What does a functional medicine stool test actually show?

Have you been considering a functional medicine stool test but don’t really understand what it’s supposed to reveal.  Or have you used one before but it left you feeling more confused or not sure about what to do? Well, this post is for you!

Consider the incredible discoveries that put gut health at the center of our long-term overall health! A functional medicine stool test can provide incredible insight into this world. And we now know they can be useful whether you’re experiencing digestive symptoms or not! If you have mental health concerns or are struggling to manage weigh for instancet, the details we can tease out cover many areas of overall health!

In this post, I’m going to explain the main takeaways gleaned from a functional medicine stool test.  The amount of data and insight they can provide when properly interpreted is priceless compared to the ticket price. They can be a pivotal routine piece of your health and wellness testing!

As Hippocrates said, “all disease begins in the gut.” A functional medicine stool test is a powerful way to see how this manifests in each of us!

What is a functional medicine gut health or stool test?

A functional medicine stool test is a foundational tool to assess our most fundamental yet profound functions.  It takes a comprehensive look at your gut health! This includes assessing digestive function, providing a perspective of balance within your microbiome, testing for problematic pathogens and parasites, and so much more!

They are usually given as a 1-3 day collection that is then analyzed and produces a detailed report. The tests are typically performed and collected in the comfort of your home. After that, you send them back directly to the lab for analysis.

Most quality functional medicine labs that offer these stool tests use a variety of testing procedures to capture this depth of information.  These include classic culture and microscopic analysis, PCR sequencing, (Polymerase Chain Reaction sequencing, the same technology used during the most recent pandemic) and several other methods.  

I won’t bore you with the details here, but the labs offer this information through their free resources as well!  As a functional medicine practitioner, it’s a tool that I use frequently and very much enjoy educating patients about! Read more about why functional medicine lab testing might be right for you here.

Differences between conventional and functional medicine stool test

There are several noteworthy procedural and philosophical differences that make comprehensive functional medicine stool tests stand apart from conventional ones.  Let’s explore a few of the ideas here:

First, there is a difference between the way conventional medicine and functional medicine approaches what is deemed “clinically significant.”  Most commonly, conventional medicine doesn’t treat potential pathogens found outside the traditional methods of biopsy or culture testing. AND symptoms must generally be present. 

A Functional medicine approach doesn’t always require symptoms to be present. We sometimes consider the mere presence of the potentially pathogenic organisms as something that can be adding to the overall inflammatory and immune burden of the individual.

Another major difference is that functional medicine is able to be an “early adopter” of newer concepts. These include the importance of the microbiome and parasitic infections as major players in a patient’s overall health experience.  

Conventional medicine sometimes takes a while to catch up because of time-consuming research. It’s often directed by agendas that prioritize emergent and pharmaceutical-based interventions.  Additionally, the individualized nature of comprehensive stool testing is difficult (though not impossible) to systematize and apply to the masses

To be clear, conventional approaches are important. Biopsy and culture testing is indeed powerful and meaningful in managing clinical infections.  A functional approach takes this a step further. It looks beyond classic infections at a more detailed, nuanced spectrum of imbalance and dysfunction.

Functional medicine stool testing shouldn’t take the place of conventional management, but rather they should supplement such approaches.  A functional medicine stool test can even suggest need for referral to a conventional specialist based on findings. (Start reading my 3-part blog series of Functional Medicine vs. Conventional Medicine)

The Components of a Comprehensive Functional Medicine Stool Test

A quality comprehensive functional medicine stool test analyzes several main areas of overall gut health.  In this section, we’ll explore the main sections of a typical functional stool test. I will also briefly explain how it’s connected to overall health!  We won’t get too much into the details, but I hope this provides a snapshot into what’s possible. (It may also reveal my level of nerdiness and passion I have in this realm!)

This image shows the 7 sections of a functional medicine stool test that are covered in the body of the blog post including microbiome analysis, digestion function assessment, pathogens and parasites, and more.

Microbiome Analysis

    This portion of a functional stool test is all about the balance of microbes that live within your gut.  Though it’s not a perfect science yet, this is among the best technology we have that is ever-improving. These tools give us a actionable look inside our own microbiomes.

    A typical stool test gives us insight on both the “good and bad” bacterial species. Most of the labs quantify the relative abundance too.  Your microbiome is all about balance and diversity. The good (commensal) species compete for resources with the bad (opportunistic or pathogenic) species.

    Practically speaking, our good microbes play roles in our overall health in countless ways. These include detoxification, vitamin production, energy production, decreasing inflammation, and regulating blood sugar.  If we see imbalance in this area of the stool test, it can have implications almost anywhere!

    Small intestinal bacterial overgrowth (SIBO) is also a popular topic of rising concern in the general population.  Though a functional stool test doesn’t test for SIBO directly, certain patterns of findings can correlate with SIBO and be suggestive of its presence. 

    Assessment of Digestive Function

      A functional stool test also measures how well we are actually digesting and absorbing our macronutrients.  This is pivotal! Even if you’re eating the right foods, you may not be breaking them down and absorbing them. All your efforts can be a moot point!

      Markers such as pancreatic elastase give us insight into the efficacy of your pancreas. This organ is supposed to produce an ideal amount of digestive enzymes for example.  This is an important section because if you’re not absorbing nutrients properly, you may experience fatigue, hormone concerns, brain fog, depression, and the list goes on!

      Inflammation Markers

        Functional stool tests also assess a few key markers of the inflammation in the gut.  Though these markers don’t necessarily uncover the specific cause of the inflammation, it can provide insight into the overall inflammatory load. Findings can also signal when a more urgent referral might be needed by a conventional specialist such as a gastroenterologist.  

        Inflammation in the gut can be due to many factors including food sensitivities, inflammatory bowel disease (IBD), irritable bowel syndrome, parasitic or other infections and overgrowths, etc.

        Immune System Markers

          In addition to important inflammatory markers, we can gain insight into the immune function within the gut. Perhaps my favorite to share with patients is a marker called Fecal Secretory IgA (aka sIgA).

          This marker is an immunoglobulin, or immune system molecule, that is found throughout the lining of our digestive tract.  It is a great indicator for the integrity of immune function in the gut. It is also affected by HPA Axis Dysfunction (aka adrenal fatigue) and chronic stress or hidden stress.

          Parasitology & Pathogens

            Another key section is where we analyze for parasites and other pathogens such as bacteria and yeast.  This is an area that functional medicine, Chinese medicine, and naturopathic medicine has given weight to for decades, even centuries.  I think it’s a fascinating area of study.

            This section tests for some of the most common parasites including giardia, blastocystis hominis, cryptosporidium, and H. pylori.  Many of these parasites and infections are linked to symptoms even outside the digestive tract. This is why it’s such important information to have, no matter your condition or symptoms.

            Some of the comprehensive stool tests use multiple techniques to find them too.  This is particularly important because many parasites have life cycles that span days to weeks. As such they may shed at different times.  Additionally, yeasts such as candida are notoriously difficult to isolate, so multiple methods can be important for accurate results!

            Markers for Gluten Sensitivity and Leaky Gut

              Finally, a functional stool test provides some insight into common, complicating issues. These two situations arise from the gut, but can affect the entire body – gluten sensitivity and leaky gut.  Though there is more comprehensive and confirmatory testing available, we get a good snapshot all in one sample with functional stool testing.

              Both gluten sensitivity and leaky gut have been connected with autoimmune conditions. They also might be related to joint pain, brain food and fatigue, food allergies, and more!  Though this test doesn’t assess and confirm the presence of celiac disease, it can prompt further investigation and referral if the findings warrant.

              Interpreting the Results of a Functional Stool Test

              First and foremost, it’s importance to work with a healthcare provider that is familiar with reading and interpreting these results.  I use the word interpretation here because the details, relationships, and patterns can be like reading another language. 

              Remember, we are not talking about classic “infections” when it comes to the microbiome.  When we see patterns of imbalance, we call it dysbiosis.  Know that there are many ways to address this, and that its a lifelong continuum. 

              I also like to tell patients that the strongest ways to influence your gut health are generally rooted in the lifestyle pillars. These are nutrition, movement and exercise, stress management, quality sleep, and social connection and sense of purpose.  Supplements are generally meant to be just that – supplemental! (Read more about my personal functional medicine philosophy)

              Lastly, it’s important to remember that if you find potential pathogens or parasites or significant dysbiosis on a functional stool test that this represents a “snapshot” in time.  Additionally, it would be prudent to retest after completing a treatment plan to ensure that the changes you’re looking for are taking place.  It’s best to do so with the same lab as well to ensure similar testing methods are being compared. 

              What are functional medicine stool tests good for?

              Whether you have digestive symptoms or not, a functional medicine stool test can reveal important insight into your overall health throughout the body.  Here is a short list of reasons that you might consider a functional stool test:

              • Weight management issues
              • Digestive Complaints
                • Bloating
                • Loose bowel movements
                • Constipation
                • Irritable bowel syndrome (IBS)
                • Inflammatory bowel disease (IBD)
                • Acid Reflux
                • Nausea, vomiting
              • Atopic dermatitis and eczema
              • Depression, anxiety
              • Women’s hormonal issues, menopause
              • Autoimmune conditions
              • Hypothyroidism
              • Brain fog
              • Diabetes
              • Allergies and sensitivities

              To be honest, I recommend a functional stool test with almost all my patients. If there are hidden sources of inflammation, pathogens, parasites, or digestion issues, it’s very difficult to positively and permanently influence virtually any condition.  This goes back to a fundamental concept of root cause medicine. 

              For example, you can take all the acid reducing medications in the world. You can try to lose weight by eating and exercising pristinely. But if there are significant pathogens or states of dysbiosis present, the underlying issues may not be addressed fully, or is very stubborn at best. 

              Not only are they great for assessing gut and microbiome issues, but they can levers for health optimization too.  In a perfect world, and with many of my patients, I recommend a stool test at least once every 1-2 years along with yearly organic acids testing. (Another incredibly powerful functional medicine test).

              What are the best functional medicine stool tests?

              Of course, we’re always looking for “best” of anything. I do have some recommendations for tests that I commonly use in my practice.  Feel free to check out their site and links to their functional stool testing below:

              Genova Diagnostics – GI Effects

              Diagnostic Solutions – GI Map

              Doctor’s Data – GI360

              There are many overlapping sections and markers used in each test as well as shared methods.  Ultimately, I like to choose a test based on the patient’s underlying issues. I recommend from there because some of the tests provide more information than others in a given section.

              In some instances it’s prudent to use two different stool testing companies for particularly stubborn digestive complaints or other complex health situations.  This ensures that you capture the most information.  You can think of a functional medicine stool test as a window that we look through. Each company offers “windows” are made of slightly different glass. 


              As you can see, a functional medicine stool test offers invaluable insight into our gut health. This can serve as a foundational tool in understanding the intricate balance within our bodies. From microbiome analysis to assessing digestive function, inflammation, immune system markers, and parasitology, these tests unveil a comprehensive picture of our overall well-being. 

              By bridging the gap between conventional and functional medicine approaches, they supplement existing testing methods. They also pave the way for personalized health management.

              Embracing the wisdom of Hippocrates, they empower us to address the root causes of disease and optimize our health journey. You might consider making them an indispensable addition to your long-term wellness plan!

              For more information about functional medicine lab testing and interpretation services, please feel free to reach out. You can reply via this post, reach out to me on Instagram or Facebook, or subscribe to my mailing list below to stay connected.  I look forward to being a continued source of information and empowerment in your personal health journey!

              About the Author

              Headshot of Dr. Kenny Mittelstadt for Author Bio in Color

              Kenny Mittelstadt is an acupuncturist and functional health practitioner based in San Antonio, Texas.  He is trained through the Institute for Functional Medicine and received both of his doctorate degrees with highest honors from Southern California University of Health Sciences. He focuses on empowering patients through creating opportunities for integrated understanding and personalized root-cause healing - starting with gut health and growing beyond!

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