The bladder microbiome or urinary microbiome (UM) is the community living inside the urinary tract. It is made up of many hundreds of microbial strains including bacteria, fungi and viruses. But how does this apply to a urinary tract infection?

UTIs are usually considered to be caused by one strain of bacteria. The most common single bacterial pathogens identified in laboratory reports for urinary tract infections are:

  • E-Coli which accounts for around 80-85% of infections
  • Klebsiella – 11%
  • Pseudomonas – 11%
  • Staphylococcus saprophyticus – 5-10%
  • Enterococcus – 7%

However researchers and specialist clinicians have recently found using enhanced microbial testing resources that chronic UTIs can be polymicrobial – caused by several different types of bacteria. This means the bacteria identified in your UTI may well be different to that found in others and can explain why people experience differing symptoms. It may also mean that the urinary microbiome plays a part in the development of a UTI – but should it be seen as a friend or a foe?

But isn’t the urinary tract is sterile?

No, this is a common misapprehension. The bladder was thought to be a sterile environment with pathogenic (infection causing bacteria) introduced externally – through the urethra – but research published in Frontiers in Cellular and Infection Microbiology in 2013 and the Journal of Clinical Microbiology  in 2012 shows bladder microbial communities including bacteria, fungi, viruses and moulds, when enhanced testing methods are used.

In the study The Urinary Microbiome and Its Contribution to Lower Urinary Tract Symptoms published in 2017, Linda Brubaker and Professor Alan J. Wolfe of the Department of Obstetrics & Gynecology, University of California San Diego; Department of Urology, University of California San Diego and Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago noted:

“Modern techniques avoiding selective culture indicate the presumption of sterility of urine is potentially wrong. There are many potential consequences of microbial influence which may be important for generation of symptoms and disease, or conceivably may be protective. To establish the relationship will require considerable research progress, but the findings potentially could be rewarding for understanding disease mechanisms and possibilities for clinical intervention”.

There is enough research now to confirm that the microbes within the urinary microbiome are not contaminants, as often noted in current laboratory analysis, and are culturable under the right conditions.

Challenges in understanding the urinary micobiome

An important first step is to understand the normal urinary microbiome and whether disruption of this can result in someone being more likely to get to UTIs. Additionally, understanding the mechanisms of how bacteria co-operate to create multi bacterial infections is also needed. Many bacteria may be harmless commensals in the urinary tract, what is the trigger that causes them to develop into infection causing microbes? And how do biofilms fit into this picture? All part of the ongoing research work taking place across key research laboratories globally.

One study published in 2019 in The Journal of Clinical Micobiology, analysed the urine of normal controls against that of patients with lower urinary tract symptoms (LUTS) and those in treatment for chronic LUTS.  Using next generation sequencing, it was found that in the normal controls 580 identifiable species were discovered, those patients with lower urinary tract symptoms had 590 species and patients in treatment for lower urinary tract symptoms had 600.  There was a 500 species overlap between all 3 groups. Indeed the 20 most common uropathogens were found in 81% of study participants with lower urinary tract symptoms as opposed to 79.0% of control recruits. With such close similarities in the 3 cohort groups, the study authors argue that definitive, specific bacterial causation for chronic cystitis is currently difficult to achieve.

In a 2020 study published in Frontiers in Microbiology, the team at Loyola University in Chicago and the University of San Diego examined the prevalence of uro-pathogenic E-coli, described as the most common cause of urinary tract infections, in symptomatic women who noted lower urinary tract symptoms (LUTS) alongside asymptomatic women with no symptoms. Their results indicated that even with the presence of E.Coli or genomic variations of E.Coli strains in urine samples, this could not predict UTI symptoms. In fact the asymptomatic women recruited for the study had higher levels of E.Coli in their samples but reported no LUTS. They hypothesized that UTI symptoms are more likely to be the result of multiple factors, including the urobiome composition and that the entire urinary microbiome should be considered when determining the cause(s) of a urinary tract infection.

Professor Alan Wolfe of  Loyola University explains more about the urinary microbiome in this video presentation from the 2019 Large Urology Group Practice Association (LUGPA) Chicago meeting (audio/video).

In 2023 the Bladder Infection and Immunity Group (BIIG) based in the Department of Renal Medicine at University College London published a discussion paper in The Society for Mucosal Immunology acknowledging that the emerging field of the urobiome fails to clarify the issue of discriminating between true UTI-causing pathogens from normal bladder commensals.

Recognising the female urinary microbiome (FUM)

Laboratories are now able to focus on the diversity of the urinary microbiome and the female urinary microbiome using enhanced metagenomic testing – analysis of the genetic DNA of microbes – and Enhanced Quantitate Urinary Cultures (EQUC) to identify strains, virulence factors and their effect on the microbiome of the bladder and bladder wall mucosa.  These identification methods are recent and were unavailable to researchers previously.

More longer term studies are needed and given the impact of intracellular/biofilm infections, analysis not just of urine but also the bladder wall mucosal microbes will add to this growing area of study.

In 2018, a study by researchers at the Hudson Institute of Medical Research identified a collection of microbes living in the bladder which co-exist in the vagina, which they have christened the ‘bladder microbiome’. These bugs appear to be important for human health.

Researchers say the discovery suggests some UTIs may be caused by this community falling out of balance. It also suggests potential new treatments which could rebalance the levels of good and bad bacteria in the bladder – rather than just killing them.

They note:

“Previously, it was thought that a healthy vaginal microbiota was the major factor in preventing ascending infections from migrating into a sterile bladder. The data presented herein suggests that microbial sharing between the vaginal and bladder microbiota is not limited to known and emerging uropathogens, such as E. coli and S. anginosus, but also includes health-associated commensal bacteria, such as L. iners and L. crispatus. Now, we propose that some bacteria that can reside in both the bladder and vagina could provide protection against urinary infection, suggesting that the microbes of these adjacent pelvic floor niches could be considered to be a single urogenital microbiota.

This insight, combined with this unique genome-sequenced culture collection, should alter the way we view the bacteria of the female pelvic floor both by enabling further research and by providing new diagnostic and treatment options for UTIs, urgency urinary incontinence, and other associated urinary tract disorders”.

In another study published in 2017: The Female Urinary Microbiota/Microbiome: Clinical and Research Implications, Linda Brubaker with Professor Alan Wolfe note:

“The FUM can be diverse. From more than 1,000 study participants, researchers have detected almost 300 different species in about 150 different genera. What are those bacteria doing? Which ones are beneficial and should be protected? Which ones are pathogenic? Do presently unknown pathogens cause disorders that currently have no etiology, such as Urinary Urge Incontinence and Painful Bladder Syndrome? Do some bacteria (e.g. Gardnerella vaginalis) facilitate colonization by uropathogens such as Uropathogenic E-coli (UPEC)? Do others inhibit the growth of pathogens? How do beneficial and pathogenic bacteria interact with the urothelium and its innate immune system?”.

Fungi and the urinary mycobiome

A further research area for the FUM is the effect of the introduction of fungal spores into the bladder environment. The vaginal microbiome is dominated by Lactobacillus which create an acidic environment thought to protect women against sexually transmitted diseases and opportunistic infections such as thrush and bacterial vaginosis. If there are changes in these lactobacillus levels, it affects the vaginal microbiome and as mentioned above, infections can arise. For example, a study published in the American Society of Microbiology in 2014 by the team at Loyola University noted that an upsurge of Lactobacillus gasseri within the bladder has been associated with urinary urgency incontinence (UUI) in women. They noted

“Given the significant overlap of UUI symptoms with those of urinary tract infections, it is possible that UUI may have a microbial component”.

More about vaginal microbiome and the important of vaginal PH.

As the term “microbiome” is frequently used to refer to the study of bacteria alone, the term “mycobiome”, a combination of microbiome and mycology or the scientific study of fungi, has been created to understand the fungal community within a specific part of the human body. This field is still in its infancy. This lack of knowledge can be attributed to the lack of advanced diagnostic tools to study fungal species up until recent years and their interactions with us the human host.

At present the interaction of fungi with the bladder urothelium are entirely uncharacterized. As yet:

  • It is not yet know whether fungi may attach directly to the wall of the bladder to form mixed biofilms with bacteria or grow in colonies in the urine itself, never making direct contact with the bladder wall.
  • Could fungi remain dormant within cells of the bladder wall, as can be seen with E. coli intracellular bacterial colonies?
  • How do fungi react to host and environmental factors and how do they react to stress that may contribute to growth conditions for these types of infections?

The effect of viruses in the urinary microbiome

In addition to bacteria, the microbial communities that inhabit the human body include other organisms such as fungi and viruses. These are involved in complex interactions with each other and surrounding human cells. Of particular note are the interactions between bacteria and their natural predators: bacteriophages (viruses that infect bacteria). Unfortunately whilst studies have focused on the human gut and the interaction between bacteria, fungi and viruses, the urinary bladder is understudied. Urinary microbiome research has primarily focused on the bacterial make up of the community, with only a few studies showing that the urinary microbiota also includes viruses.

A study published in Frontiers in Microbiology in 2015 sought to identify a whether there is a population of viruses unique to the human urinary tract and whether this community membership may be affected by the health of the urinary tract including the effect on them of bacterial UTIs.

All research is in its infancy and key questions that need to be answered are:

  • Can all microbes can be identified against known existing bacterial strains?
  • Are the microbes in the bladder commensal, pathogenic or capable of altering a healthy urinary microbiome? In other words, what are their virulence factors?
  • What influence do fungal microbes play in infection?
  • How do viruses affect the UM? Do they contribute to a urinary tract infection, help control bacterial replication through the presence of bacteriophages or simply replicate symptoms of a UTI?
  • How do factors such as age, body mass index, hormonal stresses and other health problems affect someone with a recurrent or chronic urinary tract infection?
  • Are there genetic dispositions which mean some are more prone to urinary tract infections and the risk of a chronic infection as opposed to others?

All of this will feed into how recurrent and chronic infections develop and how they may be treated in the future. This paper published in the American Journal of Microbiology in 2020 reviews many of the questions and possible answers around the urinary microbiome.