What Is the GI-MAP™ Test? A Complete Guide

Published January 2025 · 9 min read · Medically reviewed by Madison Ordway, FDN-P

If you have been struggling with chronic digestive issues, unexplained fatigue, autoimmune symptoms, or skin problems, your doctor may have suggested a stool test. The GI-MAP™ is available to order directly online — no doctor's referral required. But not all stool tests are created equal. The GI-MAP™ (Gastrointestinal Microbial Assay Plus), also commonly searched as the G.I. MAP test, GI mapping test, or GI-MAP stool test, is widely considered the most comprehensive stool analysis available, and it is increasingly becoming the test of choice for naturopaths, functional medicine doctors, and integrative health practitioners across the United States.

What Does GI-MAP™ Stand For?

GI-MAP™ stands for Gastrointestinal Microbial Assay Plus. It is developed and processed by Diagnostic Solutions Laboratory, a CLIA-certified laboratory based in the United States. The "Plus" refers to the intestinal health markers included beyond the core microbial analysis.

How Is the GI-MAP™ Different from Regular Stool Tests?

The key difference lies in the technology. Traditional stool cultures require organisms to be alive and capable of growing in a lab dish — a process that misses many important pathogens. The GI-MAP™ uses quantitative polymerase chain reaction (qPCR) technology, which detects organisms at the DNA level. This means it can identify pathogens that are present in very small quantities, organisms that are difficult to culture, and even DNA from organisms that are no longer alive but still indicate a recent infection.

Additionally, the GI-MAP™ provides quantitative results — meaning it tells you exactly how much of each organism is present, not just whether it is detected or not. This is critical for practitioners who need to gauge severity and track treatment progress.

What Does the GI-MAP™ Test For?

The GI-MAP™ analyzes over 85 biomarkers organized into several categories:

Bacterial Pathogens

The test screens for harmful bacteria including Helicobacter pylori (with 8 virulence factors), Campylobacter, Clostridioides difficile (toxins A and B), pathogenic E. coli strains, Salmonella, Shigella, and Vibrio cholerae. H. pylori virulence factor testing is particularly valuable — it helps practitioners understand the aggressiveness of an H. pylori infection and make more informed treatment decisions.

Parasitic Pathogens

The GI-MAP™ tests for common parasites including Cryptosporidium, Entamoeba histolytica, Giardia lamblia, Cyclospora cayetanensis, and others. These parasites are frequently missed by conventional stool tests and can cause persistent digestive symptoms.

Viral Pathogens

The test detects Norovirus GI/GII and Rotavirus A, two common causes of acute gastroenteritis.

Opportunistic Organisms

These are bacteria and fungi that may be part of the normal microbiome but can cause problems when present in excess. This includes various Candida species, Staphylococcus, Streptococcus, Enterococcus, Pseudomonas, and others.

Beneficial Bacteria

The GI-MAP™ quantifies levels of important beneficial bacteria including Lactobacillus species, Bifidobacterium species, Akkermansia muciniphila, Faecalibacterium prausnitzii, Roseburia, and Bacteroides fragilis. Low levels of these organisms indicate dysbiosis and may explain a range of symptoms.

Intestinal Health Markers

Beyond microbial analysis, the GI-MAP™ includes markers that assess overall gut function: Calprotectin (intestinal inflammation), Secretory IgA (mucosal immune function), Anti-gliadin IgA (gluten sensitivity), Elastase-1 (pancreatic enzyme output), Steatocrit (fat absorption), Beta-Glucuronidase (detoxification and estrogen metabolism), and Occult Blood.

Who Should Consider the GI-MAP™?

The GI-MAP™ is appropriate for anyone experiencing chronic digestive symptoms (bloating, gas, diarrhea, constipation, abdominal pain), suspected food sensitivities, autoimmune conditions, chronic skin issues, unexplained fatigue or brain fog, recurrent infections, or anyone wanting a comprehensive baseline assessment of their gut health.

Each biomarker is reported with a numeric value alongside a reference range, and many practitioners use these numbers as a baseline that can be re-tested after a course of treatment to see whether levels have moved in the right direction.

How the qPCR Technology Actually Works

Quantitative polymerase chain reaction (qPCR) is the same broad family of DNA-amplification technology that became familiar to the public during COVID-19 testing. The laboratory uses primers that are designed to bind to genetic sequences unique to each target organism. If that organism's DNA is present in the stool sample, the reaction amplifies it through repeated heating and cooling cycles, and a fluorescent signal is measured in real time. The number of cycles required before the signal crosses a detection threshold corresponds to how much starting DNA was present, which is how the test produces a quantitative result rather than a simple "detected / not detected" answer.

Because the method targets DNA directly, it does not depend on whether an organism is still alive or able to grow on a culture plate. This is one reason molecular panels generally report higher detection rates than traditional culture for many gastrointestinal targets. It is also why sample handling matters: the at-home collection kit includes a preservative designed to stabilize microbial DNA during shipping. You can see exactly what the collection process looks like on our how it works page.

How to Read Your GI-MAP™ Report

A GI-MAP™ report groups results into the categories described above and flags values that fall outside the reference range, often using color coding so that out-of-range findings stand out at a glance. A single flagged marker rarely tells the whole story on its own. For example, an opportunistic overgrowth alongside low beneficial bacteria and elevated Calprotectin paints a very different picture than one mildly elevated marker in isolation. This is why the report is intended to be interpreted in the context of your symptoms and history by a qualified practitioner rather than read as a standalone diagnosis. You can preview the layout on our sample report page before you order.

Results are not a substitute for evaluation by a licensed clinician. The GI-MAP™ is best used as one input into a broader clinical picture, and any treatment decisions, including the use of antimicrobials, antibiotics, or prescription medication, should be made with a healthcare professional who can weigh the findings against your individual circumstances.

GI-MAP™ vs. Other Stool Tests

Conventional stool testing has traditionally relied on culture and microscopy, which require organisms to grow or to be visually identified. These methods remain valuable in acute clinical settings, but they can miss organisms that are difficult to culture, present in small numbers, or no longer viable. We compare the two approaches in detail in our guide on GI-MAP™ vs. conventional stool culture. The GI-MAP™ also offers focused panels: alongside the comprehensive GI-MAP™ Standard, there is a GI-MAP™ + Zonulin option that adds a direct marker of intestinal permeability, and a standalone H. pylori profile for those whose primary concern is Helicobacter pylori and its virulence factors.

Common Questions About the GI-MAP™

Do I need to stop probiotics or medications before testing?

Many practitioners ask patients to pause probiotics, digestive enzymes, and certain medications for a window before collection because these can influence results, while others may want a sample taken during normal routine. Because the right approach depends on what you are trying to learn, this is a question to confirm with the practitioner overseeing your test rather than a fixed rule.

Is the GI-MAP™ a diagnostic test for a specific disease?

No. The GI-MAP™ is a laboratory assessment of microbial and intestinal-health markers. It can reveal patterns associated with various conditions, but it does not by itself diagnose disease. Conditions such as inflammatory bowel disease, infections, and cancers require evaluation and diagnosis by a physician using appropriate clinical methods.

How long do results take?

Turnaround is typically a couple of weeks after the laboratory receives your sample, since the full comprehensive panel is processed rather than a single targeted organism.

How to Order in the United States

You can order a GI-MAP™ test kit directly through our website. No doctor's referral is required. Kits ship free to all US addresses, and the simple at-home collection process means no clinic visits or lab appointments are needed. Order your kit or view our test packages and pricing →

Sources

This article draws on the laboratory's published test documentation and peer-reviewed literature on molecular stool testing. Always discuss your individual results with a qualified healthcare practitioner.

• Diagnostic Solutions Laboratory — GI-MAP (GI Microbial Assay Plus) test overview
• Comparison of Real-Time PCR versus a Culture-dependent Algorithm to Identify Enteropathogens in Stool Samples (Scientific Reports, 2020)
• Fecal Calprotectin for the Diagnosis and Management of Inflammatory Bowel Diseases (PMC)