It all starts in your gut

"All disease begins in the gut"

Hippocrates said this more than 2,000 years ago, but we’re only now coming to understand just how right he was.

Research over the past two decades has revealed that gut health is critical to overall health, and an unhealthy gut can contribute to a wide range of diseases including diabetes, obesity, rheumatoid arthritis, autism spectrum disorder, depression, and chronic fatigue syndrome, to name a few. Research in this field is ever evolving. This is by no means a complete list of conditions attributable to poor gut health. 

In fact, many researchers - such as Felice Jackman - who studies nutritional psychiatry and the link between anxiety and depression and gut health, believe that supporting intestinal health and restoring the integrity of the gut barrier will be one of the most important goals of medicine in the 21st century.

According to Chris Kresser, "there are two closely related variables that determine our gut health: the intestinal microbiota, or “gut flora”, and the “gut barrier". Someone with problems with their gut barrier would experience leaky gut, a condition where the permeability of their gut lining is compromised.  



Essentially, the gut flora can be explained with the following analogy. A healthy garden needs healthy soil. Our gut is home to approximately 100,000,000,000,000 (100 trillion) microorganisms. Essentially our bodies are more bacteria than anything else!

If they aren't working towards our health then we really are in trouble, we are at a disadvantage from the basic building blocks of our body.

The human gut contains 10 times more bacteria than all the human cells in the entire body, with over 1,000 known diverse bacterial species.

We’ve only recently begun to understand the extent of the gut flora’s role in human health and disease. Among other things, the gut flora promotes normal digestive function, accounts for approximately 80 percent of our bodies immune response, and helps to regulate our metabolism.

Dysregulated gut flora has been linked to diseases ranging from autism and depression to autoimmune conditions like Hashimoto’s, inflammatory bowel disease, and metabolic conditions like type 2 diabetes. For more on this, have a look at our 8 signs of an unhealthy gut article. 


Several features of modern living directly contribute to unhealthy gut flora:

  • Antibiotics and other medications like birth control and NSAIDs
  • Diets high in refined carbohydrates, sugar and processed foods
  • Diets low in fermentable fibres, aka not enough veggies
  • Foods known to cause leaky gut, gluten, seed oils and refined sugar
  • Chronic stress
  • Chronic infections

Antibiotics are undoubtedly necessary in some circumstances. I don’t have an issue with them when used correctly. They do however have huge implications on gut health.

Doctor Natasha Campbell-McBride is a gut health specialist and founder/author of the GAPS diet. She says it can take up to four years to restore and rebuild the gut biome following a course of antibiotics.

If you do require antibiotics ensure you drink bone broth to seal your gut lining and consume a diet rich in probiotic foods including kefir, kombucha and sauerkraut. The diversity of your gut flora following antibiotic use is not recoverable without these interventions.

Research also suggests infants that aren’t breastfed, are born by cesarian section or are born to mothers with bad gut flora are more likely to develop unhealthy gut bacteria, and that these early differences in gut flora may predict a person’s chances of being overweight, developing diabetes, eczema/psoriasis, depression and other health problems in the future.

We can’t change our own births or how we were fed as infants. Similarly, breastfeeding isn’t always possible for many women and c-sections have their place in ensuring the safety of mothers and babies during childbirth. In these instances it is helpful to understand gut health can be compromised but equally there are many things you can do to account for these situations. Following the suggestions at the end of this blog will help immensely.  


The gut barrier is your gatekeeper that decides what gets in and what stays out.

When you think about it, our gut is a system that operates entirely on it's own. It is a sealed passageway from our mouths to our bottom. Technically, the scope with which it interacts with other organs in our body is somewhat limited.

Anything goes in the mouth and isn’t digested will pass right out the other end. This is, in fact, one of the most important functions of the gut: to prevent foreign substances from entering the body.

When the intestinal barrier becomes permeable i.e. leaky gut syndrome, large protein molecules ‘leak’ into the bloodstream. Since these proteins don’t belong outside of the gut, the body mounts an immune response and attacks them.

The link between leaky gut and autoimmune conditions is huge.

"I have not seen a client at the BePure clinic with thyroid disease who has not had leaky gut, in particular an intolerance to gluten."

Removing gluten for these people and healing their gut has made symptom management and disease reversal possible in almost every single case.

Our own clinical experiences are supported by the findings of experts in mucosal biology, like Dr. Alessio Fasano, who now believe leaky gut is a precondition to developing autoimmunity:

"There is growing evidence that increased intestinal permeability plays a pathogenic role in various autoimmune diseases including celiac disease and type 1 diabetes. Therefore, we hypothesise that besides genetic and environmental factors, loss of intestinal barrier function is necessary to develop autoimmunity."

The phrase “leaky gut” used to be confined to the outer fringes of medicine, employed by alternative practitioners. Conventional researchers and doctors originally scoffed at the idea that a leaky gut contributes to autoimmune problems, but slowly it is becoming part of the mainstream approach to wellness.

The breach of the intestinal barrier - which is only possible with a leaky gut - by food toxins like gluten and chemicals like arsenic or BPA causes an immune response which affects not only the gut itself, but also other vital organs such as your skeletal system, the pancreas, the kidney, the liver, and the brain.



Part of the reason micronutrient deficiencies affect mental health is because of compromised gut function. Even if a person with mental illness did have access to appropriate nutrition or levels of micronutrients, leaky gut will mean they are unable to absorb them.

The inner workings of your digestive system don’t just help you digest food, but also guide your emotions.

What’s more, the function of these neurons — and the production of neurotransmitters like serotonin — is highly influenced by the billions of “good” bacteria that make up your intestinal microbiome.

"We know that serotonin production is increased when subjects take a quality probiotic" Jackman says.

These bacteria play an essential role in your health. They protect the lining of your intestines and ensure they provide a strong barrier against toxins and “bad” bacteria; they limit inflammation; they improve how well you absorb nutrients from your food; and they activate neural pathways that travel directly between the gut and the brain.



Leaky gut and bad gut flora are common because of the modern lifestyle. If you have a leaky gut, you probably have bad gut flora, and vice versa. And when your gut flora and gut barrier are impaired, you will feel less than 100%.

"Leaky gut and bad gut flora are common because of the modern lifestyle."

This systemic inflammatory response then leads to the development of autoimmunity. And while leaky gut and bad gut flora may manifest as digestive trouble, in many people it does not. Instead it shows up as problems as diverse as heart failure, depression, brain fog, eczema/psoriasis and other skin conditions, metabolic problems like obesity and diabetes and allergies such as asthma.

To adequately address these conditions, you must rebuild healthy gut flora and restore the integrity of your intestinal barrier. This is especially true if you have any kind of autoimmune disease, whether you experience digestive issues or not.



The most obvious first step in maintaining a healthy gut is to avoid all of the things I listed above that destroy gut flora and damage the intestinal barrier.

But of course that’s not always possible, especially in the case of chronic stress and infections. Nor did we have any control over whether we were breast-fed or whether our mothers had healthy guts when they gave birth to us.

If you’ve been exposed to some of these factors, there are still steps you can take to restore your gut flora:

  1. Avoid foods and chemicals that irritate the gut
  2. Eat plenty of fermentable fibers (starches like kumara, pumpkin, resistant starch from cooked and cooled potatoes or whole grains, etc.)
  3. Eat fermented foods like kefir, yogurt, sauerkraut, kimchi, etc.
  4. Consider taking a probiotic and/or a prebiotic supplement. The BePure Gut Health Pack includes BePure Gut Assist and BePure Gut Renew Probiotic. This pack designed to support complete upper and lower digestive health.
  5. Treat any intestinal pathogens (such as parasites) that may be present.
  6. Manage your stress
  7. Test your gut health


Your gut health is not just a matter of having a healthy microbiome; it's actually an incredibly complex ecosystem with endless factors. So to help you understand where to start when it comes to your gut health, you can now scientifically screening for normal liver function and balanced gut health. 


The BePure Gut and Liver Health Screening utilises urine collection methods to measure for normal levels of three organic acids, measuring bacteria and yeast levels, along with Glutathione, an important antioxidant required for liver function.

Chat with one of our BePure Holistic Health Consultants to learn about our incredible functional health testing and our personalised approach to diet, lifestyle and nutritional support.



Join me to start better understanding your precious gut and digestive system, learn why it is so central to our health, energy and happiness and more importantly, how you can support its balance naturally.

I’m touring nationwide across New Zealand from August - September 2018. See if I’m coming to a town near you here and use code WEAR to receive $10 off your ticket.


Article written by leading clinical nutritionist Ben Warren. 

Published on  Updated on