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✦ PROTOCOL · NO 03

Stomach trouble,
two ways.

Reflux, bloating, or recurring pain after meals: the symptoms that creep back no matter what you try. On the left, the conventional path through PPIs, endoscopy, and the GI specialist. On the right, the gut-first path that elimination diets, microbiome science, and vagal protocols are built on.

Omeprazole 20mg, take one daily
20% WEEKLY REFLUX
2 TRACKS · 10 STEPS
UPDATED MAY 2026
TRACK · A · conventional

Conventional medicine

Rule out structural disease, suppress acid, treat H. pylori if present, escalate to scope and specialist if persistent past 8 weeks.

TRACK · B · holistic

Gut-first / holistic

Treat the gut as a system that responds to inputs: food triggers, microbiome composition, meal timing, and vagal tone. Reset before reaching for acid blockers.

Week 0
Primary care visit

History, abdominal exam, red-flag screen (weight loss, blood, dysphagia, anemia, age >55 new onset).

$80-$220 · Family / internal medicine MD
Day 1
Symptom + meal log

Log every meal, drink, supplement, symptom severity (0-10), and sleep. Identify pattern: postprandial, fasting, nocturnal, stress-linked.

$0 · You · 7-14 day journal
Week 1-8
PPI trial + H. pylori test

Omeprazole 20-40mg daily x 8 weeks. Stool antigen or urea breath test for H. pylori; triple therapy if positive.

$15-$60 OTC PPI · $90-$220 breath test · Self-administered + lab
Week 1-6
Low-FODMAP elimination

6-week strict elimination of fermentable carbs, then structured reintroduction. Most-validated diet for IBS-type symptoms.

$0 DIY · $140-$280 dietitian visit · Monash Univ. protocol · RD-guided optional
Week 8-12
Upper endoscopy (EGD)

Direct visualization of esophagus, stomach, duodenum. Biopsy for Barrett’s, eosinophilic esophagitis, celiac, gastritis.

$650-$3,500 · Gastroenterologist · outpatient endo center
Week 6-12
Microbiome rebuild

30+ plant species / week. Targeted fermented foods (kefir, sauerkraut, yogurt). Optional stool / microbiome test for personalization.

$0 food-based · $59-$370 testing · Will Bulsiewicz MD · Tim Spector (ZOE)
Month 3+
GI specialist work-up

For persistent symptoms: pH-impedance study, gastric emptying scan, colonoscopy if indicated. Functional dyspepsia / IBS workup.

$280-$540 first visit · Gastroenterology · functional GI
Month 2+
Meal timing + vagus tone

12-14 hr overnight fast. Slow eating, no liquids with meals, post-meal walks. Vagal exercises: humming, cold face dunks, breath holds.

$0 · Self-directed · Andrew Huberman protocols
Month 6+
Procedural / surgical

For refractory GERD: Nissen fundoplication, TIF, LINX device. Hiatal hernia repair if structural.

$8,400-$18k fundoplication · GI surgeon · ASC or hospital
Ongoing
Maintenance practice

30+ plants / week. Fermented food daily. 12 hr fast. Stress regulation: breathwork, walking, sleep. Reassess every 8 weeks.

$0 · You · daily
✦ THE GUT-FIRST SOURCES

Who built
track B.

Consolidated from what these doctors, scientists, and podcasters publish, with edits where peer-reviewed work disagrees.

CONVENTIONAL MEDICINE · SOURCES
  • AGA Clinical Practice GuidelineSpecialty body
  • JAMA · PPI safety meta-analysesMeta-analysis
  • Cochrane · H. pylori eradicationSystematic review
GUT-FIRST / HOLISTIC · SOURCES
  • Will Bulsiewicz MD · @theguthealthmdGI MD · 1.4M
  • Tim Spector · ZOE HealthEpidemiologist · King’s College
  • Monash University · FODMAPResearch protocol
  • Andrew Huberman · Huberman LabStanford neuroscientist