When I was in my teens and first stepping into the health arena, I believed the brain was separate from the rest of the body – protected, highly specialised and largely unaffected by what was happening elsewhere. To me, the brain stood apart as its own independent system.
I let go of that way of thinking many, many decades ago, it no longer made sense.
Today, we understand that the brain is inseparable from the gut. In fact, the gut is often referred to as the “second brain”, containing more neurons than any other organ in the body. This makes your gut vitally important to how well you are able to express health.
In the United States, gut-related concerns affect around 80 percent of the population. Closer to home, in New Zealand, around one in seven adults are affected, and gut health complaints are now among the most common concerns people present with.
Irritable Bowel Syndrome affects roughly 20 percent of the population, while rates of Inflammatory Bowel Disease in New Zealand are among the highest in the world. Then there are reflux and heartburn, food allergies, bloating, gas, constipation, diarrhoea, fatigue, skin challenges, mood changes, attention difficulties and neurodevelopmental concerns. All of these are signs that something is not right on the inside.
Yet very little seems to be changing in how these concerns are approached within the conventional system. Drug after drug is offered to suppress symptoms, while the underlying problem continues to grow.
Let me explain what is happening in a simple way.
Your small intestine, which is around six to eight metres long, and your large intestine, which is around one and a half metres long are both lined with specialised epithelial (skin) cells. These cells form your gut barrier – your castle wall. They allow helpful substances to pass through while keeping harmful substances out. Every three to five days this lining renews itself as the cells turn over.
Living inside your small and large intestine are trillions of microorganisms, including bacteria, yeasts, fungi and archaea. These microbes are known as the gut microbiome. Their role is to support your physiology, including helping to repair and maintain the gut barrier. When this barrier is functioning properly, it helps protect the immune system.
In simple terms, there are three protective layers.
- Your microbes are the first line of protection, supporting and maintaining the gut barrier.
- Your gut barrier is the epithelial lining – your castle wall.
- Your immune system is the final line of defence.
The goal is that your microbes and your gut barrier do most of the protective work so your immune system does not need to be activated unnecessarily.
When the gut barrier becomes compromised and substances begin crossing into the body, people commonly experience digestive symptoms, skin changes, fatigue, joint and muscle aches, mood changes and brain fog to name a few. This pattern is often described as “leaky gut”.
The stronger and more diverse your microbes are, the stronger your gut barrier becomes and the less reactive your immune system needs to be. When the gut ecosystem is balanced, the immune system is signalled to respond only when truly necessary. Everything calms down. The microbiome essentially behaves like a vital organ.
When the barrier is ‘leaking’ and the immune system remains switched on for long periods of time, cytokines are constantly released. Cytokines are small signalling proteins produced by immune cells to coordinate the body’s response to injury. They are essential, but in excess they can contribute to tissue damage.
This type of immune-driven destruction has been associated with depression, mood disorders, neurodegenerative disease and chronic inflammatory conditions amongst others. The key point being the immune system and the gut microbiome are so closely connected that they cannot be separated.
Modern life is steadily destroying our microbiome. The result is disruption of the gut barrier and long-term activation of the immune system, creating chronic low-grade inflammation.
One component of modern life and one of the most powerful disruptors is antibiotics.
By the age of five in New Zealand, the vast majority of children have received antibiotics, often at a rate of one to two courses per year. While there is no widely published New Zealand data extending to age eighteen, cumulative exposure could easily reach ten to fifteen or more courses by adolescence.
In the United States, more than ninety percent of children have received at least one course of antibiotics, and cumulative exposure often exceeds ten courses by early adolescence.
What is most concerning is the recovery of the gut and microbiome after a course of antibiotics.
Rebuilding microbial communities can take up to a year after a single course, and in some people full recovery may never occur. When antibiotics are repeated, the microbiome does not have the time to rebuild and stabilise. This directly affects the gut barrier and, in turn, the immune system. Over time, this increases the risk of allergic, autoimmune and metabolic health challenges later in life. This is a key reason for the increase in childhood chronic diseases.
A sobering reality.
A child’s microbiome and immune system begin developing before birth, and the first three years of life are especially influential and critical. A child in utero is virtually microbiome free, all their nutrition comes through the placenta and hence their external skin and their internal gut are void of microbiome.
Three major factors shape early microbial and microbiome development.
The first is mode of birth. During a vaginal birth, the baby comes in contact with the maternal microbes that help seed the external skin and support early immune development. This exposure is absent during caesarean.
The second is feeding. Breastfeeding enables the infant to be in contact with the mother’s skin microbiome as well as specialised human milk oligosaccharides within the breast milk that help shape the developing gut microbiome.
The third is antibiotic and drug use, which as already mentioned profoundly disrupts microbial ecosystems.
Gut health is foundational, not secondary. Early-life gut health plays a major role in long-term health. The microbiome begins forming at birth and continues to develop throughout infancy and childhood. During this period, it helps establish immune tolerance, inflammatory thresholds and metabolic regulation. Early disruptions such as repeated antibiotic exposure, bottle feeding and caesarean reduce microbial diversity and may influence health for decades.
If the microbiome behaves like a regulatory organ, then its health becomes foundational to the body’s health. It helps shapes the biological environment in which the brain must operate. From my perspective, the microbiome’s influence on brains health moves it beyond the notion of being an optional wellness strategy and places it firmly in the realm of long-term neurological resilience.
Simply put, to adapt to life, you must be neurologically robust. Chiropractic care focuses on supporting the structural parts of your body that house your nerve system namely your brain, and your spinal cord. Given the nerve system innervates every cell, tissue and organ of the body then it makes sense to make sure your nerve system is clearly communicating so your gut microbiome, your epithelial cells and your immune system can all function as they should.
The relationship between the gut and the brain is not theoretical. It is physiological. They communicate continuously through what is known as the gut–brain axis. This involves direct neural signalling, immune communication and microbial and metabolic messengers.
One of the most important communication pathways is the Vagus nerve. It provides a direct line between the gut and the brain and plays a central role in regulating stress responses, digestion and inflammation.
From a nervous system perspective, this is profound. The gut is one of the body’s largest sensory organs. The information it sends helps the brain interpret internal safety, threat and physiological stability. The brain is constantly listening to the gut and, at the same time, influencing it.
Around seventy percent of the body’s immune system is located in the gut. Our external skin acts mainly as a barrier, however, our internal skin (our epithelial cells, our gut) needs to act both as a barrier and as a place of passage. This is why we have so many immune defences located in the gut.
The brain and the microbiome help train immune cells and shape how reactive or regulated immune responses become. When microbial diversity and balance are maintained, immune signalling is more likely to remain proportionate. When the microbiome is disrupted, immune responses often become exaggerated and inflammatory.
This matters for the brain.
Chronic low-grade inflammation is now recognised as a contributing factor in many neurological and mental health concerns. What happens in the gut does not stay in the gut. Inflammatory signals circulate through the bloodstream and influence the biological environment in which the brain must function.
In Brain Maker, David Perlmutter emphasises that inflammation is not a side issue, but a central driver of long-term brain vulnerability. Protecting the brain therefore begins with protecting the systems that regulate inflammation.
This means prevention.
Supporting gut health becomes one of the most practical upstream strategies for immune regulation and reducing inflammatory load. This includes regular chiropractic care to support neurological integrity, developing a more conscious understanding of how we define and approach health, and making dietary choices that reduce inflammatory foods such as wheat, dairy and refined sugars while increasing fibre-rich foods such as vegetables, fruits, legumes and fungi.
When fibre reaches the colon, it becomes fuel for beneficial microbes to reproduce and grow. In response, these microbes produce three important short-chain fatty acids: Acetate, Propionate and Butyrate acting as chemical communicators between systems – they support the gut wall cells, they reduce inflammation, they support healthy metabolism and appetite and they foster a healthy and balanced immune response.
A brain operating in a body dominated by chronic inflammation, persistent stress and metabolic instability is working under very different biological conditions from a brain supported by regulated immune activity, a resilient microbiome and a well-functioning nervous system.
If the microbiome is a living ecosystem, then food becomes one of its most powerful environmental inputs. Fibre-rich plant foods, dietary diversity and naturally fermented foods support microbial diversity and beneficial metabolic activity. Highly processed foods and diets dominated by refined carbohydrates, added sugars, wheat and dairy tend to promote microbial patterns associated with inflammation and metabolic dysfunction.
Food therefore becomes not only fuel for your cells and nervous system, but nourishment for your microbial community. Your everyday choices actively shape the biological environment that either supports or undermines your health.
What has changed dramatically over recent decades is modern life and its effect on microbial resilience. Frequent antibiotic use, low-fibre diets, highly processed foods, reduced contact with natural environments and chronic psychological stress all contribute to narrowing microbial ecosystems.
Less diverse microbial communities are more fragile. They are more easily disrupted and less capable of regulating immune and metabolic signalling. From a systems perspective, this reduces the body’s capacity to buffer stress and maintain stable neurological function.
The gut is not simply supporting digestion. It is shaping immune behaviour, influencing nervous system regulation, contributing to physiological balance and helping protect the brain itself.
If we truly want to support long-term cognitive health, emotional stability and neurological integrity, caring for the gut microbiome is not a secondary strategy.
It is vitally important.
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