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Why Test our Gut Microbiome?

Often as Naturopaths, we recommend Gut Microbiome testing (or testing your poop) to determine any potential underlying causes of health issues. Though these tests are quite expensive, it is always the first place to look after general pathology screening. As Hippocrates said, "All disease begins in the gut".

We would likely modify Hippocrates' saying slightly today to say that "all chronic, low grade, or systemic inflammation begins in the gut". This is not the same as acute inflammation which is our bodies necessary response to immediate danger, but rather a persistent inflammatory response when there is no immediate danger present. It is this low grade, chronic inflammation that is thought to be behind obesity, heart disease, type 2 diabetes, metabolic syndrome, Alzheimer’s disease, depression, and numerous others including the chances of developing autoimmune conditions.

It may also come as a surprise, that there is more DNA in our body from the residents in our gut microbiome, than from our own human DNA. So while we may think we are driving the decisions we make, it is actually the residents of our gut making the decisions for us. Based on this knowledge, we need to be the 'adult in the room' and take control if 'the children are making unhealthy choices' for our health and longevity.

Why Test our Gut Microbiome?

What we eat can either reduce our chronic disease risk, or increase our chronic disease risk. This is all determined by what is happening in our gut microbiome. Altering what you eat can alter your microbiome in either a beneficial way, or not so. It is a worthy exercise to consider, and get tested for, using genetic sequencing of your entire gut microbiome - hence the expense!

Graphic showing anti-inflammatory plant based foods versus pro inflammatory meat based foods
Rethinking Healthy Eating in light of the Gut Microbiome

As well as information about the residents of our gut microbiome (bacteria, parasites, fungi, archaea), we can learn valuable information about intestinal and systemic inflammation, intestinal barriers and permeability, our digestive secretions, intestinal motility, and much more.

Graphic showing impacts of pro-inflammatory foods versus anti-inflammatory foods
How Diet can contribute to Low Grade, Chronic Inflammation

How to Modify Your Risk for Autoimmune Disease

Our risk for Autoimmune Disease can be increased if we have issues in our gut like:


When the ecosystem of gut bacteria is altered, we can end up with dysbiosis. This may be in the form of:

  • Decreased beneficial species

  • An overgrowth of harmful pathogens that shouldn't be present in our gut microbiome

  • Opportunistic pathogens that see weakness in the microbiome

  • Reduced diversity and richness of species - to help us with health resiliency

How to repair - prebiotics, probiotics, and dietary interventions


  • Intestinal and systemic inflammation can drive autoimmunity (by activating pathways like NF-kB and Th17 cells)

  • Inflammatory cytokine release

How to repair - anti-inflammatories like Omega-3's and Short Chain Fatty Acids (SCFA's)

Intestinal Permeability (Leaky Gut)

  • Elevated Zonulin levels allow for our single cell epithelial layer in our gastrointestinal tract to lose their closely connected tight junctions. This can allow food antigens and pathogens to slip straight through from our intestinal lining through to our bloodstream.

  • Immune responses can result from this, and autoimmune reactions can be triggered via molecular mimicry pathways, where for example, certain foodstuffs can be thought to be actual pathogens.

How to repair - Glutamine and Saccharomyces boulardii (SB) to reinforce the gut barrier

Immune Dysfunction

  • Imbalances between effector T lymphocytes (Th17) and regulatory T cells mean we lose 'self tolerance' where we stop seeing aspects of our body as belonging to us, and see them as pathogens. This means our body targets ourself as an enemy.

  • Reviewing Lymphocyte subsets is important to determine where an imbalance may be occurring.

  • Based on results, in conjunction with a gut microbiome analysis, enables therapies to be selected that can then be used to down regulate the imbalanced side of our immune response.

How to repair - A general approach can start with Vitamin D, and then tailored.

An example of how diet and associated gut-dysbiosis is seen below where a poor diet, causes obesity and associated issues in the gut leading to a permeable gut wall (leaky gut), allowing pro-inflammatory molecules such as lipopolysaccharides (LPS) from a fatty diet and its metabolites (Trimethylamine N-Oxide or TMAO) that can tip the balance of our immune response. In this case causing hand osteoarthritis. These inflammatory substances are tested for in a gut microbiome test.

Cartoon showing leaky gut allowing inflammatory cytokines to hand osteoarthritis
Diet associated Gut Dysbiosis and Hand Osteoarthritis

How does Diet Impact on our Gut Microbiome

By eating well, including a lot of fibre and specific prebiotics, ensuring specific dietary nutrient needs are met, based on the gut microbiome results, we can:

  • Reduce Gut Inflammation

  • Improve our lipid metabolism (cholesterol and triglycerides)

  • Improve our antioxidant production

  • Improve our short chain fatty acid (SCFA) production

  • Reduce our risk of infections

  • Improve insulin sensitivity

In comparison, by eating excessive sugar, saturated fats, and high protein consumption we can:

  • Increase Gut Inflammation

  • Increase our risk of cardiovascular disease

  • Increase our lipopolysaccharide (LPS) production, or endotoxins, that can enter your bloodstream and trigger low grade, chronic inflammation

  • Reduce our anti-inflammatory short chain fatty acid (SCFA) production

  • Increase our risk of infection

  • Increase insulin resistance

Graphic showing the mechanisms behind how whole plant foods, or processed foods either help or hinder our risk of chronic disease
How to Lower your Risk of Chronic Disease

Specific Diets

In terms of the gut microbiome, one of the best dietary approaches that you can make is to follow the Mediterranean diet. This ensures we get good quality fibre for our gut microbiome, as well as good quality fats and proteins, with all the required vitamins and minerals.

It has been shown that there are different 'immune signatures' elicited by different dietary approaches. A diet focused on vegetable intake improves our innate immune response and antiviral activity, while a high protein diet can significantly up regulate our adaptive immune system, which is generally not desirable.

Other diets, may require supplementation to avoid deficits, may pose risk, and some should not be used long-term (Low FODMAP). To make life simple and uncomplicated, the best advice is to eat small amounts of a wide variety of natural foods that covers a broad diversity, with limited processed foods. This approach is best for your gut microbiome, and reduces any risk from overexposure of any one food or food type.

Table of vegan, mediterranean, paleo, low FODMAP diets and foods consumed
Comparison of Popular Dietary Food Sources Consumed

If you would like to discuss your personal circumstances, or get Gut Microbiome testing performed, or discuss your associated health issues, then please don't hesitate to make a booking with me.

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