Labs & Testing for Crohn's & Colitis

Standard medical testing often reports "normal" values even when someone is clearly unwell. This is because conventional labs focus on diagnosing severe inflammation, not identifying the biological patterns that cause that inflammation in the first place.

My approach uses advanced microbiome, toxin, immune, bile acid, mitochondrial, and intestinal barrier testing to reveal the root causes driving Crohn's and Colitis. These tests show why inflammation is happening and which pathways must be corrected for long-term healing.

Why These Tests Matter

Crohn's and Ulcerative Colitis are inflammatory expressions of deeper biological imbalances—immune pathway dominance, dysbiosis, mycotoxin exposure, bile dysfunction, mitochondrial stress, and mucosal immune collapse.

The tests below allow us to map these systems and identify the exact mechanisms triggering flares.

Core Tests I Use in My Practice

This page includes some of the tests that help to directly reveal root-cause IBD drivers. Each test examines a different biological system that contributes to inflammation, digestion, nutrient absorption, and immune regulation.

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GI-MAP (Comprehensive Stool DNA Analysis)

Primary focus: Microbiome structure, pathogens, keystone species, inflammatory markers, mucosal immunity, and digestive function.

What this test measures:

Beneficial vs. opportunistic bacteria

  • Fungal organisms (Candida, yeast)

  • Parasites

  • H. pylori

  • Calprotectin (inflammation)

  • sIgA (mucosal immune strength)

  • Occult blood

  • Pancreatic elastase (digestive enzyme output)

  • Beta-glucuronidase

  • Liver-related markers (bile metabolism patterns)

  • Short-chain fatty acid trends

Why it matters for IBD: Reveals dysbiosis patterns, immune collapse, fungal overgrowth, digestive impairment, and inflammatory activity that mirror Crohn's/Colitis behavior.

Organic Acids Test (OAT)

Primary focus: Mitochondria, mold/fungal metabolites, bacterial overgrowth, oxalates, detox pathways.

What this test measures:

  • Mold toxins (ochratoxin, gliotoxin, others indirectly)

  • Fungal metabolites

  • Mitochondrial energy markers

  • Oxidative stress

  • Neurotransmitter precursors

  • Bacterial overgrowth

  • Oxalate patterns

Why it matters for IBD:

Shows mitochondrial suppression, mold-related metabolic stress, fungal overgrowth, and oxalates - all significant triggers for modern IBD flares.

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Mycotoxin Testing (Urine Mycotoxin Panel)

Primary focus: Mycotoxin burden and immune suppression states.

What this test measures (36+ mold toxins including):

  • Ochratoxin A

  • Aflatoxins

  • Gliotoxin

  • Zearalenone

  • Trichothecenes

  • Citrinin

  • T2 toxins (if present)

Why it matters for IBD: Mycotoxins activate TLR4, suppress T-reg function, disrupt bile acids, raise histamine, damage mitochondria, and contribute to intestinal permeability—patterns frequently seen in Crohn's and Colitis.

Environmental Toxicity Panels

Primary focus: Non-mold toxins that worsen inflammation.

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What these tests measure:

  • Herbicides and pesticides (glyphosate, organophosphates)

  • VOCs

  • Plastics (phthalates, BPA)

  • Heavy metals

  • Chemical byproducts

Why it matters for IBD: Environmental toxins add immune load, damage mitochondria, alter microbial patterns, and impair detox pathways—fueling persistent inflammation.

HTMA (Hair Tissue Mineral Analysis)

Primary focus: Minerals, electrolytes, adrenal patterns, and hidden toxic metals.

What these tests measure:

Essential Minerals

Magnesium, zinc, sodium, potassium, calcium

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Mineral Balance

Copper balance and mitochondrial mineral status

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Stress Patterns

Stress/adrenal patterns

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Toxic Metals

Aluminum, mercury, arsenic, lead

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Why it matters for IBD: Mineral imbalances drive fatigue, impaired recovery, mitochondrial dysfunction, weakened mucosal immunity, and prolonged flare cycles.

Advanced Blood Panels

Primary focus: Functional interpretation of immune activation, nutrient status, and inflammatory pathways.

Key markers:

What these tests measure:

  • CBC with differential (including eosinophils, basophils, lymphocyte patterns)

  • CRP and ESR (inflammatory trends, not isolated values)

  • Ferritin, transferrin, and iron panels

  • Vitamin D, B12, folate, RBC magnesium

  • Comprehensive metabolic panel

  • Liver and pancreatic enzymes (AST, ALT, GGT, ALP, amylase, lipase)

  • Lipid markers tied to bile metabolism

  • Homocysteine and methylation markers

  • Thyroid panel (TSH, free T3, free T4, reverse T3)

Why it matters for IBD: Bloodwork tells the story of immune activation, malabsorption, chronic stress load, nutrient depletion, mitochondrial strain, and bile dysfunction.

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sIgA & Calprotectin

Primary focus: Mucosal immunity and inflammatory load.


What these tests measure:

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Why it matters for IBD: These markers show how active inflammation is and whether the gut is in resilience or collapse.

SIBO Breath Testing

Primary focus: Small-intestinal bacterial overgrowth patterns.

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What it measures:

  • Hydrogen

  • Methane

  • Hydrogen sulfide

Why it matters for IBD: SIBO worsens bloating, diarrhea, nutrient loss, and flare patterns—especially in small-bowel Crohn's.

Immune & Antibody Panels

Primary focus: Immune reactions connected to gut auto-inflammation.

What we look at:

Antibody Testing

  • Gut-associated antibodies

  • Food immune activation panels

  • Intestinal barrier antibodies

Immune Pathways

  • Immune pathway dominance patterns (T-helper profiles)

  • Histamine and mast cell markers

Barrier Function

  • Antibody patterns related to gut lining injury (e.g., zonulin, occludin, actomyosin if available in the panel you use)

Why it matters for IBD: These markers help determine whether your inflammation is driven by mast cells, food antigens, permeability, mold, microbial overgrowth, or bile acid dysfunction.

How These Tests Work Together

Each test evaluates a different biological system: immune, microbial, toxin, bile, cellular and mitochondrial, digestive, or mucosal. Together, they reveal the complete inflammatory architecture behind Crohn's and Colitis.

This is how we create targeted, step-by-step plans based on data, not guesswork.

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The power of comprehensive testing is in the connections. When we see how these systems interact, we can address the root causes systematically.

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What Testing Looks Like in My Program

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Ready to Uncover What's Driving Your Flares?

If you want to identify the biological patterns driving your bowel disease, we can use targeted testing to uncover exactly what your body needs to heal.

Book a call