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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

Nearly one in three women will experience at least one urinary tract infection by the time they are 24 years old. Almost half of all women will experience one urinary tract infection during their lifetime. With staggering numbers underscoring its ubiquity, it's clear that urinary tract infections are more than just a routine inconvenience—they're a pressing healthcare challenge that demands effective diagnosis and treatment protocols. (14)


What Are Urinary Tract Infections?

Urinary tract infections (UTIs) are infections that occur within the urinary system, which comprises the kidneys, ureters, bladder, and urethra. Most UTIs occur within the lower urinary tract, specifically the bladder (cystitis) and the urethra (urethritis).

Urinary Tract Infection Signs & Symptoms

UTI presents with three hallmark symptoms:

  • Pain with urination (dysuria)
  • Frequent urination of small volumes
  • Urinary urgency  

Other common signs and symptoms associated with UTI include (10, 26):  

  • Foul-smelling and cloudy urine
  • Blood in urine (hematuria)
  • Lower abdominal or pelvic pain
  • Confusion, fatigue, and weakness (more common in elderly patients)
  • Suprapubic tenderness on physical exam

Fever, chills, back pain (costovertebral angle tenderness on physical exam), rapid heartbeat, nausea, and vomiting indicate pyelonephritis (kidney infection).

Root Causes of Urinary Tract Infections

Understanding the root cause of a UTI helps personalize treatment plans to ensure effective eradication of the infection and prevent future ones from recurring. 

Pathogenic Organisms

UTIs are caused by the invasion of pathogenic microorganisms into the urinary tract. 

More than 90% of bladder infections are caused by Escherichia coli (E. coli), a bacteria that resides in the gastrointestinal tract. Other bacteria that cause UTIs include:

  • Enterobacter
  • Proteus
  • Enterococcus
  • Klebsiella 

While rarer, UTIs can be caused by fungi and viruses. Candida albicans is the most common fungus responsible for causing UTIs. Causes of viral UTIs include cytomegalovirus (CMV), type 1 human polyomavirus, and herpes simplex virus (HSV). (20


Women are up to 30 times more likely than men to get UTIs because of the anatomy of the female genitourinary system. The female urethra is much shorter than a man's, making it easier for bacteria to travel into and colonize the bladder. A woman's urethral opening is also close to the vagina and anus, sources of germs that cause UTIs like E. coli. (25

Anatomical abnormalities in the urinary tract can impair the ability to completely empty the bladder, increasing the risk of UTI. For instance, urethral strictures, bladder outpouchings, or urinary tract obstructions can impede the complete emptying of the bladder. Residual urine left in the bladder provides a favorable environment for bacterial growth, leading to an increased risk of infection. (27

Hormonal Changes

Drops in estrogen that occur prior to menstruation and during menopause cause thinning and dryness of urethral tissues, making them more susceptible to infection.

UTIs are one of the most common infections during pregnancy. In addition to the uterus compressing the bladder, elevated progesterone levels can cause smooth muscle relaxation, causing urinary stasis and backward movement of urine from the bladder to the kidneys. (16

How to Diagnose a Urinary Tract Infection

A comprehensive patient history is the most important tool for diagnosing UTI. The onset of urinary frequency and dysuria in the absence of vaginal discharge has a positive predictive value for UTI of 90%.

A focused physical examination and laboratory urinalysis can complement the patient's medical history and confirm the diagnosis of a UTI.

Step 1: Perform Urinalysis

Urinalysis and urine culture performed on a midstream, clean-catch urine sample improves the accuracy of a clinical UTI diagnosis. Urinalysis involves examining the physical and chemical properties of urine. Nitrites and leukocyte esterase on dipstick urinalysis strongly suggest UTI. (21

Urine culture complements urinalysis by identifying the specific microorganism causing the infection and determining their antibiotic susceptibility. A colony count greater than or equal to 103 CFU/mL of a uropathogen is diagnostic for UTI. Antibiotic susceptibility testing guides targeted antibiotic therapy, ensuring effective treatment. (10

The following are urinalysis and culture testing options:

Step 2: Testing to Uncover Root Causes of Recurrent UTIs

Additional testing can uncover the root cause(s) of UTI to prevent recurrence. Recurrent UTIs are defined as at least two urinary tract infections in six months or three in one year. In a primary care setting, 53% of women over age 55 and 36% of younger women report a UTI recurrence within one year of a resolved infection. (13)

Microbiome Analysis

Vaginal and gastrointestinal pathogens can translocate into the urethra, causing UTI. Dysbiosis in either the vaginal or intestinal environments, therefore, can be the source of recurrent UTIs. Assessing the microbial makeup of both environments can be done with comprehensive vaginal and stool cultures.

Tests to assess the vaginal microbiome: 

Tests to assess the intestinal microbiome: 

Comprehensive Hormone Testing

Imbalances in female sex hormones estrogen and progesterone can induce microbial and anatomical changes in the urogenital tract, making it easier for pathogenic organisms to cause UTIs (6).  

Chronic stress can suppress the immune system, making it harder for the body to fight infection naturally. Salivary cortisol is a testing method commonly used to assess the HPA axis as a marker of chronic stress.

These panels are options to measure female reproductive hormones and cortisol: 


Imaging may be recommended for patients with recurrent UTIs or who don't respond to treatment to examine the urinary tract for anatomical anomalies, disease, and injury. Ultrasound, computed tomography (CT), and cystoscopy are typical imaging procedures ordered for a more extensive evaluation of the urinary tract. (23


Treatment Plan for Urinary Tract Infections

Below is a step-by-step treatment plan that can be personalized for patients struggling with uncomplicated or recurrent UTIs. 

1. Eradicate Infection

Here's Why This Is Important: 

Prompt eradication of UTI prevents undesirable health complications if the infection spreads to the kidneys or into the bloodstream.

How Do You Do This?

Acute, uncomplicated UTIs can be treated with antibiotics or natural supplements.

The first-line antibiotics for treating acute, uncomplicated cystitis include: 

  • Nitrofurantoin 100mg twice daily for five days
  • Trimethoprim-sulfamethoxazole 160 mg/800 mg twice daily for three days
  • Fosfomycin 3 grams in a single dose 

Antimicrobial and antiadhesive herbs and supplements kill and prevent pathogens from adhering to the urinary tract's lining. Research shows that the following supplements effectively treat uncomplicated UTIs. 

2. Reduce Inflammation

Here's Why This Is Important:

UTIs can cause inflammation in the urinary system, contributing to symptoms even after the infection is eradicated. Anti-inflammatory measures help palliate uncomfortable urinary symptoms during treatment and prevent symptoms from lingering after active treatment is complete. 

How Do You Do This?

Water-soluble mucilage herbs, including corn silk and marshmallow root, are often taken in tea form to promote adequate hydration, increase urine flow, and help flush bacteria from the urinary system. Additionally, they soothe irritated urogenital tissues. 

3. Reestablish a Healthy Urogenital Microbiome

Here's Why This Is Important:

Lactobacilli species of bacteria predominate the genitourinary tract of premenopausal women. Lactobacilli produce hydrogen peroxide, which inhibits pathogens from adhering to the bladder walls. 

How Do You Do This?

According to a systematic review, probiotics, especially Lactobacillus rhamnosus and reuteri, effectively prevent recurrent UTIs in women. Studies on UTI treatment and prevention have used probiotic doses ranging from ten thousand to ten billion CFU daily for five days to 12 months. 

4. Establish Good Hygiene Practices

Here's Why This Is Important:

Good hygiene prevents UTI by minimizing bacterial contamination of the urethra. 

How Do You Do This? 

The following hygiene practices prevent the spreading of bacteria into the urethral opening (22, 23):  

  • Wipe from front to back after using the toilet
  • Urinate before and after sexual activity
  • Stay well hydrated by drinking at least half your body weight in ounces every day
  • Avoid douching

The Risks of Untreated Urinary Tract Infections 

Untreated UTIs increase the risk of the following serious health complications:

  • Kidney infection and kidney damage
  • Adverse pregnancy outcomes, including premature delivery and low birth weight, when UTI occurs during pregnancy
  • Urethral narrowing
  • Sepsis

UTI Case Study

Read about a real case study here:

How Megan Beat Her Recurring Urinary Tract Infections by Treating Her Gut


Key Takeaways:

  • Effective diagnosis and treatment of urinary tract infections (UTIs) are paramount in alleviating symptoms, preventing complications, and promoting overall well-being.
  • Treatment of acute infections should encompass antimicrobial and palliative therapies to eradicate infection and alleviate urinary symptoms.
  • Motivating patients to implement preventive measures can help reduce the burden of UTIs and minimize the risk of recurrent infections.
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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