Omega-3 Fish Oil

The Autoimmune Protocol removes foods commonly implicated in immune activation and gut permeability — grains, legumes, dairy, eggs, nightshade vegetables, nuts, seeds, refined sugar, alcohol, and additives — for a 30–90 day elimination, followed by careful one-at-a-time reintroduction. It is most studied in Hashimoto's thyroiditis and inflammatory bowel disease.

Typical duration: 30–90 day strict elimination, then a structured staged reintroduction over weeks to months.

AIP is restrictive and best done with a practitioner familiar with the protocol, especially when active autoimmune disease is involved or in pregnancy/lactation.

The anti-inflammatory diet is not a single protocol but a synthesis of the patterns most consistently linked to lower inflammatory markers (CRP, IL-6, TNF-alpha) in human studies — Mediterranean-style eating, oily fish, abundant polyphenols, and low intake of ultra-processed foods, refined sugar, industrial seed oils, and excessive alcohol.

Typical duration: A long-term eating pattern.

Safe and flexible. Can be combined with Mediterranean, vegetarian, or plant-forward patterns.

A classical ketogenic diet typically provides ~70–80% of calories from fat, ~15–20% from protein, and only ~5–10% (often 20–50 g/day) from carbohydrates. The metabolic shift to ketosis lowers blood glucose and insulin, raises ketone bodies (beta-hydroxybutyrate, acetoacetate), and is being studied for neurological and metabolic conditions. Variants include the Modified Atkins Diet (MAD), Medium-Chain Triglyceride (MCT) ketogenic diet, and the Low Glycemic Index Treatment (LGIT).

Typical duration: Often 3–6 months minimum to assess response; medically supervised protocols (e.g. for epilepsy) may be maintained for years.

Ketogenic therapy is a medical intervention when used for seizure disorders or oncology — work with a clinician or registered dietitian experienced in ketogenic therapy. Not recommended in pregnancy, type 1 diabetes without supervision, pancreatitis, certain fatty-acid oxidation disorders, or active eating disorders.

A whole-food vegan diet emphasizes vegetables, fruit, legumes, whole grains, nuts, and seeds. It has been associated with improvements in body weight, blood lipids, and glycemic control, and is being studied for autoimmune and inflammatory conditions. It requires deliberate planning for vitamin B12, vitamin D, omega-3 (EPA/DHA), iodine, iron, zinc, and (sometimes) calcium.

Typical duration: A long-term eating pattern.

Vegan diets can be excellent or deficient — quality depends on planning. Pregnant, breastfeeding, and growing children on vegan diets should be followed by a registered dietitian.

Vegetarian diets range from lacto-ovo (includes eggs and dairy) to lacto (dairy only) and ovo (eggs only). Done well, they are associated with lower rates of cardiovascular disease, type 2 diabetes, and some cancers. Done poorly, they can be high in refined grains and low in key nutrients (B12, iron, omega-3s, zinc).

Typical duration: A long-term eating pattern.

Nutritional adequacy depends on planning, not just food choice. A registered dietitian can help avoid common gaps.

FODMAPs (Fermentable Oligo-, Di-, Mono-saccharides And Polyols) are short-chain carbohydrates poorly absorbed in the small intestine. They draw water into the gut and are rapidly fermented by colonic bacteria, producing gas and bloating in sensitive people. The Monash University protocol uses a 2–6 week strict low-FODMAP elimination, followed by a structured reintroduction phase to identify personal triggers.

Typical duration: 2–6 week strict elimination, then 6–8 weeks of structured reintroductions, then a long-term personalized diet.

Not intended as a long-term diet. The goal is to identify personal triggers and liberalize as much as possible.

The carnivore diet is the most aggressive elimination diet — it removes every plant food (and therefore every fiber, lectin, oxalate, gluten, and FODMAP source) to isolate animal-food tolerance. Proponents use it primarily as a short-term diagnostic elimination to surface food triggers in autoimmune, gut, and inflammatory conditions. Long-term safety data is limited and observational.

Typical duration: Typically run as a 30–90 day elimination, then food reintroductions one at a time.

Long-term effects on cardiovascular markers, bone health, and the gut microbiome are not well established. Avoid in chronic kidney disease, gout flares, or active eating disorders without medical supervision.

Low vitamin D status is one of the most widespread deficiencies globally and has been linked to autoimmune disease activity (Hashimoto's, MS), mood disorders, recurrent infections, and poor skin barrier function.

Reference intake: Adults 600–800 IU/day RDA; functional medicine often targets 2,000–5,000 IU/day with monitoring.

Supplementation notes: Take with a fat-containing meal. Pair with vitamin K2 (MK-7) when supplementing higher doses long-term.

An estimated 50% of adults consume below the EAR. Low magnesium is linked to insomnia, anxiety, migraines, muscle tension, and poor blood sugar regulation.

Reference intake: 310–420 mg/day RDA depending on age and sex.

Supplementation notes: Glycinate for sleep/anxiety, citrate for constipation, threonate for cognitive/brain effects. Avoid magnesium oxide (poorly absorbed).

Low zinc is linked to recurrent infections, acne, slow wound healing, leaky gut, and impaired taste/smell. Often deficient in vegetarians and those with gut malabsorption.

Reference intake: 8–11 mg/day RDA.

Supplementation notes: Take away from iron and calcium. Long-term high-dose zinc depletes copper — pair with ~1 mg copper if dosing >30 mg/day.

Low EPA/DHA status correlates with depression, anxiety, dry skin, joint pain, and autoimmune flare risk.

Reference intake: 250–500 mg combined EPA+DHA/day baseline; 1–3 g/day therapeutic.

Supplementation notes: Choose IFOS-certified or molecularly distilled fish oils to minimize heavy-metal exposure.

Low vitamin A impairs mucosal immunity, gut barrier integrity, and skin cell turnover.

Reference intake: 700–900 mcg RAE/day; avoid >3,000 mcg/day preformed retinol in pregnancy.

Supplementation notes: Beta-carotene conversion is poor in some genotypes — preformed retinol may be needed.

Deficiency contributes to anxiety, low mood, PMS, and sleep disturbance.

Reference intake: 1.3–1.7 mg/day; avoid >100 mg/day long-term (peripheral neuropathy risk).

Supplementation notes: P-5-P (active form) is preferred for those with poor conversion.

Deficiency is linked to frequent infections, poor wound healing, easy bruising, and accelerated skin aging.

Reference intake: 75–90 mg/day RDA; 500–2,000 mg/day commonly used for immune support.

Supplementation notes: Split high doses through the day. Liposomal forms improve absorption at higher intakes.

Deficiency is common in vegetarians/vegans, older adults, and those on PPIs or metformin. Strongly implicated in neurological symptoms (MS-like presentations), fatigue, anxiety, and cognitive decline.

Reference intake: 2.4 mcg/day RDA; therapeutic 1,000 mcg/day sublingual methylcobalamin is common.

Supplementation notes: Prefer methylcobalamin or hydroxocobalamin over cyanocobalamin, especially with MTHFR variants.

Low folate (or impaired conversion in MTHFR variants) is implicated in depression, anxiety, autism spectrum biology, and pregnancy complications.

Reference intake: 400 mcg DFE/day; 600 mcg pregnancy.

Supplementation notes: Methylfolate (5-MTHF) is preferred over folic acid, especially with MTHFR C677T/A1298C variants.

Selenium reduces TPO antibodies in Hashimoto's and supports T4→T3 conversion. Deficiency is implicated in thyroid autoimmunity and viral susceptibility.

Reference intake: 55 mcg/day RDA; therapeutic 200 mcg/day studied for Hashimoto's.

Supplementation notes: Do not exceed 400 mcg/day long-term — selenium toxicity causes hair/nail loss.