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Stool Testing 101: Inside the GI EFFECTS by Genova Diagnostics

by Kate Daugherty, MS, CNS, Functional Nutritionist and Dr. Mitchell Rasmussen, DC, Certified Functional Medicine Practitioner

When it comes to Stool Testing, the GI Effects Comprehensive Stool Test by Genova Diagnostics is our go-to. The GI Effects is an at-home stool test that gets delivered to your door for a self-collection over the course of three days.

Functional stool testing using the GI Effects Stool Test is looking at your gut health at the microbial level. While traditional GI exploration (like endoscopy and colonoscopy) have their place, this goes beyond the physical/visible manifestation of gut dysfunction and looks more into the functional state of the gut.

What Does the GI Effects Measure?

Broadly, when we think about the GI Effects there are three big overarching themes of information gathered: Digestion and Absorption, Inflammation/Immunology, and the Gastrointestinal Microbiome.

Looking at these things in context help us understand how well you are digesting the food you consume, what your microbiome diversity looks like, and any underlying parasites/pathogens burdening your system. The GI Effects Stool Test gives us actionable intelligence about the state of your overall health.

Unboxing the GI Effects Stool Test by Genova Diagnostics
A Peek Inside the Test Kit

Digestion markers that the test will look at include:

  • Pancreatic Elastase: This tells us how well your pancreas is producing enzymes to help with components of digestion.

  • Fecal Fats: The GI Effects gives us a breakdown of different types of fecal fats (like cholesterol and phosolipids). When we see high amounts of fat in the stool, we know there is an issue further upstream causing an inability to digest and use these fats.

  • Products of Protein Breakdown: Similar to fats, these markers tend to be elevated in people with poor absorptive or digestive capacity. It also correlates with low enzyme function.

Big Takeaways from this information: These markers tells us your ability to produce the necessary chemicals to properly digest your food. I.e.: Can I break things down? Can I pull nutrients into my cells? Can I use that stuff to create “ME”?

<< You are not only what you eat, but what you absorb.>>

Immunology markers that the test will look at include:

  • Calprotectin: This is widely accepted as a non-invasive marker for Inflammatory Bowel Disease. It helps us rule out diseases like Crohn's and Ulcerative Colitis.

  • Eosinophilic Protein X: When this marker is elevated it hints at food or environmental allergies or presence of a parasite. If we don't see a parasite, AND we see elevated EpX we can explore potential food allergens or sensitivities.

  • Secretary IgA: SIgA is part of our immune system (an immonoglobulin) secreted by the epithelial cells of the GI Tract. Large increases or decreases are associated with leaky gut and food sensitivities/intolerances. We look at this to evaluate the status of the mucus secreted in your gut. We want a healthy response without an over exuberance. (aka Immune Tolerance)

  • Beta Glucuronidase: When we see elevations in Beta glucuronidase, you might be struggling to detoxify and properly eliminate ‘stuff’. This is an inducable enzyme by a healthy microbiome, but when it is really high we can suspect liver detox is overburdened or not working properly.

Gastrointestinal Microbiome, the crux of the test:

The GI Effects shines in that it does PCR DNA sequencing of the bugs in the GI tract. Traditional stool culture techniques miss this step. The PCR analysis takes all of the living or dead bacteria and quantifies it into phylum to get a real number of each species present. We can then see if you have a high/low amount of bacteria compared to a healthy population, what your diversity looks like, and any potential pathogens due to over abundance of subspecies.

This analysis tells us hints of dysbiosis or SIBO. Further, by seeing exactly what YOUR microbiome looks like, we can better direct probiotic strains for therapeutic benefit.

We see certain dysbiotic pattern associations with end stage conditions--even those unrelated to "gut dysfunction" like anxiety, depression, and skin problems.

The GI Effects Stool Test also includes a traditional stool culture; similar to that run by your conventional doctor. This culture shows bacteria and infections (including candida, fungal, or other yeast) as well as potential pathogens based on your total output.

Lastly, we'll look at parasitology in your stool, both microscopic and PCR. This gives a full spectrum analysis to ensure we catch any parasites or worms.


The GI Effects Comprehensive Stool Test Panel is broad with actionable intelligence. The GI tract is a paramount part of your physiology contributing to your overall health. If we don't address this interface, healing is limited. We look to the gut as a root cause of all sorts of conditions that don't seem quite related (especially brain dysfunction). The gastrointestinal tract is a major interface from 'outside' world to internal world; and there's a lot of room for an issue HERE to cause issues elsewhere.

Stool Testing Functional Lab Genova Diagnostics

Why Three Days?

When it comes to certain infections and parasites (eek, worms!), there’s a much higher chance to finding it when collected over three days versus one. While it’s more of a commitment to collect three days in a row, there is no additional cost for this extended sample.



The GI Effects Test kit looks complex, but take your time reading the instructions and it is fairly straightforward.

On Days 1 and 2, you’ll collect a stool sample in a provided “dish”. Then, you’ll carefully scoop parts of the stool into the marked test vials (green tops). You will store these vials in the refrigerator while you complete the remaining collections.

On Day 3, you’ll follow the same process but add stool samples to four vials (green, pink, white and orange tops). You’ll also collect a fecal swab from the same stool sample using the provided long handled cotton swab.

Once all vials are filled, you will repackage everything in the box and put it into the included pre-paid shipping envelope. You can drop this off at any FedEx location or drop-box.

Included in the box are a requisition form*, a health survey, and patient identification labels. Fill out your information on the labels and attach to each vial in case anything gets separated. The health survey helps Genova Diagnostics collect information and correlate it to their large database of stool test information.

*By the time you receive your kit, we have already registered the test for you. You do not need to input any billing information or diagnostic codes.

A 30-Second Overview of Stool Sample Collection:

Spotlight on Stool Testing: G.I. Effects by Genova Diagnostics

For helping us scientifically diagnose poop problems, we like the GI Effects by Genova Diagnostics. It's an at-home stool test that looks at what's coming out. The GI Effects is a PCR analysis of your microbiome (how much of every bug do you have?) + digestive function markers (how well are you digesting fats/proteins) + inflammatory markers (do you have inflammatory bowel disease?) + parasitic and pathogenic investigation (what infections do you have?).

Functional Stool Testing GI Effects
Snapshot of Stool Testing

With these results, we can help you deal with leaky gut, bacterial overgrowth, dysbiosis, eradicate pathogens or parasites (naturally), and start to normalize bowel habits.

GI Effects Sample Report
Download PDF • 2.90MB

First, We discover the WHAT ; then we address the WHY .

Functional Medicine Team at The Facility Denver
Functional Medicine Team at The Facility

Stool Testing Denver CO Functional Medicine Clinic

Wanna Know More?

We're here for you.

We always start with a Comprehensive Functional Medicine New Patient Exam. During that appointment, you'll sit with both Dr. Rasmussen (a Functional Medicine Doctor) and Kate (a Certified Nutrition Specialist) to talk through your symptoms, your diet, your lifestyle, and what you've tried. We'll order Functional Lab Testing and get started fixing your gut.


Want a free resource for understanding your diet and it's relationship to your bowel function? Click here to get Kate's 5 Day Food-Mood-Poop Journal!

Liver Detoxification Nutrients Needed
Cruciferous Vegetables, Protein, and Fiber are all important for optimal bowel function!


CLICK HERE to shop our supplement store - products are also available in our Cherry Creek Clinic.

If you're curious about building a personalized supplementation protocol for controlling and managing your detoxification capacity, contact us to book a consultation! (This can be remote).


Denver Colorado Functional Medicine Specialists

Want to work with a functional medicine doctor to run labs and assess nutrient status? Struggling with hormone imbalance, IBS, weight gain, mood changes? Let's look at BIOCHEMISTRY. Read more about Functional Medicine at The Facility here.

Not sure where to start?

CLICK HERE to schedule a FREE 15-Minute Consult with Kate to determine your best course of action!

Or reach out by email


How to do the Gi Effects Comprehensive Stool Analysis Test


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Dr. Mitchell Rasmussen - Doctor of Chiro
Kate Daugherty - Nutritionist - Function
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