What Is the GI-MAP?

The GI-MAP (Gastrointestinal Microbial Assay Plus) is a comprehensive stool test offered by Diagnostic Solutions Laboratory. It uses quantitative PCR (qPCR) technology to measure specific DNA targets from bacteria, parasites, viruses, and fungi in your stool. Unlike 16S sequencing or shotgun metagenomics that attempt to catalogue your entire microbiome, the GI-MAP targets a curated panel of clinically relevant organisms and biomarkers.

The GI-MAP has become the most widely ordered functional stool test in integrative and functional medicine, and for good reason — it provides actionable, organism-specific data alongside important digestive function markers. However, understanding what the test measures, what it does not measure, and how to interpret the results is critical for getting value from it.

Section 1: Bacterial Pathogens

The GI-MAP tests for specific bacterial pathogens known to cause gastrointestinal illness:

  • Campylobacter — one of the most common causes of bacterial gastroenteritis worldwide. Even after acute infection resolves, Campylobacter has been linked to the development of post-infectious IBS
  • C. difficile — both the organism and its toxins (Toxin A and Toxin B) are measured. Detection of the organism without toxin production may represent colonisation rather than active infection
  • E. coli (pathogenic strains) — ETEC, EPEC, EHEC, and other virulence factors are specifically tested. Non-pathogenic E. coli is normal gut flora
  • H. pylori — along with virulence factors like CagA and VacA that indicate more aggressive strains associated with higher risk of ulcers and gastric cancer
  • Salmonella and Shigella — important enteric pathogens

Section 2: Parasitology

The GI-MAP detects both pathogenic parasites and commensal organisms:

  • Giardia lamblia — a common parasitic cause of chronic diarrhoea, bloating, and malabsorption that is frequently missed on standard ova and parasite exams
  • Cryptosporidium — a protozoan parasite that can cause persistent watery diarrhoea
  • Entamoeba histolytica — the pathogenic amoeba that causes amoebic dysentery, distinguished from the non-pathogenic E. dispar
  • Blastocystis hominis — a controversial organism whose pathogenicity is debated. Some subtypes may cause symptoms while others are commensal
  • Dientamoeba fragilis — increasingly recognised as a potential cause of chronic digestive symptoms
One of the GI-MAP's greatest strengths is its sensitivity for parasites. Traditional microscopy-based ova and parasite exams miss up to 70% of parasitic infections due to the cyclical shedding patterns of many organisms. The DNA-based qPCR approach can detect parasites even when they are not actively shedding, making the GI-MAP significantly more reliable for parasite detection.

Section 3: Viral Pathogens

The test screens for cytomegalovirus (CMV) and Epstein-Barr virus (EBV) in the gut. These are primarily relevant for immunocompromised patients or those with IBD, where viral reactivation in the gut can drive inflammation and complicate treatment.

Section 4: Opportunistic and Normal Flora

This section quantifies both beneficial and potentially problematic organisms:

  • Beneficial flora — Lactobacillus, Bifidobacterium, Akkermansia muciniphila, Faecalibacterium prausnitzii, and Roseburia species. Low levels may indicate dysbiosis and reduced short-chain fatty acid production
  • Opportunistic bacteria — organisms like Pseudomonas, Staphylococcus, Streptococcus, Klebsiella, and Citrobacter that are normal at low levels but problematic when overgrown
  • Fungi — Candida species and other fungal organisms are quantified

Section 5: Intestinal Health Markers

This is where the GI-MAP goes beyond microbiology to assess digestive function:

  • Calprotectin — a marker of intestinal inflammation. Elevated levels suggest inflammatory bowel disease or other inflammatory conditions
  • Secretory IgA (sIgA) — reflects gut immune function. Low sIgA indicates impaired mucosal immunity; high sIgA suggests active immune response to infection or inflammation
  • Anti-gliadin IgA — a screening marker for gluten-related immune activation
  • Pancreatic elastase — measures exocrine pancreatic function. Low levels indicate pancreatic insufficiency, meaning you may not be producing enough digestive enzymes to properly break down food
  • Steatocrit — measures faecal fat content, indicating fat malabsorption
  • Beta-glucuronidase — a bacterial enzyme involved in estrogen and toxin recirculation. Elevated levels may contribute to estrogen dominance and impaired detoxification
  • Zonulin — a marker of intestinal permeability (leaky gut), though its reliability is debated in the research community

Making Sense of Your Results

A GI-MAP report can be overwhelming, with dozens of markers across multiple categories. The key principles for interpretation are: context matters more than any single marker, patterns across multiple markers are more informative than isolated findings, and results must be correlated with your actual symptoms. A finding of elevated opportunistic bacteria is only clinically significant if it corresponds to symptoms you are experiencing.

Working with an experienced practitioner is strongly recommended for GI-MAP interpretation. Additionally, having detailed symptom data to correlate with test findings dramatically improves clinical decision-making. GutIQ can provide this symptom context, giving your practitioner a clear picture of your daily digestive patterns alongside your lab results for more targeted and effective treatment planning.