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Upper Fermenting Gut Protocol

Jun 23, 2025

Overview

Discussion centered on the concept of "upper fermenting gut," its health consequences, and a detailed protocol for addressing it through dietary changes and targeted supplementation, with supporting commentary on conventional medical practices, toxins, and practical advice for implementation.

The Upper Fermenting Gut: Problem and Symptoms

  • Upper fermenting gut is frequently overlooked by conventional medicine but drives significant pathology.
  • It results from excessive carbohydrate intake overwhelming the gut's natural defenses, leading to bacterial and fungal overgrowth.
  • Symptoms include bloating, reflux, indigestion, nocturnal cough, burping, belching, and systemic effects like brain fog and fatigue.
  • The overgrowth produces toxic byproducts requiring detoxification by the liver and can contribute to various chronic diseases.

Diet and Addiction

  • Carbohydrate and sugar consumption is described as addictive, contributing to the persistence of upper fermenting gut.
  • A carnivore (meat, fish, eggs) or ketogenic, low-carb diet is recommended to "starve" pathogenic microbes.
  • The "addiction test" is suggested: avoid foods you can't stop eating after the first taste.

Protocol to Eliminate Upper Fermenting Gut

  • Two-pronged approach: restrict carbohydrates and kill remaining microbes.
  • Three recommended tools: high-dose vitamin C (contact-kills microbes), iodine (broad-spectrum microbial killer), and MSM (kills upper gut microbes, acts as a prebiotic in lower gut).
  • Emphasis on low cost and practicality for sustained use.

Supplementation and Maintenance

  • Maintenance includes ongoing vitamin C, iodine, and periodic MSM dosing with mineral replenishment.
  • Additional supplements: multivitamin, multi-mineral, fish oil, and high-dose vitamin D (10,000 IU daily).
  • Epsom salt baths and heating regimes suggested for detoxification of fat-soluble toxins.

Addressing Conventional Wisdom and Misconceptions

  • LDL and high cholesterol are not considered harmful; lowering them via vegetable oils or statins is criticized.
  • Modern dietary guidelines and the use of processed foods, gluten, and dairy are discouraged.
  • The negative influence of "big pharma" and "big food" on medicine and public health policy is highlighted.

Micronutrient and Fat Considerations

  • Butter may be tolerated; other dairy products and gluten grains are not recommended.
  • Animal fats, tallow, cold-pressed organic oils (olive, avocado) are favored; industrial seed oils are rejected.

Fasting and Meal Timing

  • Intermittent fasting (eating within a 6-hour window), occasional one-meal days, and periodic multi-day fasts are encouraged for autophagy and metabolic health.

Recommendations / Advice

  • Address the fermenting gut with diet and targeted supplements before focusing on broader detox or maintenance.
  • Start interventions slowly if health is poor; increase gradually.
  • Apply practical, affordable solutions over expensive or complicated regimens.

Action Items

  • TBD – Individual: Begin low-carb or carnivore diet to starve upper gut microbes.
  • TBD – Individual: Implement vitamin C (first thing in the morning), iodine (midday), and MSM (three days a week).
  • TBD – Individual: Add a multivitamin, mineral supplement, fish oil, and vitamin D daily.
  • TBD – Individual: Consider Epsom salt baths or gentle heating regimes for detox support.
  • TBD – Individual: Avoid gluten, most dairy, and industrial seed oils; include healthy animal and cold-pressed fats.

Questions / Follow-Ups

  • Source of MSM remains to be confirmed.
  • Further clarification may be needed for those with specific health issues (e.g., severe thyroid dysfunction, extreme sensitivity to detox).