Specialty Testing Guide › GI-MAP Gut Testing
The GI-MAP is a stool test that looks for the DNA of specific microbes rather than trying to grow them in a dish. The lab uses a method called quantitative PCR (qPCR) to find and count the genetic fingerprints of bacteria, parasites, fungi and viruses, and it runs a separate set of protein tests that reflect digestion, gut immunity and inflammation.
That design makes the panel sensitive and gives numbers rather than a simple yes or no. It also creates the test's main limit: finding an organism's DNA tells you it was there, not that it is alive or making you sick.
Key takeaways
- The panel counts microbial DNA in a single stool sample using qPCR, a well-established lab method.
- DNA detection is sensitive, but a positive result can reflect dead organisms, harmless carriage or passing exposure rather than active infection.
- Alongside the microbes, the report includes markers of digestion, inflammation and gut immunity measured by antibody-based assays.
- It is a lab-developed test that does not diagnose SIBO and does not replace colorectal cancer screening.
Who makes it and how it is regulated
The GI-MAP is made by Diagnostic Solutions Laboratory, a CLIA-certified lab in Alpharetta, Georgia.1 Each page of its report states that the assays were developed and their performance characteristics determined by the lab itself.2
That makes it a lab-developed test: the lab designed and validated it in-house rather than selling a kit cleared by the FDA for a specific diagnosis. This is common in specialty testing and does not mean the results are wrong. It does mean the clinical meaning of many results rests on the lab's own reference ranges and research rather than on outside diagnostic standards. Our guide to lab-developed tests explains the oversight in more detail.
How qPCR works in plain terms
PCR copies a short, unique stretch of an organism's DNA over and over until there is enough to detect. In quantitative PCR, the machine measures the DNA as it is being copied, so it can estimate how much was in the sample to begin with.
The lab describes the process this way: the sample is screened for DNA sequences chosen to be specific to each target organism, and the result is converted into an estimated count.
- Units. Results are reported as genome equivalents per gram of stool, a way of estimating how many microbes are present per gram.2
- Notation. Numbers appear in scientific notation, so 3.5e7 means 35 million per gram.
- Below detection. "<dl" means the target was below the test's detectable limit.
On repeat testing of the same sample, the lab reports that its microbial assays vary by less than 10%.3 That is a measure of lab precision. It tells you the number is reproducible, not that the number explains your symptoms.
DNA detection is not the same as culture
A traditional stool culture grows live bacteria. A microscope exam looks for parasites and eggs. qPCR does neither: it finds DNA, whether the organism was alive, dead or just passing through from food or a recent exposure.
The lab notes that because the test is DNA-based, toxin results reflect strains carrying toxin genes, not the toxin proteins themselves. It also states that not everyone with a positive pathogen finding will have symptoms.1
Infectious disease specialists make the same point about PCR stool panels in general. A 2026 review warned that positive results may reflect colonization, prolonged shedding or organisms of uncertain pathogenicity rather than active infection.4
This is why a result reads "detected" and why a clinician has to decide what it means. We cover that step in how to read GI-MAP results.
What the panel groups cover
The current sample report groups results into these sections. Add-ons are ordered separately, so ask our team which version the clinic orders for you.
| Section | What it reports | Method |
|---|---|---|
| Pathogens | Bacteria, parasites and viruses known to cause gastroenteritis, such as Salmonella, Giardia and norovirus | qPCR |
| H. pylori | H. pylori level, virulence genes and antibiotic resistance genes | qPCR |
| Commensal bacteria | Common resident groups such as Bifidobacterium, Lactobacillus and Akkermansia | qPCR |
| Dysbiotic and overgrowth bacteria | Organisms that are normal in small amounts, such as Streptococcus and Staphylococcus | qPCR |
| Fungi, viruses, parasites | Candida and other yeasts, two viruses, protozoa such as Blastocystis, and worms | qPCR |
| Intestinal health markers | Elastase, steatocrit, beta-glucuronidase, occult blood, secretory IgA, anti-gliadin IgA, eosinophil protein, calprotectin | Protein and antibody assays |
| Optional add-ons | Zonulin, stool gluten peptide, wider antibiotic resistance genes, bile acids and short-chain fatty acids | Varies |
Each intestinal health marker has its own strength of evidence. Calprotectin is well studied; others are more experimental. See secretory IgA and other stool markers for a marker-by-marker view.
What the test cannot do
- Diagnose SIBO. Small intestinal bacterial overgrowth is a small bowel problem. A stool sample reflects the colon, and the clinic does not run SIBO tests.
- Screen for colorectal cancer. The report includes an occult blood marker, but that is not a screening program. Average-risk adults should follow the US Preventive Services Task Force advice to begin colorectal cancer screening at age 45.5
- Diagnose a whole-body disease. It describes your gut, not your thyroid, joints or skin.
- Prove cause. An organism being present does not show it is causing your symptoms.
How the sample is collected
The lab specifies a single stool sample sent at room temperature in the vial provided.1 The clinic's version is an at-home kit, so Pennsylvania patients collect the sample privately at home. Medication pauses, shipping and turnaround through the clinic are not something we can state here: ask our team. Through the clinic, the GI-MAP is a $404 add-on to an assessment. For the practical steps, see GI-MAP at-home collection, and the GI-MAP hub lists every article on the test.
Frequently asked questions
Is a DNA stool test more accurate than a standard stool test?
It is more sensitive for the targets it includes, so it finds low levels that culture or a microscope can miss. More sensitive also means more findings of uncertain meaning, so "more accurate" depends on the question being asked.
Does the GI-MAP sequence my whole microbiome?
No. It measures a chosen list of organisms with targeted tests. It does not read every species in your stool the way research sequencing does.
Can a result change from week to week?
Yes. Diet, travel, medicines and normal day-to-day variation change what is in stool, so one sample is a snapshot rather than a fixed portrait of your gut.
Related reading
This article is for general education and is not medical advice. Decisions about testing and treatment should be made with your clinician. If you have severe symptoms, call 911. For a suspected poisoning, call Poison Control at 1-800-222-1222.
