Conditions, Cystitis, Interstitial Cystitis, Overactive Bladder, Urinary Incontinence

Is A Healthy Bladder Really Sterile? A Look at the Urinary Microbiota.

The human bladder and urine have long been considered to be sterile. Emerging evidence challenges this paradigm.

Recent advances in gene sequencing have made it possible to look at the human microbiome (the collective bacteria that live in and on our bodies) and more and more studies are showing an important link between the microbiome and our health.

Standard urine testing methods are limited in their ability to show the true bacterial composition of the urine and their main use is to show certain strains of bacteria that typically overgrow in urinary tract infections.

Genetic screening of the bacterial ‘16S rRNA’ gene has made it possible to look at all the different bacteria living in and on our body.

New studies using this method have shown that urine is in fact not sterile, but harbours communities of living bacteria.

The Urinary Microbiota

The gut microbiome and its role in health and disease has received much attention in recent years. Other body sites have not received the same attention with regards to their individual microbiota but so far we know that the organs with a connection to the outside of the body seem to have their own microbiota – including the bladder.

There is insufficient data to determine what the urinary microbiota should really look like.

A healthy ‘core’ microbiota may exist but we don’t know exactly what it is yet. As with the gut microbiome the problem here is finding people that have not been negatively affected by modern lifestyle who could be representative for a perfectly healthy bladder.

Studies so far have shown that the urinary microbiota fluctuates between the sexes and between different age groups.

Fluctuations have also been found in diseased bladders compared to healthy ones.

Around 85 different species of bacteria have been found in urine so far.

The Urinary Microbiota and Bladder Health

Several studies have shown significant differences between the urinary microbiota of healthy individuals and people with clinical symptoms relating to the urinary tract.

For example, those with symptoms had different types and proportions of Lactobacilli, a bacterial species known to play a role in urogenital health.

Specifically, the strain Lactobacillus Crispatus seemed to be present in healthy bladders, whilst missing or reduced in diseased bladders.

The urinary microbiota seems to change with age, a potential factor in increasing risk for bladder dysfunction in later life.

It is known that the gut microbiota, for example, plays an important role in immunity and, if healthy, can ‘out-crowd’ pathogens and therefore help protect us against infections. The same has been suggested to be true for the bladder.

The urinary microbiota seems to be different compared to healthy individuals in both people with existing symptoms and those who later developed urinary tract infections or other problems.

In those who had symptoms but whose standard urine tests had come back negative the gene sequencing showed raised levels of bacteria that cannot normally be picked up on a standard urine culture test.

Therefore, if you feel like you have an UTI but your tests come back negative it may just be a different type of bacteria!

Hopefully in time better testing will be available.

The urinary microbiota may play a huge role in the health and disease of the urinary tract and with more knowledge we’ll hopefully have more therapeutic options.

More Than Just Bacteria

While the 16S rRNA sequencing allows us to look at the different types of bacteria present in the urine, it does not tell us about other microorganisms that are not bacteria such as yeasts/fungi, protozoa and viruses. Neither do the standard culture tests used by most doctors.

These other microorganisms have also been implicated in bladder conditions and some of them may also be a part of the urinary microbiota.

Other testing methods would be required to capture pathogens that aren’t bacterial – new methods of metagenomics have the ability to sequence bacteria, fungi and viruses.

Again, if you suffer from symptoms but your tests return negative consider that the problems may be caused by a virus or fungi instead of bacteria.

Have you had UTIs without a positive urine culture? Share your story in the comments!

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Nienhouse, V. et al Interplay between bladder microbiota and urinary antimicrobial peptides: mechanisms for human urinary tract infection risk and symptom severity. PLoS One. 2014 [Dec 8;9(12):e114185] available at:

Lewis, DA et al The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol. 2013 [Aug 15;3:41] available at:

Hilt, EE et al Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol. 2014 [Mar;52(3):871-6] available at:

Brubaker, L.; Wolfe, AJ The new world of the urinary microbiota in women. Am J Obstet Gynecol. 2015 [Nov;213(5):644-9] available at:

Whiteside, SA et al The microbiome of the urinary tract–a role beyond infection. Nat Rev Urol. 2015 [Feb;12(2):81-90] available at:

Groah, SL et al Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction. J Urol. 2016 [Aug;196(2):579-87] available at:

Schneeweiss, J. et al The human urinary microbiome and how it relates to urogynecology. Int Urogynecol J. 2016 [Sep;27(9):1307-12] available at:



  • Reply


    February 7, 2017

    Great writing as usual – well researched and easy to understanding. Fascinating bit on the Lactobacillus Crispatus, as it’s also the ‘superhero’ of the vagina:

    • Reply


      February 7, 2017

      Thanks, Sheryl! And also thanks for the link, very interesting!

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