However, the gut also can act independently of our first brain as it oversees our digestive processes.

How our thoughts and reactions affect our gut

Known as the gut brain axis, the two brains regularly communicate with one another through molecules produced by bacteria in the gut which then enter the bloodstream. An example of how our first brain affects the gut is how we respond to stressors, whether real or imagined. I know from my own experience that before exams my gut motility tended to go into overdrive and I would also lose my appetite. Once my exams were over I felt fine and my gut health returned to normal.  

Stress in general tends to diminish healthy bacteria and boosts unhealthy bacteria because as cortisol levels rise energy is diverted away from digestion. This reduces digestive enzymes and food is improperly digested. With less nutrient absorption the quality of our gut bacteria is affected.

How our health is impacted by our gut flora

The environment of the gut microbiome is a fragile and adaptive one that changes according to what and how we eat, the health of our digestive tract and the presence of beneficial bacteria. Our gut health is dependent on sufficient bile flow, hydration and the production of adequate Hydrochloric acid that is needed to digest our food. Without sufficient HCL the undigested food in our gut can lead to bacterial, viral and fungal overgrowth and parasitic infections.

The 100 trillion intestinal bacteria that make up what is called the human microbiome can determine how long we live, whether or not we are slender or prone to weight. Gut bacteria alters the way in which we store body fat and how we respond to hormones that make us feel hungry or full.

Healthy gut bacteria help us extract energy from our food and churn out natural antibodies that prevent pathogens from invading the body. 70% of our immune system is dependent on the gut being able to expel and kill foreign invaders.

Gut bacteria plays a role in the production of B vitamins needed for the healthy functioning of our nervous system and vitamin K which is needed for blood clotting, healthy bones and protection against heart disease. 

Lactobacillus for instance is capable of producing B vitamins such as B9- folic acid/ folate. Propionibacterium and Lactobacillus Reuteri can help produce vitamin B12. Bacillus Subtilis is the bacteria that produces K2. Inflammation is perpetuated by the presence of pathogenic bacteria in the gut while beneficial gut bacteria reduce inflammation and prevent leaky gut, present in most autoimmune and neurological conditions.

Leaky gut?

Healthy gut bacteria help us maintain a healthy gut lining. However high levels of inflammation favour the proliferation of unhealthy bacteria which can cause the normally tight junctions in the gut to open and become hyperpermeable. Large molecules of food and toxins can then pass through the gut lining which initiates an immune response. Antibodies are produced against these foreign proteins that mimic proteins already in the body such as those found in the pancreas and in the thyroid. A leaky gut in strongly implicated in autoimmune conditions such as diabetes, Hashimotos’s disease, and asthma. It is linked to neurological conditions such as autism. Leaky gut is also present in conditions of the gastrointestinal tract such as IBS, Ulcerative Colitis and Coeliac disease.

A leaky gut is a cause of poor nutrient absorption of minerals such as iron, zinc and magnesium and vitamin B12. This can lead to depression and anxiety.

Mighty mouse

Mice experiments conducted by Stephen Collins of McMaster University in Hamilton showed that when microbes of anxious mice were implanted in bolder mice they became timid. Aggressive mice calmed down when scientists altered their microbes by changing their diet and feeding them probiotics.

The absence of a single specific species of gut bacteria causes social deficits in mice. When mice were given lactobacillus it enhanced social behaviour and when given another bacteria called L – Reuteri it helped promote the production of oxytocin which is known to play a role in social bonding.

How our gut affects our mental health

There is growing evidence that gut bacteria can influence how we think. According to Dr Emeran Mayer, Professor of Medicine and Psychiatry at the University of California, Los Angeles, bacteria in our digestive tract may help us to mould brain structure as we are growing up, influencing our moods, behaviour and feelings as an adult.

There is a tendency to think of brain involvement in conditions such as anxiety and depression. Yet many of our calming neurotransmitters such as serotonin, dopamine and GABA (Gamma-Amino butyric Acid) are made in our gut. 50% of dopamine and almost all of our serotonin originate in our intestines. Moreover, the brain’s serotonergic system which plays a key role in emotional activity does not develop in the absence of microbes. Serotonin is the neurotransmitter that helps regulate our moods, appetite, sleep and helps us to learn.

A 2004 study in the Journal of Paediatric Gastroenterology and Nutrition, Integrative Immunologist Michael Bailey discovered that monkeys whose mothers had been startled by loud noise in pregnancy had fewer lactobacilli and Bifidobacterium. So stress directly impacts our gut bacteria. We need lactobacillus and Bifidobacterium to help produce GABA, a neurotransmitter that lessens our stress response and keeps us calm. Lactobacillus plantarum is a healthy microbe that is capable of enhancing memory which could prove to be very beneficial around exam times!!!

The origin of our gut bacteria

When babies pass through the birth canal they inherit their mother’s bacteria such as lactobacilli, which help them to digest milk. They continue to build up the diverse community of their gut microbes in the following weeks. Breastfeeding helps populate the baby’s gut bacteria from the skin contact between mother and child.

Some babies are born by Caesarean section which means they don’t have the opportunity to get the necessary bacteria from their mothers. Dr Perlmutter advises that before a baby is delivered an organic sponge should be placed in the birth canal before any antibiotics are administered. Once the baby is born the sponge is to be placed over the baby’s face which helps to colonise their gut.  

How can I help my gut? 

We need to create a healthy environment in which our gut bacteria can thrive and multiply. Prebiotics helps to fuel the growth of healthy gut bugs and are found in onions, garlic, leeks and in dandelion greens and asparagus. Prebiotics provide the food for probiotics and keep them living and growing as they should.

A nutrient rich diet high in natural anti -oxidants and minerals favours a healthy gut flora. The presence of beneficial lactobacillus are found in lacto fermented foods such as sauerkraut, kefir and natural yoghurt(only if dairy is not a problem) A teaspoon of sauerkraut is teeming with beneficial bacteria which is really helpful following a stomach bug to help recolonize the gut. Cruciferous vegetables such as broccoli and cauliflower and kale contain Sulphur metabolites which are broken down by microbes to reduce inflammation in the gut. This lessens the risk of cancers.

Bone broth contains collagen and the amino acids proline and glycine which, according to Dr Natasha Campbell McBride are excellent to help” heal and seal” the gut lining.

Gelatine contains the amino acid glycine which helps to control inflammation and strengthen the gut lining. Gelatine also has the added bonus of helping us produce GABA, a calming neurotransmitter which acts as an antidote to anxiety.

The mineral magnesium plays an important role in the maintenance of a healthy gut biome. A study was conducted in a University in Brussels showed the difference in the gut bacteria between mice who were fed a magnesium rich diet and mice who were fed a diet low in magnesium. The magnesium deficient diet was linked to greater intestinal inflammation and a drop in Bifidobacterium, a bacteria that protects us from unhealthy pathogens.  

Living with a dog is not just good for us emotionally but their presence also helps us diversify our gut flora. A 2013 study showed that adults share more microbes with their own dogs than with dogs owned by other people. Children in dog owning households are less likely to suffer with allergies and asthma.

What harms my gut?

A diet high in sugars including an excess of fructose favors the growth of unhealthy bacteria such as Candida Albicans which attacks the intestinal wall. Sugar is processed too easily and starves those microbes who need healthy foods to munch on. The presence of sugar in the diet makes bacteria in the gut extract more calories from food, which is not good news for those trying to lose weight.

Inflammation starts a cascading response in the gut that triggers the release of proinflammatory cytokines and chemicals that induce depression.

Antibiotics can cause massive collateral damage as they target the killing of certain pathogenic bacteria and end up wiping out our healthy colony of microbes. This is when a course of probiotics is needed to help repopulate the gut.

Other prescription medications also negatively affect the gut flora such as the birth control pill and anti- inflammatory drugs. Our current obsession with hygiene has people buying anti-bacterial wipes and household cleaning products. However, this over sanitisation of our homes is wiping out every bacteria in sight and some exposure to bacteria is needed for the development of our immune system.   

Love your gut

Deep breathing exercises extending into the abdomen will send messages of relaxation to the gut. Eating slowly allows for more efficient digestion and keeps the gut calm and relaxed. Thinking happy positive thoughts and learning to reframe negative situations reduces the stress response which has a knock on effect on the health of our microbes.

A healthy diet breeds healthy microbes that favor the release of happy brain chemicals such as serotonin, dopamine and GABA. A healthy gut affords us immunity from outside pathogens and enables us to extract energy from our food. Seeing as we are more microbe than human (we have more microbes in our body than cells) maybe it’s time we gave them a little more thought and a lot more love.


Perlmutter D, 2015, The Power of Gut microbes to heal and protect your brain for life, Yellow Kite, Great Britain.

Campbell McBride, N, 2010, Gut and Psychology Syndrome, Medinform Publishing, UK


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