Functional Fermentation: Naturopathic Treatment of Entamoeba histolytica

Lauren Geyman, ND

This case highlights how a naturopathic protocol—combining antiparasitic botanicals, targeted probiotics, and fermented foods—successfully eradicated Entamoeba histolytica while restoring gut balance and reducing inflammation.

Abstract:

Infection with the parasite Entamoeba histolytica remains a clinical challenge, often requiring pharmaceutical intervention. However, integrative protocols may offer effective, lower-impact alternatives. This case report details the successful eradication of E. histolytica in a 32-year-old female using a naturopathic approach combining botanical antimicrobials, targeted fermented foods, and gut-repairing nutraceuticals.

The standard of care for treatment of E. histolytica involves treating both symptomatic and asymptomatic cases to prevent spread, typically with metronidazole or tinidazole. In naturopathic medicine, we can provide effective alternatives that go beyond the eradication of the pathogen, individualizing treatment plans to create a more diverse and resilient microbiome. This case exemplifies the potential of botanical medicines in the eradication of intestinal parasites. It also underscores the potential for fermented foods and probiotics to play an active therapeutic role beyond microbial replenishment. Their natural antimicrobial metabolites, postbiotics, and immunomodulatory properties may enhance the effectiveness of botanical protocols and support host-microbe symbiosis.

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Introduction:

Entamoeba histolytica is a protozoan spread by fecal-oral contact, usually through contaminated food or water sources. It infects the intestines and can also cause extra-intestinal manifestations, with the potential to affect the liver, respiratory tract, heart, and brain. Ninety percent of cases are asymptomatic; however, up to ten percent of asymptomatic individuals can develop disease over time.¹ E. histolytica is responsible for 100,000 deaths per year worldwide, though only about five annually in the United States, where amebiasis infections are rare.

Gastrointestinal symptoms are typically gradual in onset (1–3 weeks) and may include diarrhea, bloody stools, weight loss, and abdominal pain. The most common extraintestinal complication is amoebic liver abscess formation, which can cause fever, right upper quadrant pain, hepatomegaly, or jaundice, but which may not present for months to years after infection.¹ Given the risk of spread and severity of potential extraintestinal manifestations, both symptomatic and asymptomatic E. histolytica infections should be treated.¹ Metronidazole is the first-line treatment. While generally well tolerated, some patients may seek alternatives to reduce possible side effects or the potential for antibiotic resistance.³

Herbal medicine has historically been used throughout the world to treat intestinal parasites and can provide a safe and effective alternative to prescriptions.⁵ Using whole plants in combination creates a broad-spectrum effect, where many active constituents can modulate the gut microbiome and target pathogens. Probiotics (fermented food and targeted supplements) can also be used to compete with pathogenic bacteria and address deficiencies in commensal bacteria, building resistance in the gut microbiome.²

Case Presentation:

Patient Profile: 32-year-old female, no significant medical history

Symptoms and Examination: Daily nausea and diarrhea. Intermittent acute upper abdominal pain lasting several hours.

Diagnostic Testing: Comprehensive stool analysis utilizing PCR, ELISA, and LC-MS revealed Entamoeba histolytica infection. Stool analysis also provided information about commensal bacteria.

Timeline:

• September 23, 2024: Patient presents with daily nausea and diarrhea, present for several months. She also reports three episodes within a one-month period of sharp upper abdominal pain accompanied by burping and nausea lasting several hours. Stool analysis is ordered.
• September 28, 2024: Initial stool sample collected.
• October 14, 2025: Stool analysis results reveal high levels of pathogenic E. histolytica and a pattern of dysbiosis. Standard of care is discussed, and the patient declines in favor of a naturopathic protocol, including a broad-spectrum antiparasitic botanical formula, pulsed every other week × 10 weeks (five weeks of active treatment), daily proprietary probiotic containing Akkermansia muciniphila and Bifidobacterium lactis, and daily inclusion of lactofermented vegetables.
• January 18, 2025: Second stool sample collected.
• February 3, 2025: Stool analysis confirms eradication of protozoan infection. Symptoms of sharp abdominal pain, burping, and nausea resolved. Soft stools persist; advised to reduce daily beet intake. Continue probiotics and fermented foods.

Differential Diagnosis:

The differential diagnosis for E. histolytica intestinal amebiasis includes:

• Pathogenic bacteria (Shigella, Escherichia coli, Salmonella, Campylobacter, Clostridioides difficile) — ruled out on stool analysis.

• Inflammatory bowel disease — no blood or inflammatory markers present.

• Irritable bowel syndrome (diarrhea type) — new onset warranted further workup.

Interventions:

Treatment Overview:

• Fermented Foods:
  • Daily intake of at least a combined ¼ cup of lactofermented ginger carrots and red cabbage

• Broad-spectrum antiparasitic herbal formula [Brand name omitted]:
  • Annual Wormwood (Artemisia annua) (Aerial Parts) (4:1 Extract)… 150mg
  • Black Walnut (Juglans nigra) (Hulls) … 150mg
  • Oregano (Origanum vulgare) (Leaves) (4:1 Extract)… 150mg
  • Quassia (Quassia amara) (Bark) … 150mg
  • Clove (Syzygium aromaticum) (Flower Buds)… 100mg
  • Garlic (Allium sativum) (Bulb)… 100mg
  • Plantain (Plantago major) (Leaves) … 100mg
  • Pumpkin (Cucurbita pepo) (Seed) (Extract)… 100mg
  • Barberry (Berberis vulgaris) (Root) (Bark)… 50mg
  • Goldenseal (Hydrastis canadensis) (Aerial Parts)… 50mg
  • Grapefruit (Citrus paradisi) (Seed) (8:1 Extract)… 50mg
  • Thyme (Thymus vulgaris) (Leaves) (4:1 Extract)… 50mg
  • Undecylenic Acid (as calcium undecylenate) … 50mg
  • Berberine Sulfate … 30mg
  • Fennel (Foeniculum vulgare) (Seed)… 20mg
  • Gentian (Gentiana lutea) (Root)… 20mg

DOSAGE: 2 capsules 3x per day for 7 days every other week for 5 repetitions

• Probiotic [Brand name omitted]:
  • Proprietary blend (Akkermansia muciniphila MucT®, Bifidobacterium lactis B420™) with inulin. Proprietary names retained for reproducibility; subsequent references use species names only.

DOSAGE: 1 capsule daily on weeks, also taking the herbal formula, 1 capsule 2x per day on off weeks.

Outcome and Follow-Up:

Following a 10-week pulsed antiparasitic protocol, stool analysis confirmed resolution of E. histolytica. Symptoms resolved except for mild soft stools, which improved with dietary adjustments. Long-term follow-up in April 2025 confirmed stable bowel habits; the patient canceled the July 2025 follow-up due to absence of GI distress.

Discussion:

While protozoan infections are relatively rare in the U.S., gastrointestinal infections remain a leading cause of morbidity worldwide. Stool analysis is a valuable diagnostic tool in patients with abdominal pain or altered bowel habits.^1,3,4 Pharmacological interventions are vital, but alternative modalities merit consideration given concerns about antibiotic resistance and adverse effects of medications like metronidazole.³

Research on the anti-amoebic potential of whole plants and flavonoids is growing.^3-5 Beyond expanding treatment options, a naturopathic lens that considers diet, lifestyle, and microbiome composition can also provide a holistic approach that is individualized and builds resiliency.

Addressing dysbiosis of commensal bacteria may reduce susceptibility to pathogens, and mitigating disruption of the intestinal barrier plays a key role in reducing gut inflammation. In this case, the patient’s deficiency in Akkermansia, Bifidobacterium, and Lactobacillus species provided rationale for targeted supplementation. Recent research highlights the beneficial effects of Akkermansia muciniphila in supporting intestinal flora and barrier integrity.⁶ Additionally, lactofermented vegetables, rich in naturally occurring Lactobacillus species, are well recognized for their role in increasing microbiome diversity and reducing inflammation.⁷

Conclusion:

Broad-spectrum antiparasitic herbal medicine successfully eradicated E. histolytica in this patient, with probiotics and fermented foods—both selected based on the patient’s commensal bacteria deficiencies—complementing treatment to restore microbiome balance and reduce inflammation. This case suggests that naturopathic protocols may offer a safe, individualized approach to managing gastrointestinal infections.

References

1. Akhtar, N., et al. (2024). Prevalence and antimicrobial resistance patterns of Entamoeba histolytica in human infections: A systematic review and meta-analysis. Gut Pathogens, 16, 11. https://doi.org/10.1186/s13099-024-00635-7
2. Calderaro, A., & Bianchi, L. (2023). Current and emerging therapeutic approaches for amoebiasis. Pathogens, 12(12), 1410. https://doi.org/10.3390/pathogens12121410
3. Júnior, L. J. Q., et al. (2024). A review of medicinal plants with activity against Entamoeba histolytica. Journal of Medicinal Plant Research. Advance online publication. https://www.researchgate.net/publication/391775020_A_Review_of_Medicinal_Plants_with_activity_against_Entamoeba_Histolytica
4. National Center for Biotechnology Information. (2020). Amoebiasis. In StatPearls (Internet). StatPearls Publishing. https://www.ncbi.nlm.nih.gov/books/NBK557718/
5. Sandberg-Lewis, S. (2017). Functional gastroenterology: Assessing and addressing the causes of functional gastrointestinal disorders (2nd ed.). Inside Health Education. https://www.functionalgastroenterology.com/product-page/functional-gastroenterology
6. Shirley, D.-A. T., Farr, L., & Watanabe, K. (2018). Impacts of amoebiasis on human health. Pathogens and Global Health, 112(7), 357–365. https://doi.org/10.1080/20477724.2018.1506957
7. Wastyk, H., Fragiadakis, G. K., Perelman, D., et al. (2021). Fermented-food diet increases microbiome diversity, decreases inflammatory proteins, study finds. Stanford Medicine News Center. https://med.stanford.edu/news/all-news/2021/07/fermented-food-diet-increases-microbiome-diversity-lowers-inflammation.html