Protocols
Stool Test
The cheapest, most informative diagnostic in functional medicine
1. Stool pH between 5.7 and 6.2
Hydrion paper, 6-8 range. Press against stool on TP, or defecate on newspaper. Take the most alkaline reading. Do not test stool that has gone into toilet water. Blue = alkaline (trouble). Green = neutral (not terrible, not great). Yellow-green / unchanged = acidic (success).
2. No toilet paper needed
A fully formed stool with adequate fiber and normal mucus leaves nothing behind. Toilet paper is like tissue paper. You only need it if you’re sick. Extensive wiping = upstream issue.
3. Two or more bowel movements per day
Below this, transit extends into the range where conjugated toxins are increasingly deconjugated and reabsorbed.
4. Transit time under 36 hours
Measure with chlorophyllin: 1 tsp — time until bright green stool appears. Optimal: 18-24 hours. Acceptable: up to 36. Beyond 36: deconjugation becomes serious.
Note: Daily passage of stool does not guarantee passing transit time. A patient can have one bowel movement per day and still have 48+ hour transit.
5. Sinking stool — minimal gas
Healthy stool sinks, and a healthy microbiome creates little to no flatulence. Dysbiosis creates gas from unused H₂ and unwanted methane production, which, when entrapped in stool, causes it to float.
If any test fails → Colon Protocol
All five tests must pass. Any failure indicates the colon environment needs restoration before other protocols can work effectively.
If all five pass → Small Intestine Protocol
The colon environment is already sound — uncommon, but possible. There is nothing to restore, so the Colon Protocol can be skipped; proceed to the Small Intestine Protocol.
Colon Protocol
pH is the master variable. Protocol entry point determined by stool pH reading.
Test stool pH
Use Hydrion paper (6-8 range). Patient may prefer to wear gloves for any method.
- Method 1: Press pH paper against stool on toilet paper. This becomes harder as the microbiome heals and less stool remains on the paper.
- Method 2: If stool smears on the pH paper, leave it in contact for 5 seconds, then wipe the smear off with fresh toilet paper. The color embedded in the paper reads clearly once the smear is cleared.
pH paper only registers on damp material. If the stool is dry on the surface, press the paper into the inside of the stool. In all cases, take the most alkaline reading. Do not test stool that has gone into the toilet water.
Result determines entry point below.
pH ≥7.2 — Dysbiosis (severe)
Severely alkaline. Urease-producing organisms (primarily Proteobacteria) dominant. The LAB seed bank may be empty.
SCFA supplementation (Phylamet) is appropriate here for systemic support — the body is starved for SCFAs, which regulate function everywhere. Oral SCFAs do not reach the colon in meaningful quantity, so they do not suppress colonic bacteria directly — that requires the patient’s own microbiome producing SCFAs locally, which the rest of the protocol works toward.
Consider Acidulem: 6 per meal · Bacillimet: 4 per meal · Pokegeshi: 4 per meal · Phylamet: 4 per meal · Bifidus probiotics* · Zoiben: 1 tsp a day for 5 days (do not repeat) · Ellagica: 2 per meal · Clinical Electron Charger · Sextaphage* (Russian bacteriophage)
pH 6.8–7.2 — Dysbiosis (moderate)
Urease-producing organisms (primarily Proteobacteria) still active. SCFA supplementation (Phylamet) supports the systemic SCFA pool — the body is short on SCFAs for immune, gut barrier, and mood regulation. Oral SCFAs do not reach the colon in meaningful quantity and so do not suppress colonic bacteria; that requires the patient’s own microbiome producing SCFAs locally, which the rest of the protocol works toward. Zoiben and Ellagica provide direct antimicrobial pressure in the meantime.
Consider Acidulem: 4 per meal · Bacillimet: 3 per meal · Phylamet: 2 per meal. Zoiben: 1/2 tsp a day for 5 days (do not repeat) · Ellagica: 1 per meal
pH 6.2–6.8 — Microbiome transition zone
The saccharolytic populations are recovering and starting to produce SCFAs locally, lowering colonic pH and suppressing alkaline-loving bacteria at the site of production. Patient-side production is still below what the body needs systemically — Phylamet bridges the gap, supporting the systemic SCFA pool (immune, gut barrier, mood) while the microbiome continues to rebuild local production.
Consider Acidulem: 2 per meal · Bacillimet: 2 per meal · Phylamet: 1 per meal · Panaceum: 4 per meal
pH 5.7–6.2 — Microbiome quality restored
Two conditions must both be met before supplementation can be retired: stool pH 5.7–6.2 (quality — the right bacteria are present, producing real SCFAs locally) and 3 bowel movements per day (quantity — enough throughput for patient-side production to meet the body’s systemic SCFA needs). At optimal pH but fewer than 3 BM/day, the patient’s microbiome is doing the colonic job (suppressing alkaline-loving bacteria at the site of production) but not yet producing enough SCFAs for systemic supply — continue Phylamet until both conditions are met. Maintain with prebiotics and spore bacteria.
Consider Acidulem: 1 per meal · Bacillimet 1 per meal · Panaceum: 2 per meal
*pH ≤6.0 — Check for carbohydrate malabsorption
A pH at the acidic end of the strip reflects acid in the colon, and that acid can come from healthy SCFA production or from pathological fermentation of carbohydrate that was never absorbed upstream. The Hydrion strip will not read below 6.0, so a true success reading and a malabsorption reading look identical on paper.
The deciding factor is context. In a patient who has not been on the protocol, an acidic reading is far more likely to be carbohydrate malabsorption than a pristine microbiome. Rule out carbohydrate malabsorption, short bowel syndrome, celiac disease, fructose intolerance, or lactose intolerance before treating the reading as a success.
A 1–2 week reset that runs underneath the protocol
The supplements work against, or with, what the patient eats. For established dysbiosis, a short 1–2 week dietary window removes what feeds the wrong organisms while the selective substrate feeds the right ones. Run it alongside the supplementation above — it is not a separate phase.
- Carbohydrate — selective only. Cooked-and-cooled starch (resistant starch) and the HMOs (Acidulem). Exclude fruit and all simple sugar: the unabsorbed fraction is fermented by the facultative Proteobacteria you are trying to starve. This is a high-selective-carbohydrate window, not a high-carbohydrate one.
- Fat — glyceryl monolaurate, supplied directly. Adults do not reliably liberate monolaurin from dietary triglyceride the way an infant does. Supply the monoglyceride already formed, in small divided amounts.
- Protein — branch on tolerance. If casein is tolerated, use slow-digesting casein (a low-lactose micellar casein isolate covers patients who react to milk sugar rather than the protein). If casein is not tolerated, restrict instead: withhold animal protein — red meat especially — for the window, since concentrated animal protein is the substrate most favorable to the proteolytic, urease-bearing organisms. Take only the modest plant protein incidental to the vegetable and starch base.
If the client cannot tolerate or access lactulose: HMOs (Acidulem) can accomplish much of the same acidification when dosed in bulk — roughly 2 Tbsp per meal equivalent — with less gas, bloating, and cramping, though at higher cost.
Small Intestine Protocol
Wants low microbial density — match the agent to the pathobiont. The two foundational columns come first; the three targeted agents follow. Ordered easy (top) to hard (bottom) to suppress.
| Pathobiont (signature) | Bacillimet (Bacillus) |
Bile (Glytamins) |
Zoiben (EO + bitters) |
Sextaphage (phage) |
Fructan-free allicin |
|---|---|---|---|---|---|
| Fermentative gram-negativesKlebsiella, E. coli — H₂, fermentation | F | F | S | S* | S |
| Histamine / amine producersMorganella, Enterobacter — histamine, putrescine, cadaverine | F | F | S | P | S* |
| Streptococcusfermentative gram-positive — lactate, D-lactate, H₂ | F | F | S | S* | S |
| Staphylococcusopportunist gram-positive — toxins, inflammation | F | F | S | S* | S |
| Proteolytic / putrefactiveProteus, Clostridia, Fusobacterium — ammonia, amines | F | F | S* | P | S |
| Fungi / SIFOCandida albicans | F | F | S* | R | S |
| Enterococcusbile-resistant gram-positive (VRE-type) — lactate, broad intrinsic resistance | F | F | S | S* | S |
| SulfidogensBilophila wadsworthia, Desulfovibrio — H₂S | F | F | S* | R | S |
| MethanogensMethanobrevibacter smithii — CH₄ | F | F | P | R | S* |
Bile flow, the migrating motor complex, and the fasting window
Bile (detergent against overgrowth, FXR antimicrobial peptides at the terminal ileum, peristalsis, Bacillus germination), the migrating motor complex (a sweeping wave every 90 minutes that needs fasting to fire), and the 12–14 hour overnight fast hold the compartment beneath the whole table. The agents above act on overgrowth once established; these keep it from recurring. Stop eating 3 hours before sleep — the overnight window is the most important MMC window, and eating too close to sleep suppresses it.
Consider 4 Bacillimet a day · 1 box of Glytamins · and 1/4 tsp Zoiben once a day for one week.
Gallbladder (Bile)
Bile is location-dependent: beneficial in intestines, caustic if retrograde
Step 1 — Consider Glytamins, 1x per day for 10 days
Step 2 — Continue Glytamins + therapeutic ultrasound
Another 10 days with therapeutic ultrasound over gallbladder, 5 min/session. For liver stones, apply over liver.
Optional — Traditional flush after 10 days
Standard olive oil / Epsom salt flush can be done after completing at least 10 days of the protocol, but is unnecessary. True stones sink — floating material is typically saponified oil (artifact).
Sinus & Brain Detox
Where the brain, immune system, lungs, and circulation converge
Step 1 — Detox stage
Bind fat-soluble toxins (mycotoxins, bacterial lipid toxins), dissolve biofilm matrix, recover mucin layer architecture, and support ciliary clearance. Add salt water sinus rinses to support clearance as needed.
Consider Ventrimet 6 sprays a day each nostril
Step 2 — Postbiotic spray
Provide postbiotics to suppress mold and toxic bacteria, normalize immune response, and decrease neuro-inflammation. Run in parallel with Step 1.
Consider Sentrimet 6 sprays a day each nostril
Step 3 — Sinus probiotics
- Corynebacterium pseudodiphtheriticum
- Dolosigranulum pigrum
- Commensal Staphylococcus epidermidis
Consider Floramet 6 sprays a day each nostril
Sleep Apnea
The condition we sleep through
Step 1 — Identify location(s)
Experience: one or both nostrils become stuffy or blocked.
Protocol: Ventrimet, Sentrimet, and Floramet. Nasal strips can open the airway.
Experience: snoring.
Protocol: Ventrimet and Sentrimet sprayed into the back of the throat.
Experience: airway closes when resting on one’s back.
Protocol: in addition to the sinus protocol, consider a Nightshift belt (3rd party, prescription) or a positional backpack (tennis-ball or wedge style). Warning: positional aids worsen sinus-driven apnea — where the sinuses are also involved, pair them with head-of-bed incline to keep the sinuses draining.
Experience: apnea.
Protocol: not an airway blockage — the brain intermittently fails to send the signal to breathe, often tied to unstable CO₂/bicarbonate buffering and chronic hyperventilation. Work up acid-base status — see the Saliva & Urine pH protocol.
Step 2 — Read the severity
Two ways to read the same story. The instrumented workup measures it; the dream and sleep signs cost nothing.
Instrumented — SpO₂ and/or heart rate monitoring during sleep:
- Number of apneic events
- Depth of desaturation (O₂ drop)
- Length of desaturation
- Elevated heart rate without desaturation indicates the apneic event was short enough not to desaturate
Free — dream and sleep signs:
- Violent or suffocation dreams → apnea
- Frustration dreams (running, stuck, searching) → hypopnea
- Pounding heart or sweat-soaked sheets on waking → sympathetic surge from oxygen desaturation
- Sheets and blankets in disarray → restless sleep from repeated arousal events
Step 3 — Identify and address the inflammatory trigger
Mold/bacteria in home air and bedding, dust mites in bed, pollen season, pet allergies, allergens in diet, infection in sinuses/teeth/throat. See book for full differential.
The most common driver is the home itself — mold and bacteria in the air and bedding. Remediate it. See Home Detox tab.
Saliva & Urine pH
Morning resting reading, confirmed by a stimulated follow-up
Step 1 — First test on rising
Resting saliva, first thing upon rising, — before food, toothpaste, or any rinse. Read urine pH at the same time, and test the urine fresh — a sample left sitting reads falsely alkaline.
Optimal reading
Resting saliva 6.8, urine 6.5, and saliva rises more alkaline on the stimulated follow-up — bicarbonate flood intact.
Consider Autonomis 1-2 caps a day during stressful moments
Step 2 — Follow-up: stimulated saliva
Rinse mouth with water, then gently gnaw the tongue until saliva flows, then re-read. If no saliva comes, find the cause: dehydration, stress, or medications.
- Alkaline → drops to acidic: the resting alkalinity was overnight oral ammonia, not buffering reserve — address oral flora and hygiene. But stimulated saliva that falls acidic instead of rising to 7.5–8 still points to bicarbonate failure; work it up as below.
- Acidic → alkaline (rises toward 7.5–8): bicarbonate reserves intact.
- Acidic → stays mostly acidic (<6.6): bicarbonate failure. Rule out chronic hyperventilation (lowers CO₂). Consider bicarbonates, chelation, and zinc. Check blood CO₂ if possible.
Consider our Metal Detox Protocol
True bicarbonate deficit
A bicarbonate deficit that resists correction often points upstream to toxic metal burden. Once low flow, oral causes, and hyperventilation are excluded: consider heavy metal chelation.
Metal Detox
Nature uses relay races, so should we
Step 1 — Identify metals
Hair, blood, urine, transdermal testing. See book for strengths and weaknesses of each method. Include mercury filling history (especially if removed improperly or gums turned dark) and history of MRIs with gadolinium contrast injection.
Step 2 — Measure kidney function
Bloodwork (BUN, creatinine, eGFR) or urine test strips to determine detox capacity.
Step 3 — Raise urine pH to 7.5 during chelation. Verify with pH paper.
Acidic urine can cause redistribution. For urine alkalinization, consider one Bicarbamet per 25 lb body weight and chelators in 8 oz of water on an empty stomach first thing in the morning, then wait 30 minutes before eating.
Why a relay
Every tier used alone risks redistribution — solubilizing a metal in one place and dropping it in another. The relay hands the metal up an affinity gradient: a fast, small Tier 1 mobilizer reaches into crystalline deposits and tight binding pockets, passes its cargo to a more stable Tier 2, which passes it to a rigid Tier 3 terminal catcher that rarely lets go. Match the donor chemistry to the metal — hard donors for hard metals, soft donors for soft (HSAB; see remedylink.com/charts).
Hard-metal relay — good kidney function
- Tier 1 — citrate or malate (malate where histamine is an issue): fast mobilizer; dissolves crystalline deposits and reaches small spaces
- Tier 2 — EDTA (Medicardium V2O): stable mid-relay carrier
- Tier 3 — DOTA (Captimet): macrocyclic terminal catcher
- Add silica (methylsilanetriol) if aluminum is present
Soft-metal relay — good kidney function
- Tier 1 — alpha-lipoic acid (ALA): fat-soluble soft-metal mobilizer; reaches lipid compartments
- Tier 2 — MiaDMSA (Dasimet): stable mid-relay carrier
- Tier 3 — DOTA (Captimet): the macrocyclic cage out-holds sulfur-donor chelators (Hg log K 26.4 vs DMSA 16.5), so DOTA is the terminal catcher for soft metals too
Mixed burden — most patients
Most patients carry both chemistries. Run the hard relay and the soft relay together. DOTA (Captimet) is the shared Tier 3 terminal catcher for both sides — arsenic being the one exception, held by MiaDMSA.
Stage one tier at a time, by tolerance
Begin with the most stable runner and add the next mobilizer only once the current combination is shown to be tolerated, so anything a mobilizer frees always meets a more stable catcher already in place. Never mobilize more than you can capture.
1 — Tier 3 alone (DOTA / Captimet), low dose
The macrocyclic Tier 3 carries little redistribution risk — its stability keeps it from dropping cargo back into circulation, which makes it the safest single agent to start with. If 100 mg of a Tier 3 alone is tolerated, then go to 200 mg. If 200 mg is tolerated, you can add in Tier 2.
2 — Add Tier 2 once Tier 3 is tolerated
It is not about plateauing — it is about tolerance. Once Tier 3 is shown to be tolerated at the doses above, add the Tier 2 — EDTA for hard-metal coverage and/or MiaDMSA for soft. For sensitive patients, the molar dose of Tier 2 must always be lower than Tier 3.
3 — Add Tier 1 once Tiers 3 + 2 are tolerated together
Add Tier 1 if and only if Tiers 2 and 3 run at the same time are tolerated. Add citrate and malate for hard metals, alpha-lipoic acid for soft. Tier 1 reaches the small spaces the larger chelators cannot enter — protein binding pockets, crystal interstices, and enzyme active sites where the metal sits in the position of the missing essential cofactor. For sensitive patients, Tier 1 amounts must never exceed the molar dose of Tier 2 or Tier 3.
Standard Dosing schedule
1 Captimet, 1 Dasimet, 1 Medicardium V2O and 6 Bicarbamet 5 days on, 2 days off, with re-mineralizing on the off days — especially zinc, and magnesium and copper as needed.
Methyl DOTA (Vellumet) — intracellular reach
Fat-soluble macrocyclic; crosses cell membranes and demethylates to active DOTA inside the cell. This is the most aggressive level of the standard protocol, and the risk of mineral stripping is real. Bring magnesium and zinc to normal levels before starting, and replenish them on the off cycle (3–5 days on, 2 days off). Vellumet must always be taken with magnesium glycinate before, during, and after.
Run Vellumet for only 3 days, then follow with Captimet (DOTA). Always keep a gradient from the brain to the body — Vellumet frees metal from intracellular and brain compartments, and the Captimet that follows keeps it moving outward instead of redistributing back.
Sensitive / compromised kidney function consider:
- Begin with 100mg DOTA (1 Captimet) a day 5 days on 2 days off for one month
- If well tolerated, then try adding 100 mg EDTA (1 Medicardium V2O) for hard and borderline metals or 100 mg MiaDMSA (1 Dasimet) for soft metals
- If both are needed, start with EDTA, then add MiaDMSA one week later
Capsules can be opened and absorbed sublingually if there are no metal fillings present in the mouth. Sensitive clients can start with 1/2 capsule.
Chemical Detox
Build in reverse order: Phase III before Phase II before Phase I
Step 1 — Identify ongoing exposures (including mold)
Remediate or avoid toxic exposure. No protocol overcomes continuous re-exposure.
Step 2 — Baseline testing
Blood or urine test for toxicity baseline. If labwork is unavailable, firm pressure on acupuncture point LV3. Monitor for decreasing discomfort as protocol progresses.
Step 3 — Complete Gallbladder protocol
Bile flow is the primary exit route for Phase II conjugated chemicals. Gallbladder (Bile) protocol precedes chemical detox.
Step 4 — Lower stool pH to 6.5
See Colon Protocol. Dysbiotic gut bacteria produce beta-glucuronidase and sulfatases that strip Phase II conjugation tags, causing toxin reabsorption. Colon Protocol precedes chemical detox.
Step 5 — Phase III support
Recover ATP necessary to power Phase III (ABC cassette pumps). Be at least 2 weeks into Metal Detox protocol before starting Chemical detox, or have blood CO₂ of 27.
Step 6 — Phase II support
Supply conjugants: glutathione, glucuronolactone, sulfate, TMG, and B5.
In acute crisis, consider additional liposomal glutathione, glycine, alanine, glucuronolactone, and Calcium D-Glucarate.
Consider Xeneplex
Step 7 — Phase I support
Oxidation (CYP450): fat-soluble toxin → reactive intermediate.
Consider Xeneplex
Cyclodextrin binding — lipophilic toxins
HPBCD cyclodextrins encapsulate fat-soluble toxins, rendering them water-soluble for excretion — a parallel route to bile and oral binders for the lipophilic fraction.
Consider Albedextrin
Home Detox
If the building’s delivery rate of toxins exceeds the body’s clearance rate, no protocol will produce sustained improvement.
Why modern homes are vulnerable
OSB sheathing (broken cellulose surfaces). Paper-backed drywall. Cellulose insulation if borates leach. Roof penetrations (solar panels, skylights, vents). Vapor wrapping the home. Particle board furniture. All are pre-digested food for mold or moisture traps. Lignin in solid timber provides armor that processed wood products lack.
Assessment tools
Remediation principles
Remove the water source first. Contaminated porous building materials should be removed, not cleaned. Non-porous surfaces can be treated. HEPA filtration during and after work.
HVAC
Ductwork distributes contamination to every room. Skin shed (~2 lbs/year per occupant) feeds organisms in ducts.
Fogging
HEPA vacuuming of areas beforehand is highly recommended.
Consider our Home Fogging System
Porous surfaces
Clothing: usually recoverable with multiple wash cycles using mycotoxin-specific enzyme formulations. Carpets and upholstery: typically not recoverable — plan on replacement. Hard surfaces clean readily. The line falls at porosity.
Spike Protein Protocol
Never cleave without binding
Indication
History of complications after a COVID infection or COVID vaccination. Long COVID symptoms (fatigue, brain fog, cardiovascular symptoms, POTS).
Step 1 — Cleave: proteolytic enzymes
Liposomal proteolytic enzymes (serrapeptase, lumbrokinase, nattokinase). Liposomal delivery is required — non-liposomal enzymes will not reach the bloodstream. Cleaves intact spike protein.
Consider 6 Protelase 3x a day
Critical warning
Cleaved spike protein breaks into approximately 7 prion fragments. Each fragment can template neighboring proteins into misfolded configurations. Proteolytic enzymes without cyclodextrin binding = iatrogenic prion exposure. Do not trade cardiovascular disease for neurodegeneration.
Step 2 — Bind: cyclodextrins (simultaneous with Step 1)
HPBCD cyclodextrins encapsulate the prion fragments produced by cleavage, rendering them water-soluble for excretion. Steps 1 and 2 must run together — never cleave without binding.
Consider Albedextrin 1x a day