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A Functional Medicine UTI Protocol: Specialized Testing, Therapeutic Diet, and Supplements

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A Functional Medicine UTI Protocol: Specialized Testing, Therapeutic Diet, and Supplements

Urinary tract infections (UTIs) are the most common outpatient infection in women. Up to 60% of women experience at least one UTI in their lifetime, and many of these infections will be recurrent. The standard of care treatment for UTIs is antibiotics. However, the rising concern over antibiotic resistance and the recurrence of UTIs has led to exploring alternative treatment options. Integrative and functional medicine offers a promising avenue for managing and preventing recurrent UTIs.


What Is a UTI?

A UTI is an infection in the urinary system, which includes the kidneys, ureters, bladder, and urethra. Most UTIs involve the lower urinary tract: the bladder (cystitis) and the urethra (urethritis). Recurrent UTIs are defined as two urinary tract infections in six months or three in one year. (7

Women are up to 30 times more likely to get UTIs than men due to several anatomical and physiological factors. One key factor is the shorter length of the female urethra compared to the male urethra. The urethra is the tube through which urine exits the body. It is relatively shorter in women, making it easier for bacteria to travel into the bladder and cause infection. Additionally, the close proximity of the female urethra to the anus creates a higher risk of bacterial contamination from the intestinal tract. Hormonal changes during menstruation, pregnancy, and menopause can also affect the urinary tract, making it more susceptible to infection. (7

Although rarer, UTIs can also affect children and male adults. It is estimated that 2.5% of children and 12% of men will develop a UTI in their lifetime. (14)

UTI Signs & Symptoms

The hallmark symptoms of a UTI are pain with urination (dysuria), urinary frequency, and blood in the urine (hematuria) (7). A UTI may also present with some or all of these (14): 

  • Foul-smelling and/or cloudy urine
  • Urinary urgency with little urinary output
  • Pain and pressure in the lower abdomen or pelvis
  • Confusion, fatigue, and weakness (more common in older patients)

Fever, back pain, chills, nausea, and vomiting are symptoms that indicate the infection has reached the kidneys. Pyelonephritis is more serious than lower UTIs and requires immediate medical intervention. (16

What Causes UTIs?

UTIs are caused by the invasion of microorganisms within the urinary system. More than 90% of bladder infections are caused by Escherichia coli (E. coli), a bacteria that resides in the gastrointestinal tract. However, other bacteria and yeast can also cause UTIs when they are translocated from the vagina, skin, and anus into the urethra. This can happen due to improper wiping techniques after bowel movements, sexual intercourse, or the use of unclean or contaminated objects during genital contact. (7)

Certain factors can increase the risk of developing UTIs, such as anatomical urinary tract abnormalities, urinary catheterization, a weakened immune system, hormonal changes, and conditions that hinder complete bladder emptying. Sexual activity and using spermicides or diaphragms can also contribute to UTI development. (22

Functional Medicine Labs to Test for Root Cause of UTIs

Functional medicine labs should be used to confirm the diagnosis of UTI and the causative pathogen. For patients with recurrent UTIs, specialty labs also assist in a holistic diagnostic evaluation, getting to the root cause of dysbiosis and immune system dysfunction that can contribute to repeat infections. 


The presence of nitrites and leukocyte esterase measured by urinalysis are the most accurate indicators of acute UTI in symptomatic patients. A colony count of at least 103 colony-forming units per mL of a uropathogen on culture is diagnostic of UTI. (8

Assessment for Dysbiosis

For patients with recurrent UTIs, excluding dysbiotic vaginal and gastrointestinal patterns is very important because pathogens originating from the vagina and/or digestive tract can recolonize the urinary. Stool and vaginal tests are available to assess the gastrointestinal and vaginal microbiomes, screening for dysbiotic patterns and overgrowth of pathogenic microorganisms that act as the source for recurrent infections.

Comprehensive Hormone Panel

Low estrogen contributes to reductions in healthy Lactobacillus bacteria, thinning of the vaginal tissues, and weaker bladder contractions (7). These changes make it easier for pathogenic organisms to cause UTIs. Additionally, chronic elevations in cortisol, such as what happens during chronic stress, suppress certain aspects of the immune system, making it harder for the body to fight off infection naturally. A comprehensive hormone panel helps identify reproductive and stress hormone imbalances that may contribute to recurrent UTIs. 

Other Lab Tests to Check 

Functional medicine providers may also recommend the following labs better to tailor treatment recommendations for patients with recurrent UTIs.

Complete Blood Count (CBC)

A CBC with differential is a panel that provides valuable information regarding the distribution and number of white blood cells in the blood. It is common to see elevations in white blood cell counts during acute, active infection. However, low white blood cells can indicate the presence of chronic infection and/or immunosuppression, indicating the need for additional evaluation. 

Comprehensive Metabolic Panel (CMP)

A CMP is a comprehensive panel that includes markers of kidney function and blood glucose. Diabetes mellitus, indicated by elevated blood sugar, can increase the risk for UTI and other infections. Untreated UTIs and pyelonephritis can damage the kidneys, so monitoring kidney function markers may be an essential aspect of preventive care for some patients.

Nutritional Assessment

Imbalances in essential vitamins, minerals, and antioxidants may contribute to systemic inflammation and a suppressed immune system. Using a nutritional assessment to screen for these imbalances can help tailor recommendations regarding diet and supplements to support the patient's natural immune system to fight and prevent infection.


Imaging, including ultrasound, computed tomography, and cystoscopy, may be recommended for patients with recurrent UTIs or who don't respond to treatment to examine the urinary tract for urogenital anomalies, disease, and injury. (7)


Conventional Treatment for UTIs

Conventional treatment for UTIs typically involves using antibiotics to eliminate the bacteria causing the infection. The choice of antibiotic depends on factors such as the type of bacteria involved and the individual's medical history. Commonly prescribed antibiotics for UTIs include trimethoprim-sulfamethoxazole and nitrofurantoin. The duration of antibiotic treatment is typically around 3 to 7 days, although it may vary depending on the severity of the infection. Low-dose daily prophylactic antibiotic treatment may be recommended for patients prone to UTI. (1

Functional Medicine Treatment Protocol for UTIs

Through a functional medicine lens, the goal of treating UTIs is to eliminate active infections and address underlying factors that increase the risk for recurrent infections. Prescription medications may be recommended as antimicrobial therapy in some instances, but functional medicine doctors often utilize antimicrobial botanicals as first-line options to reduce the risk of antibiotic resistance. While individual circumstances and lab results should always be used to customize treatment plans, the rest of this article will provide a framework for a functional medicine protocol to treat and prevent UTIs. 

One of the best ways to prevent UTIs is by practicing good genital hygiene practices, which include wiping from front to back, regularly changing menstrual products, avoiding douching and thong underwear, and thoroughly cleaning sex toys after use. Additionally, urinating before and after sex is important to flush out bacteria introduced into the urethra during sexual activities. Using birth control methods aside from diaphragms and spermicidal agents can also reduce the risk of UTI. (7

Therapeutic Diet and Nutrition Considerations for UTIs

Drinking an adequate amount of water is crucial for maintaining proper urinary tract health. Sufficient hydration helps flush out bacteria from the urinary system, reducing the risk of infection (14). General recommendations suggest drinking at least half of your body weight in ounces of water daily to prevent dehydration

Maintaining an overall healthy, balanced, and anti-inflammatory diet supports immune function and limits the consumption of foods that can irritate the urinary tract, such as alcohol and artificial sweeteners. Research suggests that a vegetarian diet can help prevent UTIs because it limits exposure to E. coli through meat products. Additionally, plant-based diets are rich in fruits, vegetables, and whole grains, which contain essential nutrients with natural antimicrobial and anti-inflammatory properties. (7)

An anti-Candida diet may be considered for patients with UTI caused by Candida spp or other yeast. This diet eliminates or reduces the intake of sugar, refined carbohydrates, high glycemic fruits, dairy, and alcohol - foods that potentially promote the overgrowth of yeast in the body.

Supplements Protocol for UTIs

The following supplements can be recommended as natural alternatives to antibiotic therapy in treating and preventing UTIs. 

Not included in this protocol is an antimicrobial agent specific to treating dysbiosis or infection within the gastrointestinal tract and/or vagina. Establishing healthy intestinal and vaginal microbiomes is important for long-term success, so this should not be overlooked. Based on the patient's labs, customize antimicrobial and probiotic treatment recommendations to eliminate opportunistic pathogens and restore balance to the microbiota.


This botanical formula by Thorne, containing uva ursi, buchu, echinacea, and berberine, can be used as an alternative to antibiotics in uncomplicated UTIs. These naturally antimicrobial herbs kill and prevent unwanted bacteria from attaching to the walls of the urinary tract and soothe irritated tissues.

Dose: 3 capsules four times daily

Duration: 7 days

*Note: Patients should be advised to contact their doctors immediately if UTI symptoms worsen during treatment or do not resolve after completing one week of therapy.


In 2020, the FDA authorized a health claim that stated cranberry products help reduce the risk of UTI in healthy females. Multiple meta-analyses have shown cranberry can reduce the risk of recurrent UTIs, including those in high-risk populations, by up to 51%. (13, 23

Active Infection: 1,000 mg three times daily for seven days

Prevention: 1,000 mg daily 


D-mannose inhibits bacterial adhesion to the lining of the urinary tract, preventing the colonization of infectious bacteria in the urinary tract (7). Studies support using D-mannose in treating and preventing UTIs. (19)  

Active Infection: 2 grams twice daily for seven days

Prevention: 1 gram daily


Probiotics reduce the risk of recurrent UTIs by regulating and restoring a healthy urogenital microflora. Lactobacillus spp., especially L. rhamnosus and L. reuteri, most effectively prevent recurrent UTIs in women. (11

Dose: 1-10 billion CFU daily

Duration: 7 days to 12 months

When to Retest Labs

Any active infections identified on baseline labwork should be monitored after antimicrobial therapy to confirm eradication. Additional labs can be remeasured 3-6 months after baseline to monitor nutrient deficiencies, dysbiosis, blood sugar dysregulation, and inflammation. 



Functional medicine offers a comprehensive and holistic approach that goes beyond conventional methods to treat and prevent UTIs. This article explores the application of functional medicine principles in managing UTIs, emphasizing the importance of identifying underlying root causes such as imbalances in gut health, hormonal disruptions, and immune system dysfunction. By addressing these factors through simple hygiene practices, personalized dietary modifications, and targeted supplementation, functional medicine aims to provide long-lasting relief from UTIs and prevent recurrence. This integrative approach to UTI treatment offers a promising avenue for those seeking a more holistic and individualized approach to their urinary health.

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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