Comprehensive Nutrient & Micronutrient Testing

The Cofactor Problem

Every enzyme in the human body requires cofactors — vitamins, minerals, amino acids, fatty acids — to function. Without adequate cofactors, enzymes slow down, stall, or produce aberrant products. Mitochondria cannot generate ATP without magnesium, CoQ10, B vitamins, and iron. The liver cannot detoxify without zinc, selenium, glycine, and glutathione. Neurotransmitters cannot be synthesized without B6, iron, folate, and amino acid precursors. Hormones cannot be metabolized without methylation cofactors, sulfation substrates, and Phase I/II enzyme support.

The IFM recognizes nutrient status as foundational — not supplementary, not optional, foundational. You cannot correct hormonal imbalance, immune dysregulation, or mitochondrial dysfunction if the raw materials for those corrections are missing. And yet, standard medical practice rarely assesses nutrient status beyond the most basic markers.

Why Standard Blood Levels Mislead

Serum nutrient levels reflect what is circulating in the blood at the moment of the draw. For many nutrients, this tells you about recent dietary intake, not tissue stores or functional adequacy. Serum magnesium is the classic example: only 1% of total body magnesium is in the blood. A patient can be profoundly magnesium-depleted in muscles, bones, and cells while maintaining a normal serum level — the body pulls from tissue stores to maintain serum homeostasis until the deficit becomes severe.

Functional and intracellular testing addresses this gap. Functional markers measure the downstream metabolic consequence of deficiency — if the metabolic pathway that requires nutrient X is producing excess byproduct Y, then nutrient X is functionally insufficient regardless of its blood level. Intracellular testing measures nutrient concentrations inside cells — where the nutrients actually work.

Comprehensive Testing Panels

NutrEval by Genova Diagnostics

The NutrEval is the Swiss army knife of nutrient testing. A single blood draw plus first morning urine yields: organic acid markers (functional B vitamins, CoQ10, methylation, oxidative stress), plasma amino acids (20+ amino acids with ratios), essential and metabolic fatty acids (omega-3 index, AA:EPA ratio, saturated/monounsaturated/polyunsaturated balance), oxidative stress markers (lipid peroxides, 8-OHdG, glutathione), toxic elements (mercury, lead, arsenic, cadmium), and nutrient element levels (zinc, copper, selenium, manganese, chromium, vanadium).

The NutrEval essentially combines what would otherwise require an OAT, amino acid panel, fatty acid panel, heavy metal panel, and micronutrient panel into one test. For clinicians who can only order one comprehensive test, this is a strong choice.

SpectraCell Micronutrient Test

SpectraCell takes functional intracellular testing to its logical endpoint. The lab isolates the patient’s lymphocytes and cultures them in media deficient in one nutrient at a time. If the lymphocytes cannot grow without supplemental nutrient X, the patient is functionally deficient in X. This tests 33 nutrients: vitamins (A, B1, B2, B3, B5, B6, B12, biotin, folate, C, D, E, K2), minerals (calcium, magnesium, zinc, copper, manganese), amino acids (asparagine, glutamine, serine), fatty acids (oleic acid), metabolites (CoQ10, cysteine, glutathione, carnitine, choline, inositol, alpha-lipoic acid), and antioxidant capacity (SPECTROX score).

The advantage: directly tests cellular function. The limitation: lymphocytes have a 4-6 month lifespan, so SpectraCell reflects nutrient status over the preceding months — it will not show acute changes from recent supplementation.

Vibrant Micronutrient Panel

Vibrant America measures both intracellular (within cells) and extracellular (serum) nutrient levels simultaneously. This dual measurement reveals patterns: low intracellular with normal extracellular means the nutrient is in the blood but not getting into cells (transport or absorption issue). Normal intracellular with low extracellular suggests recent dietary insufficiency but adequate tissue stores. Low in both compartments is straightforward depletion.

Key Nutrients: Optimal Ranges and Clinical Significance

Vitamin D (25-Hydroxy Vitamin D)

The conventional reference range of 30-100 ng/mL is misleadingly broad. Functional optimal is 50-80 ng/mL. Below 50 is insufficient for immune modulation, mood regulation, and hormone production. Vitamin D is not merely a vitamin — it is a secosteroid hormone with nuclear receptors in virtually every tissue.

At 50+ ng/mL, vitamin D modulates over 200 genes involved in immune function, cell differentiation, and inflammation. Studies consistently show that optimal vitamin D levels reduce risk of autoimmune disease, infections (including respiratory viruses), depression, and colorectal cancer.

Repletion protocol: 5,000-10,000 IU daily for 8-12 weeks, then retest. Maintenance typically 2,000-5,000 IU depending on absorption, body composition (adipose tissue sequesters vitamin D), and sun exposure. Always co-supplement with vitamin K2 as MK-7 (200mcg daily) — K2 activates matrix Gla protein and osteocalcin, directing calcium into bones and teeth and away from arterial walls. Without K2, high-dose vitamin D supplementation can promote arterial calcification. Check calcium and PTH alongside vitamin D to rule out primary hyperparathyroidism.

Magnesium

Serum magnesium is clinically useless for assessing tissue status. RBC magnesium is the accessible functional marker — optimal range 5.5-6.5 mg/dL. Ionized magnesium is more accurate but less widely available. The OAT markers for mitochondrial function indirectly reflect magnesium status, since magnesium is required for every ATP-generating reaction.

Estimates suggest 60-80% of the Western population is magnesium deficient. Modern agriculture depletes soil magnesium. Processing removes it from food. Stress, alcohol, caffeine, proton pump inhibitors, and diuretics accelerate excretion.

Clinical selection of magnesium forms matters: magnesium glycinate for calming, anxiety, and sleep (glycine is an inhibitory neurotransmitter); magnesium threonate for cognitive function and neuroprotection (the only form proven to cross the blood-brain barrier, from MIT research); magnesium malate for energy production and fibromyalgia (malate feeds the Krebs cycle); magnesium taurate for cardiovascular health (taurine stabilizes cardiac cell membranes); magnesium citrate for bowel motility and constipation (osmotic effect). Dosing: 200-600mg elemental magnesium daily in divided doses. Bowel tolerance (loose stools) is the practical upper limit.

Zinc

Serum zinc optimal is 90-120 mcg/dL. RBC zinc provides a longer-term picture. A clinical proxy: alkaline phosphatase (ALP) below 50 U/L strongly suggests zinc deficiency, since ALP is a zinc-dependent enzyme. Low ALP with low zinc is essentially diagnostic.

Zinc is critical for: immune function (T-cell maturation, natural killer cell activity), testosterone synthesis (zinc is required for the enzyme that converts androstenedione to testosterone), wound healing, taste and smell perception, and stomach acid production (zinc is needed for carbonic anhydrase in parietal cells — zinc deficiency contributes to hypochlorhydria, which compounds nutrient malabsorption).

The zinc-to-copper ratio should be 8-12:1. Excess copper relative to zinc promotes oxidative stress, anxiety, and estrogen dominance (copper increases ceruloplasmin, which carries estrogen). High copper is common with oral contraceptive use, copper IUDs, vegetarian diets (copper-rich, zinc-poor), and copper water pipes.

Supplementation: zinc picolinate or zinc bisglycinate, 30-50mg daily with food. Always supplement with 1-2mg copper for every 15mg zinc to prevent copper depletion. Zinc carnosine (75mg twice daily) is specifically formulated for GI mucosal repair — used in Japan as a prescription medication for gastric ulcers.

Vitamin B12

Serum B12 optimal is above 600 pg/mL. The conventional cutoff of 200 pg/mL is the level below which overt megaloblastic anemia develops — a catastrophically low bar. Neurological symptoms of B12 deficiency (peripheral neuropathy, cognitive decline, depression) begin long before anemia manifests.

Methylmalonic acid (MMA) is the most sensitive functional marker. Elevated MMA (above 0.4 mcmol/L) indicates functional B12 deficiency regardless of serum B12 level. Homocysteine elevation also suggests B12 deficiency (or folate, or B6 — homocysteine sits at the intersection of all three).

B12 forms for clinical use: methylcobalamin supports methylation (the methionine synthase reaction), most useful for patients with MTHFR variants or methylation demands. Hydroxocobalamin is the naturally occurring form with the longest half-life — excellent for detoxification support (scavenges cyanide and nitric oxide) and sustained delivery. Adenosylcobalamin is the mitochondrial form — directly participates in the methylmalonyl-CoA mutase reaction (the one that MMA tests).

Sublingual or intramuscular routes bypass GI absorption issues. Many B12-deficient patients have low stomach acid, intrinsic factor insufficiency, or SIBO — all of which impair oral B12 absorption.

Folate

RBC folate (optimal above 800 ng/mL) is superior to serum folate because it reflects tissue stores accumulated over the red blood cell’s 120-day lifespan. Serum folate fluctuates with recent intake. FIGLU (formiminoglutamic acid) on the OAT is the functional marker — elevated FIGLU means folate is insufficient for the histidine degradation pathway.

Always assess folate alongside B12. They are metabolically codependent — folate donates a methyl group to homocysteine (via methionine synthase, which requires B12), regenerating methionine. Supplementing folate alone can mask B12 deficiency by normalizing the blood picture (MCV returns to normal) while neurological damage continues unchecked. This is why the FDA mandated folic acid fortification alongside B12 assessment.

Methylfolate (5-MTHF, 400-1000mcg) is the biologically active form that bypasses MTHFR enzyme variants. Folinic acid (5-formylTHF) is an alternative that enters the folate cycle at a different point — useful for patients who do not tolerate methylfolate (overmethylation symptoms: anxiety, insomnia, irritability).

Omega-3 Index

The Omega-3 Index measures EPA plus DHA as a percentage of red blood cell membrane fatty acids. Optimal is above 8%. Below 4% is the high-risk zone — associated with increased cardiovascular mortality, systemic inflammation, depression, and cognitive decline.

The AA:EPA ratio (arachidonic acid to EPA) measures the balance between pro-inflammatory and anti-inflammatory fatty acids. Optimal is below 3:1. The standard American diet produces ratios of 10:1 to 25:1 — massively tilted toward inflammation.

Supplementation: EPA-heavy formulas (2-3g EPA daily) for inflammatory conditions, depression, and cardiovascular risk. DHA-heavy formulas for brain development, cognition, and pregnancy. Combined EPA/DHA (2-4g total) for general anti-inflammatory support. Triglyceride form fish oil absorbs 70% better than ethyl ester form. Test and retest — target an Omega-3 Index above 8% and an AA:EPA ratio below 3:1.

Iodine

Spot urine iodine above 100 mcg/L is considered adequate. Between 50 and 100 is mild deficiency. Below 50 is moderate deficiency. The 24-hour iodine loading test (take 50mg iodine, collect urine for 24 hours, measure excretion) is more comprehensive — if you excrete less than 90% of the load, tissues are retaining iodine, indicating deficiency.

Iodine is essential for thyroid hormone synthesis (T4 contains four iodine atoms, T3 contains three) and has roles in breast tissue health, immune function, and as an antimicrobial agent. Deficiency is more common than assumed, particularly in populations that avoid iodized salt, dairy, and seafood.

Caution with Hashimoto’s thyroiditis: excess iodine can flare autoimmune thyroid inflammation by increasing thyroid peroxidase activity and hydrogen peroxide production. In Hashimoto’s patients, ensure adequate selenium status (selenium is required for glutathione peroxidase, which neutralizes the hydrogen peroxide generated by iodine utilization) before introducing iodine, and start with low doses (150-325mcg) rather than milligram-level doses.

Selenium

Serum selenium optimal is 125-150 ng/mL. Selenium is the essential cofactor for deiodinase enzymes (which convert T4 to active T3), glutathione peroxidase (the primary peroxide-neutralizing antioxidant enzyme), and thioredoxin reductase (redox regulation and DNA synthesis).

Brazil nuts are the most concentrated food source — one to two nuts daily provide approximately 200mcg. Do not exceed 400mcg daily — selenium toxicity (selenosis) causes garlic breath, hair loss, nail brittleness, and neurological symptoms. Selenomethionine is the preferred supplemental form.

Vitamin A (Retinol)

Serum retinol optimal is 50-80 mcg/dL. Vitamin A is critical for mucosal immunity (maintains the epithelial barrier in gut, respiratory tract, and urogenital tract), gut barrier integrity, vision (rhodopsin synthesis), and thyroid function (vitamin A is required for thyroid hormone receptor expression).

Beta-carotene conversion to retinol depends on the BCO1 enzyme. Genetic variants (SNPs) in BCO1 reduce conversion efficiency by 30-70% — up to half the population may be poor converters. These individuals need preformed retinol from animal sources (liver, egg yolks, cod liver oil, dairy) rather than relying on plant-source carotenoids. This is a significant concern for vegans and vegetarians with BCO1 variants.

CoQ10 (Ubiquinone/Ubiquinol)

Serum CoQ10 optimal is above 1.0 mcg/mL. CoQ10 is the electron carrier in mitochondrial Complex III — without it, the electron transport chain stalls and ATP production drops. Statins block HMG-CoA reductase, which sits upstream of CoQ10 synthesis in the mevalonate pathway — every statin user is being depleted of CoQ10, which explains statin-induced myopathy and fatigue.

Ubiquinol (the reduced, active form) is better absorbed than ubiquinone (oxidized form), particularly in patients over 40 whose conversion capacity declines. Dosing: 100-200mg daily for maintenance, 200-400mg for therapeutic repletion, 600-1200mg in mitochondrial disease or advanced heart failure.

Amino Acids

A quantitative amino acid panel (plasma or urine) reveals multiple clinical layers simultaneously. Globally low amino acids across the board suggest protein maldigestion — low stomach acid, low pancreatic enzymes, or insufficient dietary protein. Check elastase on GI-MAP and consider HCl and enzyme support.

Specific patterns: low tryptophan with low 5-HIAA suggests serotonin precursor deficiency — the raw material for serotonin is not available. Low tyrosine with low HVA suggests dopamine precursor deficiency. Low glycine, taurine, and cysteine indicate compromised Phase II hepatic conjugation capacity — the liver cannot detoxify efficiently. Low glutamine points to gut barrier vulnerability (glutamine is the primary fuel for enterocytes). Elevated homocysteine with low methionine confirms impaired methylation.

Branched-chain amino acids (leucine, isoleucine, valine) are critical for muscle protein synthesis and mTOR signaling. Low BCAAs in a fatigued patient suggest either insufficient intake, malabsorption, or excessive utilization during catabolic states.

Building the Nutrient Protocol

The IFM approach does not treat lab values — it treats patients. A comprehensive nutrient panel reveals the pattern of deficiency, which points to the root cause. Global depletion suggests malabsorption (fix the gut first). Specific B vitamin depletion suggests methylation demand or genetic variants. Antioxidant depletion suggests toxic burden (find and remove the exposure). Mineral depletion suggests soil depletion in food supply and may require long-term supplementation alongside dietary optimization.

Repletion follows a hierarchy: remove obstacles to absorption (heal the gut, optimize stomach acid, address SIBO), then replete depleted nutrients at therapeutic doses for 8-12 weeks, then retest, then transition to maintenance doses. The goal is not lifelong high-dose supplementation — it is restoring sufficiency, maintaining it with diet and targeted support, and periodically verifying with functional testing.

The body is not a collection of isolated nutrient levels. It is an interconnected metabolic network where zinc status affects B6 function, which affects neurotransmitter synthesis, which affects cortisol regulation, which affects magnesium retention. Pull one thread and the whole tapestry shifts. Comprehensive nutrient testing reveals the entire pattern at once — and that pattern, read skillfully, tells you exactly where to intervene.