The Functional Medicine Supplement Formulary

The Quality Problem Nobody Talks About

Walk into any pharmacy or health food store and you’ll find a wall of supplements. Same label claims, wildly different prices. A consumer might reasonably ask: what’s the difference between the $8 fish oil at the grocery store and the $45 one from a practitioner?

The difference is everything.

The supplement industry in the United States operates under DSHEA (Dietary Supplement Health and Education Act of 1994), which places the burden of proof for safety on the FDA — after a product is already on the market. This means supplements can be sold without proving they contain what the label says, in the amounts listed, free of contaminants. Independent testing has repeatedly found supplements containing less active ingredient than labeled, wrong species of herbs, heavy metal contamination, and undeclared pharmaceutical drugs (particularly in weight loss and sexual enhancement products).

This is not an argument against supplements. It is an argument for ruthless quality standards. The right supplement, from the right manufacturer, at the right dose, for the right indication, can be transformative. The wrong one is expensive urine at best and a liver toxin at worst.

Quality Benchmarks: What to Demand

Manufacturing Standards

• GMP Certification (Good Manufacturing Practices): The FDA minimum, but not all companies follow it rigorously. Look for NSF GMP registration or TGA (Australian Therapeutic Goods Administration) compliance, which is stricter.
• Third-Party Testing: Independent verification of identity, potency, purity, and contamination. The gold standards are USP (United States Pharmacopeia), NSF International, and ConsumerLab. IFOS (International Fish Oil Standards) specifically for omega-3 products.
• Professional-Grade Lines: Companies like Thorne, Pure Encapsulations, Designs for Health, Metagenics, Integrative Therapeutics, Ortho Molecular, and Xymogen sell primarily through practitioners. Their quality control budgets are substantially higher than mass-market brands.

Red Flags on a Label

• “Proprietary blend” — hides individual ingredient doses, making it impossible to evaluate therapeutic amounts
• Artificial colors (FD&C dyes), titanium dioxide, or unnecessary fillers
• Magnesium stearate in excessive amounts (though small amounts are generally benign)
• No lot number or expiration date
• Claims that sound too good to be true (“cures cancer,” “reverses diabetes”)
• Mega-doses without clinical justification (50,000 IU vitamin A daily, for instance)

Core Categories and Specific Recommendations

Multivitamin/Mineral Foundation

The multivitamin is the insurance policy — covering micronutrient gaps that even a good diet leaves open. Modern soil depletion, food processing, and increased metabolic demands from stress and toxin exposure mean that nutrient sufficiency is harder to achieve through diet alone than it was a century ago.

What to look for:

• Methylated B vitamins: methylfolate (5-MTHF) instead of folic acid, methylcobalamin or hydroxocobalamin instead of cyanocobalamin. Roughly 30-40% of the population has MTHFR polymorphisms that impair folic acid conversion.
• Chelated minerals: magnesium glycinate or malate instead of oxide, zinc picolinate or bisglycinate instead of sulfate, selenium as selenomethionine instead of selenite. Chelation dramatically improves absorption.
• Active vitamin B6 as pyridoxal-5-phosphate (P5P), not pyridoxine HCl
• Mixed tocopherols for vitamin E, not just alpha-tocopherol
• Vitamin A as mixed carotenoids plus some preformed retinol, not just beta-carotene
• No iron (unless specifically indicated — iron should be dosed separately based on labs)

Top picks: Thorne Basic Nutrients 2/Day, Pure Encapsulations O.N.E. Multivitamin, Designs for Health Complete Multi.

Fish Oil (Omega-3 Fatty Acids)

The omega-3 index (percentage of EPA + DHA in red blood cell membranes) is an independent cardiovascular risk factor. Target range is 8-12%. Most Americans are between 3-5%.

What to look for:

• IFOS certification (5-star rating): Tests for oxidation, heavy metals, PCBs, and dioxins
• Triglyceride form (rTG): Better absorbed than ethyl ester form. Check the label — if it says “ethyl ester” or just “fish oil concentrate,” it’s the cheaper form
• EPA:DHA ratios by indication:
  • General health: balanced EPA:DHA (roughly 2:1)
  • Inflammation/pain/autoimmunity: high EPA (1000-2000mg EPA daily)
  • Brain health/depression/cognition: high DHA (1000-1500mg DHA daily)
  • Pregnancy: DHA-dominant (at least 300mg DHA daily, some guidelines say 600mg)
  • Cardiovascular: high dose combined (2000-4000mg EPA+DHA daily, per AHA guidelines for elevated triglycerides)
• Total EPA+DHA per serving, not total “fish oil.” A 1000mg fish oil capsule might contain only 300mg of actual EPA+DHA. Read the Supplement Facts panel.

Top picks: Nordic Naturals ProOmega (IFOS certified, rTG form), Thorne Super EPA Pro, Designs for Health OmegAvail Hi-Po.

Probiotics

The probiotic market is a minefield of hype. Not all probiotics are equal, and more CFUs (colony-forming units) does not automatically mean better.

What to look for:

• Strain specificity: Probiotics work at the strain level, not the species level. Lactobacillus rhamnosus GG has robust evidence; a random L. rhamnosus without a strain designation might do nothing. Look for named, researched strains.
• Indication-matched strains:
  • IBS/general GI: Lactobacillus plantarum 299v, Saccharomyces boulardii, Bifidobacterium infantis 35624 (Align)
  • Antibiotic-associated diarrhea: Saccharomyces boulardii, Lactobacillus rhamnosus GG
  • Mood/anxiety: Lactobacillus helveticus R0052 + Bifidobacterium longum R0175 (the “psychobiotic” combination)
  • Immune support: Lactobacillus rhamnosus GG, Lactobacillus paracasei
  • Histamine issues: Avoid L. casei, L. bulgaricus, L. reuteri (histamine producers). Use Bifidobacterium species and L. rhamnosus
• CFU count: 10-50 billion for general maintenance; 100+ billion for acute therapeutic use (post-antibiotics, active dysbiosis). More is not always better — some conditions respond to lower doses.
• Shelf stability: Shelf-stable formulations (desiccant packaging, protective technology) vs. refrigerated. Both can be effective if properly manufactured.
• Delayed-release capsules: DR or enteric-coated capsules survive stomach acid better than standard capsules.

Top picks: Klaire Labs Ther-Biotic Complete, Seed Daily Synbiotic, Designs for Health ProbioMed 50, Microbiome Labs MegaSporeBiotic (spore-based).

Vitamin D3 + K2

Vitamin D is arguably the most important single nutrient to optimize. It functions as a hormone, influencing over 200 genes. Deficiency (below 30 ng/mL) affects an estimated 40% of Americans; insufficiency (below 50 ng/mL) affects far more.

Dosing by serum level (25-OH Vitamin D):

• Below 20 ng/mL: 10,000 IU daily for 8-12 weeks, then recheck
• 20-30 ng/mL: 5,000 IU daily for 8-12 weeks, then recheck
• 30-50 ng/mL: 2,000-5,000 IU daily maintenance
• Target range: 50-80 ng/mL (functional medicine optimal, not just “normal”)
• Toxicity concern: generally above 100 ng/mL, though rare below 150 ng/mL

Why K2 matters: Vitamin D increases calcium absorption. K2 (specifically MK-7 form, menaquinone-7) directs that calcium into bones and teeth rather than arteries and soft tissues. Without K2, high-dose D supplementation theoretically increases vascular calcification risk. Dose: 100-200 mcg MK-7 per 5,000 IU D3.

Format: Liquid drops (D3+K2 in MCT oil) offer flexible dosing and better absorption than tablets. Capsules with fat-based carrier are second choice.

Top picks: Thorne Vitamin D/K2 Liquid, Designs for Health D Supreme, Pure Encapsulations D3+K2.

Magnesium

The unsung mineral. Involved in over 300 enzymatic reactions. The standard American diet provides roughly 50% of the RDA. Serum magnesium is a poor marker — only 1% of body magnesium is in the blood. RBC magnesium is somewhat better but still imperfect.

Form matters enormously — match the form to the indication:

Form	Best For	Notes
Magnesium glycinate (bisglycinate)	Sleep, anxiety, muscle tension	Calming, well-absorbed, gentle on stomach
Magnesium L-threonate	Brain fog, cognitive support, neuroprotection	Crosses blood-brain barrier (Magtein brand)
Magnesium citrate	Constipation, general repletion	Osmotic laxative effect at higher doses
Magnesium malate	Muscle pain, fibromyalgia, energy	Malic acid supports mitochondrial ATP production
Magnesium taurate	Cardiovascular support, arrhythmia	Taurine adds cardiac and vascular benefits
Magnesium oxide	Avoid in most cases	Only 4% bioavailability, primarily a laxative

Dosing: 200-800 mg elemental magnesium daily, split into 2-3 doses. Start low and increase. Loose stools are the dose-limiting side effect (bowel tolerance).

Top picks: Thorne Magnesium Bisglycinate, Life Extension Neuro-Mag (threonate), Natural Vitality CALM (citrate powder).

Curcumin

The most well-studied botanical anti-inflammatory. Native turmeric root contains only 3-5% curcuminoids, and curcumin itself has notoriously poor oral bioavailability — most of it gets metabolized in the gut and liver before reaching systemic circulation. The delivery system is everything.

Bioavailability-enhanced forms:

• Meriva (Phytosome technology): Curcumin bound to phosphatidylcholine. 29x better absorption. Strong evidence for joint pain and inflammation.
• Longvida (SLCP technology): Solid lipid curcumin particle. Designed to cross the blood-brain barrier. Best for neuroinflammation and cognitive support.
• BCM-95 (CurQfen): Curcumin combined with turmeric essential oils. 7-8x better absorption. Good general-purpose option.
• C3 Complex + BioPerine: Standardized curcuminoids with piperine (black pepper extract) to inhibit glucuronidation. 20x better absorption. Caveat: piperine also affects drug metabolism (CYP3A4, CYP2D6), so avoid with medications sensitive to these pathways.
• Theracurmin: Nano-particle curcumin in colloidal dispersion. 27x better absorption. Japanese formulation with good clinical data.

Dosing: Depends on formulation. Meriva: 500-1000mg twice daily. Longvida: 400-800mg daily. BCM-95: 500mg twice daily. Always take with a meal containing fat.

Top picks: Thorne Meriva 500-SF, Designs for Health Curcum-Evail (BCM-95), Integrative Therapeutics Theracurmin HP.

Dispensary Models

In-Office Dispensary

Keep a curated inventory of your top 30-50 products. Patients leave with what they need the same day. Mark-up of 20-40% is standard and ethical — you’re providing expertise in selection, quality assurance, and convenience. Keep it clean: never recommend supplements you wouldn’t use yourself or give to your family.

Online Dispensaries

• Fullscript: Largest selection, practitioner-set discounts (typically 15-25% off MSRP), auto-refill, adherence tracking, education resources. Integrates with most EHRs.
• Wellevate (Emerson Ecologics): Similar model to Fullscript, strong professional-grade catalog. Merged with Fullscript parent company.
• Direct-to-Patient (Thorne, Pure Encapsulations): Some companies offer practitioner portals where patients order directly. Lower margin for practitioner but zero inventory risk.

Supplement Timing

Timing affects absorption, efficacy, and side effect profile.

With food (ideally containing fat):

• Fat-soluble vitamins: A, D, E, K
• Curcumin, CoQ10, omega-3s
• Most multivitamins (reduce nausea)

Empty stomach (30-60 minutes before meals):

• Amino acids (L-theanine, NAC, glutamine, GABA)
• Thyroid medication (separate by 4 hours from calcium, iron, magnesium)
• Certain probiotics (depends on strain — check manufacturer instructions)
• Activated charcoal or binders (2 hours away from all other supplements and medications)

Morning:

• B vitamins (energizing, can disrupt sleep if taken late)
• Adaptogens (ashwagandha is an exception — can be taken at night for sleep)
• CoQ10 (energy production)
• Iron (morning on empty stomach with vitamin C, away from coffee and calcium)

Evening/Bedtime:

• Magnesium glycinate (promotes sleep)
• Melatonin (30-60 minutes before bed)
• Ashwagandha (calming, cortisol-lowering)
• Phosphatidylserine (cortisol-lowering when taken at night)

Spacing from medications:

• Thyroid medications: 4 hours from calcium, iron, magnesium, fiber
• Antibiotics: 2-3 hours from probiotics, minerals, dairy
• Blood thinners: maintain consistent vitamin K intake; flag fish oil and other anticoagulant herbs with prescriber
• Binders (charcoal, clay, cholestyramine): 2 hours away from everything else

Cost Management

Functional medicine supplements can easily run $200-400 per month. Most patients cannot sustain this indefinitely, and financial stress is itself a health risk.

The essential 3-5 strategy: Identify the 3 to 5 supplements that will make the biggest difference for this specific patient at this specific time. Everything else can wait. A patient with severe vitamin D deficiency, gut dysbiosis, and chronic inflammation might start with D3/K2, a targeted probiotic, and curcumin — and add the rest later as budget and compliance allow.

Cycling strategies: Not every supplement needs to be taken continuously. Probiotics can be cycled (3 months on, 1 month off). Antimicrobial herbs are typically pulsed (2-4 weeks on, 1-2 weeks off). Even foundational supplements can be titrated down as lab values normalize.

Generic switches: When a patient is stable on a professional-grade product and cost is a barrier, switching to a quality retail brand (NOW Foods, Life Extension, Jarrow) for maintenance is reasonable — as long as the quality benchmarks are met.

Food first: Every supplement conversation should include the food-first caveat. Fermented foods instead of probiotics for maintenance. Sardines instead of fish oil capsules. Brazil nuts (2 per day) instead of selenium supplements. Magnesium-rich foods (pumpkin seeds, dark chocolate, spinach) to reduce supplemental dose.

If the supplement protocol feels like a second meal plan, something has gone wrong. What is the smallest intervention that produces the largest shift?