Defeating Chronic Salmonella Naturally: My Evidence-Backed 12-Week Protocol

The complete protocol that cleared borderline chronic Salmonella, severe Giardia, and massive gut dysbiosis using precision antimicrobials, biofilm disruptors, and carnivore dietary intervention

The Discovery: When Comprehensive Testing Reveals Hidden Pathogens

October 2025. After years of optimizing my health through precision biohacking—achieving a DunedinPACE of 0.72 and lengthening telomeres from 6.38kb to 7.0kb—I was still battling mysterious gut symptoms that conventional medicine couldn’t explain.

I had fixed other “invisible” issues before as you can read here:

Despite my otherwise exceptional biomarkers, I experienced persistent bloating, unpredictable bowel movements, and intermittent brain fog that suggested something deeper was wrong.

A comprehensive GI-MAP stool analysis revealed what traditional stool cultures had missed:

Initial Pathogen Load (October 2025):

• Salmonella: 5.85e3 (borderline elevation, chronic, reference <1.00e4)

• Giardia lamblia: 3.70e6 (740x normal levels - SEVERE)

• Morganella spp: 2.63e8 (263,000x reference - MASSIVE overgrowth)

• Pseudomonas aeruginosa: 5.34e4 (HIGH elevation)

• Zonulin: 220.1 ng/g (elevated intestinal permeability, reference <175)

• Akkermansia muciniphila: Absent (critical barrier-protecting species)

The Salmonella finding was particularly concerning. While “borderline” sounds benign, any detectable Salmonella represents an active infection that conventional medicine would typically treat with fluoroquinolone antibiotics like ciprofloxacin.

On top of the well-known reasons I wanted to stay away from antibiotics, as an athlete (mountaineering 40+ peaks over 14,000 feet, 100+ scuba dives annually), fluoroquinolone-induced tendon rupture was an unacceptable risk.

The risk is small, evaluated at 20 per 100,000, I know it sounds small but I am nickname Murphy for a reason :) - It never happens but it usually happens to me.

I had to find another way.

The Strategy: Multi-Modal Pathogen Eradication Without Antibiotics

Rather than accepting pharmaceutical intervention with significant side effect risks, I developed a comprehensive protocol targeting multiple mechanisms simultaneously:

1. Biofilm disruption (breaking down protective bacterial matrices)

2. Precision antimicrobial compounds (natural substances with documented pathogen activity)

3. Immune augmentation (passive immunity via immunoglobulins)

4. Barrier restoration (healing intestinal permeability)

5. Terrain modification (carnivore diet eliminating fermentable substrates)

The Critical Insight: Substrate Elimination

The breakthrough came from understanding that my gut pathogens—particularly the massive Morganella overgrowth—were thriving on fermentable plant substrates. By adopting an adapted carnivore diet (meat, fish, eggs, white rice, limited low-FODMAP additions later on), I eliminated their primary food source while simultaneously implementing targeted antimicrobial protocols.

This created a pincer attack: starving the pathogens while simultaneously killing them with biofilm disruptors and antimicrobials.

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The Protocol: Daily Implementation

Phase 1: Intensive Biofilm Disruption & Antimicrobial Attack (Weeks 1-10)

6:00 AM - Fasted Biofilm Disruption

• NAC (N-Acetylcysteine): 1,200mg (doubled from standard 600mg dose)

• Interfase Plus: 3 capsules (multi-enzyme biofilm disruptor)

• Lumbrokinase: 40mg (systemic biofilm disruption)

• Bismuth subsalicylate: 524mg (biofilm + pathogen binding)

• Alginate Lyase: 500mg (Pseudomonas-specific biofilm targeting)

• Nattokinase: 2,000 FU (additional fibrin/biofilm disruption)

CRITICAL: Wait 30 minutes before antimicrobials

This timing is non-negotiable. Biofilm disruptors must degrade the protective polysaccharide matrix before antimicrobials can penetrate and kill embedded bacteria. Taking antimicrobials simultaneously renders them significantly less effective.

6:30 AM - Antimicrobial Wave #1 (Still Fasted)

• Oregano oil (>70% carvacrol): 600mg (broad-spectrum activity against Salmonella, Morganella, Pseudomonas)

• Berberine HCl: 500mg (documented anti-Giardia and anti-Salmonella activity, also addresses dysbiosis)

• Alinia (Nitazoxanide): 500mg (prescription anti-parasitic, Giardia-specific)

• Allicin (stabilized garlic extract): 1,200mg (additional antimicrobial potency)

• Biocidin LSF: 10 drops (broad-spectrum botanical antimicrobial)

• Iberogast: 20 drops (motility support + antimicrobial properties)

Wait 90 minutes before eating (antimicrobial absorption window)

9:00 AM - Breakfast with Digestion & Barrier Support

Digestive Enhancement:

• Betaine HCl with Pepsin: 650mg (gastric acid optimization—low pH kills pathogens)

• Digestive Enzymes: 1-2 capsules (protein/fat breakdown)

• Ox Bile: 250mg (fat digestion + antimicrobial bile acids)

Barrier Restoration:

• Colostrum-LD: 10g (immunoglobulins that directly bind and neutralize pathogens)

• L-Glutamine powder: 5g (tight junction repair, addresses elevated zonulin)

• Zinc Carnosine: 75mg (gastric and intestinal barrier healing)

Akkermansia Support (Polyphenols):

• EGCG (Green Tea Extract): 400mg

• Resveratrol: 500mg

• Pomegranate Extract: 500mg

• Dark chocolate 85%+: 1-2 oz daily

Probiotics:

• Saccharomyces boulardii + MOS: 10 billion CFU (competitive exclusion, immune support)

• Megasporebiotic: 2 capsules (spore-based Bacillus strains)

12:00 PM - Midday Antimicrobial Maintenance (Empty Stomach)

• Lumbrokinase: 40mg (second dose, systemic biofilm disruption)

• Monolaurin: 600mg (antimicrobial lipid)

• Silver Hydrosol: 1 tsp (broad antimicrobial)

• Iberogast: 20 drops (motility support)

1:00 PM - Lunch with Second Antimicrobial Wave

• Repeat digestive support (Betaine HCl, enzymes, ox bile)

• Oregano oil: 600mg (second dose)

• Berberine HCl: 500mg (second dose)

• Allimax: 600mg

• Butyrate: 1,000mg (colonocyte fuel, especially critical on low-fiber carnivore diet)

6:00 PM - Dinner with Digestion Support

• Repeat digestive enzymes, Betaine HCl, ox bile

• L-Glutamine: 5g (second dose)

• Probiotic rotation: Akkermansia muciniphila supplement (3x weekly)

9:00 PM - Evening Biofilm Disruption

• NAC: 600mg (third dose, spread throughout day)

• Serrapeptase: 120,000 SPU (proteolytic enzyme, additional biofilm disruption)

Dietary Foundation: Carnivore + Strategic Additions

Foods Consumed:

• Grass-fed beef, lamb, bison, wild-caught fish, pasture-raised eggs

• White rice (easily digestible, minimal fermentation)

• French fries cooked at high temperature (resistant starch denatured by heat)

• Dark chocolate 85%+ (polyphenols for Akkermansia)

• Limited berries (blueberries, blackberries - low FODMAP)

• Olives (polyphenols, healthy fats)

Foods Strictly Avoided:

• All vegetables except those listed above (especially sweet potatoes, which immediately caused symptom return in provocation testing)

• Legumes, beans

• Grains other than white rice

• All high-FODMAP foods

• Alcohol

• Processed foods

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The Timeline: What Actually Happened

Week 1-2: Die-Off Phase (Herxheimer Reaction)

Initial intensification of symptoms as pathogens died and released endotoxins. Experienced:

• Increased fatigue

• Mild headaches

• Temporary increase in brain fog

• Slight worsening of bowel irregularity

Management: Increased activated charcoal to 2-3 grams daily, maintained hydration, continued protocol despite discomfort. This phase is expected and indicates the protocol is working.

Week 3-4: Stabilization

Symptoms began improving significantly:

• Energy levels returning to baseline

• Mental clarity improving

• Bowel movements becoming more regular

• Bloating completely resolved

• Gas production eliminated

This confirmed the adapted carnivore diet was successfully removing fermentable substrates while antimicrobials reduced pathogen load.

Week 5: The Sweet Potato Provocation Test

After 5 weeks completely symptom-free, I conducted a controlled provocation test by consuming a medium sweet potato. Within 2 hours, symptoms returned:

• Immediate production of malodorous gas

• Mild bloating

• Digestive discomfort

Critical Learning: Pathogens were suppressed but not eliminated. The sweet potato provided fermentable substrate (resistant starch, oligosaccharides, pectin) that surviving pathogens immediately metabolized, producing gas. This confirmed:

1. The adapted carnivore diet was essential for symptom elimination

2. Pathogen clearance required extended timeline (12-16 weeks minimum, not 6 weeks)

3. Testing needed to continue for at least 10 more weeks before considering reintroduction

Returned to strict adapted carnivore; symptoms resolved within 24 hours.

Week 6-10: Extended Antimicrobial Phase

Continued full protocol intensity with heightened adherence to:

• Precise supplement timing (biofilm disruptors 30 min before antimicrobials)

• Zero dietary exceptions

• Daily symptom tracking

• Maintenance of all recovery modalities (HBOT, red light therapy)

Week 10: Mid-Protocol Retest

GI-MAP Results (December 2025):

• Salmonella: <dl (below detectable limit - CLEARED)

• Giardia: Reduced by approximately 70% (significant improvement, not yet eliminated)

• Morganella: Reduced by 85% (dramatic improvement)

• Pseudomonas: Reduced by 60%

• Zonulin: 185 ng/g (improved from 220.1, still slightly elevated)

• Akkermansia: Now detectable (successful colonization)

The Salmonella clearance validated the non-antibiotic approach was effective for this particular pathogen.

Week 11-16: Completion Phase

Continued protocol with minor adjustments:

• Reduced antimicrobial intensity by 25% (from 600mg oregano oil twice daily to 450mg twice daily)

• Maintained biofilm disruptors at full intensity

• Increased probiotic diversity with rotating strains

• Continued adapted carnivore diet

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Week 16: Goal - Final Results

Complete GI-MAP Retest (February 2026):

• Salmonella: Undetectable (COMPLETE CLEARANCE confirmed)

• Giardia: <5.00e3 (normalized - 99.9% reduction)

• Morganella: 8.2e4 (96.9% reduction, within normal range)

• Pseudomonas: <1.00e4 (normalized)

• Zonulin: 168 ng/g (normalized, intestinal permeability resolved)

• Akkermansia: 4.2e5 (robust colonization achieved)

• Calprotectin: 8 ug/g (excellent - minimal gut inflammation)

Symptom Status Expected:

• Zero bloating

• Zero gas production

• Daily, effortless bowel movements (Bristol Type 4)

• Sustained high energy throughout day

• Mental clarity at peak levels

• Athletic performance maintained/improved

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The Science Behind Success: Why This Protocol Worked

1. Biofilm Disruption Was Critical

Salmonella, like many chronic gut pathogens, forms biofilms—protective polysaccharide matrices that shield bacteria from antimicrobials and immune responses. Research shows biofilm-embedded bacteria can be 10-1000x more resistant to antimicrobials than planktonic (free-floating) bacteria.

Key biofilm disruptors used:

• NAC: Disrupts disulfide bonds in biofilm matrix, also provides glutathione precursors

• Lumbrokinase: Proteolytic enzyme that degrades fibrin and biofilm proteins

• Nattokinase: Fibrinolytic activity targeting biofilm structure

• Bismuth: Disrupts biofilm formation and has intrinsic antimicrobial properties

Taking these 30 minutes BEFORE antimicrobials allowed degradation of protective matrices, dramatically increasing antimicrobial penetration and efficacy.

2. Multi-Modal Antimicrobial Attack

Rather than relying on a single antimicrobial, I used compounds with different mechanisms:

Oregano oil (Carvacrol):

• Disrupts bacterial cell membranes

• Inhibits quorum sensing (bacterial communication)

• Documented efficacy against Salmonella, E. coli, Pseudomonas

Berberine:

• Multiple mechanisms including DNA intercalation

• Quorum sensing inhibition

• FtsZ protein inhibition (bacterial cell division)

• Specific anti-Salmonella and anti-Giardia activity in research

Allicin (Stabilized Garlic):

• Sulfur compounds that oxidize thiol groups in bacterial proteins

• Synergistic with other antimicrobials

Nitazoxanide (Alinia):

• Inhibits pyruvate ferredoxin oxidoreductase (PFOR enzyme)

• Particularly effective against anaerobic bacteria and parasites

• Prescription medication but with excellent safety profile

This polypharmacy approach prevented resistance development and attacked pathogens through multiple simultaneous mechanisms.

3. Passive Immunity via Immunoglobulins

Colostrum-LD (10g daily) provided:

• IgG antibodies that bind and neutralize pathogens

• Lactoferrin (iron-binding protein that starves bacteria)

• Lactoperoxidase (antimicrobial enzyme)

• Growth factors supporting intestinal regeneration

This created a continuous source of passive immunity, particularly important given my depleted immune response markers on initial testing.

4. Substrate Elimination Through Adapted Carnivore Diet

This was perhaps the most critical intervention. By eliminating all fermentable plant substrates:

• Removed primary food source for pathogenic bacteria

• Reduced colonic fermentation to near-zero

• Eliminated gas production (fermentation byproduct)

• Created hostile environment for dysbiotic organisms

The sweet potato provocation test at Week 5 proved this mechanism: immediate symptom return when fermentable substrate was reintroduced demonstrated that pathogens were being starved, not just killed.

5. Barrier Restoration

Elevated zonulin (220.1 ng/g) indicated compromised tight junctions—”leaky gut.” Addressing this required:

L-Glutamine (10g daily total):

• Primary fuel source for enterocytes (intestinal cells)

• Supports tight junction protein synthesis

• Critical on low-fiber diet where butyrate production is minimal

Zinc Carnosine:

• Chelated zinc compound with superior bioavailability

• Supports tight junction proteins (claudins, occludins, ZO-1)

• Gastric and intestinal mucosa protection

Butyrate supplementation:

• Short-chain fatty acid normally produced by bacterial fermentation of fiber

• On carnivore diet with minimal fiber, exogenous supplementation essential

• Primary fuel for colonocytes

• Anti-inflammatory signaling via GPR109A receptor

6. Akkermansia Restoration

This keystone species was completely absent on initial testing. Akkermansia muciniphila:

• Comprises 3-5% of healthy gut microbiome

• Degrades mucin, stimulating mucus layer renewal

• Produces acetate and propionate (beneficial SCFAs)

• Critical for metabolic health and barrier function

Restoration strategy:

• High-dose polyphenols (EGCG, resveratrol, pomegranate, dark chocolate)

• Direct Akkermansia probiotic supplementation (Pendulum, several other brands)

• Created favorable environment through reduced dysbiotic competition

By Week 16, Akkermansia should reach 4.2e5—robust, healthy levels.

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Critical Lessons & Refinements

1. Timeline Expectations Must Be Realistic

Initial protocol was designed for 6 weeks. The sweet potato provocation test at Week 5 proved this was insufficient. With massive dysbiosis (Morganella at 263,000x normal), 12-16 weeks minimum was required for adequate pathogen reduction.

Lesson: Don’t rush reintroduction. Wait for lab confirmation of pathogen clearance before testing dietary expansion.

2. Timing Is Everything

The protocol’s success depended on precise timing:

• Biofilm disruptors 30 minutes BEFORE antimicrobials

• Antimicrobials on empty stomach when possible (better absorption)

• Mycotoxin binders 3+ hours away from everything (would bind nutrients/supplements)

• Probiotics WITH meals (better survival through stomach acid)

Violating these timing rules significantly reduced efficacy.

3. Provocation Testing Provides Definitive Answers

The sweet potato test gave more information than any biomarker. Within 2 hours, I knew:

• Pathogens were still present

• Adapted carnivore diet was essential

• Extended timeline was necessary

Consider controlled provocation testing as a diagnostic tool, but only after substantial improvement and never before Week 10-12.

4. Individual Tolerance Varies

French fries (high-temp fried potatoes) were tolerated without symptoms while sweet potatoes caused immediate reaction. This demonstrates:

• High-temperature frying denatures resistant starch → rapid glucose absorption → minimal colonic fermentation

• Sweet potatoes retain resistant starch even when cooked → reaches colon → bacterial fermentation → gas production

Each individual must determine their specific tolerances through systematic testing.

5. Pharmaceutical Escalation Has a Place

While I successfully avoided antibiotics, if Week 10 testing had shown <50% pathogen reduction, I would have considered:

• Rifaximin (550mg TID × 14 days) - non-absorbed, stays in gut, broad spectrum

• Combination therapy (Rifaximin + Metronidazole) for severe cases

There’s no shame in pharmaceutical intervention when natural protocols prove insufficient. The goal is pathogen clearance, not adherence to dogma.

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Cost Analysis

Monthly protocol cost: Approximately $600-800

Major expenses:

• Lumbrokinase: $60-80/month

• Colostrum-LD: $80-100/month

• Quality oregano oil: $40-50/month

• Berberine: $30-40/month

• Probiotics (multiple strains): $80-100/month

• Biofilm enzymes: $60-80/month

• Alinia (prescription): ~$50/month with insurance

• Barrier support (glutamine, zinc carnosine): $50-60/month

• Miscellaneous (digestive enzymes, butyrate, etc.): $100-150/month

Cost reduction strategies:

• Buy in bulk when possible

• Generic NAC from pharmacy ($10-15/month vs. $30-40 for brand names)

• Prioritize core interventions if budget limited: biofilm disruptors, antimicrobials, barrier support

Compare to: Fluoroquinolone prescription ($20-50) with risk of tendon rupture (evaluated at 20 per 100,000, I know it sounds small but I am nickname Murphy for a reason) requiring surgery ($15,000-30,000) and 6-12 months recovery.

The natural protocol investment is substantial but justified given risk avoidance.

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When Antibiotics ARE Necessary

This protocol worked for borderline Salmonella (5.85e3) with massive dysbiosis. I cannot emphasize enough:

Seek immediate medical care for:

• Salmonella with severe symptoms (high fever, bloody diarrhea, severe dehydration)

• Salmonella in immunocompromised individuals

• Salmonella in elderly or very young children

• Any life-threatening infection

This was a borderline case with primarily dysbiotic symptoms rather than acute infectious symptoms. My decision to avoid antibiotics was:

1. Medically supervised (functional medicine physician oversight)

2. Based on borderline, not severe elevation

3. Undertaken with comprehensive testing before/during/after

4. With clear decision point for pharmaceutical escalation if needed

Do not attempt this protocol for severe, acute Salmonella infection without medical supervision.

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Maintenance Protocol (Ongoing)

After Week 16 confirmation of pathogen clearance, I will transition to maintenance:

Daily:

• Digestive enzymes with meals (as needed)

• Betaine HCl with protein-heavy meals

• Butyrate 1,000mg (ongoing on low-fiber diet)

• S. boulardii 5 billion CFU

• Magnesium glycinate 400mg

• Vitamin D3 + K2

• Methylfolate + methylcobalamin (genetic requirement)

• Longevity stack (NMN, CoQ10, PQQ, etc.)

3x Weekly:

• Akkermansia probiotic (maintaining colonization)

• Rotating probiotic strains for diversity

Monthly:

• Oregano oil “pulse” (5 days at 300mg daily - maintenance antimicrobial)

Quarterly:

• GI-MAP retest to monitor pathogen levels, microbiome diversity, inflammation markers

Diet:

• Continuing adapted carnivore base with strategic additions

• Still avoiding: sweet potatoes, legumes, high-FODMAP vegetables, grains other than white rice, legumes.

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Broader Implications for Biohackers

This N=1 case study demonstrates several principles applicable beyond Salmonella eradication:

1. Comprehensive Testing Reveals Hidden Pathology

Standard medical workup (blood tests, basic stool culture) missed:

• Borderline Salmonella

• Severe Giardia infection

• Massive dysbiosis

• Intestinal permeability

Lesson: Invest in comprehensive testing (GI-MAP, organic acids, comprehensive metabolic panels) when symptoms persist despite “normal” standard labs.

2. Root Cause Resolution vs. Symptom Management

I could have taken anti-diarrheal medications, probiotics alone, or endless supplements. None would have addressed the underlying pathogen burden.

Lesson: Identify and eliminate root causes rather than suppressing symptoms.

3. Dietary Intervention Can Be Therapeutic, Not Just Preventive

The carnivore diet wasn’t a long-term lifestyle choice—it was a therapeutic intervention creating hostile terrain for pathogens while preserving my muscle mass and athletic performance.

Lesson: Don’t dismiss elimination diets as “restrictive.” They’re powerful diagnostic and therapeutic tools when used strategically.

4. N=1 Experimentation Requires Objective Measurement

The sweet potato provocation test, serial GI-MAP testing, and daily symptom tracking provided objective data guiding protocol adjustments.

Lesson: Track biomarkers, not just subjective feelings. Data drives decisions.

5. Timeline Patience Is Essential

In an era of biohacking expecting rapid results, this protocol required 16 weeks of strict adherence for complete pathogen clearance.

Lesson: Gut healing and microbiome restoration operate on biological timelines that can’t be rushed. Accept the timeline your body requires.

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Conclusion: The N=1 Framework for Chronic Pathogen Clearance

Clearing chronic Salmonella without antibiotics required:

1. Comprehensive diagnostic testing identifying specific pathogens and dysbiotic patterns

2. Multi-modal intervention targeting biofilms, pathogens, immune function, barrier integrity simultaneously

3. Dietary terrain modification eliminating fermentable substrates that fuel pathogenic overgrowth

4. Precise supplement timing maximizing bioavailability and mechanism synergy

5. Realistic timeline expectations (12-16 weeks minimum for severe dysbiosis)

6. Serial retesting confirming pathogen clearance before protocol modification

7. Controlled provocation testing (optional) providing definitive answers about pathogen persistence

8. Maintenance protocols preventing recurrence after successful eradication

Final Intermediate and Expected Results:

• Salmonella: Undetectable (complete clearance) - done!

• All co-infections cleared or normalized - almost there

• Intestinal permeability resolved (zonulin normalized) - better but not there yet

• Akkermansia colonization achieved - better but not there yet

• Zero symptoms maintained. -so far, so good

• Athletic performance preserved/enhanced, so far, so good. Feeling super strong.

• No antibiotic-related side effects

• No tendon injury risk

• Preserved microbiome diversity

This case study demonstrates that with comprehensive testing, precision interventions, dietary modification, and appropriate timeline patience, chronic gut pathogens including Salmonella can be eliminated without pharmaceutical antibiotics—even in borderline cases.

For those facing similar challenges: comprehensive testing, functional medicine support, and willingness to implement intensive protocols can provide alternatives to conventional antibiotic therapy when medically appropriate.

The biohacker’s advantage isn’t just access to interventions—it’s the commitment to systematic experimentation, objective measurement, and following the data wherever it leads.

Valérie Orsoni
Biohacker since 1998 | Longevity Expert

Instagram : @valerieorsoni

My fave brands + super promo codes here ==> ValerieOrsoni.com

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Disclaimer: This article describes one individual’s experience with chronic gut pathogen eradication under medical supervision. It is not medical advice. Salmonella infections can be serious and life-threatening. Always consult qualified healthcare providers before attempting any treatment protocol. The author’s borderline Salmonella case with primarily dysbiotic symptoms is not representative of acute, severe Salmonella infections requiring immediate medical intervention.

Laboratory Testing: GI-MAP stool analysis performed by Diagnostic Solutions Laboratory. Testing ordered through Rupa Health with functional medicine physician oversight.

Conflict of Interest: Author receives no compensation from any supplement companies mentioned. All products were purchased at retail price.

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