Lab Reference Library / Organic Acids (Urine) Gut & Immune

Organic Acids (Urine)

Q: What does the organic acids test measure?

The OAT measures 70+ urinary organic acid metabolites organized into categories: Krebs cycle and mitochondrial energy markers (revealing mitochondrial efficiency), gut dysbiosis markers (arabinose for Candida, HPHPA for Clostridia, tartaric acid), neurotransmitter metabolism markers (vanilmandelic acid, homovanillic acid, 5-HIAA reflecting dopamine, norepinephrine, and serotonin catabolism), B vitamin functional markers (methylmalonic acid for B12, xanthurenate for B6), oxidative stress markers (8-hydroxy-2-deoxyguanosine), and detoxification capacity markers (pyroglutamic acid for glutathione).

Q: What is arabinose on the organic acids test?

Arabinose is a 5-carbon sugar produced by Candida species as a fermentation byproduct. Elevated urinary arabinose is the most specific OAT marker for intestinal Candida overgrowth, even in patients who test negative on standard stool cultures. Arabinose above the reference range strongly suggests Candida colonization of the gut and supports initiating antifungal therapy or dietary sugar restriction alongside the full clinical picture.

Q: How is the organic acids test collected?

The OAT requires a first-morning urine collection, taken before eating or drinking, on a day when the patient has avoided fruit (particularly apples, grapes, pears) and antibiotics for 48 hours prior, as these can falsely alter several markers. The sample is collected in the laboratory-provided container, refrigerated immediately, and shipped with ice packs. Great Plains Laboratory (now MosaicDX) and Genova Diagnostics offer the most comprehensive and clinically validated OAT platforms.

OAT · Organic Acids Test · Urine Organic Acids

Urine organic acids test interpretation and why this comprehensive metabolic snapshot reveals gut dysbiosis markers, mitochondrial function, B vitamin cofactor status, neurotransmitter metabolism, and detoxification capacity from a single first-morning urine collection.

Comprehensive MetabolicDysbiosis Marker

CollectionFirst Morning Urine

Reveals50+ Biomarkers

Key MarkersArabinose, D-Arabinitol

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Category: Gut & Immune | Also known as: OAT, Urine Organic Acids, Organic Acid Test, Metabolic Organic Acids Panel

1. What This Test Measures

The organic acids test (OAT) measures over 70 urinary organic acid metabolites in a first-morning urine sample. Organic acids are small molecules produced as byproducts of cellular metabolism, gut microbial fermentation, neurotransmitter catabolism, amino acid breakdown, and detoxification processes. They are excreted in urine at measurable concentrations that reflect the functional activity of the biochemical pathways that produced them. Abnormal patterns indicate where in the metabolic, microbial, or nutritional web a disruption is occurring, often before clinical symptoms are severe enough to trigger investigation through conventional testing.

The OAT is distinctive among functional medicine laboratory tests in its breadth: a single urine collection provides simultaneous information about Krebs cycle and mitochondrial energy efficiency, gut dysbiosis from bacterial and fungal overgrowth, neurotransmitter synthesis and catabolism, B vitamin cofactor sufficiency, oxidative stress burden, glutathione status and detoxification capacity, and fatty acid oxidation efficiency. No other single test provides this scope of metabolic insight from a single sample, which is why the OAT has become a foundational diagnostic tool in functional and integrative medicine for patients with complex, multi-system presentations.

Two major laboratory platforms offer comprehensive OAT panels with overlapping but distinct marker sets: MosaicDX (formerly Great Plains Laboratory) and Genova Diagnostics. Both are clinically validated and widely used in functional medicine practice. Results include individual marker values with reference ranges and flagging of abnormal values; interpretation requires understanding the metabolic pathways connecting related markers rather than evaluating individual values in isolation.

2. Test Collection Requirements

Requirement	Details
Collection time	First void of the morning; concentrated overnight urine provides highest metabolite detection
Dietary restrictions 48h before	Avoid all fruit (apples, grapes, pears especially); avoid apple juice; these contain organic acids that cross-react with OAT markers
Antibiotics	No antibiotics for 4 weeks before testing; antibiotics suppress gut bacteria producing dysbiosis markers and produce false-negative bacterial OAT findings
Probiotics	No probiotic supplementation for 48 to 72 hours before testing; probiotics alter dysbiosis marker production
Sample handling	Refrigerate immediately; ship on ice packs Monday through Wednesday to avoid weekend laboratory delays
Medications	Document all medications and supplements; many alter OAT marker values (acetaminophen, aspirin, SSRIs, riboflavin supplements)

3. Key OAT Marker Categories and Clinical Interpretation

The OAT should be read as a metabolic story, not as a list of individual values. The most clinically informative approach is to identify which categories of markers are abnormal, how they cluster together, and what upstream dysfunction explains the observed pattern. Isolated single-marker elevation is less informative than a pattern of multiple abnormalities pointing toward the same root cause, such as multiple Krebs cycle markers elevated together indicating mitochondrial dysfunction, or multiple dysbiosis markers elevated together indicating multi-organism gut overgrowth.

4. Major Marker Categories

Gut Dysbiosis Markers

Arabinose (D-Arabinitol): the most specific and widely validated OAT marker for intestinal Candida overgrowth; arabinose is produced by Candida species as a fermentation byproduct and appears in urine in proportion to gut Candida burden; positive arabinose with clinical symptoms is strong evidence for Candida overgrowth regardless of negative stool culture; reference range varies by laboratory but values above the 95th percentile indicate clinically significant Candida activity
HPHPA (3-[3-Hydroxyphenyl]-3-hydroxypropionic acid): the most specific OAT marker for Clostridia bacterial species overgrowth; Clostridia produce HPHPA from dietary phenylalanine; elevated HPHPA produces excess dopamine through inhibition of dopamine-beta-hydroxylase (the enzyme converting dopamine to norepinephrine), contributing to elevated dopamine relative to norepinephrine; associated with autism spectrum disorder, OCD, tic disorders, and attention difficulties
Tartaric and citric acid (if abnormal): tartaric acid can reflect Aspergillus or Candida yeast production; citric acid elevation in the absence of dietary citrus can indicate yeast fermentation
Hippuric acid: produced by Clostridia difficile and other Clostridia from toluene and benzoate; mildly elevated with many gut bacterial species; markedly elevated warrants Clostridia-specific evaluation
Phenylpropionic acid: marker of Clostridia and certain streptococcal species; part of the phenolic dysbiosis pattern
Benzoic acid and 4-hydroxyphenylacetic acid: markers of Clostridia and certain other anaerobic bacteria; elevated together with HPHPA confirms Clostridia dysbiosis

Mitochondrial and Energy Markers

Succinate, fumarate, malate, 2-oxoglutarate (alpha-ketoglutarate): Krebs cycle intermediate organic acids; elevation above reference range indicates accumulation upstream of a block in the cycle, typically from cofactor deficiency (CoQ10, NAD+, B vitamins), mitochondrial dysfunction, heavy metal inhibition, or inherited organic acidemias in children
Hydroxymethylglutarate (HMG): elevated with HMG-CoA reductase activity increase or statin use; the only OAT marker that actually reflects statin therapy; useful for documenting statin metabolic effects
Methylmalonic acid (MMA): elevated with B12 functional deficiency (more sensitive than serum B12 alone); B12 is required for the methylmalonyl-CoA mutase reaction producing succinate from MMA; elevated MMA is the first biochemical marker of intracellular B12 insufficiency before peripheral blood counts change
Lactic and pyruvic acids: elevated together indicate impaired pyruvate dehydrogenase (PDH) complex function from B1 (thiamine) deficiency, arsenic toxicity, or mitochondrial disease; the pyruvate-to-lactate ratio provides insight into PDH efficiency
Adipic and suberic acids: markers of impaired fatty acid beta-oxidation; elevated with carnitine deficiency, riboflavin (B2) deficiency, or impaired mitochondrial fatty acid transport

Neurotransmitter Metabolite Markers

Homovanillic acid (HVA): the primary urinary metabolite of dopamine; low HVA indicates reduced dopamine catabolism (low dopamine synthesis or low dopamine turnover); elevated HVA indicates excess dopamine catabolism (may reflect high dopamine synthesis or increased dopaminergic activity); paired with HPHPA for Clostridia-dopamine pattern evaluation
Vanilmandelic acid (VMA): the primary urinary metabolite of norepinephrine and epinephrine; low VMA with normal or elevated HVA suggests impaired dopamine-beta-hydroxylase conversion of dopamine to norepinephrine, which can be a consequence of Clostridia-produced HPHPA inhibiting that enzyme
5-Hydroxyindoleacetic acid (5-HIAA): the primary urinary metabolite of serotonin (5-HT); low 5-HIAA indicates reduced serotonin catabolism, often from low serotonin synthesis (tryptophan deficiency, B6 deficiency, inflammation-driven IDO activation diverting tryptophan to kynurenine); elevated 5-HIAA in the context of carcinoid tumor warrants further investigation
Quinolinic acid: a neurotoxic kynurenine pathway metabolite produced when inflammation activates IDO enzyme and diverts tryptophan away from serotonin; elevated quinolinic acid is an NMDA receptor agonist associated with excitotoxicity, depression, and neuroinflammation
Kynurenate: protective kynurenine pathway metabolite that antagonizes NMDA receptors; the quinolinate-to-kynurenate ratio reflects neurotoxic vs neuroprotective kynurenine pathway balance

Nutritional and Detoxification Markers

Xanthurenate and kynurenate: both produced from tryptophan via kynurenine in a B6-dependent reaction; elevated xanthurenate specifically indicates functional B6 (PLP) deficiency; the most sensitive functional B6 status marker available, more sensitive than direct serum PLP in many cases
Methylmalonic acid (MMA): functional B12 status marker; elevated MMA indicates intracellular B12 insufficiency affecting the methylmalonyl-CoA mutase reaction; can be elevated even when serum B12 is within laboratory reference range if cellular uptake or methylation is impaired
Pyroglutamic acid (5-oxoproline): a marker of glutathione depletion and oxidative stress; elevated pyroglutamate indicates the gamma-glutamyl cycle is upregulated to regenerate cysteine for glutathione synthesis when glutathione is depleted by chronic oxidative burden, chronic acetaminophen use, or sulfur amino acid deficiency
8-Hydroxy-2-deoxyguanosine (8-OHdG): a marker of oxidative DNA damage; elevated values indicate significant nuclear DNA oxidative stress burden; one of the most direct measures of oxidative damage available from a non-invasive urine collection
Glucarate: a marker of liver phase I detoxification activity; elevated glucarate indicates upregulated cytochrome P450 enzyme induction from chemical exposure, medication load, or high xenobiotic burden

5. Common Clinical Patterns and What They Indicate

Pattern	Markers Elevated	Clinical Implication	Primary Intervention
Candida overgrowth	Arabinose, tartaric acid, citric acid	Intestinal Candida fermentation; correlate with stool antigen and Candida antibodies	Antifungal protocol; dietary sugar elimination; probiotic restoration
Clostridia dysbiosis	HPHPA, hippuric acid, 4-hydroxyphenylacetic acid; low HVA/VMA ratio	Clostridia bacterial overgrowth inhibiting dopamine-norepinephrine conversion; associated with neurological and behavioral symptoms	Targeted antibiotics (metronidazole, vancomycin pulsing); prebiotic and probiotic restoration
Mitochondrial dysfunction	Multiple Krebs cycle intermediates elevated; lactic acid elevated; adipic and suberic acids elevated	Impaired cellular energy production; evaluate heavy metals, B vitamin cofactors, CoQ10, carnitine	CoQ10, NAD+ precursors, B vitamins, carnitine, magnesium; heavy metal assessment if indicated
Inflammation-driven IDO activation	Quinolinic acid elevated; low 5-HIAA; kynurenate elevated; tryptophan depleted	Inflammatory cytokines (IFN-gamma) diverting tryptophan away from serotonin toward neurotoxic kynurenine pathway	Reduce upstream inflammation; anti-inflammatory protocol; tryptophan and B6 support
B6 functional deficiency	Xanthurenate elevated	Impaired pyridoxal phosphate availability regardless of serum B6 level; affects neurotransmitter synthesis, DAO activity, and transaminase function	P5P supplementation 25 to 50mg daily; address B6 antagonists (oral contraceptives, alcohol)
Glutathione depletion	Pyroglutamic acid elevated; 8-OHdG elevated	Oxidative stress exceeding glutathione buffering capacity; assess acetaminophen use, sulfur amino acid intake, and total toxic burden	N-acetylcysteine, glycine, glutathione supplementation; reduce oxidative load

6. Related Lab Tests

Candida AntibodiesConfirm OAT Arabinose with Antibody and Stool Antigen

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SIBO Breath TestBacterial Dysbiosis Markers Complement Breath Testing

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Plasma TryptophanOAT Kynurenine Pathway Markers Contextualize Tryptophan Depletion

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Vitamin B12OAT Methylmalonic Acid Is the Most Sensitive Functional B12 Marker

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Vitamin B6OAT Xanthurenate Is the Most Sensitive Functional B6 Marker

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NAD+OAT Mitochondrial Markers Reflect NAD+ Cofactor Sufficiency

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7. Clinical Perspective

Clinical Perspective

The organic acids test is the diagnostic tool I reach for when a patient presents with a constellation of symptoms that span multiple organ systems and no conventional workup has provided a unifying explanation. Brain fog, fatigue, anxiety, recurrent infections, digestive symptoms, and chemical sensitivities all in one patient, with normal standard labs, is exactly the presentation where the OAT tells a complete metabolic story in one test. I have opened OAT reports and seen the entire picture at once: Candida arabinose elevated, multiple Krebs cycle intermediates accumulated indicating mitochondrial dysfunction, xanthurenate flagged for functional B6 deficiency that is simultaneously impairing DAO activity and neurotransmitter synthesis, and pyroglutamic acid indicating glutathione depletion. Every one of those findings interconnects. The B6 deficiency explains the impaired DAO and the impaired serotonin synthesis. The Candida overgrowth explains the arabinose and contributes to the mast cell activation and the brain fog. The mitochondrial dysfunction explains the fatigue and the chemical sensitivity. One test, one morning urine collection, and the clinical picture that had been fragmented across years of specialist visits suddenly has a metabolic architecture that a targeted protocol can address systematically.

Brian Lamkin, DO | Founder, The Lamkin Clinic | Edmond, Oklahoma

8. Frequently Asked Questions

What does the organic acids test measure?

The OAT measures 70+ urinary organic acid metabolites from a first-morning urine collection. Categories include: Krebs cycle and mitochondrial energy markers (mitochondrial efficiency), gut dysbiosis markers (arabinose for Candida, HPHPA for Clostridia), neurotransmitter metabolites (HVA for dopamine, VMA for norepinephrine, 5-HIAA for serotonin, quinolinic acid for neuroinflammation), B vitamin functional markers (methylmalonic acid for B12, xanthurenate for B6), oxidative stress markers (8-hydroxy-2-deoxyguanosine), and detoxification capacity markers (pyroglutamic acid for glutathione status).

What is arabinose on the organic acids test?

Arabinose (D-arabinitol) is the most specific and widely validated OAT marker for intestinal Candida overgrowth. It is produced by Candida species as a fermentation byproduct and appears in urine in proportion to gut Candida burden. Elevated arabinose confirms Candida fermentation activity in the gut regardless of stool culture results, which frequently miss Candida overgrowth. It is the primary OAT marker prompting antifungal therapy in functional medicine practice.

What does HPHPA indicate on the organic acids test?

3-(3-Hydroxyphenyl)-3-hydroxypropionic acid (HPHPA) is produced by Clostridia bacterial species from dietary phenylalanine. Elevated HPHPA indicates Clostridia overgrowth, which inhibits dopamine-beta-hydroxylase, the enzyme converting dopamine to norepinephrine, producing an elevated dopamine-to-norepinephrine ratio. This Clostridia-dopamine pattern is associated with autism spectrum disorder, OCD, tic disorders, and attention difficulties. Treatment typically involves targeted antibiotics (metronidazole or oral vancomycin pulsing) alongside probiotic restoration.

How is the organic acids test collected?

First-morning void, before eating or drinking, after avoiding all fruit and fruit juice for 48 hours (fruit organic acids cross-react with OAT markers). No antibiotics for 4 weeks before testing. No probiotics for 48 to 72 hours before testing. Document all medications and supplements. Refrigerate the sample immediately and ship with ice packs on Monday through Wednesday to ensure laboratory receipt before the weekend.

Can the organic acids test replace other functional medicine tests?

The OAT provides a unique breadth of metabolic information from a single collection but does not replace tests that provide different information types. It does not replace comprehensive stool analysis for detailed microbiome characterization, breath testing for SIBO (OAT shows dysbiosis markers but not bacterial location), blood testing for hormones and inflammatory markers, or Candida antibody testing for immune response characterization. The OAT is most powerful when integrated into a broader diagnostic picture rather than used as a standalone assessment.

Content authored and clinically reviewed by Brian Lamkin, DO, founder of The Lamkin Clinic in Edmond, Oklahoma. Brian Lamkin, DO has 25+ years of experience in functional and regenerative medicine. This page reflects current functional medicine practice standards and is updated as new clinical evidence becomes available.

The OAT provides gut dysbiosis markers, mitochondrial function, B vitamin status, neurotransmitter metabolism, and detoxification capacity from a single first-morning urine collection. No other single test covers this metabolic territory.

The organic acids test is the starting point for patients with complex multi-system presentations that conventional testing has not explained. Schedule a consultation for an OAT-based functional medicine evaluation.

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Medical Disclaimer: This content is provided for educational purposes only and is not intended as a substitute for professional medical advice, diagnosis, or treatment. Lab interpretation should always be performed in clinical context by a qualified healthcare provider. Reference ranges and optimal targets may vary based on individual patient history, clinical presentation, and laboratory methodology. Schedule a consultation to discuss your specific results with Dr. Lamkin.