The GI-MAP test is a stool test that uses quantitative PCR to count specific gut bacteria, parasites, viruses and yeast, and adds a few digestion and inflammation markers.[1] It is a laboratory-developed assay with lab-set reference ranges, and the one independent validation study we found reported many false positives.[2] Treat results as a prompt for a clinical conversation, not a diagnosis.
This guide walks through each section of the report, what the evidence says about the markers, and how to weigh the results. It is balanced on purpose: the test can detect real organisms, and the evidence for acting on many of its numbers is thin.
What does the GI-MAP test measure?
The GI-MAP measures microbial DNA in stool by qPCR and reports it per gram of stool, alongside a handful of protein markers.[3] A sample report from the laboratory's format, which we retrieved in October 2026, is organized into the sections below.[3]
| Report section | Examples on the sample report | What it is meant to show |
|---|---|---|
| Pathogens | Campylobacter, C. difficile toxins A and B, Shiga-toxin E. coli, Salmonella, Giardia, Cryptosporidium, norovirus | Organisms known to cause gastroenteritis |
| H. pylori and virulence factors | Helicobacter pylori, cagA, vacA, babA | Presence of the stomach bacterium and some of its virulence genes |
| Commensal bacteria | Bifidobacterium, Lactobacillus, Akkermansia muciniphila, Faecalibacterium prausnitzii, Roseburia | Amounts of common resident bacteria compared with a lab range |
| Opportunistic and overgrowth microbes | Staphylococcus aureus, Pseudomonas, Klebsiella, Citrobacter, Desulfovibrio | Bacteria that can cause trouble when they overgrow |
| Fungi and yeast | Candida species, Geotrichum, Rhodotorula | Yeast levels |
| Viruses, protozoa and worms | Cytomegalovirus, Epstein-Barr virus, Blastocystis hominis, Dientamoeba fragilis, tapeworm and roundworm targets | Parasites and some viruses |
| Intestinal health markers | Elastase-1, steatocrit, secretory IgA, calprotectin, occult blood (FIT), anti-gliadin IgA | Digestion, immune function and inflammation |
| H. pylori resistance genes | Markers linked to amoxicillin, clarithromycin, fluoroquinolone and tetracycline resistance | Reported when H. pylori is detected |
Zonulin is sold as an optional add-on and is not on the base sample report, so we cover it separately below.[3]
How do you get a GI-MAP test done, and what should you avoid beforehand?
A GI-MAP test at home means collecting the stool sample yourself: the ordering clinic or laboratory supplies a kit with collection instructions, and the sample goes back to the laboratory for analysis.[1] Follow the instruction sheet in your own kit exactly. We could not retrieve the laboratory's current collection instructions during this review, so we are not listing kit-specific rules such as supplement or medication holds.
Two general points are supported by guidelines:
- Antibiotics and acid blockers can change H. pylori results. For confirming that H. pylori has cleared, the American College of Gastroenterology (ACG) guidance summary advises waiting at least 4 weeks after antibiotics and at least 2 weeks off proton pump inhibitors or potassium-competitive acid blockers, with antacids or H2 blockers allowed to bridge.[4] That advice is written for test-of-cure testing, so ask your clinician how it applies to you.
- Do not stop prescribed medication on your own. Ask the ordering clinician before changing any prescription for a stool test.
Results timing varies by lab, so ask the ordering clinic. In a separate study of seven consumer sequencing services, reports arrived 2 to 8 weeks after shipping.[5]
How do you read GI-MAP results?
Start with what was flagged, then ask whether it fits your symptoms. A flag means a number fell outside the laboratory's own range. The sample report itself notes that not everyone with a positive finding develops symptoms, and that the organism's virulence factors and the person's immune and digestive health all matter.[3]
Pathogens: a detection is not the same as an infection
The pathogen section lists organisms such as Campylobacter, Salmonella, Giardia and Cryptosporidium. Validated clinical PCR panels perform well here: a meta-analysis of two widely used multiplex gastroenteritis panels found specificity of 0.98 or higher for nearly all targets.[6]
Still, DNA detection can outrun disease. In a Zanzibar case-control study of children, at least one pathogen was found in 94% of children with acute diarrhea and 84% of controls without it.[7] In a large reanalysis of a childhood diarrhea study, researchers needed model-derived quantitative cutoffs to decide which detected pathogen was likely responsible in a given child.[8] Those were studies of children with diarrhea, so they do not map one-to-one onto adults, but they show why a single positive needs context.
If the report names a well-known pathogen and you have diarrhea, fever or blood in the stool, call a clinician rather than waiting for an appointment to interpret the report. Our pages on Clostridioides difficile, Giardia and Entamoeba histolytica explain what each organism does.
H. pylori and virulence factors
The report includes H. pylori and its virulence genes. The ACG guideline covers who to test and when to confirm eradication after treatment.[9]
A commentary on it advises against ordering an H. pylori test unless you intend to treat.[4] In the validation study, the GI-MAP reported H. pylori as "high" in nine aliquots whose antigen tests were consistently negative, though the authors could not confirm the PCR result against a reference PCR.[2] If your report flags H. pylori, ask about confirming it with a standard clinical test before treatment. Our H. pylori guide covers the organism.
Commensal and opportunistic bacteria: where the evidence is thinnest
This is the section most people mean when they ask how to read GI-MAP results. It compares amounts of bacteria such as Bifidobacterium, Akkermansia and Faecalibacterium with laboratory ranges, and flags groups such as Klebsiella, Citrobacter and Streptococcus when high.[3]
The problem is the reference range. A 2025 international consensus statement concluded that evidence supporting the clinical usefulness of microbiome diagnostics is scarce and that commercial tests lack consensus on regulation and proven value.[10] In the NIST-led comparison of seven consumer services, each company used a different "healthy" comparison group, and the reports sometimes gave conflicting health scores for identical material.[5] That study evaluated sequencing-based services, not the GI-MAP, but it shows that "high" and "low" depend on whose range you use.
Treat a flagged commensal or opportunistic organism as a hypothesis. Our guide to opportunistic bacteria explains why many of these organisms are harmless at normal levels, and the pages on Klebsiella oxytoca and Blastocystis hominis show how contested a single stool finding can be.
Digestive, immune and inflammation markers
Some of the report's protein markers have much better-studied counterparts in ordinary clinical care.
| Marker | What the evidence says | Practical reading |
|---|---|---|
| Calprotectin | A meta-analysis of 17 studies (1,956 adults) found sensitivity of 85.8% and specificity of 91.7% for telling inflammatory bowel disease from irritable bowel syndrome[11] | A raised value needs a clinician's follow-up. A normal value makes IBD less likely |
| Elastase-1 | A meta-analysis of 14 studies reported pooled sensitivity of 0.77 and specificity of 0.88 against the secretin test[12] | Low values can point to pancreatic enzyme insufficiency. Mild cases are often missed[13] |
| Secretory IgA | We found no guideline-endorsed use for stool secretory IgA | Interpret only with a clinician |
| Zonulin (optional) | Commercial serum zonulin assays were found not to detect the actual protein[14] | Do not use as proof of "leaky gut" |
Two details matter for calprotectin. At a 1% prevalence of IBD, the meta-analysis calculated a negative predictive value of 99.8% but a positive predictive value of only 9%, so a raised result is not proof of IBD.[11] And for elastase-1, one study found sensitivity of 16.7% for mild and 12.5% for moderate pancreatic insufficiency, versus 72.2% for severe disease.[13]
On zonulin, the Monash study tested serum kits, not the stool assay used in some GI-MAP add-ons, so it does not directly invalidate the stool version. It does show that "zonulin" results from commercial immunoassays are not a settled measure of gut permeability.[14] Our page on leaky gut covers what is and is not established.
How accurate is the GI-MAP test?
Independent accuracy data are limited. When we searched PubMed for GI-MAP studies, the only validation paper that turned up was a 2020 spiked-stool evaluation.[2] In that study:
- Investigators spiked pooled stool from one donor with 14 bacterial and 2 parasitic targets, plus 7 unspiked controls, and compared the GI-MAP with the BioFire FilmArray panel.[2]
- The GI-MAP detected the added organism in 12 of 16 spiked samples (80% sensitivity). Its specificity was 26% because of many false positives, while BioFire scored 100% on both.[2]
- Yersinia and Vibrio cholerae were reported below the lab's "normal" threshold and counted as misses.[2]
Read this study with its limits in mind. It used one stool matrix, a small number of samples and a comparator the authors described as not a true gold standard. It was funded by Doctor's Data, a competing laboratory, and it dates from 2020, so the assay may have changed since.[2] We did not find an independent follow-up.
The authors also argued that quantity in stool has no established clinical relevance, because stool volume and density shift with diet, hydration and fiber intake.[2] Repeat results within one laboratory's workflow can be consistent, as the NIST group found for sequencing services, but consistency is not the same as being right. The same study found that differences between providers were as large as differences between people.[5]
Is the GI-MAP test worth it?
It can be reasonable when a clinician has a specific question and will act on a clear result, and it is hard to justify as a general gut check. Two sets of guidance frame the decision:
- For irritable bowel syndrome, the ACG recommends checking fecal calprotectin and C-reactive protein in people with diarrhea and no alarm features to help rule out inflammatory bowel disease, and recommends against routine stool testing for enteric pathogens in all people with IBS.[15]
- For microbiome diagnostics generally, the 2025 international consensus statement warns that unproven tests risk wasting money and driving poor management.[10]
If you already have a diagnosis, the useful question is whether a result would change treatment. If it would not, the money may be better spent on a dietitian visit or on guideline-recommended tests. For a wider comparison of stool and other options, see our microbiome testing guide.
Can the GI-MAP test help with acne?
Possibly as a research curiosity, but not as a proven acne work-up. A narrative review describes a "gut-skin axis" and notes that clinical trials of oral probiotics for acne are scarce, though the reported results were positive.[16]
Those trials tested probiotics, not GI-MAP-guided care. In our search we found no trial showing that choosing treatment by GI-MAP results improves acne. Our acne page and gut-skin axis article go deeper.
When should you see a doctor instead of ordering a stool kit?
See a clinician first if you have symptoms that guidelines treat as alarm features. The ACG IBS guideline lists blood in the stool or black stool, unintentional weight loss, an older age at symptom onset, and a family history of inflammatory bowel disease or colon cancer.[15] Those need a medical evaluation, not a mailed kit.
Also talk to a clinician before acting on any result if you are pregnant, immunocompromised, taking prescription medication, or managing a diagnosed condition. Do not start antimicrobial herbs or stop medication based only on a report. In the validation study, the authors warned that false positives could lead to treatment with antibacterial or antiparasitic drugs in the absence of a true pathogen.[2]
This article is for general educational purposes and is not medical advice. Laboratory methods, reference ranges and prices change, and we have not tested the GI-MAP ourselves. It does not replace testing or evaluation by a qualified clinician. Talk to a qualified healthcare professional before ordering a stool test or changing treatment, particularly if you are pregnant, immunocompromised, taking prescription medication, or managing a diagnosed condition.
Frequently Asked Questions
How much does a GI-MAP test cost?
The price depends on the laboratory, the ordering practitioner, and whether the optional zonulin add-on is included, and the practitioner's own consultation fees are usually billed separately. We could not verify a current price from a primary source in this review, so we are not quoting one. Ask the ordering clinic for the all-in cost, including interpretation, before you agree to the test.
Is the GI-MAP test covered by insurance?
We did not find an authoritative source confirming routine insurance coverage for the GI-MAP, so assume it may be out of pocket until your insurer confirms otherwise. Coverage depends on your plan, the ordering clinician, and the stated reason for testing. Standard tests that guidelines recommend, such as fecal calprotectin for suspected irritable bowel syndrome with diarrhea, are more likely to be covered.
Do you need a doctor to order and interpret a GI-MAP?
A clinician is worth involving. Reports use laboratory-defined reference ranges, positive findings do not always mean illness, and the sample report itself notes that not every person with a positive finding has symptoms. A clinician can also check whether a guideline-recommended test would answer your question first.
Can a GI-MAP diagnose IBS or IBD?
No. The American College of Gastroenterology suggests diagnosing irritable bowel syndrome with a positive, symptom-based strategy, and checking fecal calprotectin and C-reactive protein to help rule out inflammatory bowel disease in people with diarrhea and no alarm features. A GI-MAP report includes a calprotectin line, but it is not a substitute for that clinical work-up.
How do you check your gut microbiome?
A stool sample is the standard starting point, analyzed either by a targeted panel such as the GI-MAP or by sequencing, and a 2025 international consensus statement found evidence for clinical usefulness of these tests is scarce. For the main options, what each can and cannot show, and typical use cases, see our complete guide to microbiome testing.
What abnormalities can a stool test show?
The GI-MAP sample report flags detections of pathogens such as Campylobacter, Giardia or C. difficile toxins, occult blood, high calprotectin, low elastase-1, and counts of bacteria or yeast outside the laboratory's ranges. Each flag has different reliability, and none is a diagnosis alone. A clinician should match it to symptoms and, where needed, a confirmatory test.
What are the signs of a bad gut microbiome?
Persistent bloating, gas, irregular stools, abdominal pain, and fatigue are commonly linked to gut problems, but none of them proves a microbiome imbalance, and a stool test cannot confirm one by itself. Our guide to the signs of poor gut health covers the common symptoms and which ones deserve a medical check.
How is the GI-MAP different from sequencing-based gut tests?
The GI-MAP reports a fixed panel of named targets using quantitative PCR, so it can only report what is on the panel. The consumer gut tests NIST evaluated used 16S rRNA or shotgun sequencing to profile much larger sets of microbes. Both approaches have open questions about standardization and clinical use.
References
- Precision Point Diagnostics. GI-MAP (Stool), laboratory partner product page, retrieved October 2026. Precision Point Diagnostics. 2026. Available at: https://precisionpointdiagnostics.com/test/gi-map/ ↩
- Gingras BA, Maggiore JA. Performance of a new molecular assay for the detection of gastrointestinal pathogens. Access Microbiology. 2020;2(10):acmi000160. doi:10.1099/acmi.0.000160 ↩
- Precision Point Diagnostics. GI-MAP sample report (Diagnostic Solutions Laboratory report format), retrieved October 2026. Precision Point Diagnostics. 2023. Available at: https://precisionpointdiagnostics.com/wp-content/uploads/2023/11/GI-MapSampleReport11323.pdf ↩
- Schoenfeld P. ACG Guideline on Treatment of Helicobacter pylori: New Recommendations... Will Practice Change?. Evidence-Based GI, American College of Gastroenterology. 2024. Available at: https://gi.org/journals-publications/ebgi/schoenfeld_sep2024/ ↩
- Servetas SL, Gierz KS, Hoffmann D, Ravel J, Jackson SA. Evaluating the analytical performance of direct-to-consumer gut microbiome testing services. Communications Biology. 2026;9(1):269. doi:10.1038/s42003-025-09301-3 ↩
- Chang LJ, Hsiao CJ, Chen B, et al.. Accuracy and comparison of two rapid multiplex PCR tests for gastroenteritis pathogens: a systematic review and meta-analysis. BMJ Open Gastroenterology. 2021;8(1):e000553. doi:10.1136/bmjgast-2020-000553 ↩
- Elfving K, Andersson M, Msellem MI, et al.. Real-Time PCR Threshold Cycle Cutoffs Help To Identify Agents Causing Acute Childhood Diarrhea in Zanzibar. Journal of Clinical Microbiology. 2014;52(3):916-923. doi:10.1128/jcm.02697-13 ↩
- Liu J, Platts-Mills JA, Juma J, et al.. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. The Lancet. 2016;388(10051):1291-1301. doi:10.1016/s0140-6736(16)31529-x ↩
- Chey WD, Howden CW, Moss SF, et al.. ACG Clinical Guideline: Treatment of Helicobacter pylori Infection. American Journal of Gastroenterology. 2024;119(9):1730-1753. doi:10.14309/ajg.0000000000002968 ↩
- Porcari S, Mullish BH, Asnicar F, et al.. International consensus statement on microbiome testing in clinical practice. The Lancet Gastroenterology & Hepatology. 2025;10(2):154-167. doi:10.1016/s2468-1253(24)00311-x ↩
- Dajti E, Frazzoni L, Iascone V, et al.. Systematic review with meta-analysis: Diagnostic performance of faecal calprotectin in distinguishing inflammatory bowel disease from irritable bowel syndrome in adults. Alimentary Pharmacology & Therapeutics. 2023;58(11-12):1120-1131. doi:10.1111/apt.17754 ↩
- Vanga RR, Tansel A, Sidiq S, El-Serag HB, Othman MO. Diagnostic Performance of Measurement of Fecal Elastase-1 in Detection of Exocrine Pancreatic Insufficiency: Systematic Review and Meta-analysis. Clinical Gastroenterology and Hepatology. 2018;16(8):1220-1228.e4. doi:10.1016/j.cgh.2018.01.027 ↩
- Naruse S, Ishiguro H, Ko SB, et al.. Fecal pancreatic elastase: a reproducible marker for severe exocrine pancreatic insufficiency. Journal of Gastroenterology. 2006;41(9):901-908. doi:10.1007/s00535-006-1884-0 ↩
- Ajamian M, Steer D, Rosella G, Gibson PR. Serum zonulin as a marker of intestinal mucosal barrier function: May not be what it seems. PLOS ONE. 2019;14(1):e0210728. doi:10.1371/journal.pone.0210728 ↩
- Lacy BE, Pimentel M, Brenner DM, et al.. ACG Clinical Guideline: Management of Irritable Bowel Syndrome. American Journal of Gastroenterology. 2021;116(1):17-44. doi:10.14309/ajg.0000000000001036 ↩
- Sánchez-Pellicer P, Navarro-Moratalla L, Núñez-Delegido E, et al.. Acne, Microbiome, and Probiotics: The Gut–Skin Axis. Microorganisms. 2022;10(7):1303. doi:10.3390/microorganisms10071303 ↩