Protocols
Stool Test
The cheapest, most informative diagnostic in functional medicine
1. Stool pH between 5.7 and 6.2
6.0-8.0 pH paper strips. Press against stool on TP, or defecate on newspaper. Read the strip at 15 seconds, and 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. Sinking stool — minimal gas
Healthy stool sinks. Dysbiosis creates methane which causes stool to float.
4. Transit time under 36 hours
Measure transit 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. At least 2 fully formed stools per day.
Stool quantity is directly related to microbiome output.
6. Odor — faint, not foul
A healthy gut creates stool with minimal smell and CO₂ gas with no odor. A strong fecal or sulfurous odor points to a fermentation imbalance.
If any test fails → Colon Protocol
All six tests must pass. Any failure indicates the colon environment needs restoration before other protocols can work effectively.
If all six 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 6.0-8.0 pH paper strips, read at 15 seconds. Patient may prefer to wear gloves for any method.
Press pH paper against stool on toilet paper. This becomes harder as the microbiome heals and less stool remains on the paper. 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.
pH ≥7.6 — Dysbiosis (extreme)
Urease-producing organisms (primarily Proteobacteria) are active. SCFA production is likely offline. The LAB seed bank may be empty.
Consider Acidulem: 4 per meal · Acetalac · Bacillimet: 3 per meal · Phylamet: 2 per meal. Zoiben: 1 tsp a day for 5 days (do not repeat) · Ellagica: 1 per meal
pH 7.2-7.6 — Dysbiosis (high)
This is due to low SCFA output and/or urease-producing organisms (primarily Proteobacteria) dominant. The LAB seed bank may be empty.
Consider Acidulem: 6 per meal · Acetalac · Bacillimet: 4 per meal · Pokegeshi: 4 per meal · Phylamet: 4 per meal · Bifidus probiotics* · Zoiben: 1/2 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)
Elevated pH is likely due to low SCFA production.
Consider Acidulem: 4 per meal · Bacillimet: 3 per meal · Phylamet: 2 per meal. Zoiben: 1/4 tsp a day for 5 days · Ellagica: 1 per meal
pH 6.2–6.8 — Microbiome transition zone
SCFAs are being produced, but not yet at optimal levels.
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
As long as the low pH is not due to carbohydrate malabsorption, the microbiome is fully producing SCFA. Congratulations.
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 pH 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.
Stool floats
Methane is being produced. Consider Allimet. Garlic extracts also lower propionate producers. Take the minimum dose for the minimum amount of time needed to achieve desired effect.
Hard to pass and infrequent
Drink more water and add organic psyllium powder mixed in water to the diet.
Mushy with pH 5.7–6.4
Something is irritating the stool. Look at spices, supplements, and drugs.
With elevated stool pH, consider lowering meat intake to 10% of the diet, and focusing on vegetables. For grains, consider flaked oats fermented with Lactobacillus Plantarum and millet.
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) | Bacillus spores (Bacillimet) |
Bile flow (Glytamins) |
EO + bitters (Zoiben) |
Bacteriophage (Sextaphage) |
Thiosulfinate (Allimet*) |
|---|---|---|---|---|---|
| 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* |
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
Two independent readings — saliva reads the bicarbonate system, urine reads the acid load
Step 1 — Morning saliva test
First thing on rising — before food, toothpaste, or any mouthwash. Rinse the mouth with water, then gently gnaw the tongue until saliva flows, and read the saliva pH at 15 seconds.
Step 2 — Morning urine test
Read urine from mid stream flow at 15 seconds.
Consider Autonomis 1-2 caps a day during stressful moments
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