• Allison Fahrenbach

The Gut, the Microbiome & Pain

As a gut centered coach, I am constantly interested in learning more about the role of the gut, it’s health, and how microbial balance impact all facets of well-being.

Over the last decade or so gut health has become an increasingly trendy topic. Our gut has been shown to be one of the keys to our overall health and wellbeing.

  • It has been called our “second brain” due to the intricate nervous system (the enteric nervous system aka the ENS) it houses and how it communicates with our brain (via the gut-brain axis).

  • It has been shown to play a vital role in the production of serotonin, which has been one of the keys to understanding the role it plays in mood, mental and emotional health, and sleep.

  • It has been shown to play a vital role in our stress (via the hypothalamic pituitary adrenal (HPA) axis) and relaxation (through the vagus nerve) response.

  • It is home to 100 trillion microorganisms and their genetic material, known as microbiome, and scientists are only just unlocking the potential (and the power) of the microbiome

  • Some of the most interesting areas being explored by scientists include the role our gut plays in immunity, inflammation and pain.

To understand the importance of our gut and the role it plays in health and wellbeing, it is important to have a clear understanding of what (exactly) the gut is, what it does, why it matters and how it relates to pain.



In this blog I’ll discuss what the gut is, what the microbiome is, how the lining of the gut supports the immune system, and the link between the gut, the immune system and pain.


What is your gut?

When I say the word “gut” you probably think of your stomach.


But the “gut”, also known as the gastrointestinal system, gastrointestinal tract, digestive system and digestive tract is not just the stomach.


It is made up of many organs including: the mouth, salivary glands, oesophagus, stomach, panaceas, liver, gallbladder, appendix, small intestine, large intestine, rectum and anus.

Our gut uses the process of digestion to break down food into the nutrients and energy we need to live and thrive. At each level of our digestive system – from our mouth to large intestine – food is being broken down and converted, so that we can breathe, walk, talk, concentrate, build muscle, repair, grow and survive.


The saying “you are what you eat” is true: what we eat and drink literally becomes the foundation of our overall health and wellbeing, making up the structure, function and integrity of every single cell in our bodies.

The food we eat is used for:

  • Brain and memory function

  • Eye function

  • Digestion and transportation of waste products

  • Heart and blood health

  • Bone, muscle and ligament repair and strengthening

  • Energy for mental and physical activities

  • Building and strengthening our immune system

  • Repairing cells and tissues

I stumbled into this video, which explains, over 40-50 hours our gut converts the food we eat into the nutrients, vitamins and minerals we need to get through the day. But food conversion is only one piece of the puzzle.


Our gut also performs many other vital functions including:


What is the gut microbiome?

Our gut microbiome is made up of 100 trillion microorganisms and their genetic material which live within our gut. These micro-organisms include more then just bacteria they also include parasites, viruses, and fungi.


What’s more, microbial composition varies from person to person. No two gut microbiomes are the same. In fact while our genomes may be 99.9% the same, our gut microbiomes can be 100% different. Your microbial environment is unique to you.

Factors that play a role in the type, variety and quantity of our microbiome include:

All of these factors make up our “unique bacterial fingerprint”. This unique bacterial fingerprint serves many vital functions which support our overall health and wellbeing, including:

A healthy gut has a diverse and abundant microbial colony and is what’s referred to as “Eubiosis“. The opposite of that, would be a low, irregular or poor balance of the microbiome – known as “dysbiosis

Dysbiosis has been linked to many disease states including depression, inflammatory bowel disease, fibromyalgia, complex regional pain syndrome, multiple sclerosis, autism spectrum disorder and Alzheimer’s disease.


This is still what I’d consider to be a relatively “new” area of science that researchers are looking into, trying to determine whether dysbiosis causes these diseases, or is a result of these diseases, or if the relationship isn’t even a cause and effect relationship at all.

What is the link between our gut microbiome and pain?

Changes to gut bacteria in people with painful gastrointestinal issues such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) has long been recognized.


However, emerging research looking into specific painful conditions such as fibromyalgia, inflammatory pain, headache, neuropathic pain and even opioid tolerance, has helped reinforce the relationship the gut microbiome has with other forms of chronic pain.


Researchers in this area believe that signal-carrying molecules – which are by-products of microbiota (the cells which are made up of your microbiome), metabolites (comes directly from our food), neurotransmitters (produced in the gut) and neuromodulators – regulate peripheral and central sensitization.


This has an impact on the development and chronicity of pain.

These researchers claim that changes to diet (nutritional intervention) and the introduction of specific probiotic therapies may assist with the management of specific types of chronic pain.


In other words, pain can be managed through management of the gut.


This is an area that is currently undergoing more research, but has some exciting possibilities for the future of pain management.

How does the lining of our gut support our immune system?

Gut permeability refers to how easily nutrients, including proteins, move from your digestive system into the blood stream.


The permeability of the gut is important, but needs to be balanced. You want properly digested microscopic food particles to move across into the blood stream where they can be used to support health and wellbeing.


But what happens when the intestinal lining gets so inflamed that it becomes more permeable then it should be, allowing both the good AND the bad bacteria and toxins to “permeate” or “leak” into your bloodstream?


“Leaky” gut is what happens. "Leaky gut" is the term that refers to when poorly digested, microscopic fragments of food may pass from the gut into the bloodstream causing issues with inflammation, food sensitivities, immune function and abdominal discomfort.


A healthy gut ensures our health and wellbeing, and assists with the prevention of diseases of the gut and other organs within the body by contributing to a healthy immune system.


It’s only logical then to look at how an unhealthy gut relates to immune system dysfunction and disease.

There has been alot of research looking into how our gut and immune system are linked:

  • Our microbiome is a teacher to our immune system: we are born with a very basic immune system and are protected by the antibodies we receive from our mothers. From here we develop our own antibodies from the food we eat, the environment we live and the bugs we fight off.

  • Gut bacteria maintains immune system balance: our nose, lungs and gut constantly expose our immune system to “new things” such as pollen, dust, dirt and food. The role of our immune system is to identify what is “ok” or safe, and what is not ok, or what it needs to fight off. The diverse range of bacteria, fungi and microorganisms that live within our gut, help the immune system to build a resilience to “new things”. The importance of the relationship is further highlighted by the fact 70-80% of our immune cells are found within our gut.

  • The gut wall is a communication channel between our body and the microbiota: as I mentioned earlier the gut acts as a barrier allowing certain molecules to pass into the bloodstream while disallowing others. The purpose of this is to support immune and brain function. The gut wall is made up of a:

  • Physical barrier: epithelial cells that line the gut, the molecules on their surface and mucus they produce.

  • Chemical barrier: inflammatory molecules (cytokines), antibodies, and antimicrobial substances produced by epithelial and immune cells.

  • Preliminary findings on endotoxins and zonulin and inflammation:

  • An endotoxin is a lipopolysaccharides (LPS) (large molecules found in some bacteria) which elicits a strong immune response when absorbed by the body. The endotoxin is released when the bacteria dies and cell wall breaks down. This can produce an immune response and the release of pro inflammatory cytokines when "leaky gut' allows movement of endotoxins into the blood supply.

  • Zonulin is a protein produced by our body in response to gluten and specific bacteria, which has been linked to increasing gut permeability. When zonulin, endotoxins and cytokines enter the circulation they trigger an immune and inflammatory response. One way to test for leaky gut is to test zonulin levels.


What is the link between our gut, immune system and pain?

A really interesting area of research has been looking at how gut permeability affects inflammation and pain, particularly with conditions such as irritable bowel syndrome (IBS).


Scientists have noted that sensitization of visceral afferent (sensory) pathways may contribute to pain and changes to the brain characterized by IBS.


Some interesting findings include increased gut permeability, increased immune system activation, and an imbalance in descending pain inhibition. There has also been some preliminary studies looking at two painful conditions: fibromyalgia and complex regional pain syndrome and their relationship to gut permeability. These studies show higher permeability in the gut of both conditions. Researchers are investigating how improving gut health may improve gut permeability and these painful conditions.

It’s also worth mentioning that 50% of people living with chronic pain, also suffer from depression or anxiety. Researchers have been looking at the links between anxiety, depression and gut permeability. They have identified changes to the gut microbiome, including dysbiosis, as well as biomarkers for endotoxins and zonulin. Although this area of research requires alot more study, it shows a clear relationship between the disease state of the gut and mood disorders/mental health.

This study released in 2020 discusses the evolving science looking beyond genetic predisposition and environment, and towards the changes to gut permeability, immune activation, and changes to the microbiome, in chronic inflammatory diseases.

The ongoing challenge in this area of science is determining if the changes occur as a result of the disease or are the cause of the disease, and whether improving the gut will improve the disease.


The Bottom Line;

  1. The gut is not simply your stomach, it is a network of organs that are central to whole body health

  2. The gut microbiome has been linked to a wide variety of diseases

  3. Signal carrying molecules from the gut impact the development and chronicity of pain.

  4. Gut bacteria also help maintain balance in the immune system

  5. Gut permeability affects inflammation and pain, particularly in cases of IND and IBS.


In next weeks blog I’ll get into this topic more in depth, by explaining what the gut-brain connection is, and the tole it, and the ENS play, in pain.

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