Understanding the GI Map Stool Test: A Comprehensive Guide

By Fernando Bernall, DOM, CFMP

The GI Map Stool Test, serves as an informative resource for anyone interested in understanding more about their gut health and the advanced testing options.In this article I’ll share with you what the GI Map Stool Test is, how it works, and why it can be a valuable resource for understanding and improving your gut health.

In our Optimal Digestion Blueprint Masterclass, I laid out a simple 3 step system to address digestive disorders.  I stated that my first discovery, which led to the development of the Optimal Digestion Blueprint program was that The Poop Doesn’t Lie.

In that video, I addressed the importance of a visual examination of our stool and contrast its appearance to one of the seven types found in the Bristol Stool Scale (BSFS).1 Despite limited data regarding its validity and reliability, the BSFS is already widely used to measure stool form in the clinical and research setting.

The importance of colonic transit time was discussed, and I included the 3 main functions of the large intestine: absorb water and electrolytes, produce vitamins and propel the feces towards the rectum.

But in order to get a better picture, so to speak, of the amount and types of bacteria in the small and large intestine, I emphasized the importance of a stool test. As you may know from reading this site or from seeing me in my clinic, I believe in blood chemistry analysis and use it as a tool to help me formulate programs that address your reason for seeing me.

However, while the blood can give us a lot of information about our biochemistry, it falls short of explaining many conditions that have their origin in the gut. Which is why we always hear in the clinic patients saying that their doctor said their blood labs all came back normal, yet he or she, still does not feel well.

Before discussing the stool test, let me point out that symptoms of an imbalanced microbiome (dysbiosis)6 are not always of a digestive nature: anxiety, depression, skin conditions, insomnia, and a host of other conditions that seem unrelated to our gut, are indeed rooted deep within our bowels.

I think that as physicians, we need to keep reminding ourselves of what Hippocrates — the father of modern medicine, said: “all disease begins in the gut”; and, while that may not be 100% correct, evidence does suggest that most chronic conditions originate, or are worsen by an imbalanced microbiome. And to find that out, we need to test the stool.

What is the GI Map Stool Test?

The GI Map Stool Test, short for Gastrointestinal Microbial Assay Plus, is a comprehensive stool analysis created by Diagnostic Solutions Laboratory,7 that provides a detailed overview of the bacteria, viruses, fungi, and parasites present in the GI tract. It uses quantitative polymerase chain reaction (qPCR) technology2 to identify and measure the DNA of various microorganisms in our microbiome, and offering precise and accurate results. For a refresher on what the microbiome and microbioata are, watch this segment of our masterclass.

How Does the GI Map Stool Test Work?

  • Sample Collection: The test begins with the collection of a small stool sample, which can be done in the comfort of your own home. The sample is then sent to a specialized laboratory for analysis.
  • Laboratory Analysis: In the lab, the sample undergoes qPCR testing. This technique amplifies and quantifies the DNA of the microorganisms present in the stool, allowing for the detection of specific pathogens and the overall microbial balance.
  • Results: The results are typically available within 5-10 business days and provide a detailed report on the various microorganisms found in the sample. The report includes information on beneficial bacteria, pathogenic bacteria, fungi, viruses, and parasites. It also provides insights into markers of inflammation, digestion, and immune function.

Why is the GI Map Stool Test Important?

The GI Map Stool Test offers several benefits that make it a valuable tool for both healthcare providers and patients:

  • Comprehensive Analysis: Unlike traditional stool tests that may only identify a limited number of pathogens, the GI Map provides a comprehensive analysis of the gut microbiome. This includes both beneficial and harmful microorganisms, offering a complete picture of gut health.
  • Personalized Health Insights: The detailed report allows healthcare providers to tailor treatment plans to the specific needs of the patient. Whether addressing bacterial overgrowth, dysbiosis, or infections, the test results provide actionable insights.3
  • Early Detection: Identifying imbalances or infections in the gut early on can prevent more serious health issues down the line. The GI Map can detect low-level infections and subclinical imbalances that might not be apparent with other testing methods.4
  • Holistic Health Approach: Gut health is linked to various aspects of overall health, including immune function, mental health, and chronic disease prevention. By understanding the state of the gut microbiome, individuals can make informed decisions about diet, lifestyle, and supplementation to improve their overall well-being.

Who Should Consider the GI Map Stool Test?

The GI Map Stool Test is beneficial for anyone experiencing chronic digestive issues, unexplained symptoms, or conditions that may be linked to gut health. This includes:

  • Individuals with chronic gastrointestinal symptoms such as bloating, diarrhea, constipation, or abdominal pain.
  • Those with autoimmune diseases, as gut health is closely linked to immune function.5
  • Patients with chronic inflammatory conditions, such as IBS or IBD.
  • Individuals experiencing unexplained fatigue, skin issues, or mood disorders, which can all be influenced by gut health.


The GI Map Stool Test is a powerful tool for assessing and improving gut health. By providing a comprehensive analysis of the gut microbiome, it offers valuable insights that can lead to personalized treatment plans and better overall health. Whether you’re dealing with chronic health issues or simply looking to optimize your well-being, the GI Map Stool Test can be a crucial step in your health journey.