GI-MAP vs GI Advanced: Which Comprehensive Stool Test Is Better?

Most people don't think about stool testing until something is clearly wrong, and has been for a while. But by the time symptoms like chronic bloating, IBS, brain fog, or recurring infections appear, gut imbalances have often been present for a long time. Functional stool testing, or comprehensive stool analyses can reveal what's actually driving symptoms. But not all stool tests are created equal. The two most popular functional options, the GI-MAP and the GI Advanced stool tests, differ in meaningful ways.

Is a comprehensive stool test worth it?

If you're dealing with chronic bloating, IBS symptoms, constipation, diarrhea, food sensitivities, autoimmune issues, brain fog, or recurring digestive problems, a functional stool test can often provide deeper answers than standard testing. Modern gut health tests can evaluate pathogens, microbiome balance, inflammation, digestion, intestinal permeability (“leaky gut”), and immune activity all from an at-home stool test. In this article, we’ll compare two of the most popular comprehensive stool analysis options, the GI-MAP stool test and the GI Advanced stool test, to help you determine which test may be the better fit for your needs.

Who should consider functional stool testing?

Someone with new or long standing digestive symptoms can generally benefit greatly from a comprehensive stool analysis. Especially if treatment has not corrected the problem. Common symptoms include:

• IBS diagnosis

• IBD diagnosis (Crohn's disease or Ulcerative Colitis or Proctitis)

• Chronic constipation

• Chronic diarrhea

• Bloating, indigestion

• Chronic acid reflux

• Slow digestion

• Food intolerances or sensitivities

• Autoimmune conditions

• Brain fog linked to gut function and digestion

• History of antibiotic use or recurrent infections

• Chronic yeast infections

Many patients are surprised how often digestive symptoms overlap with skin, immune, or fatigue complaints.

What does a comprehensive stool test actually measure?

Most standard stool tests ordered through a primary care office or gastroenterologist are primarily designed to identify acute infections causing symptoms like severe diarrhea, food poisoning, bloody stools, nausea, vomiting, or fever. These tests commonly evaluate pathogens such as Salmonella, Shigella, Campylobacter, C. difficile, Giardia, and Cryptosporidium.

More advanced stool testing expands beyond acute infections and evaluates microbiome balance, beneficial bacteria, yeast and fungi, digestion, intestinal inflammation, intestinal permeability (“leaky gut”), and broader patterns of gut dysfunction.

This is often where the bigger picture starts to emerge, not just whether a pathogen is present, but whether imbalances in the microbiome, inflammation, digestive dysfunction, or intestinal permeability may be contributing to chronic symptoms.

Sometimes the most helpful findings aren’t pathogens at all, but poor microbiome diversity or digestive dysfunction

Why Most Doctors Don't Order These Tests

Most traditional MD/DOs and NPs aren't familiar with the opportunities advanced stool testing offers. Standard stool tests only evaluate for acute infections. Even gastroenterologists, who diagnose and treat the digestive system as a specialty, routinely tell our patients that "their diet has nothing to do with their digestion". The digestive system, microbiome, and immune system are deeply interconnected, and research continues to uncover how strongly gut function can influence inflammation, immunity, metabolism, and even neurological symptoms.

Most conventional stool testing is designed to identify acute infections or serious pathology, not to evaluate microbiome balance, digestive function, intestinal permeability, or subtle inflammatory patterns. As a result, many patients with chronic digestive symptoms are told their testing is “normal” despite continuing symptoms.

"Some stool tests only look for pathogens. Others evaluate the entire gut ecosystem."

How the GI-MAP stool test works

This test is qPCR only. This is a highly accurate quantitative DNA detection, single stool sample, strong at identifying pathogens and some functional markers including zonulin. Well-established, widely used by functional medicine practitioners. Approximately 40+ markers with a 10–12 business day turnaround.

How the GI Advanced stool test works

The GI Advanced from US Biotek is a RT-PCR plus microbial culture. It's this dual methodology that adds another layer of characterization and antimicrobial sensitivity information.

The GI Advanced also measures 127+ markers across 15 categories. It includes viral pathogens, short-chain fatty acids, antimicrobial sensitivities, and 8 potential autoimmune triggers, which the GI-MAP does not include. It's also a single-day collection, which is much preferred by patients over 3 day collection tests which require 3 separate samples on 3 separate days. That's a lot of poop collection!

Head-to-head comparison

Key: ✓ = included in base price | * = add-on cost | — = not offered

BACTERIAL PATHOGENS

Marker	GI-MAP	GI Advanced
Campylobacter	✓	✓
C. difficile Toxin A	✓	✓
C. difficile Toxin B	✓	✓
C. difficile Hypervirulent strain	—	✓
E. coli – EPEC/EHEC	✓	✓
E. coli O157	✓	✓
Enteroaggregative E. coli	—	✓
Enteroinvasive E. coli/Shigella	✓	✓
Enterotoxigenic E. coli LT/ST	✓	✓
Shiga-like Toxin E. coli stx1/stx2	✓	✓
Salmonella	✓	✓
Aeromonas species	—	✓
Vibrio	✓	✓
Yersinia	✓	✓

H. PYLORI & VIRULENCE FACTORS

Marker	GI-MAP	GI Advanced
Helicobacter pylori	✓	✓
H. pylori Antigen	—	✓
Virulence factor: babA	✓	✓
Virulence factor: cagA	✓	✓
Virulence factor: oipA	✓	✓
Virulence factor: vacA	✓	✓
Virulence factor: virB	✓	✓
Virulence factor: virD	✓	✓
Virulence factor: dupA	✓	—
Virulence factor: iceA	✓	—
Antibiotic resistance genes (Clarithromycin, Fluoroquinolone, Tetracycline, Rifabutin, Metronidazole)	✓	✓ (Clarithromycin)

OPPORTUNISTIC / DYSBIOTIC BACTERIA

Marker	GI-MAP	GI Advanced
Bacillus species	✓	✓
Bacteroides fragilis	✓	✓
Bacteroides thetaiotaomicron	—	✓
Phocaeicola vulgatus	—	✓
Enterobacter cloacae complex	✓	✓
Enterococcus faecalis	✓	✓
Enterococcus faecium	✓	✓
Morganella species	✓	✓
Pseudomonas species	✓	✓
Pseudomonas aeruginosa	✓	✓
Staphylococcus species	✓	✓
Staphylococcus aureus	✓	✓
Streptococcus species	✓	✓ (agalactiae, anginosus, mutans, oralis, salivarius)
Desulfovibrio species	✓	✓
Methanobacteriaceae / Methanobrevibacter smithii	✓	✓

POTENTIAL AUTOIMMUNE TRIGGERS (named dedicated section, in the GI Advanced)

Marker	GI-MAP	GI Advanced
Citrobacter species	✓ (in dysbiosis section)	✓ (dedicated section)
Citrobacter freundii	✓	✓
Klebsiella species	✓	✓
Klebsiella pneumoniae	✓	✓
Prevotella copri	✓	✓
Proteus species	✓	✓
Proteus mirabilis	✓	✓
Fusobacterium species	✓	✓
M. avium subsp. paratuberculosis	✓	—

Note: GI-MAP includes these markers but distributes them across sections rather than grouping them as a dedicated autoimmune category.

NORMAL FLORA / COMMENSAL BACTERIA

Marker	GI-MAP	GI Advanced
Akkermansia muciniphila	✓	✓
Faecalibacterium prausnitzii	✓	✓
Bifidobacterium spp. (total)	✓	✓
Bifidobacterium adolescentis	—	✓
Bifidobacterium bifidum	—	✓
Bifidobacterium breve	—	✓
Bifidobacterium longum	—	✓
Lactobacillus spp. (total)	✓	✓
Lactobacillus acidophilus	—	✓
Lactobacillus casei	—	✓
Lactobacillus delbrueckii	—	✓
Lactobacillus plantarum	—	✓
Lactobacillus rhamnosus	—	✓
Lactobacillus salivarius	—	✓
Enterococcus species	✓	✓
Escherichia species	✓	✓
Roseburia spp.	✓	—
Clostridium species	—	✓
Oxalobacter formigenes	—	✓

BACTERIAL PHYLA / MICROBIOME DIVERSITY

Marker	GI-MAP	GI Advanced
Firmicutes	✓	✓
Bacteroidetes	✓	✓
Firmicutes:Bacteroidetes Ratio	✓	✓
Actinobacteria	—	✓
Proteobacteria	—	✓
Verrucomicrobia	—	✓
Euryarchaeota	—	✓

FUNGI / YEAST

Marker	GI-MAP	GI Advanced
Candida spp. (general)	✓	✓
Candida albicans	✓	✓
Candida dubliniensis	—	✓
Candida famata	—	✓
Candida glabrata	—	✓
Candida guilliermondii	—	✓
Candida krusei	—	✓
Candida parapsilosis	—	✓
Candida tropicalis	—	✓
Geotrichum species	✓	✓
Microsporidium species	✓	—
Rhodotorula species	✓	✓
Saccharomyces cerevisiae	—	✓

PARASITES — PROTOZOA

Marker	GI-MAP	GI Advanced
Blastocystis hominis	✓	✓
Cryptosporidium	✓	✓
Cyclospora	✓	✓
Dientamoeba fragilis	✓	✓
Entamoeba histolytica	✓	✓
Giardia	✓	✓
Chilomastix mesnili	✓	—
Endolimax nana	✓	—
Entamoeba coli	✓	—
Pentatrichomonas hominis	✓	—
Enterocytozoon species	—	✓

PARASITES — WORMS / HELMINTHS

Marker	GI-MAP	GI Advanced
Ancylostoma (Hookworm)	✓	✓
Ascaris (Roundworm)	✓	✓
Enterobius vermicularis (Pinworm)	—	✓
Necator americanus (Hookworm)	✓	✓
Strongyloides	—	✓
Taenia (Tapeworm)	✓	✓
Hymenolepis (Tapeworm)	—	✓
Trichuris trichiura (Whipworm)	✓	✓

VIRUSES

Marker	GI-MAP	GI Advanced
Adenovirus 40/41	✓	✓
Norovirus GI/II	✓	✓
Astrovirus	—	✓
Rotavirus A	—	✓
Sapovirus	—	✓
Cytomegalovirus	✓	—
Epstein-Barr Virus	✓	—

GI FUNCTIONAL MARKERS

Marker	GI-MAP	GI Advanced
Calprotectin (inflammation)	✓	✓
Pancreatic Elastase-1	✓	✓
Secretory IgA	✓	✓
Zonulin (leaky gut)	* add-on	✓
β-Glucuronidase	✓	✓
Steatocrit (fat digestion)	✓	✓
Transglutaminase IgA (celiac marker)	—	✓
Anti-gliadin IgA	✓	—
Gluten Peptide	* add-on	—
Eosinophil Activation Protein (EDN/EPX)	✓	—
Occult Blood / FIT	✓	✓
Stool pH	—	✓
Macroscopy (color, form, mucus)	—	✓

SHORT-CHAIN FATTY ACIDS

Marker	GI-MAP	GI Advanced
Total SCFAs / Beneficial SCFAs	* add-on (StoolOMX)	✓
Acetate	* add-on	✓
Butyrate	* add-on	✓
Propionate	* add-on	✓
Valerate	* add-on	✓
Bile acids (25 markers)	* add-on (StoolOMX)	—

ANTIMICROBIAL SENSITIVITIES

Marker	GI-MAP	GI Advanced
Culture-based sensitivity testing	—	✓

METHODOLOGY

	GI-MAP	GI Advanced
Primary method	qPCR only	RT-PCR + microbial culture
Stool collection days	1 day	1 day
Results delivery	7–10 business days	14 business days

NOTE: Not every abnormality on a stool test is clinically significant, which is why interpretation matters.

Which one is right for you?

The GI-MAP may be sufficient for straightforward pathogen investigation, but the GI Advanced is the stronger choice for chronic, complex, or autoimmune presentations where a fuller picture matters.  The GI-MAP's qPCR is quantitative (tells you how much of an organism is present), while the GI Advanced culture component adds confirmatory accuracy and antimicrobial sensitivity data as well.

While the GI Advanced is a more comprehensive test, many patients prefer having a broader evaluation upfront rather than needing multiple rounds of testing later.

Ready to investigate your gut health more deeply?

You can see your naturopathic or your functional medicine provider to get a more personalized recommendation based on your unique needs. Our office provides a Complimentary Virtual 15-min Consult if would like to see if our office is a good fit for you.

For patients looking for a more comprehensive look at digestion, microbiome balance, inflammation, intestinal permeability, and potential pathogens, we often find the GI Advanced provides the most complete overall picture.

The GI Advanced stool test can be ordered directly through our Functional Labs page and completed entirely at home, with optional interpretation support available if desired.

GI Advanced Comprehensive Digestive Test

From$464.00

Buy Now

FAQ

1. Is the GI Advanced the same as the GI-MAP?

   1. No, they're two different tests from two different labs. The GI-MAP is made by Diagnostic Solutions Laboratory and uses qPCR-only technology. The GI Advanced is made by US Biotek and uses a dual method of RT-PCR plus microbial culture, which adds a layer of confirmatory accuracy. They cover many of the same markers, but the GI Advanced includes more: 127+ markers across 15 categories compared to roughly 40+ on the GI-MAP base panel. The GI Advanced also includes a dedicated autoimmune trigger section, more Candida species, more viral pathogens, short-chain fatty acids, and antimicrobial sensitivities — all in the base price.

2. Can I order stool testing without a doctor?

   1. Yes! You can order the GI Advanced directly from our Functional Labs page without a doctor's visit or a prescription. Once you order, a collection kit is shipped to you, you collect your sample at home in a single day, and send it back to the lab. Results are delivered securely and you can add an optional review session with one of our naturopathic doctors or functional nutritionists if you'd like help understanding what your results mean.

3. What's the difference between PCR and culture in stool testing?

   1. PCR (polymerase chain reaction) detects the DNA of microorganisms in your stool. It's fast, highly sensitive, and can find even very small amounts of an organism. qPCR, which the GI-MAP uses, takes this a step further by also quantifying how much of an organism is present, not just whether it's there. Culture-based testing actually grows the organisms from your sample in a lab, which allows for more detailed characterization and importantly, antimicrobial sensitivity testing, meaning you can see which treatments a particular organism responds to. The GI Advanced uses both methods together, which is why it can offer antimicrobial sensitivities that a PCR-only test cannot.

4. Does the GI Advanced test for leaky gut?

   1. Yes. The GI Advanced includes Zonulin as part of its base panel, so no add-on required. Zonulin is currently one of the best available markers for intestinal permeability, commonly referred to as leaky gut. It's a protein that regulates the tight junctions between cells lining the gut wall. When zonulin is elevated, it suggests those junctions may be more permeable than they should be, allowing bacteria, food particles, and toxins to cross into the bloodstream and drive inflammation. The GI Advanced also includes Calprotectin for gut inflammation and Transglutaminase IgA for gluten-related gut reactivity, giving you a more complete picture of gut barrier and immune function.

5. What's the best stool test for bloating and IBS?

   1. There isn't one single "best" stool test for everyone, but more comprehensive stool tests often provide better answers for chronic digestive symptoms like bloating, IBS, constipation, diarrhea, food sensitivities, and unexplained gut inflammation. The GI Advanced includes broader microbiome analysis, short-chain fatty acids, autoimmune-related bacteria, and antimicrobial sensitivities, making it especially useful for more chronic or complex gut issues.

6. Can stool testing help identify autoimmune-related gut problems?

   1. It can help identify patterns commonly associated with autoimmune disease and immune dysregulation. The GI Advanced includes several bacteria that have been associated in research with autoimmune conditions, including certain species of Klebsiella, Proteus, Prevotella, Citrobacter, and Fusobacterium. It also evaluates intestinal inflammation, gut barrier function, and microbiome balance, all of which may play a role in immune system regulation.

7. Can stool testing detect Candida or yeast overgrowth?

   1. Yes! Both the GI-MAP and GI Advanced evaluate for Candida and other fungal or yeast organisms in the digestive tract. The GI Advanced includes a broader range of Candida species than the GI-MAP base panel, which may be helpful in patients with chronic yeast-related symptoms, recurrent infections, bloating, sugar cravings, or digestive dysfunction.

8. Can stool testing detect parasites?

   1. Yes! Both the GI-MAP and GI Advanced test for many common parasites, protozoa, and intestinal worms, including Giardia, Blastocystis hominis, Cryptosporidium, Entamoeba histolytica, and several helminths. The GI Advanced includes additional parasite markers beyond the GI-MAP base panel. Both tests are phenomenally more comprehensive than standard stool tests.

      
      

      Most standard stool tests ordered through a primary care office or gastroenterologist are primarily designed to look for acute infections causing severe diarrhea, food poisoning, bloody stools, fever, nausea, or vomiting. These tests commonly evaluate pathogens such as Salmonella, Shigella, Campylobacter, C. difficile, Giardia, and Cryptosporidium.

9. Are stool microbiome tests accurate?

   1. Modern stool microbiome testing uses advanced molecular methods such as PCR and RT-PCR, which are highly sensitive for detecting microbial DNA. The GI Advanced also incorporates microbial culture, which can provide additional confirmation and antimicrobial sensitivity testing. No test is perfect, but comprehensive stool analysis can provide valuable clinical information when interpreted in the context of symptoms and medical history.

10. Does insurance cover GI-MAP or GI Advanced testing?

    1. Most functional stool tests are considered specialty laboratory testing and are typically self-pay rather than insurance-covered. However, many patients choose these tests because they provide significantly more information than standard stool testing ordered through conventional medical offices. HSA and FSA funds may sometimes be used depending on your plan.

11. How is the GI Advanced stool test collected?

    1. The GI Advanced is an at-home stool test collected over a single day. A collection kit is mailed directly to your home with instructions and return packaging. Once completed, the sample is shipped back to the lab for analysis and results are typically available within approximately 2 weeks. Please note, it is best to discontinue any probiotics about 3 weeks before collection, and some digestive medications or supplements need to be discontinued a few days before collecting the test.

12. Is stool testing better than a colonoscopy?

    1. They evaluate very different things. A colonoscopy is used to directly visualize the colon and look for structural disease such as polyps, bleeding, inflammatory bowel disease, or colon cancer. Comprehensive stool testing evaluates microbiome balance, pathogens, digestion, inflammation, intestinal permeability, and immune activity. In some cases, both tests may be appropriate depending on symptoms and medical history. A functional stool test will never take the place of a colonoscopy when evaluating for polyps, bleeding, inflammatory bowel disease, or colon cancer.

References

1. Diagnostic Solutions Laboratory. GI-MAP Product Information and Test Methodology. Accessed May 2026.

2. US BioTek Laboratories. GI Advanced Stool Profile Product Information and Marker Overview. Accessed May 2026.

3. Mullish BH, McDonald JAK, Pechlivanis A, et al. Microbial bile salt hydrolases mediate the efficacy of fecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut. 2019;68(10):1791–1800.

4. 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. Clin Gastroenterol Hepatol. 2018;16(8):1220–1228.e4.

5. Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev. 2011;91(1):151–175.

6. Manzotti G, Breda D, Di Gioacchino M, Burastero SE. Serum zonulin as a marker of intestinal permeability in autoimmune diseases and allergies. Scand J Gastroenterol. 2021;56(5):517–528.

7. Tibble J, Sigthorsson G, Foster R, Forgacs I, Bjarnason I. Use of surrogate markers of inflammation and Rome criteria to distinguish organic from nonorganic intestinal disease. Gastroenterology. 2002;123(2):450–460.

8. Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16(6):341–352.

9. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.

10. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823–1836.

11. Arasaradnam RP, Brown S, Forbes A, et al. Guidelines for the investigation of chronic diarrhoea in adults. Gut. 2018;67(8):1380–1399.

12. Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial ecology along the gastrointestinal tract. Microbes Environ. 2017;32(4):300–313.

13. Kelly JR, Minuto C, Cryan JF, Clarke G, Dinan TG. Cross talk: the microbiota and neurodevelopmental disorders. Front Neurosci. 2017;11:490.

14. Kho ZY, Lal SK. The human gut microbiome – a potential controller of wellness and disease. Front Microbiol. 2018;9:1835.

15. National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). Symptoms & Causes of Irritable Bowel Syndrome. Accessed May 2026.

16. American Gastroenterological Association. Clinical Practice Guidelines on the Role of Biomarkers for the Management of Inflammatory Bowel Disease. Accessed May 2026.

Disclaimer: The entire contents of this website are based upon the opinions of physicians at Pacific Clinic of Natural Medicine, unless otherwise noted. Individual articles are based upon the opinions of the respective author, who retains copyright as marked. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of our physicians and their community. PCNM encourages you to make your own health care decisions based upon your research and in partnership with a qualified health care professional. If you are pregnant, nursing, taking medication, or have a medical condition, consult your health care professional before using products based on this content.

If you want to use an article on your site please direct to and cite the original article page. This content may be copied in full, with copyright, contact, creation, and information intact, without specific permission, when used only in a not-for-profit format. If any other use is desired, permission in writing from PCNM and the original author is required.