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A Functional Medicine Recurrent Bacterial Vaginosis Protocol: Comprehensive Testing, Supplements, and Nutritional Considerations

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A Functional Medicine Recurrent Bacterial Vaginosis Protocol: Comprehensive Testing, Supplements, and Nutritional Considerations

Up to 75% of women will experience a vaginal yeast infection in their lifetime, so it's understandable why many women will assume they have a yeast infection when they begin to experience vaginal symptoms. However, other conditions can present with similar symptoms, and one study showed that only about one-third of women are correct in self-diagnosing vulvovaginal candidiasis. 

Bacterial vaginosis (BV) is actually the most common vaginal condition in women ages 15-44, affecting 21.2 million (29.2%) of women ages 14-49 in the United States. Conventional treatment options focus on quick symptom relief but fail to address the underlying imbalances contributing to recurrent infections that will occur in up to 80% of women after treatment. This article explores the principles of functional medicine and its potential in treating BV, providing a sample treatment protocol that healthcare providers can use and adapt in clinical practice.


What Is Bacterial Vaginosis?

Bacterial vaginosis (BV) is a common vaginal condition characterized by an imbalance in the naturally occurring bacteria within the vagina. Beneficial Lactobacillus bacteria dominate in a healthy vaginal environment. However, in BV, dysbiosis results in an overgrowth of various anaerobic bacteria, such as Gardnerella vaginalis and Prevotella. Without protective Lactobacillus to keep the vagina naturally acidic, vaginal pH rises, and the disruptive bacterial species cause vaginal symptoms. (5

Several factors have been identified as potential contributors to the development of BV. The three main factors responsible for the decline in vaginal Lactobacillus include sexual intercourse without condoms, vaginal douching, and broad-spectrum antibiotics. Although BV is not considered a sexually transmitted infection (STI), sexual activity, multiple sexual partners, and the presence of STIs have been associated with an increased risk of developing BV. Additionally, disruptions to the vaginal microbiome can occur due to hormonal imbalances and gastrointestinal dysbiosis. (5

Untreated BV can lead to several health complications, including an increased risk of contracting an STI (e.g., HIV, HSV, chlamydia, gonorrhea), infection after gynecological surgery, pelvic inflammatory disease, and pregnancy-related complications.

Symptoms of Bacterial Vaginosis

BV doesn't always present with symptoms, so many people don't know they have it. When symptoms do present, the main symptom is copious amounts of thin vaginal discharge with a malodorous, fishy smell. Vaginal discharge can be white, gray, or green. Patients may also report vaginal itching, pain with urination, and pain with sex. (17

Functional Medicine Labs to Test for Root Cause of Bacterial Vaginosis

Diagnosis of BV is typically presumed based on patient-reported symptoms and confirmed by obtaining a vaginal swab and creating a wet mount slide. According to the Amsel Criteria, BV can be diagnosed when at least three of the following criteria are met:

  • Homogenous vaginal discharge is present
  • Vaginal fluid pH is greater than 4.5
  • "Whiff test" is positive: an amine odor is observed when 10% potassium hydroxide solution is added to vaginal secretions
  • Clue cells are visualized on a wet mount

Functional medicine providers may also order the following labs to diagnose BV, identify contributory factors (especially in patients with recurrent BV), and personalize treatment options. These lab results can help doctors personalize treatment recommendations to improve patient outcomes and prevent BV recurrence.

Comprehensive Vaginal Assessment

Various tests can evaluate the health and microbiome of the vagina comprehensively. A vaginosis panel is a helpful tool in differentiating between bacterial vaginosis and vulvovaginal candidiasis; it also includes antimicrobial susceptibility testing to prescriptive and natural agents for identified bacterial and fungal species to guide appropriate treatment recommendations.

For patients with recurrent BV, a vaginal microbiome analysis can identify dysbiotic shifts in the vaginal microbiota, predisposing an individual to overgrowth of opportunistic bacteria. 

Given that BV predisposes an individual to an increased risk for STIs, your doctor may recommend routine STI screening, especially if you are between ages 15-24, have multiple sex partners, have unprotected sex, or have sex while under the influence of drugs or alcohol (5).

Comprehensive Gut Assessment

Patients with recurrent BV should be screened for intestinal dysbiosis, especially if they also experience regular gastrointestinal symptoms. Given the proximity of the vagina and the anus, it is easy for opportunistic pathogens to travel from the gut to the vagina, altering the vaginal microflora. A stool test can be ordered to screen for intestinal dysbiosis and gastrointestinal infections.

Comprehensive Hormonal Assessment

Estrogen stimulates Lactobacillus growth, which produces lactic acid to maintain an acidic pH that discourages harmful bacteria. With low estrogen, Lactobacillus populations decrease, causing an imbalance in the vaginal microbiota and increasing BV risk (16). Additionally, low estrogen leads to thinner, drier vaginal tissues, making them more vulnerable to infection, and alters the vaginal pH, creating a favorable environment for anaerobic bacteria associated with BV (16, 19). A female hormone panel provides a broad assessment of sex hormones important to women's health to screen for hormonal imbalances contributing to poor vaginal health.

Micronutrient Panel

A primary focus of a functional medicine BV treatment protocol is enhancing the immune system to support the body's natural defense mechanisms against infections while promoting a healthy vaginal microbiome. It is important to address any deficiencies in specific micronutrients that can weaken the immune system. Micronutrients such as vitamins A, C, and E, copper, selenium, and zinc play crucial roles in immune function. Micronutrient panels help healthcare practitioners assess the patient's nutrient status and tailor a targeted treatment plan to provide immune support.


Conventional Treatment for Bacterial Vaginosis

Conventional treatment options for BV involve using antibiotics, typically metronidazole or clindamycin, available in oral, vaginal gel, or cream forms. These antibiotics aim to eliminate the overgrowth of harmful bacteria within the vagina. Treatment duration typically lasts for 5 to 7 days. (15

Functional Medicine Treatment Protocol for Recurrent Bacterial Vaginosis

More than 50% of patients treated with first-line antibiotics will experience a recurrence of BV and its associated symptoms within six months of completing treatment. Alternative approaches aim to address the predisposing factors to vaginal dysbiosis to prevent recurrence and reduce reliance on frequent antibiotic use. 

Therapeutic Diet and Nutrition Considerations for Recurrent Bacterial Vaginosis

Diets high in refined carbohydrates and sugars can disrupt the natural balance of the intestinal and vaginal microbiomes, leading to dysbiosis. By limiting the intake of refined carbohydrates and sugars and increasing the intake of fiber-rich foods, it is possible to prevent the development of dysbiosis and maintain a healthy microbiome. 

Certain dietary components have been associated with a decreased risk of severe BV. Adequate intake of dietary folate, vitamin A, and calcium has been shown to have a protective effect. Foods rich in folate include various fruits, vegetables, grains, and legumes. Vitamin A can be obtained from liver, fish, eggs, dairy products, and orange/yellow vegetables. Calcium-rich foods include dairy products, bone-in fish, cruciferous vegetables, and tofu. (5

Probiotics are beneficial bacteria that can help restore and maintain a balanced vaginal microbiome. Probiotic-rich foods like yogurt, kefir, sauerkraut, and kimchi can introduce beneficial bacteria to the gut, improving intestinal and vaginal health.

Supplements Protocol for Recurrent Bacterial Vaginosis

The following sample protocol utilizes natural oral and intravaginal supplements to treat active BV and prevent recurrence. These agents focus on eliminating unwanted vaginal bacteria while re-establishing the intravaginal dominance of Lactobacillus spp. Treatment protocols should be tailored to the patient's needs and focused on addressing the root cause of recurrent BV. The patient's past medical history, symptoms, and lab results should guide treatment recommendations. 

Boric Acid Suppositories

Boric acid restores the acidic pH of the vagina, which creates an inhospitable environment for the overgrowth of harmful bacteria associated with BV. Additionally, it disrupts biofilms produced by bacteria, which can cause treatment resistance and contribute to BV recurrence. Studies show that intravaginal boric acid can be used alone or with antibiotics to treat BV successfully. (1)

Dose (Acute Infection): insert 600 mg intravaginally nightly for seven days

Dose (Maintenance): insert 300-600 mg intravaginally twice weekly for six months

V-Fresh® Suppositories

This vaginal suppository made by Vitanica highlights vitamin C. Vitamin C's acidic and antimicrobial properties have been shown to restore the acidic pH and promote a healthy vaginal environment. One study found that 250 mg of intravaginal vitamin C reduced BV recurrence by nearly 50%.

Dose: insert one suppository intravaginally nightly for six consecutive days per month after menses


Lactobacillus species, particularly Lactobacillus rhamnosus and Lactobacillus reuteri, are commonly used in probiotic formulations for BV treatment. These strains can help restore the natural acidity of the vagina and produce antimicrobial substances that inhibit the growth of BV-causing bacteria. (1)

Probiotic supplements are available in various forms, including oral capsules, vaginal suppositories, or creams. Oral supplementation can help restore the overall microbial balance in the body, including the vaginal microbiota. Vaginal suppositories or creams deliver probiotics directly to the vaginal area, providing more targeted relief. Fem-Dophilus® is Lactobacillus probiotic formula specific to vaginal and urinary tract health that can be taken orally and inserted vaginally.   

Oral Dose: take one capsule by mouth daily for at least three months

Intravaginal Dose: insert one capsule intravaginally once daily for at least three months

When to Retest Labs

A repeat vaginosis panel can be used to confirm the eradication of infection after completing a one-week course of treatment. Chronic dysbiotic patterns and hormonal imbalances typically take at least 3-6 months to correct; repeat microbiome analyses and hormone panels should be postponed at least three months after initiating treatment protocols to accurately assess patient response. 



BV is a common vaginal infection that affects millions of women and often reoccurs after treatment. Unlike conventional approaches that focus on symptom management, functional medicine seeks to identify and address the root causes of BV, such as hormonal imbalances, immune system dysfunction, and disruptions in the human microbiome. By employing a comprehensive and personalized strategy, including dietary modifications, targeted supplementation, and microbiome restoration, functional medicine aims to restore vaginal health and prevent recurrent BV.

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

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4. Chow, K., Wooten, D., Annepally, S., et al. (2023). Impact of (recurrent) bacterial vaginosis on quality of life and the need for accessible alternative treatments. BMC Women's Health, 23(1).

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14. Krasnopolsky, V.N., Prilepskay, V.N., Polatti, F., et al. (2013). Efficacy of Vitamin C Vaginal Tablets as Prophylaxis for Recurrent Bacterial Vaginosis: A Randomised, Double-Blind, Placebo-Controlled Clinical Trial. Journal of Clinical Medicine Research, 5(4).

15. Majeroni, B.A. (1998). Bacterial Vaginosis: An Update. American Family Physician, 57(6), 1285–1289.

16. Olson, O.T. (2022, June 20). Can estrogen improve vaginal health for postmenopausal women? Fred Hutch.

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18. Sobel, J.D. (2007). Vulvovaginal candidosis. Lancet (London, England), 369(9577), 1961–1971.

19. Sweetnich, J. (2023, February 22). An Integrative Medicine Approach to Estradiol Imbalance. Rupa Health.

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