🩺 Root-cause framework with explicit dual-axis design (one axis well-supported, one hypothesis-generating). This protocol is built around two parallel mechanisms thought to drive estrogen-related inflammation in endometriosis and adenomyosis:
- Liver Phase 2 estrogen clearance (methylation, sulfation, glucuronidation, glutathione conjugation) — well-supported by published research; the primary target of standard functional medicine estrogen-clearance work
- Microbiome-mediated handling of cleared estrogens (gut and vaginal bacteria producing β-glucuronidase and sulfatase enzymes) — biologically plausible based on the published estrobolome literature, but the quantitative interaction with Phase 2 interventions has not been directly tested in cohort research
The protocol’s design assumes the integrative dual-axis framing is correct — that addressing both axes produces a more complete clinical response than addressing only the first — but this assumption is hypothesis-generating, not confirmed by cohort data. A reader’s experience may differ from the author’s case-study results depending on their specific Phase 2 status and microbiome composition.
The mechanistic basis is in
why-this-works.md; the case-study evidence is incase-studies/001-core-restore-no-bc/including the integrativemicrobiome-estrogen-axis.mdhub document, which explicitly frames the integrative thesis and where the research is well-supported vs. sparse.📊 Derived from the case study:
case-studies/001-core-restore-no-bc/. The case study shows what happened in one person; this protocol generalizes what worked.⚠️ Not medical advice. Practitioner-supervised use recommended. This is structured education to bring to your functional medicine practitioner, OBGYN, or REI. Supplement names and dose ranges are referenced for context; your practitioner determines what’s right for your body.
🚺 Developed without hormonal contraception or suppression. If you are currently on BC, hormonal endo suppression, or HRT, review the supplement list with your prescriber first. See
research/birth-control-context.md.
A 30-day structured protocol to:
The protocol is built in four weekly phases:
| Week | Focus | Goal |
|---|---|---|
| Week 1 — Foundation | Reduce inbound load | Eliminate the most common inflammatory food triggers and toxicant exposures |
| Week 2 — Activation | Activate Phase 2 pathways | Add targeted methylation, conjugation, and detox-support nutrients |
| Week 3 — Clearance | Optimize elimination | Maximize fiber, hydration, sauna cadence; block enterohepatic recirculation |
| Week 4 — Integration | Sustainable maintenance | Reintroduce foods strategically; identify long-term keepers |
The full mechanistic justification is in why-this-works.md.
Pick the framing closest to where you are:
“You have 2–12 weeks before laparoscopy. Lower your inflammatory baseline going in, and the surgery does less work + you recover faster.”
“You’re 1 day to 12 weeks post-op. Surgery removed lesions but didn’t remove the underlying inflammatory + hormonal milieu that grew them. This is the window where the body is most responsive.”
“You’re trying to avoid or postpone surgery. The full root-cause protocol may meaningfully reduce symptoms enough that you and your practitioner can re-evaluate whether surgery is still the right call.”
Each pillar maps to a documented mechanism (see why-this-works.md):
| # | Pillar | What it targets | Concrete daily action |
|---|---|---|---|
| 1 | Reduce inbound estrogen load | Xenoestrogens, conventional dairy/meat estrogen residues | Switch to glass/stainless containers for hot foods; clean personal care (no parabens/phthalates); filter water; choose organic dairy/meat when possible |
| 2 | Phase 1 → safer 2-OH direction | Shift estrogen metabolism toward safe 2-hydroxy pathway | Cruciferous vegetables daily (broccoli, kale, cabbage, brussels sprouts, broccoli sprouts) |
| 3 | Phase 2 methylation | COMT methylates 4-OH estrogens to safer 2-MeO estrogens; restores SAMe | Methylation-support nutrients: B12 (methylcobalamin), B6, methylated folate (5-MTHF), magnesium glycinate, choline — practitioner-guided dosing |
| 4 | Phase 2 sulfation | SULT enzymes conjugate estrogens for excretion | Sulfur-rich foods: garlic, onion, eggs, cruciferous, MSM; consider NAC (practitioner-guided) |
| 5 | Phase 2 glutathione conjugation | Clears reactive 4-OH estrogen quinones | NAC, glycine, vitamin C, selenium, alpha-lipoic acid (practitioner-guided); prioritize sleep — glutathione regenerates during deep sleep |
| 6 | Block enterohepatic recirculation | Prevent gut β-glucuronidase from un-conjugating cleared estrogens back into circulation | 30+ g fiber daily; calcium-D-glucarate (practitioner-guided); fermented foods; sauerkraut, kefir if tolerated |
| 7 | Skin clearance route | Sweat eliminates lipid-soluble xenoestrogens (BPA, phthalates, PCBs) | Infrared sauna 3–4x/week, 30–45 min |
| 8 | Anti-inflammatory baseline | Lower the inflammatory background that worsens endo | Omega-3 (EPA/DHA 2–3 g/day), curcumin, ginger; eliminate gluten + dairy for the 30-day trial |
| 9 | Stress / cortisol axis | Reduce cortisol-driven progesterone depletion that worsens estrogen dominance | 8h sleep target, magnesium glycinate evening, daily breath practice (4–6 ratio), restorative movement |
| 10 | Track your data | Know if it’s working — objectively | Daily symptom log + wearable (WHOOP/Garmin) + pre/post bloodwork (homocysteine, vitamin D, hs-CRP at minimum) |
Important: the supplements below are referenced for educational context. Do not start any of them without your practitioner’s review. Dose ranges are typical functional medicine ranges, not prescriptions. Several of these (DIM, calcium-D-glucarate, sulforaphane extracts, St. John’s Wort) interact with hormonal medication and the CYP450 enzyme system.
| Supplement | Mechanism | Typical adult range | Cautions |
|---|---|---|---|
| Methylated B12 (methylcobalamin) | Methylation cycle cofactor | 500–2,500 mcg/day | Generally safe; flag with practitioner if MTHFR variant |
| Methylated folate (5-MTHF / L-methylfolate) | Methylation cycle cofactor | 400–1,000 mcg/day | Match form to genetic context |
| Vitamin B6 (P5P preferred) | Methylation, neurotransmitter synthesis | 25–50 mg/day | High doses (>200 mg/day) can cause neuropathy |
| Magnesium glycinate | Methylation cofactor + sleep + muscle relaxation | 200–400 mg evening | Bowel tolerance for higher doses |
| NAC (N-acetylcysteine) | Glutathione precursor | 600–1,800 mg/day | Generally safe; flag asthma/respiratory conditions |
| Sulforaphane (broccoli sprout extract) | Phase 2 enzyme inducer via Nrf2 pathway | 10–30 mg/day | Can interact with thyroid; flag with practitioner |
| DIM (diindolylmethane) | Shifts estrogen metabolism toward 2-OH pathway | 100–200 mg/day | ⚠️ Interacts with hormonal contraception; potency varies; practitioner-only |
| Milk thistle (silymarin) | Hepatoprotective; modulates CYP enzymes | 150–300 mg/day | Flag if on medications metabolized by CYP3A4 |
| Curcumin (with piperine or phytosome form) | Anti-inflammatory; NF-κB modulator | 500–1,500 mg/day | Blood thinners interaction — flag if pre-surgery |
| Calcium-D-glucarate | Inhibits β-glucuronidase; blocks enterohepatic recirculation of estrogens | 500–1,500 mg/day | ⚠️ Can lower hormonal contraception levels; flag with prescriber |
| Omega-3 (EPA/DHA fish oil) | Anti-inflammatory; reduces prostaglandins | 2–3 g EPA+DHA/day | Mild blood thinning; pause 1 week pre-surgery |
| Vitamin D₃ (with K₂) | Immune modulator; documented endo pain reduction | 2,000–5,000 IU/day (based on labs) | Test 25-OH D level first |
| Vitamin C | Glutathione regenerator; anti-inflammatory | 500–1,000 mg/day | High doses can cause GI upset |
Pre-surgical caution: stop blood-thinning supplements (omega-3, curcumin, vitamin E, garlic extract, fish oil) at least 7 days before surgery unless your surgeon advises otherwise.
tracking/ templates)Likely (based on the case study):
Possible but not guaranteed:
Unlikely:
Possible negative effects:
README.md — this overviewwhy-this-works.md — full mechanistic explanationweek-1-foundation.md — Days 1–7week-2-activation.md — Days 8–14week-3-clearance.md — Days 15–21week-4-integration.md — Days 22–30for-pre-surgery.md — audience-specific guidancefor-post-surgery.md — audience-specific guidancefor-surgery-hesitant.md — audience-specific guidancetracking/ — daily logs and templatesFor the personal results that informed this protocol — full WHOOP data, biomarker shifts, cycle-phase analysis, and honest confounders — see: