GUT/BRAIN AXIS 101 “The body’s second brain”

Before we were born, we didn’t have to worry about anything. All the building blocks to form the cells in our growing body were provided to us, in utero, by our mothers, filtered and ready to use. This is the case until the moment the umbilical cord is cut. SNIP! From this point, we are on our on own, and our bodies immediately need to acquire it’s many nutritional building blocks or raw materials  to carry out its biological functions from the outside world, while at the same time doing its best to keep out whatever it doesn’t need, and whatever is potentially harmful to the host. Though it serves many minute and precise functions, the guts most important – and difficult function is to acquire the necessary building blocks from the outside world in order for the body to build and run itself. It does this through the food we consume, while at the same time making sure that nothing foreign gets into the body, which could threaten it survival.

Biologically speaking, the body has two brains: one in the head & in one in the gut. And just like the brain controls is own nervous system – the central nervous system (CNS), the gut also independently controls its own nervous system… the enteric nervous system (ENS). Then there’s the autonomic nervous system (ANS) that is shared between the two: Even though these systems are independent in terms of their functions; both communicate with each other, and can indirectly influence each other’s functional commands out outcomes.

The brain in your head is the hardware for our thoughts. But when we experience a “gut feeling,” or “intuition”, the tiny sparks of bio-electricity show up within the neurons in your second brain. While your first brain serves as your intellectual hardware, your second brain – the gut – is your spiritual and emotional GPS or satellite navigation. Without it, your lost. This is what’s known as the gut:brain axis, or referred to as the gut:brain connection where two separate organs are synergistically hard-wired together, exchanging information via the vagus nerve.

When was the last time you experienced some form of physical or emotional stress, that made you feel nauseated after. This was the brain & the gut communicating, as well as other organs in the chain. In this situation, the stimulus signals the brain to react to what is perceived. This then triggers a whole cascade of events downstream. The hypothalamus secretes corticotropin releasing hormone (CRH), which stimulates the anterior pituitary gland to release adrenocorticotropic hormone (ACTH) which signals the adrenal glands to produce cortisol from the cortex. It also increases the release of chemical compounds that trigger the release of other sympathetic hormones into the bloodstream such adrenaline & noradrenaline. In this scenario – within a nano-second; the brain dials up the gut and says, ‘look, we’re experiencing a potential threat to our survival up here. Just to let you know, we’re going to be sending some cortisol & adrenaline your way. Please don’t be alarmed. We’ll be temporarily shutting off digestive function, detoxification, sex hormone production, immune cell regeneration until further notice… oh, we’ll also be down-regulating thyroid function. We hope to have things back to normal as soon as possible. Sorry for any inconvenience’.

If any of you reading this have followed any of my previous published content or FM work you would have heard me talk about systems-biology before. The foundations of the above analogy is a very simplistic example of just some of systems-biology that is effected as a result of one external stress signal, and the biological dominoes that then fall downstream.

The following definition of the gut that I’m about to go on to write about is my own analogical creation, in order to make things more digestible, and palatable to the reader (no pun intended). But first, let’s take a tour of the one of the bodies remarkable systems, that is part of systems-biology – the gut, and its four main parts that I’ve listed below which I’ll be talking about each one individually.


An easy analogy I’m going to use to help you understand how your gut functions is it to think of it in terms of a country. Every country has its own land and borders. Every country has in place specific infrastructure and communication systems. Every country has citizens and the its department of homeland security . Using these analogical comparisons below, I’ve broken it down into its different parts to make it easier to understand.


Sticking with the analogy of countries and borders – the digestive tube is your bodies busiest border of all. Only 3 major organs come into physical contact with the outside world: your skin, your lungs, and your digestive tract, or tube. This hollow tube runs through the entire body from one end to the other, yet despite being housed ‘inside my the body, it is actually classed as ‘outside’ the body.

When it comes to our skin – even though toxins can be absorbed through the outer dermal layer if applied topically – for the most part, healthy skin is uninterrupted. Most things tend to bounce off it without any harm being caused. The other two borders on the other hand are a little more complicated. When you breathe, air enters the body. Even though oxygen (O2) comes in, it’s also classed as ‘outside’ the body until it passes into the lungs, pulmonary capillaries, and is carried away by red blood cells (RBC’s).

The same is true for food & drink. When you swallow food, it disappears from our view and travels down the digestive tube, which as I mentioned earlier is technically classed as “outside” of you until it’s broken down and absorbed through the intestinal wall. Hence, the skin, lungs, and digestive tract encompass the three “borders” where the body draws a line between what is inside and what is outside.

Of these three organs, your digestive tube is the largest and busiest of all three. The intestinal wall is also unique in that, unlike the lungs, it is constantly in touch with foreign stuff such as food, drink, and all the chemicals that are often either purposely added to both, or indirectly contaminated via exposure to other substances from the environment before it enters the body. In addition to this there is also foreign (pathogenic) organisms such as bacteria, yeast, parasites, viruses, among others, that can commute into the body via the solids & liquids that we consume. And unlike the skin, which is designed to keep most things out, and let very few things pass through it, the intestinal wall is designed to absorb everything that is useful to the body.

The digestive tube itself measures between 10 and 15 feet, running from your mouth to your anus. Along this border, some of the most important functions for survival of your body are fulfilled, such as breaking down food (digestion), absorbing nutrients essential for life (absorption), eliminating waste from your blood circulation (elimination), and housing the intestinal microflora (protection). The digestive tube also functions as a structural framework within and around the other parts of the gut – the GALT and ENS are organised.

As humans evolved, food was scarce. The architectural structure of our digestive tube adapted over the years to ensure the cells of the intestinal walls would come into contact food. This gave the body a better chance of absorbing whatever nutrients it could find. The body achieved this incredible task by creating folds and sub-folds of the intestinal wall also known as villi and microvilli, which are finger-like projections which increases the contact surface area to 200 times the area of the skin covering the body. I’ve written about this in more detail in previous articles. Its here the body acquires the nutrients necessary for survival through digestion.

Even though the large intestine (or colon as it’s more commonly known) plays an important functional role in the health of host – when it comes to the digestive process, as the human GI tract evolved, the large intestine became shorter, and we became less dependent on it. The large intestine harbours lots of bacteria to help break down & utilise hard-to-digest food such we fibrous plant matter. This process is known as fermentation. When our ancestors starting sourcing & eating easy-to-digest, calorie-rich foods such as proteins, fats, ripe fruits, and certain cooked starches that require minimal bacterial digestion (fermentation) in the large intestine, and instead utilise the small intestine for digestion. This led to the large intestine shortening as they didn’t need the lengthy digestive tract as much. This shift is reflected in our current intestinal anatomy with the small intestine representing over 56% of the intestinal tract, with the large intestine only around 20%.

Digestion is the process by which we break down food into smaller pieces. It’s done both mechanically by chewing, and chemically via gastric juices/pancreatic/brush-border enzymes; involving different satellite organs, such as the salivary glands, liver, gallbladder, and pancreas. Absorption occurs once the broken down food find the cells of the intestinal wall (IW), the first layer of the body cells to come into direct contact with the outside world. The cells of the IW let the smaller building blocks of food into the body selectively through the cells or in between them, where they are tightly joined together in what I called “tight-junctions.” This is essentially how nutrients get into the bloodstream and then are distributed to the cells and tissues.

Under the microscope the cells of the intestinal will look very much like a brick wall construction. Each cell is closely attached to other cells by the tight junctions. But these bricks are not normal bricks. No sir! These are highly intelligent ‘semi-porous’ bricks. They keep what is foreign to the body (undigested food in microorganisms) out while simultaneously letting in whatever the body needs such as digested food. Cells of the intestinal wall release an antibacterial mucus coating that keeps bacteria at distance from the cell membrane. Certain species of beneficial flora adhere to this mucus membrane as a second layer of immune protection. The cells select what they let in and want to keep out, much like what happens at customs and immigration. They normally let digested food in, in the form of nutrients, And do their best to keep undigested food out of the bloodstream, as well as any foreign invaders such as microorganisms. Even the good bacteria must be stopped from entering the bloodstream.

One common entry point for Candida is via the mucosal/intestinal border. In a healthy subject, the mucous layer lines & protects the various entry points of the body (such as the digestive tract, nasal passages, lungs, vaginal canal etc) with additional security coming from the host microflora that also resides on its surface. Weakened mucosal immunity often means lower levels of protection coming from beneficial flora (as it requires mucous to adhere to) making it easier for yeast & bacteria to infiltrate/gain entry to the bloodstream and become systemic. For this reason, intestinal wall cells must always remain intact and their tight junctions must remain ‘tight’. A missing cell or a loose junction would allow undigested food, and good and bad bacteria inside the digestive tube directly into the body. This would result in an immune system reaction, and antigenic tagging. A dscontinuation of intestinal wall cells or a loosening of the tight junctions (actual holes in the wall) leads to a condition called intestinal hyper-permeability, commonly referred to as leaky gut. This is a component, or pathological mechanism that can lead to many illnesses that I deal with in FM practice. One major one being autoimmunity – an dysfunctional/overactive/confused/ immune system which it cannot distinguish between self, and non-self, and ends up attacking the host cells, tissues, glands & organs.

Continuing where I left off – In addition – intestinal cells are in charge of exporting metabolic and other toxic waste outside the body into the digestive tube for elimination. Accompanying any food the body didn’t/couldn’t absorb. Most people think of their faces as whatever the body didn’t want or need to absorb from the food they eat. This is only half the story. The cells of the intestinal wall are capable of capturing other waste, such as mucus, fat, metabolic waste, and toxins from my blood, and dumping it into the gut for elimination. This is the exact reverse of absorption. Even if you eat nothing, your body can form faeces with this waste. The average person usually passes remnants of food within two days, even if the system is backed up. During extended/assisted detoxification/fasts, the body will continue to pass waste even though no food has been consumed. How can this be? Well, it comes to a point where the the body will start to dig deep into the tissues for old waste matter, and dump it into the digestive tube for elimination. I’ve seen black mucoid plaque shaped like the foldings of the colon being passed during assisted detoxification protocols utilising colonics. Like scrubbing the inside of a dirty pot.


Now back to the analogy. The GALT could be compared to your body’s department of homeland security. As with any animal on the planet in competition with billions of other organisms for resources, our bodies have to function in the world as individual organisms. Big organisms like tigers and bears can tear us apart limb from limb, and eat us for their dinner, but even miniature or microscopic organisms, such as viruses, parasites & bacteria, can kill us just as readily. Large predators attack you from the outside your body, while microscopic ones kill you from the inside.

The Fortunately for me as a Functional Medicine (FM) clinician, I don’t have to don my loin cloth & sword, and help patients fight off large external predators such as large wild animals – it’s more about educating them about modern-day external threats such as exposure to toxicity in all all its forms, and dealing with internal threats in the form of microbiological, immunological, metabolic, hormonal, and digestive disorders & dysfunctions, whilst educating/coaching to form new lifestyle habits/behaviours.

Whilst on the subject of modern-day external threats – foreign materials & foreign organisms harmful to the body must be kept outside the host organism. As I explained before, the first barrier that encounters anything foreign foreign as it transits down the digestive tube is the intestinal wall. The intestinal flora are actually the first barrier, although bacteria are not considered your own cells. Under ideal circumstances, the IW cells with its tight junctions would be enough to fend off everything that is not completely digested food. However, some foreign materials (such as incompletely digested food or toxic chemicals) or organisms may sometimes sneak through. This is where the bodies GALT comes into play.

The body’s immune system works a lot like the Department of Homeland Security. It is in charge of detecting anything that comes into contact with your inside that is not recognised as simple nutrients or as part of host. Your body’s homeland security has many different divisions and uses an array of elaborate weapons, including immunoglobulins, or antibodies. Your immune system has B-cells, T-cells, mast cells, phagocytes, plus many others which all service specific functions. As an example, Monocytes attack viruses, while neutrophils attack bacteria. Eosinophils are involved in allergic-type reactions, and killer T-cells attack cancerous cells, the body’s terrorists. The different cells, just like the US employs the army, navy, CIA, and FBI in its war on terror.

Even though the cells of the immune system are located and circulate throughout the body, most troops and bases are deployed at the borders where the greatest danger lurks. This is why we find immune cells right beneath the skin and around the lungs. But 80% of the body’s security troops are deployed in the gut, right next to the border with the most traffic – the intestinal wall. In-fact, the GALT makes up the biggest part of the body’s entire immune system.

Our immune system cells are constantly scanning the environment to detect organisms and molecules that are foreign and hostile. It’s accomplishes this by recognising lots of different surfaces. It helps to think of this system as similar to the scanning devices in supermarkets or shops. A simple scan of a tag will tell the retailer what a particular item is, how much it costs, and how many are left in stock. The body uses a coded system called the HLA(human leucocyte antigen) system, which works in a similar fashion. It gives a code to all surfaces that it scans/detects. One of the jobs of the Immune cells is to identify various surfaces . Everything has a surface, whether it be your own cells, a microorganism, or a piece of food. When your immune system scans interior surfaces of your body, it compares each to a list of pre-approved codes, the ones it classifies as “self.” If the immune system detects a surface with a threatening code (an antigen) it releases weapons and recruits other immune-system cells to attack the foreign surface as a way of defending the host (you) and survive.

When food is broken down, however, the individual services of its building blocks are too small to be coded. As a result, the immune system interprets them as neutral. This is how you are able to absorb nutrients through your intestinal wall without alarming your mean system right underneath it. But if the services of a larger pieces of undigested food are presented to the immune system, it reads them as an antigen. Another way of saying this is that digested food is no longer antigenic; it no longer has a recognisable surface. This system goes haywire in autoimmune cases as there is a induced coding system malfunction, and healthy functional tissues that molecularly resemble antigens are attacked by mistake.

Here is where things can go wrong. Faced with a threat, the immune system launches a defence strategy that involves not only the immune system cells in the cut, but also the immune cells around the body. The body goes into full defence mode. It goes to war with with threatening surfaces, both animate (organisms) and inanimate (undigested food and toxic chemicals). for example, some of the immune system the divisions work best at a high temperature. This is conveyed to the brain in the gut, which conserves heat by shutting down circulation to the skin to prevent heat loss as when it’s triggering muscle movement such a shivering, creating a fever in the process. A high temperature when you’re sick he’s not a mistake; he allows the immune system to perform or efficiently. What do you mean system requires a whole other set of conditions. They set of conditions is what we call inflammation. Often turned on by dysfunction in the gut, inflammation is the bodies best example of adapting surviving.


If we view host body is the home, then the intestinal microflora could be viewed as the tenants.

The giant folded area that lines the wall of your intestines is prime real estate for microorganisms to take up residence. They absolutely love it there. It’s warm and cosy, humid, protected from the elements, and food falls from the sky. It is bacteria heaven. Throughout our natural evolution, we have become so friendly with a number of them that we have offer them permanent lodging and free meals. In return, they show their gratitude & pay us back by handling heavy workload. And the gut is filled with these bacteria. In fact, there are more of them in a healthy gut then there are human cells in the entire body. A ratio of approximately 10 trillion to one. There are also hundreds of different species of the bacteria. Altogether these bacteria can weigh as much as the liver, sometimes even heavier.

These microorganisms called the intestinal flora, perform many important functions. Though the good bacteria of the intestinal flora don’t share your DNA, they can, and should, be considered to some of your own tissues, or even organs, given everything they do on your bodies behalf. they are the first things other organisms in counter in the digestive tube, and they fight to protect their territory and prevent other organisms from taking hold. In this way, the intestinal flora helps the immune system for invaders.

Even when there is no threat of invasion, intestinal flora remain hard at work, constantly stimulating the GALT. Their effect on the GALT is known as immunomodulation. One of the most fascinating functions of the intestinal flora is their ability to regulate immune system. Throughout the digestive tube different immune system “station “are located directly on the other side of the intestinal wall, opposite where the good bacteria settle. these could bacteria help keep the immune system in check. Immune system generally attacks bacteria, but it seems to have a truce with the bacteria of the intestinal flora, as long as they don’t try to get in the bloodstream through the intestinal wall, which, as I mentioned previously must always remain intact.

The presence of the cats beneficial bacteria signals to the immune system that things are working well. The presents also means that the climate and the guys healthy. The immune system can’t directly contact the intestinal flora, but one type of immune system sale, dendritic cells, since filaments into the digestive tube through the intestinal wall together information of the conditions there and look for the presence of good bacteria. This is known as “snorkelling “. The cellular activity of been constantly on the lookout for intestinal flora is what keeps the immune system awake and alert, ready for, but not engaged in, attack. You could say the good bacteria regulate the immune system is baseline/foundational activity.

The intestinal flora do many other things as well. They digest part of our food for us. Certain nutrients, such as the B-vitamins, have to be predigested by bacteria before the body can absorb them. Bacteria in general have different digestive systems from ours and can only do certain chemical tricks with food that our bodies can’t. Some of the digestive processes that the good bacteria perform are very useful to us. a healthy gut acts like a fermentation tank inside you. Because so many peoples inner fermentation tanks are not populated with the good bacteria, it can be beneficial to consume (pre) fermented foods. “Fermented” is another term for food that had been digested by bacteria. In contrast, opportunistic bacteria and other organisms produce toxic waste as a bi-product of their digestion, such as flammable gasses (methane), often seen in cases of small intestinal bacterial overgrowth (SIBO) or neurotoxins, which paralyse the nerve-muscle terminals on the intestines leading to abdominal distention, and constipation, among other things.

The intestinal flora is also a key contributor in detoxification, ridding the body of 40% of the toxins coming from food. In this sense, they serve as a satellite liver. In other words; guts with poor intestinal flora means the liver has to work almost twice as hard.

Although the gut continues to be one of the most studied subjects, and although we are learning more; the reality is, we are only just scratching the surface. Our understanding of how many of which species of good bacteria, and what segment of the digestive tube they should be in (small or large) is still in its infancy. We are just starting to fully understand what goes on in a healthy gut and, even more recently, how opportunistic microorganisms in our gut, such as viruses, parasites, yeast, and pathogenic bacteria, or lack of good bacteria, or associated with many more problems than we ever thought. Look no further than the latest research in this fascinating area of study do you understand the value of your intestinal flora, which is part of what is called the human microbiome. Only recently for instance, studies emerge showing a strong connection between the state of your guts ecosystem in cancer. The headline said it all: “what if a key factor ultimately behind a cancer was not genetic defect but ecological? “

I believe there are many more discoveries to be made regarding how the intestinal flora communicate with cells in our bodies and help us thrive and survive. But current research leaves no doubt that they have an essential role in our ability to thrive, stay healthy, adapt, and survive. Thinking of the intestinal flora as an integral part of our biology give us more incentive to protect them and learn about them, as we do with every other organ in our bodies.


Within the walls of the digestive tube are many different layers of tissues. The intestinal wall, made of cells that absorb and eliminate food and waste, he is one layer in direct contact with the outside world. Yes you heard it, just one cell layer thick. Around the intestinal wall is a layer of connective tissue, which holds it in place the little blood vessels that collect whatever is absorbed. Another concentric layer of muscle cells squeezes the contents of the digestive tube forward. In between is a discontinuously immune system cells, organise mostly in bulks, or patches on his ‘payers patches.’ Tiny nerve filament touch the intestinal wall cells, muscle cells, and immune cells that form the walls of the digestive tube, directing, regulating, modulating, and coordinating their functions. Muscle cells in the digestive tract, for instance, are responsible for peristalsis. The time of contraction of the cells, the strength, and the duration are all governed by these nerve filaments, which are extensions of neurons that live around the gut, essentially the brain in the gut.

The same is true with the intestinal wall cells, the GALT cells, and the arteries and veins inside the gut. These nerve filament, spread throughout the gut like a net, send and receive information to and from our gut neurones, which coordinate, modulate, and regulate all of them at the same time, continuously. In other words, the neurons in your gut orchestrate peristalsis and digestion, and modulate immunity and the hormonal system. Without them, they got with cease to work.

As the tiny nerve filaments that innervate the neighbouring cells join with one another, they form nerves, which are bundles of axons, extensions of the neurones that live in the gut. Amazingly, if you where to isolate these neurones and plant them all together, they would form a mass of neurones larger than the ones in your head. In fact, the brain in your gut is way more active in the production of neurotransmitters than the brain in your head. Serotonin, neurotransmitter responsible for the feeling of happiness and well-being, is primarily manufactured in the gut. Around 90% of it in-fact.

On top of all this activity, the brain in the gut helps run your intuition, communicating with you through feelings. These feelings are generated electrically inside your body by the neurones in your gut. That’s why we call it a “gut feeling”. It’s a parallel, powerful sense of knowing. Listening to your gut is one of the most important lessons you can learn. All reasons why the digestive system is a very important part of systems-biology.

If you are looking for a highly skilled & experienced practitioner of Functional & Naturopathic Medicine to help design a roadmap to guide you back on the road to functional wellness then head on over to book a free 30 minute consultation and see if we are the right fit to work together.

Thank you for your attention

*By Steve Hawes