Testing for Gut Pathogens 101

Harmful organism (pathogens) in the gut are linked to a myriad of health problems.

But, like many of the health issues I help my clients investigate and address, pathogenic infections or overgrowths can remain hidden for many years. All the while causing you distress.

In this brief article, I’ll go over:

  • How bad bacteria, yeasts, and parasites can undermine your health.
  • When you’d want to consider running a test to screen for pathogens
  • My favourite stool test for such purposes, the GI-MAP.

How Pathogens Harm You

Some of the ways in which pathogens wreak havoc in the body include:

  • Keep the body in a state of chronic stress (which can contribute to other dysfunction)
  • Promote inflammation
  • Promote autoimmunity
  • Damage the intestinal lining
  • Increase oxidative stress levels
  • Contribute to liver congestion and dysfunction
  • Produce a variety of harmful products
  • Contribute to decreased beneficial bacteria
  • Cause malnutrition or nutrient deficiencies
  • Weaken the immune system
  • Increase food sensitivities
  • Create an environment conducive to proliferation of secondary overgrowths, biofilms, and further infestation

If that doesn’t sound fun to you, I can attest that it’s not. All the test results below are mine, and as you’ll see, I’ve had a bunch of parasites, bacteria, and yeasts roaming around in my gut.

I was ignorant to the fact for a long time, and it took a hormone test with shocking results (testosterone lower than a 60-year old man’s) to prompt me to investigate further.

What is Dysbiosis?

Dysbiosis is a term we use for a disruption or imbalance in the microbiota (the community of microbes in your gut), that has a negative effect on your health. It generally means that the good microbes have decreased and the bad ones have increased in numbers.

Dysbiosis can be caused by a combination of factors such as the following:

  • Pathogenic organisms (parasites, bacteria, yeast/fungal infections)
  • Medications (antibiotics, antacids, anti-inflammatories)
  • Poor diet
  • Digestive dysfunction
  • Immune dysfunction
  • Toxin exposure (chemicals, pesticides, heavy metals)
  • Food sensitivities
  • Leaky gut / intestinal permeability

It’s not always bad bugs that cause the dysbiosis – sometimes poor lifestyle choices can create the ripe conditions for harmful organisms to take hold in the gut.

That’s why “fixing the gut” is much more than just eradicating the pathogens.

We can generally observe three types of dysbiosis:

  • Insufficiency dysbiosis: This where the numbers of your beneficial bacteria have been reduced. These beneficial bacteria provide support for healthy intestinal and immune function, and when their numbers decrease your risk of infection, inflammation, immune dysfunction, and leaky gut increases dramatically.
  • Inflammatory dysbiosis: In this type of dysbiosis we can often see a proliferation of pathogens (e.g. Giardia, C. Difficile, Campylobacter) and opportunistic organisms including Citrobacter, Klebsiella, Morganella and Candida. A lot of these produce toxic by-products that are inflammatory in nature.
  • Digestive dysfunction dysbiosis: This is where we see digestive issues such as low stomach acid, digestive enzyme insufficiencies, poor absorption, and altered intestinal motility.

The good news is that all of the above can usually be improved in unison with the right approach.

The first step in doing something about a gut infection is knowing what organisms have made a cosy little home in your intestines. To do that, you need to run a gastrointestinal (GI) pathogen screening, or stool test for short.

When to Run a Stool Test

You should consider running a GI pathogen screening test when you have:

  • Gastrointestinal issues (heartburn, cramping, bloating, constipation, diarrhea, excessive gas etc.)
  • Had food poisoning in the past
  • Numerous food sensitivities
  • A history of foreign travel
  • Leaky gut / intestinal permeability
  • Suspected heavy metal toxicity (or shown on a test)
  • Hormone imbalances (e.g. elevated nighttime cortisol)
  • Been swimming in questionable waters or touched animals that may have been harbouring pathogens


One of the best stool tests on the market is Diagnostic Solutions Laboratory’s Gastrointestinal Microbial Assay Plus (GI-MAP).

The lab uses DNA analysis technology (qPCR) that has very high accuracy and high specificity. This greatly reduces errors and false negatives (testing negative for a pathogen that you do have) that are often seen with traditional culture-based stools tests.

Below are some areas the test covers.


These are bacterial, parasitic, and viral pathogens you generally don’t want inhabiting your GI tract.


Other than the above three parasites, the GI-MAP also screens for various protozoa and worms.

Fungi / Yeast

Several fungal species are tested for:

Opportunistic Bacteria

These guys are everywhere in our environment – on our food, in our water, in the soil, and even in our gut. Usually they only become a problem when your immune system is compromised or you have dysbiosis. They can then take hold, or if already present in the GI tract, they can begin to overgrow and cause you problems.

Potential Autoimmune Triggers

Opportunistic bacteria that have been associated with autoimmunity. For example, Citrobacter freundii, Klebsiella pneumoniae, and Proteus mirabilis are associated with rheumatoid arthritis.

Normal Bacterial Flora

Beneficial intestinal flora do the following for us:

  • Keep pathogenic and opportunistic organisms in check
  • Promote a healthy intestinal barrier
  • Contribute to immune balance
  • Support the ecology of the gut
  • Create beneficial compounds through their own metabolism such as vitamins and short-chain fatty scids (SCFAs) such as butyrate.

Butyrate is the principal fuel for gut and immune cells, and promotes healthy intestinal barrier function. SCFAs like butyrate have positive immune-regulating, anti-inflammatory, and other properties.

Intestinal Health Markers (Digestion, GI Markers, Immune Response, Inflammation)

  • Elastase-1 is a marker for pancreatic enzyme production. It is not affected if you take digestive enzymes as they would never contain it. Low levels of Elastase-1 can cause malasbsorption of your food.
  • Steatocrit is a measure of fat absorption. High levels may indicate malasbsorption or even pancreatic insufficiency.
  • b-Glucuronidase: You don’t want your b-Glucuronidase levels to get too high as it can disrupt the body’s ability to detoxify hormones and toxins. It is naturally produced by your liver, kidneys and intestinal epithelium but can also be produced by certain bacteria such as Bacteroides fragilis, Escherichia coli, and Staphylococcus.
  • Secretory IgA (SigA) is your first line of immune defence in the gut. It forms complexes with allergens and pathogens to prevent them from crossing the intestinal barrier. If SigA is low it may increase your risk of infection and inflammation. Chronic stress affects SigA negatively.
  • Anti-gliadin IgA: Gliadin is the protein found in gluten that is most commonly problematic for people. If the anti-gliadin IgA marker is elevated, it points to an immune response to gluten.
  • Calprotectin is the most studied marker of GI inflammation. Levels between 50-150 may indicate inflammation due to pathogen infection or food sensitivities, whereas levels higher than that would likely require the attention of a GI specialist doctor.

Sample collection and shipping

Once your provider orders the GI-MAP for you, the kit should arrive in a couple of business days. The day before sample collection, you would need to call the courier to schedule a pickup. Then on the day of pickup, you simply poop on some paper included in the kit which slots over your toilet seat, then use the spork in the sample collection bottle to fill it up with your specimen. Close the bottle, shake it and you’re done!

You can be in and out in under 5 minutes – not the most pleasant thing in the world to do, but the data it provides you is well worth the few minutes of discomfort.


I hope you found this article helpful. Stool testing has come a long way in the last decade and Diagnostic Solutions Lab and their GI-MAP are at the forefront of innovation and advancement. The data provided by the GI-MAP is invaluable when seeking to build-up or optimise your health.

If you need personalised advice, based on your individual circumstances, please do not hesitate to schedule a free 15-minute discovery session.