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How Microbiome-Informed Treatment Could Revolutionize UTI Care

Chances are, you’ve never heard of the urobiome—but it could hold the key to more effective UTI treatment and prevention.

7 minutes

33 Citations

Escherichia coli (a bacterium that can cause urinary tract infections) under a microscope

Pictured above: Escherichia coli (a bacterium that can cause urinary tract infections) under a microscope.

If you’ve ever had a urinary tract infection (UTI), you know how debilitating it can be. Inflammation of the urinary tract leads to the intense urge to pee and a burning sensation that just won’t let up. 

To relieve yourself of the painful infection, you probably took a round of antibiotics or drank copious amounts of cranberry juice to varying degrees of success. Well, it turns out that tending to your vaginal microbiome can lead to more effective prevention and treatment. Wondering what the microbes in your vagina have to do with infections in your urinary tract? Let’s explore.

What Are UTIs and How Do I Know If I Have One?

UTIs are bacterial infections that usually happen in the lower urinary tract.1 Most often, they are caused by Escherichia coli (E. coli) bacteria.2 When certain species of E. coli are present in the gut, they’re nothing to worry about, but when they spread to the urinary tract (often via stool), they become inflammatory and pathogenic, intent on multiplying and expanding into other organs. Klebsiella pneumoniae, Proteus mirabilis, and Staphylococcus saprophyticus can also be microbial culprits of UTIs.2 

Typically, these UTI-causing microbes multiply rapidly in the tissues around the urethra opening, then in the urethra itself, making their way up into the bladder. If not properly treated, they can ascend further up the urinary tract and reach the kidneys to cause kidney infection (pyelonephritis).2,3 

How do these microbes end up in the urinary tract in the first place? Close proximity has something to do with it. There’s only a short distance between the rectum and the urethra opening (just above the vaginal entrance) in women. If you wipe from back to front after using the bathroom, you run the risk of spreading these microbes to the urethra. If you have a vagina, the urethra is a relatively short 1.5-inches long, which means pathogens don’t have to travel very far to flip the urinary microbiome into infection mode. (Thanks, anatomy!) By comparison, those with penises have a lower rate of UTIs, because their urethras are much longer, around 7-8 inches.4 

A woman’s body does have a built-in defense system against these pathogens, though, and it lives in the nearby vaginal microbiome (VMB). (Yes, your vagina has its own microbiome, and your urinary tract does too!)5 

Research shows that a certain family of bacteria in the VMB, Lactobacillus, protect against UTIs by producing lactic acid, hydrogen peroxide, and other compounds that compete with E. coli and other microbial threats before they can reach the urinary tract. Research shows that women who do not have urogenital disease conditions tend to have VMBs dominated by two Lactobacillus species in particular—Lactobacillus crispatus and Lactobacillus jensenii.6 

Similarly to a healthy vaginal microbiome, female urinary microbiomes (or urobiomes) that are protective against pathogenic microbes tend to be dominated by lactobacilli. Just like in the vaginal microbiome, not all Lactobacillus species are created equal: Lactobacillus crispatus seems to be especially beneficial to the urinary ecosystem, while Lactobacillus gasseri has been linked to urinary symptoms.7,8 

Telltale signs of a UTI include feeling as if you need to empty your bladder right away, experiencing painful urination, not being able to fully empty your bladder, or having urine that’s cloudy or slightly bloody.9 Sometimes, it can be hard to distinguish a UTI from a more serious renal infection, so you should always see your doctor when presenting with these symptoms. Seek help right away if you experience fever, back pain, nausea, or vomiting, as these can also be signs that the infection has spread to your kidneys.3

A doctor will be able to diagnose you with a UTI using a quick urine sample. Most likely, they will then prescribe you antimicrobial medication. These should clear things up within a few days, though recurrent infections are common (more on these below).10 

Potential Causes and Contributors to UTIs

UTIs have a way of sneaking up on people of all ages: before the age of 24, one-third of women will have at least one physician-diagnosed UTI, while menopause makes infections more common yet again.3,11,12 This likely has to do with the way hormonal changes during menopause impact the vaginal microbiome—lower estrogen levels correlate to less protective lactobacilli.3,13 

A decline in Lactobacillus species in the vaginal microbiome can also contribute to bacterial vaginosis (BV). Those with BV seem to be more at risk of a urinary tract infection, further suggesting a link between vaginal microbiome imbalance and urinary tract disruption.14,15 

All of this to say: One way to protect against UTIs is to build a strong and resilient vaginal microbiome. To reduce the spread of E. coli and other UTI-causing microbes to the urinary tract, always wipe from front to back after using the bathroom and use a clean washcloth when cleaning the vaginal area to avoid contamination.

While UTIs are not sexually transmitted infections, having sex can increase your risk by transferring potentially pathogenic bacteria from the vagina to the urethra.2,10 Additionally, your partner can introduce new bacteria into the vaginal microbiome that threaten Lactobacillus species dominance.16 Be sure to practice good sexual hygiene to reduce your risk of infection. Urinating after sex may help clear pathogenic bacteria introduced during intercourse, too, though the research on how effective this is is mixed.17

The Genetics of Urinary Tract Infections

Those with structural abnormalities in the urinary tract run a higher risk of infections, and women with relatives who suffer from recurrent UTIs seem to be more likely to get them too, suggesting a family predisposition.9,18

UTI Treatment and Prevention

E. coli can be fickle, and research shows it’s increasingly developing resistance to the antimicrobials typically prescribed for UTIs.19 This means that UTI medications don’t always clear away infections completely, and approximately 26% of women will have an infection return within 6 months of treatment.20 

Studies in mice suggest that recurrent UTIs (at least three infections per year) can cause long-lasting changes to the urinary tract due to inflammation and damage to the mucosal layers of the urethra and bladder.20,21 This remodeling can make it easier for pathogens to reactivate or reinfect these urinary tracts, rendering them more susceptible to future UTIs too.

D-mannose, a simple sugar naturally found in fruits, shows promise as an alternative UTI treatment with a lower recurrence risk than antimicrobials, but more trials on the supplement are needed.22

In the meantime, it’s worthwhile to take a protective approach to UTIs by keeping your urinary (and vaginal!) microbial environments in tip-top shape. Here are a few ways to do so in the name of preventing harmful bacteria from taking hold:

  • Take vaginal probiotics: When your vaginal microbiome is strong and resilient—and most likely, rich in lactobacilli—it has a protective effect against UTIs. Researchers have found that taking a Lactobacillus crispatus intravaginal suppository probiotic after antimicrobials can help prevent recurrent UTIs in premenopausal women.23 Separate research has found that vaginal probiotics tend to be more effective at preventing UTI recurrence than oral ones alone.24
  • Stay hydrated: Staying hydrated can help flush your system of potentially harmful bacteria, and research suggests that drinking an extra 1.5 liters (4-6 cups) of water daily can help prevent recurrent UTIs.25 Drinking cranberry juice may also help reduce the risk of UTIs, but the research on it actually isn’t as strong as old wives’ tales would lead you to believe.26,27
  • Keep your urinary and vaginal microbiomes in good shape: Peeing when you need to, avoiding douching and unnecessary feminine hygiene products, and quitting cigarette smoking are a few more ways to maintain healthy microbial landscapes.28-30

Interestingly, your food choices and gut health might also influence your risk: One study found that 64% of microbes found in urinary microbiota could also be found in the gut, while other research concluded that recurrent UTIs occurred less frequently after fecal transplants.31,32 

These findings offer an exciting new potential for UTI treatment. The next wave of microbiology is holistic and interconnected, traveling from one bodily ecosystem to another.

Putting an End to Painful UTIs

As we learn more about UTIs, we’re finding that there is a strong microbial component to the painful infections.5,33 In the future, treatments that target the vaginal and urinary microbiomes might become the norm—especially as antibiotic resistance increases. 


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