The GI-MAP Test

A Deep Dive Into Your Gut Microbiome & Its Impact on Body Health

Your gut is more than just a digestive system—it’s a central hub for your immune health, brain function, hormone regulation, metabolism, and more. The GI-MAP (GI Microbial Assay Plus) is one of the most advanced stool tests available to assess the balance of microorganisms in your gastrointestinal tract and identify root causes of chronic symptoms, inflammation, and disease.

Used by functional and integrative practitioners around the world, the GI-MAP utilizes quantitative PCR (qPCR) technology to accurately detect and measure the DNA of microbes in your stool—including bacteria, viruses, fungi, parasites, and inflammatory markers. Unlike traditional stool tests, it’s not culture-based, meaning it identifies hard-to-detect or slow-growing pathogens and reflects actual microbial DNA, not just presence under a microscope.

What Does the GI-MAP Test Analyze?

The GI-MAP is divided into several key categories:

1. Pathogenic Bacteria

These are disease-causing bacteria. Elevated levels are often associated with infections, diarrhea, and gut inflammation.

Examples:

  • Clostridium difficile (Toxin A & B)
  • Salmonella, Shigella, Campylobacter
  • Enteropathogenic E. coli (EPEC, EHEC, EAEC, etc.)

Impact:
High levels can cause food poisoning, inflammation, autoimmune flares, and post-infectious IBS. They often increase intestinal permeability (“leaky gut”) and immune activation.

2. Parasitic Pathogens and Protozoa

GI-MAP screens for parasites that can persist in the gut and contribute to bloating, fatigue, IBS, and nutrient loss.

Examples:

  • Giardia lamblia
  • Entamoeba histolytica
  • Blastocystis hominis
  • Cryptosporidium

Impact:
These may impair nutrient absorption, lead to iron or B12 deficiency, alter neurotransmitter production, and trigger chronic immune activation.

3. Fungi and Yeast (e.g., Candida)

Measures DNA of Candida albicans and other yeast strains.

Impact:
Overgrowth can contribute to brain fog, sugar cravings, recurrent yeast infections, fatigue, eczema, and GI discomfort. Yeast produces acetaldehyde and other toxins that burden liver detoxification and worsen mood and cognitive symptoms.

4. Viruses

Tests for reactivation of viruses often latent in the gut.

Examples:

  • Cytomegalovirus (CMV)
  • Epstein-Barr virus (EBV)
  • Norovirus
  • Rotavirus

Impact:
May worsen chronic fatigue, autoimmunity, and neurological symptoms. Reactivation is common in immune-compromised or highly stressed individuals.

5. Normal and Beneficial Bacteria

Assesses levels of healthy commensal bacteria.

Examples:

  • Bacteroides, Bifidobacterium, Lactobacillus, Akkermansia muciniphila, Faecalibacterium prausnitzii

Impact:
These bacteria produce short-chain fatty acids (like butyrate), regulate inflammation, support immunity, protect the gut lining, and influence brain chemicals like serotonin and GABA. Low levels may impair digestion, immune tolerance, and mood.

6. Opportunistic Bacteria

Normally present in small amounts but can cause issues when overgrown.

Examples:

  • Morganella, Klebsiella, Citrobacter, Pseudomonas, Proteus

Impact:
Associated with histamine intolerance, autoimmunity, brain fog, SIBO-like symptoms, and inflammation. Overgrowth often arises from antibiotics, stress, poor diet, or low stomach acid.

7. H. pylori (with Virulence Factors)

Detects presence of Helicobacter pylori and tests for virulence genes (e.g., CagA, VacA).

Impact:
H. pylori reduces stomach acid, impairs protein digestion, disrupts B12 and iron absorption, and can contribute to GERD, ulcers, or stomach cancer. The presence of virulence genes increases the risk of damage.

8. Intestinal Health and Immune Markers

These markers reflect gut inflammation, immune function, and barrier integrity.

Key markers:

  • Secretory IgA (sIgA): First-line immune defense in the gut. Low = weak mucosal immunity. High = immune activation or food sensitivity.
  • Calprotectin: Marker of inflammation; elevated in IBD, infections, or NSAID use.
  • Anti-gliadin IgA: Marker of gluten sensitivity.
  • Beta-glucuronidase: Enzyme affecting estrogen detox; elevated in estrogen dominance.
  • Elastase-1: Marker of pancreatic enzyme output. Low = digestive insufficiency.


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How GI-MAP Findings Affect the Body

The gut interacts with every organ system. Imbalances in GI-MAP results may affect:

Mood & Brain Function:

  • Low butyrate-producing bacteria and high opportunistic microbes impair serotonin, GABA, and dopamine production, contributing to anxiety, depression, and brain fog.

Hormones:

  • Dysbiosis or high beta-glucuronidase can impair estrogen clearance, contributing to estrogen dominance (PMS, fibroids, PCOS).

Immunity & Autoimmunity:

  • Leaky gut, parasites, or high sIgA may trigger systemic immune activation, worsening autoimmunity or causing food sensitivities.

Nutrient Absorption:

  • Low enzyme output or H. pylori affects B12, iron, and protein digestion, leading to fatigue, anemia, or thyroid symptoms.

Skin Health:

  • Gut pathogens and Candida may worsen acne, eczema, or psoriasis through systemic inflammation and histamine burden.

Histamine Intolerance:

  • Some bacteria (Morganella, Proteus, Klebsiella) produce histamine or block DAO enzyme activity, leading to flushing, rashes, headaches, or mast cell activation.

How to Fix Abnormal GI-MAP Findings

Treatment is individualized but often follows the 5R framework: Remove, Replace, Reinoculate, Repair, and Rebalance.

1. Remove

  • Antimicrobials (herbal or pharmaceutical) for parasites, H. pylori, or overgrowth
  • Examples: Berberine, oregano oil, garlic extract, Matula tea, mastic gum
  • Address food sensitivities and eliminate inflammatory triggers

2. Replace

  • Digestive enzymes and stomach acid support (e.g., betaine HCl, pancreatic enzymes)
  • Bile salts if fat digestion is impaired

3. Reinoculate

  • Probiotics (strain-specific): Bifidobacterium, Lactobacillus, and Saccharomyces boulardii
  • Prebiotics: inulin, PHGG, acacia fiber (if tolerated)

4. Repair

  • L-glutamine, zinc carnosine, aloe vera, slippery elm
  • Vitamin A, D, and omega-3s to rebuild mucosal barrier

5. Rebalance

  • Address stress, sleep, circadian rhythm
  • Optimize diet with high-fiber, polyphenol-rich foods (berries, olive oil, greens)
  • Consider neurotransmitter support for mood or energy issues

When to Order a GI-MAP Test

Consider testing if you experience:

  • Chronic bloating, constipation, or diarrhea
  • Fatigue, brain fog, or mood swings
  • Skin conditions (eczema, acne, rosacea)
  • Hormonal imbalance (PMS, PCOS, estrogen dominance)
  • Histamine symptoms (rashes, flushing, insomnia)
  • Autoimmune disease (Hashimoto’s, RA, lupus)
  • Nutrient deficiencies (iron, B12) with no clear cause
  • 

The GI-MAP offers an extraordinary window into your internal ecosystem. More than just a stool test, it reveals how your gut is affecting your brain, hormones, skin, mood, and immune system. Unlike symptom-chasing or restrictive diets, GI-MAP helps you target the root cause—allowing you to address the “why” behind persistent symptoms.

With personalized interpretation and a tailored protocol, this test can become a roadmap to healing and long-term vitality.


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