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A Root Cause Medicine Protocol for Patients With Ear Infections: Testing, Therapeutic Diet, and Supportive Supplements

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A Root Cause Medicine Protocol for Patients With Ear Infections: Testing, Therapeutic Diet, and Supportive Supplements

The standard medical approach to treating ear infections is antibiotics. However, roughly 80% of children with acute ear infections improve without antibiotic treatment, and studies show that delaying antibiotic use and implementing a "watchful waiting" approach does not increase the likelihood of developing serious illness for uncomplicated infections. (21

Parental factors and concerns about health complications are commonly reported barriers to adopting a watchful waiting treatment approach (20). Functional and integrative medicine offers another avenue for successfully treating ear infections by addressing key causative factors and utilizing natural nutritional supplements and botanical medicines. 


What Are Ear Infections?

Otitis media is the medical term for an infection of the middle ear space. In the emergency department, ear infections are the second most common pediatric diagnosis, following upper respiratory infections. 80% of children will experience a case of otitis media during their lifetime. Although it can occur at any age, ear infections are most common in children aged 6-24 months. (5

There are two main types of otitis media. Acute otitis media (AOM) is a bacterial or viral infection that causes ear pain, fever, and other symptoms. Bacterial pathogens, Streptococcus pneumoniae, Haemophilus influenza, and Moraxella catarrhalis are responsible for more than 95% of AOM. Otitis media with effusion (OME) is accompanied by fluid accumulation in the middle ear. (5, 19

Ear Infection Signs and Symptoms

Ear infections are often preceded by an upper respiratory infection or allergy, characterized by cough, sore throat, runny nose, fatigue, and mild fever (14, 22). 

Symptoms indicating the presence of an ear infection include unilateral ear pain and muffled hearing. The pain can range in severity. Sudden relief of pain, accompanied by ear drainage, is characteristic of a ruptured tympanic membrane. On physical exam, the tympanic membrane is bulging, red, and has reduced mobility. (11

Many young children will present with non-specific signs and symptoms, including pulling or tugging at the ears, irritability, headache, disturbed sleep, poor feeding and decreased appetite, vomiting, diarrhea, and low-grade fever (5). 

What Are the Possible Causes of Ear Infections?

Ear infections are typically caused by bacteria or viruses that enter the middle ear. These microorganisms can lead to inflammation and the accumulation of fluids in the middle ear, resulting in pain and other symptoms. Various factors can contribute to the development of ear infections, and certain conditions increase the risk of experiencing them. 

The Eustachian tubes connect the middle ear to the back of the throat. Dysfunction of these tubes, which can be caused by factors like allergies, colds, or sinus infections, can lead to inadequate fluid drainage from the middle ear, creating an environment conducive to infection. In children, the Eustachian tubes are shorter, more horizontal, and less efficient at draining fluids than adults. This makes children more susceptible to ear infections. (8, 11

Other primary risk factors for otitis media are food allergies, daycare attendance, secondhand smoke exposure, bottle feeding, pacifier use, family history of ear infections, and a weakened immune system. These genetic and environmental factors increase the likelihood of infection, inflammation, and fluid accumulation in the middle ear. (5)  

Functional Medicine Labs to Test for Root Cause of Ear Infections

For children or adults with recurrent ear infections, labs can help determine underlying factors that create an environment within the inner ear conducive to fostering infection. Results help identify causative factors for infection so doctors can tailor treatment recommendations to expedite healing and prevent future infections. 

Complete Blood Count

A complete blood count (CBC) is a set of labs that measures red and white blood cells to diagnose blood disorders, such as anemia, and imbalances in the immune system, either infection or immunodeficiency. A 2001 study noted that in a group of 680 children with frequent AOM, 20% had a low hemoglobin level. This study confirmed that anemic children have a higher prevalence of AOM than nonanemic children and showed a direct relationship between the severity of anemia and number of AOM episodes.

Allergy Testing

The findings of eosinophils in middle ear mucosal biopsies and histamine in middle ear fluid of patients with chronic OME suggest the causative relationship of allergy to otitis media. Identification and avoidance of allergens results in improvement or resolution of chronic OME. The Full Immunology Panel by Genova Diagnostics includes the measurement of IgE antibodies to food and environmental allergens and IgG antibodies to food sensitivities to screen for allergic causes of ear infections.

Micronutrient Panel

Having optimal micronutrient status is essential to immune function; suboptimal nutrient status in vitamins A, C, E, D, and B12, selenium, and zinc can lead to increased infection rates, inflammation, and allergy. A comprehensive nutritional assessment evaluates antioxidants, vitamins, minerals, fatty acids, and amino acids to detect dietary deficiencies and imbalances.

Conventional Treatment for Ear Infections

In 2004, the American Academy of Pediatrics (AAP) released new recommendations for diagnosing and managing AOM in children, stating clear guidelines for which children should be treated with antibiotics and which can follow a "watchful waiting" course. When observation is used, the doctor should ensure follow-up with the patient and begin antibiotic therapy if the child worsens or fails to improve within 48-72 hours of symptom onset. 

Antibiotic treatment is indicated in the following scenarios (10): 

  • Bilateral or unilateral AOM in children six months or older with severe signs or symptoms, which include moderate-to-severe ear pain, ear pain for at least 48 hours, and fever of at least 102.2°F
  • Nonsevere bilateral AOM in children 6-23 months without severe signs or symptoms

Postponing antibiotic therapy and adopting a watchful waiting approach can be recommended in the following scenarios (10):

  • Unilateral AOM in children 6-23 months without severe signs or symptoms
  • Bilateral or unilateral AOM in children 24 months or older without severe signs or symptoms

These guidelines also propose assessing the patient for pain and, if present, recommending treatment to reduce pain, such as acetaminophen or ibuprofen, regardless of whether antibiotics or watchful waiting is employed (10). 

Integrative Medicine Protocol for Ear Infections

An integrative approach combines conventional and non-mainstream modalities to holistically treat patients and support them in achieving wellness. Regardless of whether antibiotics are employed for treating an acute infection, integrative medicine practitioners will also emphasize complementary lifestyle, diet, and nutritional supplement recommendations customized to the patient based on their risk factors and lab findings.

Therapeutic Diet for Ear Infections

Consumption of refined sugar impairs immune function. Studies have concluded that consuming refined sugars increases systemic inflammation and reduces the activity of neutrophils, a type of immune cell critical in fighting bacterial infections (17). In contrast, an anti-inflammatory, nutrient-dense diet, like the Mediterranean diet, can foster immunity and prevent illness by providing essential nutrients for immune function. (15

An elimination diet that removes allergenic foods from the diet, customized based on allergy testing results, may also be important in treating chronic or recurrent ear infections. Studies suggest a significant association between food allergy and recurrent OME. Perhaps more importantly, elimination diets implemented by patients with identified food allergies significantly improve infection rates. (13, 16

Best Supplements for Managing Ear Infections

The following natural topical and oral supplements can be considered part of a natural, evidence-based treatment protocol for ear infections.

Garlic Oil

Garlic oil ear drops are a popular treatment alternative to antibiotics amongst naturopathic doctors for treating ear infections. Studies indicate that garlic and its active constituent, allicin, are equally or more effective than antibiotics at treating various bacterial species. Specific to otitis media, garlic ear drops have been shown by several studies to be as effective as their prescription antibiotic counterparts in treating otitis media and its associated symptoms (1, 18).

Dose: 3-5 drops applied to the affected ear twice daily

Duration: 3-5 days, or until symptoms resolve completely

Vitamin D

Vitamin D deficiency is common in children with recurrent AOM; serum vitamin D levels less than 30 ng/mL are associated with increased infection recurrence. Daily vitamin D supplementation has significantly reduced the incidence of AOM in children with a history of recurrent infection. (12

Dose: at least 1,000 IU daily; dose may vary based on serum vitamin D level

Duration: Ongoing


Xylitol is a 5-carbon polyol sugar alcohol naturally present in birch sap. A 2011 Cochrane review concluded that prophylactic administration of xylitol in healthy children attending daycare can reduce AOM occurrence by 25%. (10

Dose: Xylitol chewing gum or lozenge administered 3-5 times daily

Duration: Ongoing for infection prophylaxis

When to Retest Labs

For acute infection, patients should be advised to follow up within 72 hours if otitis media symptoms do not improve or worsen on the treatment plan. Retesting labs is unnecessary if clinical symptoms resolve and infection recurrence does not occur. In some cases, a repeat CBC or micronutrient panel may be warranted within 1-3 months to monitor abnormal results observed at baseline.



Ear infections can occur in anyone but are most common in young children. Conventional treatment options include antibiotic therapy or watchful waiting. However, there are many known risk factors and contributing factors to otitis media. A functional and integrative medicine approach considers these, eliminating triggers and supporting immune function to treat and prevent ear infections naturally.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

1. Alhelo , S., Al-Abbasi, A. M., & Saeed, Z. K. (2008). Efficacy of Garlic oil in Treatment of Active Chronic Suppurative Otitis Media. Kufa Med. Journal, 11(1).

2. Azarpazhooh, A., Lawrence, H. P., & Shah, P. S. (2016). Xylitol for preventing acute otitis media in children up to 12 years of age. Cochrane Database of Systematic Reviews, 8.

3. Bhatwalkar, S. B., Mondal, R., Krishna, S. B. N., et al. (2021). Antibacterial Properties of Organosulfur Compounds of Garlic (Allium sativum). Frontiers in Microbiology, 12(613077).

4. Conner, V. (2022, August 26). 9 Evidence Based Remedies That Help Alleviate Acute Ear Infection Pain. Rupa Health.

5. Danishyar, A., & Ashurst, J. V. (2022, January 21). Acute Otitis Media.; StatPearls Publishing.

6. Esaki, Y., Ohashi, Y., Furuya, H., et al. (1991). Histamine-induced mucociliary dysfunction and otitis media with effusion. Acta Oto-Laryngologica. Supplementum, 486, 116–134.

7. Golz, A., Netzer, A., Goldenberg, D., et al. (2001). The association between iron-deficiency anemia and recurrent acute otitis media. American Journal of Otolaryngology, 22(6), 391–394.

8. Hamrang-Yousefi, S., Ng, J., & Andaloro, C. (2021, July 19). Eustachian Tube Dysfunction.; StatPearls Publishing.

9. Hurst, D. S., & Fredens, K. (1997). Eosinophil cationic protein in mucosal biopsies from patients with allergy and otitis media with effusion. Otolaryngology--Head and Neck Surgery: Official Journal of American Academy of Otolaryngology-Head and Neck Surgery, 117(1), 42–48.

10. Lieberthal, A. S., Carroll, A. E., Chonmaitree, T., et al. (2013). The Diagnosis and Management of Acute Otitis Media. American Academy of Pediatrics, 131(3), e964–e999.

11. Limb, C. J., Lustig, L. R., & Durand, M. L. (2023). Acute otitis media in adults. UpToDate.

12. Marchisio, P., Consonni, D., Baggi, E., et al. (2013). Vitamin D Supplementation Reduces the Risk of Acute Otitis Media in Otitis-prone Children. Pediatric Infectious Disease Journal, 32(10), 1055–1060.

13. Nsouli, T. M., Nsouli, S. M., Linde, R. E., et al. (1994). Role of food allergy in serous otitis media. Annals of Allergy, 73(3), 215–219.

14. Paul, C. R., & Moreno, M. A. (2020). Acute otitis media. JAMA Pediatrics, 174(3).

15. Preston, J. (2022, December 20). Building Natural Immunity During Flu Season. Rupa Health.

16. Ruokonen, J., Paganus, A., & Lehti, H. (1982). Elimination diets in the treatment of secretory otitis media. International Journal of Pediatric Otorhinolaryngology, 4(1), 39–46.

17. Sanchez, A., Reeser, J. L., Lau, H. S., et al. (1973). Role of sugars in human neutrophilic phagocytosis. The American Journal of Clinical Nutrition, 26(11), 1180–1184.

18. Sarrell, E. M., Cohen, H. A., & Kahan, E. (2003). Naturopathic Treatment for Ear Pain in Children. PEDIATRICS, 111(5), e574–e579.

19. Searight, F. T., Singh, R., & Peterson, D. C. (2020). Otitis Media With Effusion. PubMed; StatPearls Publishing.

20. Smolinski, N. E., Antonelli, P. J., & Winterstein, A. G. (2022). Watchful Waiting for Acute Otitis Media. Pediatrics, 150(1).

21. Treating ear infections in children. (2017, January 23). Harvard Health.

22. Upper Respiratory Infection. (2021). Cleveland Clinic.

23. Zernotti, M. E., Pawankar, R., Ansotegui, I., et al. (2017). Otitis media with effusion and atopy: is there a causal relationship? World Allergy Organization Journal, 10(1), 37.

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