The GI-MAP (Gastrointestinal Microbial Assay Plus) is a comprehensive stool test that uses DNA-based technology to detect and measure bacteria, parasites, fungi, and other organisms living in your gut. It’s made by Diagnostic Solutions Laboratory and is primarily ordered through functional medicine practitioners, naturopaths, and integrative health providers. Unlike a standard stool culture you might get at a hospital, the GI-MAP provides numerical values for dozens of organisms, giving a detailed snapshot of your gut ecosystem.
How the Technology Works
The GI-MAP uses a method called quantitative polymerase chain reaction, or qPCR. Instead of trying to grow bacteria in a lab dish (the traditional culture method), qPCR targets the specific DNA of each organism in your stool sample. This matters for two reasons. First, many gut organisms are difficult or impossible to grow in a lab, so cultures miss them entirely. Second, qPCR provides true numerical results, not just a positive or negative. It can tell the difference between a trace amount of a bacterium and an overgrowth, which helps practitioners figure out whether a finding is clinically relevant or just background noise.
Standard PCR tests can detect whether an organism is present but can’t tell you how much of it there is. The quantitative version used in the GI-MAP measures the actual amount of an organism’s DNA in the sample, expressed as a precise number. That distinction is important because many gut bacteria are perfectly normal in small amounts but cause problems when they overgrow.
What the Test Measures
The GI-MAP casts a wide net. It covers several categories of organisms and gut health markers in a single panel.
Pathogens
The test screens for known disease-causing organisms, including bacteria like Salmonella, Campylobacter, and several strains of harmful E. coli. It checks for parasites such as Giardia, Cryptosporidium, and Entamoeba histolytica. Viral targets include norovirus, rotavirus, and adenovirus. It also detects H. pylori, the bacterium linked to stomach ulcers and gastritis, along with specific virulence factors that indicate how aggressive a particular H. pylori strain may be.
Beneficial Bacteria
Your gut relies on a community of helpful organisms, and the GI-MAP measures several of the most important ones. These include Lactobacillus and Bifidobacterium (the species you’ll recognize from probiotic labels), along with keystone species like Akkermansia muciniphila, which helps maintain the gut lining, and Faecalibacterium prausnitzii, one of the most abundant beneficial bacteria in a healthy colon and a major producer of short-chain fatty acids that fuel intestinal cells. Roseburia, Bacteroides fragilis, and Enterococcus species are also tracked. Low levels of these organisms can point to an imbalanced gut environment.
Opportunistic Bacteria
This is the category that often generates the most questions. Opportunistic organisms are bacteria that exist harmlessly in small numbers but can cause problems when they multiply beyond normal levels. The GI-MAP tests for about 20 of these, including Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas, Citrobacter, Proteus, and Fusobacterium. It also measures sulfate-reducing bacteria (Desulfovibrio) and methane-producing organisms (Methanobacteriaceae), both of which have been associated with bloating, gas, and altered bowel habits when elevated.
Because the test is quantitative, your results will show a number next to each organism along with a reference range. A result slightly above the threshold means something different than one that’s ten times the upper limit, and practitioners use that scale to prioritize what needs attention.
Digestive and Inflammatory Markers
Beyond organisms, the GI-MAP includes markers that reflect how well your digestive system is functioning. One key marker is fecal elastase-1, an enzyme produced by the pancreas. Normal pancreatic function shows elastase levels above 400 micrograms per gram of stool. Levels between 200 and 400 suggest intermediate function, and anything below 100 indicates severe pancreatic insufficiency, a condition where your pancreas doesn’t produce enough enzymes to properly break down food. This leads to maldigestion and malabsorption, often showing up as chronic diarrhea, oily stools, or unexplained nutrient deficiencies.
The panel also includes markers related to intestinal inflammation and immune activity, helping practitioners distinguish between an active inflammatory process and a simple microbial imbalance.
How Collection Works
The GI-MAP is a single stool sample collected at home. You’ll receive a kit with a specimen vial that contains a pink preservation liquid (don’t pour it out). Using the small spoon attached to the cap, you fill the vial to the indicated line, cap it tightly, and shake it vigorously for about 30 seconds to mix the sample with the preservative. You then seal it in the provided specimen bag with an absorbent pad and ship it to the lab.
A few practical notes: try to urinate before collecting the sample so urine doesn’t mix in. Don’t overfill the vial. You don’t need to stop prescription medications unless your doctor says otherwise, though some practitioners recommend pausing certain supplements like probiotics, antimicrobials, or digestive enzymes for a period before testing so results reflect your baseline gut environment. It’s worth confirming specific preparation steps with whoever ordered the test.
Cost and Insurance
Most insurance plans do not cover the GI-MAP. The out-of-pocket cost typically falls between $350 and $600, depending on the provider and whether the price includes a consultation to review results. Some patients have gotten partial reimbursement when the test is clearly deemed medically necessary, but this is the exception rather than the norm. Many functional medicine practices offer payment plans or bundle the cost with an initial visit.
How It Differs From Standard Stool Tests
If your primary care doctor orders a stool test, it’s usually a targeted panel looking for a specific infection, like C. difficile or Salmonella, often using culture or basic PCR. These tests answer a yes-or-no question: is this particular pathogen present? They’re appropriate when you have acute symptoms like food poisoning or traveler’s diarrhea.
The GI-MAP takes a broader approach. It’s designed for people dealing with chronic gut issues: persistent bloating, irregular bowel movements, food sensitivities, or unexplained digestive symptoms that haven’t been resolved by standard testing. By measuring beneficial bacteria, opportunistic organisms, digestive markers, and pathogens all in one panel, it aims to reveal patterns of imbalance that a targeted pathogen test would never look for.
That said, the GI-MAP is not a diagnostic tool in the way a colonoscopy or endoscopy is. It won’t detect structural problems, polyps, or cancer. It’s best understood as a window into the microbial and functional landscape of your gut, one that practitioners use alongside your symptoms and health history to guide treatment decisions around diet, supplements, or antimicrobial protocols.