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

Urinary Dysbiosis: The Underlying Factor Of Bladder Conditions

In last week’s post I talked about the urinary microbiota – the bacterial communities that have recently been discovered to be present in the urinary tract.

We know now that microbes that live in and on our bodies play a crucial role in health and illness. There are friendly and pathogenic microbes (bacteria, fungi etc.) plus opportunistic microbes that can become pathogenic when left unchecked.

When the delicate balance of good vs bad microbes is disturbed we become prone to an array of health conditions and infections. This is called a ‘dysbiosis’.

We know, for example, that dysbiosis of the gut microbiota can predispose us to allergies and autoimmune conditions.

Although we don’t quite know what a healthy urinary microbiota looks like yet, a disturbance of the microbiota has been implicated in different bladder conditions such as chronic UTIs, interstitial cystitis and chronic pelvic pain syndrome.

The Healthy Urinary Microbiota

Bacteria make up 90% of all cells in the body and the symbiotic relationship we have with these microbes is crucial for our optimal health and development.

Although we don’t know what exactly constitutes a healthy urinary microbiota, we already have some ideas about which bacteria should or shouldn’t be present in large quantities in the bladder.

Generally the studies so far show that a healthy microbiota has an increased bacterial diversity and richness compared to some bladder conditions like interstitial cystitis.

However, some conditions such as chronic pelvic pain syndrome actually show a higher diversity of microbes compared to healthy people.

Logically, a healthy bladder also lacks high numbers of pathogens known to cause symptoms, such as E.Coli.

The urinary microbiota seems to differ between sexes and age groups. Both sexes have bacteria of the phylum Firmicutes but females overall have more different kinds of bacteria, especially of the phyla Actinobacteria and Bacteroidetes.

There is some evidence that the number of classes of bacteria (but not necessarily the number of total bacteria) is reduced and/or changed in the elderly and in people receiving antibiotic treatment.

Similar to the vaginal microbiota, the ‘healthy’ female urinary microbiota also harbours high numbers of Lactobacillus. This is followed by Streptococcus, Bifidobacterium and Staphylococcus.

The bacteria most strongly associated with a healthy female urinary microbiota (and vagina) is Lactobacillus Crispatus. Perhaps a potential treatment option for bladder problems? Vaginal suppositories containing this strain are already available but I have not been able to find any preparations for the bladder.

In males, the bacterium Staphylococcus haemolyticus seems to be associated with a healthy bladder.

A lot of work still needs to be done in this field. So far the studies have been small and not necessarily representative of a 100% healthy population.

The Urinary Microbiota in Urinary Tract Infections

UTIs are the most common urologic disease in industrialized nations. Most commonly, UTIs are caused by the well-known pathogen E.Coli.

E.Coli can be detected through the standard culturing methods.  So can other pathogens such as certain strains of Staphylococci, Streptococci, Pseudomonas, Enterobacter, Proteus and Klebsiella.

However, some bacteria are anaerobes, meaning they can’t survive in a culture outside of the body.

Also, UTIs don’t always seem to be caused by only one single species but sometimes by 2 or 3.

Genetic sequencing has made it possible to look at these bacteria as well. It turns out that although E.Coli is still the most common pathogen, there are a number of potentially pathogenic bacteria not showing up in a standard urine culture test:

  • Enteroccocus Faecalis
  • Actinobacteria
  • Bacteroides
  • Facklamia
  • Gardnerella vaginalis
  • Lactobacillus
  • Prevotella


Interestingly, some of these species (such as Lactobacilli) are indicated in a healthy bladder as well but are called ‘opportunistic pathogens’, meaning they can overgrow if other bacteria are diminished.

Therefore, balance seems to be important. If there is a diversity of good bacteria, pathogens can normally not overgrow easily and neither can opportunists.

If your standard urine test consistently shows up negative, it may just be an anaerobic bacteria that is causing all the hassle.

Unfortunately, 16s rNA testing is not yet commercially available for urine testing but hopefully in time it will be.

The Urinary Microbiota in Other Bladder Conditions

A shift in the urinary microbiota has been indicated in several bladder conditions. It may well be that it is the composition of the microbes that determines the condition.

  • Interstitial Cystitis: Overall, IC urine has a much higher proportion of the phylum Firmicutes. It is missing several phyla and the phylum Nitrospirae seems to be only present in IC urine. The types of bacteria seem to be reduced in IC overall but interestingly the amount of Lactobacilli seems to be increased whilst also containing Enterococcus, Atopobium, Proteus and Cronobacter that were not present in healthy urine. Lactobacillus, Gardnerella and Streptococcus have been indicated as possible culprits for IC in several studies. Lactobacilli are generally considered to be ‘friendly’ bacteria and are often found in probiotics. However, there is some evidence that an increased abundance of these bacteria in the urinary tract can be problematic.
  • Overactive Bladder: People suffering from OAB seem to have a reduced overall abundance of bacteria, although the diversity is similar to that of healthy people. Aerococcusand Actinobaculum seem to be exclusive to OAB. Actinobaculum is a possible pathogen.
  • Chronic Prostatitis/Chronic Pelvic Pain: In these conditions, bacterial abundance and diversity seems to be increased rather than decreased. Specifically, higher counts of Clostridia bacteria have been found. Non-bacterial microbes that cannot commonly be detected through urine culture or 16s rNA sequencing have also been found. These included higher counts of fungi such as Candida and
  • Neuropathic Bladder: Actinobaculum sp. Have been found specifically in neuropathic bladder.
  • Urinary Urgency Incontinence: The microbiota of women with Urinary Urgency Incontinence also seems to be more diverse. The species strongly associated with UUI are: Actinobaculum schaalii, Aerococcus urinae, 2 Corynebacteriumspecies, Lactobacillus gasseri, Gardnerella vaginalis and Streptococcus anginosus.

What Can Disrupt the Urinary Microbiota

We know from the gut that several factors can disrupt the microbiome. Although they have not been properly established for the bladder, here are some likely factors:

Antibiotics: Antibiotics (especially the broad-spectrum antibiotics commonly used for UTIs) generally kill all bacteria and not just the pathogens.

Diet: A diet high in processed foods and especially sugar may weaken the immune system and pathogens like to feed on simple sugars.

Exercise: A lack of exercise has been implicated in reduced bacterial diversity.

Stress: Stress can change the pH in the body and different bacteria thrive in different pHs.

Hygiene: The ‘Hygiene Hypothesis’ has implicated that our increased hygiene has led to a loss of bacterial diversity. Antibacterial toiletries and cleaning products are the main culprits.

How to Maintain a Healthy Urinary Microbiota

Again, we don’t have enough data to tell us exactly how to manipulate the urinary microbiota but from what we know the following steps may be helpful:

  • Eat a diet high in fruits and vegetables, especially fibre-rich ones.
  • Eat an ancestral nutrient-dense diet such as outlined in my protocols.
  • Eat probiotic fibres such as inulin and oligo-fructosaccharides.
  • Limit processed foods and sugary drinks.
  • Only use antibiotics if absolutely necessary.
  • Avoid GMOs and pesticides (especially Glyphosate).
  • Don’t use antibacterial soaps, wipes and switch to natural cleaning products.
  • Drink probiotic beverages such as Kombucha, Kefir and Kvass.
  • Move your body, get sunlight and sleep.
  • Reduce or manage stress.


Do you expect your urinary microbiota to be out of balance? What steps have you taken to mitigate this? Let me know in the comments!

Pin it for later:


Schneeweiss, Jenifer et al The human urinary microbiome and how it relates to urogynecology International Urogynecology Journal September 2016 [Volume 27, Issue 9, pp 1307–1312] available at:

Lewis, Debbie A. et al The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults Front. Cell. Infect. Microbiol., 15 August 2013. Available at:

Groah, Suzanne L. et al Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction The Journal of Urology August 2016 [Volume 196, Issue 2, Pages 579–587] 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:

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:

Shoskes, Daniel A. et al The Urinary Microbiome Differs Significantly Between Patients With Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as Between Patients With Different Clinical Phenotypes Urology June 2016 [Volume 92, Pages 26–32] available at:

Imirzalioglu, C. et al Hidden pathogens uncovered: metagenomic analysis of urinary tract infections Andrologia April 2008 [Volume 40, Issue 2, Pages 66–71] available at:

Siddiqui, Huma et al Alterations of microbiota in urine from women with interstitial cystitis BMC Microbiology 2012 [12:205] available at:

Nickel, JC et al Assessment of the Lower Urinary Tract Microbiota during Symptom Flare in Women with Urologic Chronic Pelvic Pain Syndrome: A MAPP Network Study. J Urol. 2016 [Feb;195(2):356-62] available at:


  • Reply


    August 21, 2018

    Hi Layla
    I thought you should know that MicrogenDX is now taking samples from overseas. I am in Australia and had my Microgen test done a month ago. I just called them directly and paid over the phone, it came to $380 AUD which included FedEx delivery both ways. Im sure it will be similar for the UK.
    I was horrified (but not really surprised) to find large counts of enteroccocus faecalis, ureaplasma, prevotella bivia and rhodotulura mucilaginosa. I’m now trying to find a doctor prepared to work with the test results.
    Thanks for a great blog, I always look forward to your posts. I often take them with me to my naturopath visits.

    • Reply


      August 25, 2018

      Hi Lisa,
      Many thanks for letting me know, that’s great news 🙂
      I hope you find a doctor who can help you!

  • Reply


    August 21, 2018

    Very interesting! My IC has been stable for a good 4 years but 4 weeks ago I got a bladder infection and had to take a course of Nitro. Since then my bladder has NOT been happy! I’ve been flaring like never before and I totally agree that my bladder and bowel microbiome has been disrupted. I’ve changed my diet and started bone broth. Unfortunately probiotics are causing flares at the moment but I will reintroduce when my bladder is stronger.

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