What causes recurrent SIBO?

The Host Capacity Model identifies colonocyte bioenergetic failure as the upstream driver of recurrent SIBO. When colonocyte mitochondrial respiration fails, oxygen leaks into the lumen and reshapes the ecology toward facultative and sulfidogenic overgrowth—so antimicrobials clear the symptom but not the cause.

How is MCAS different from other mast cell conditions?

BiomeLogic stratifies MCAS into Pattern A/B/C/D activation phenotypes based on upstream drivers (barrier, neuroimmune, infectious, or connective-tissue mediated). Treatment differs by pattern, which is why generic mast-cell stabilizers fail in many patients.

Do you provide medical care or diagnoses?

No. BiomeLogic provides independent systems-biology consultation and mechanistic case analysis. It is not medical care, not a diagnosis, and does not replace your physician.

Is post-COVID gut dysfunction the same as other dysbiosis?

No. Post-COVID dysbiosis is driven by viral-mediated mitochondrial damage. NAD+ depletion is more severe, recovery takes longer (4–6 months versus 2–3), and treatment requires intensive NAD+ restoration on top of the standard dysbiosis protocol.

How long before I feel better on the recovery protocol?

Energy improves around weeks 2–3 as NAD+ repletes. GI symptoms ease weeks 4–6. Bloating, brain fog, and energy show noticeable improvement weeks 8–10. Most patients are 70–80% improved by week 12 and substantially recovered by month 6.

Do I need IV NAD+ or is oral enough?

IV is faster (2–4 weeks to significant improvement) but expensive ($2,400–6,000). High-dose oral NMN (1,000–2,000 mg daily) is slower (4–8 weeks) but $200–400/month. Many post-COVID patients respond well to intensive oral dosing alone; start there for 4 weeks and escalate to IV only if response is inadequate.

What if I have persistent stool SARS-CoV-2 RNA?

Viral persistence perpetuates dysbiosis — treating dysbiosis alone won't work because the virus keeps driving it. You need intensive NAD+ restoration to support antiviral immunity, an extended antimicrobial phase, and a Long-COVID specialist consultation to consider antivirals.

Is long-COVID GI dysfunction permanent?

No. Most post-COVID gut dysfunction resolves with intensive mechanistic protocol over 4–6 months. The key requirement is sustained adherence — continuing NAD+ support, avoiding dysbiosis-promoting diet, and ongoing probiotics.

Can I prevent post-COVID relapse?

Yes, with maintenance: indefinite NAD+ support (500–1,000 mg daily), ongoing anti-inflammatory support, dysbiosis-prevention diet, continued probiotics, and quarterly IV NAD+ boosts if relapsing. Most relapses occur when the maintenance protocol is abandoned.

What about persistent post-viral syndrome components?

Post-COVID gut dysfunction is often part of broader post-viral syndrome (brain fog, fatigue, POTS, exertional malaise). NAD+ depletion is central to PVS, so the same restoration protocol benefits most components, though POTS and exercise intolerance need additional management.

How do I know if my dysbiosis is post-viral or another cause?

Temporal relationship is key — post-viral dysbiosis starts within weeks to months after a confirmed COVID infection. Testing also helps: post-viral cases show severe NAD+ depletion (often <300 μM), elevated lactate, and a specific Klebsiella-dominant dysbiotic pattern.

Condition framework

Post-COVID Gut Dysfunction: Mechanistic Root-Cause Analysis

Post-viral gut dysfunction traced through mitochondrial injury, colonocyte bioenergetic failure, and the hydrogen-sulfide SIBO pathway.

How SARS-CoV-2 damages the gut

Post-COVID gut dysfunction follows a mechanistic pattern distinct from other dysbiosis. SARS-CoV-2 damages mitochondrial function through several converging pathways.

Spike-protein-mediated mitochondrial damage. Spike crosses the intestinal barrier, binds ACE2 on enterocytes and endothelial cells, triggers ROS production, and damages mitochondrial Complex I/III/IV — impairing electron transport capacity.

Viral proteases inhibit NAD+ synthesis. SARS-CoV-2 3CL protease cleaves PARP, which normally recycles NAD+. The result is acute NAD+ depletion during infection, which persists post-viral if no recovery protocol is implemented.

Endothelial damage increases permeability. Damaged endothelial tight junctions raise intestinal capillary permeability, allowing bacterial LPS translocation and perpetuating dysbiosis-driven inflammation.

Dysbiosis establishes from epithelial damage. ACE2-expressing colonocytes are directly damaged. Dysbiotic species — Klebsiella and other gram-negatives — exploit the weakened environment, and the dysbiosis persists post-viral if host capacity is not restored.

Why post-COVID dysbiosis persists

Standard dysbiosis treatment (antimicrobials plus diet) fails post-COVID because the primary lesion is viral-mediated mitochondrial damage, not bacterial overgrowth. Colonocyte NAD+ depletion is the bottleneck. Antimicrobials suppress dysbiosis temporarily, but the energy crisis persists, so dysbiosis returns. Recovery requires direct restoration of mitochondrial NAD+ capacity.

Phase 1: Bioenergetic assessment & inflammation quantification (weeks 1–2)

Panel: Organic Acid Test (Krebs cycle intermediates, lactate/pyruvate ratio, oxidative stress markers); intracellular NAD+ panel (often <300 μM post-viral; target >500 μM); mitochondrial damage markers (serum lactate, 8-hydroxy-2-deoxyguanosine, carnitine); inflammation and viral persistence (hs-CRP, IL-6, TNF-α, LPS/LBP, calprotectin); shotgun metagenomics; SCFA panel; barrier markers.

Interpretation: NAD+ <300 with high lactate and high hs-CRP indicates severe viral mitochondrial damage requiring intensive NAD+ restoration. NAD+ 300–400 with moderate lactate suggests standard recovery protocol. NAD+ 400–500 with normal lactate allows accelerated recovery.

Phase 2: Dysbiosis & viral persistence assessment (weeks 2–4)

Post-viral dysbiosis often shows a specific pattern: high Klebsiella, high gram-negatives, low Faecalibacterium and Roseburia, severely low butyrate, elevated zonulin. If viral persistence is suspected, run stool PCR for SARS-CoV-2 RNA and serum D-dimer; consider Long-COVID specialist evaluation if symptom burden is significant.

Phase 3: Recovery protocol (weeks 4–16)

Intensive NAD+ restoration (primary). Three options. Option 1: IV NAD+ 500 mg weekly for 8–12 weeks (most effective; $2,400–6,000 total; noticeable improvement by week 4–6). Option 2: high-dose oral NMN 1,000–2,000 mg daily, split four times daily, for 12–16 weeks. Option 3: combination — IV weeks 1–4, then oral 1,000 mg weeks 5–12, maintenance 500 mg thereafter. Target intracellular NAD+ >500 μM by week 12.

Post-viral dysbiosis protocol (weeks 4–12). Antimicrobials concurrent with NAD+ restoration: allicin extract 450 mg three times daily; berberine 500 mg twice daily; oil of oregano 75–150 mg three times daily; bismuth subnitrate 240 mg twice daily. If inadequate by weeks 8–10, add rifaximin 550 mg twice daily for 14 days. Dietary support: MCT oil 1–2 tablespoons daily, polyphenol-rich foods, high-quality amino acids, small frequent protein feeds. Butyrate restoration: sodium butyrate 1–2 g daily for 12–16 weeks (longer than standard); prebiotics (inulin 5–15 g) post-week 8.

Mitochondrial support and inflammation management (weeks 4–16+). Higher doses than standard: ubiquinol 300–400 mg, B2 150–200 mg, B3 100 mg, L-carnitine 2,000–3,000 mg, magnesium 400–600 mg daily. Iron only if ferritin <50. Anti-inflammatory: curcumin (BCM-95) 500–1,000 mg twice daily, resveratrol 500–1,000 mg, omega-3 2–4 g, vitamin D 4,000–6,000 IU daily if deficient. Mucosal healing at higher doses for persistent post-viral barrier damage: L-glutamine 10–15 g, zinc carnosine 300 mg, bone broth 12–16 oz, slippery elm 2–3 g daily.

Phase 4: Long-term recovery & prevention (weeks 16+)

Timeline: weeks 1–4 NAD+ repletion begins; weeks 4–8 dysbiosis suppression; weeks 8–12 bioenergetic recovery; weeks 12–16 transition to maintenance; week 16+ indefinite maintenance. NAD+ support continues indefinitely (~500–1,000 mg daily, or quarterly IV). Discontinue antimicrobials. Continue dysbiosis support until metagenomics normalize. Transition butyrate to food-based sources. Probiotics from week 8 onward, indefinite. Anti-inflammatory support continues indefinitely.

Maintenance baseline (daily): high-dose NMN, resistant starch, polyphenol-rich foods, probiotics, MCT oil, omega-3. Weekly: intermittent fasting, stress management, breathwork. Quarterly: optional IV NAD+ boost if symptoms recur.

Frequently asked questions

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