Conditions, Interstitial Cystitis

The Bladder Microbiota and Interstitial Cystitis

If you have been following this blog for a while you’ll hopefully know about the role of the microbiome in health, including bladder health. I’ve posted about this topic several times. Today I’d like to look more specifically at the bladder microbiota and interstitial cystitis (IC).

Although a diagnosis of interstitial cystitis is usually made when there are urinary symptoms in absence of an infection, this doesn’t mean that no microbes are present. In fact, we know now that the bladder is not sterile as previously believed but harbours its very own microbiota.

We also know that current gold standard testing misses many microbes and therefore misses infections.

The Bladder Microbiota in Interstitial Cystitis Sufferers

Different researchers have looked into the microbiota in IC sufferers and have come up with very different findings.

Two things were the same in all the studies though: the microbiota in IC sufferers was different from healthy people and it was less diverse than that of healthy people [1, 2].

However, the individual microbiota were still quite different, even amongst the IC sufferers [1].

A recent study concluded that IC sufferers seemed to have less Lactobacilli bacteria and specifically less of the strain Lactobacillus acidophilus [1].

However, a previous study had shown that IC sufferers (although having reduced diversity) had a 30% increase of Lactobacilli compared to healthy controls [2]. Other bacteria identified were Prevotella, Peptoniphilus, Anaerococcus, Staphylococcus, Finegoldia, Gardnerella (a bacterium normally found in the vagina, known to trigger repeated infections), Streptococcus and Dialister.

IC sufferers also showed raised levels of inflammatory chemicals produced by macrophages, which are cells that can ‘scavenge’ pathogens. Whilst it is not clear whether these raised inflammatory chemicals could have changed the composition of the bladder microbiota [1], the presence of macrophages does suggest one thing: infection.

Lactobacilli: Friend or Foe?

You may have heard of Lactobacilli bacteria as being some of the ‘friendly’ bacteria commonly found in supplements and you might be surprised to hear the name in relation to disease.

Well, Lactobacilli doesn’t equal Lactobacilli – it is the ‘genus’ (or class) of bacteria, which contains many different species, some beneficial and some maybe not so much.

Take Lactobacillus acidophilus for example. This strain is commonly found in beneficial bacteria supplements. It is believed to support the health of the vaginal microenvironment and when it was present in IC sufferers it was associated with less severe symptoms [1] than those sufferers who didn’t have it.

Generally, Lactobacilli are considered to be non-pathogenic, rarely causing an infection in humans. However, there is some evidence that certain species of Lactobacilli (for example Lactobacillus delbrueckii [3]) may in fact cause urinary tract infections. For example, it has been found that reduction of Lactobacilli coincided with reduction of symptoms [2].

Generally, Lactobacilli in urine samples are believed to be contaminants and not infectious organisms – therefore, they are probably not even looked for in an urine culture.

Why Diversity is Important

Unfortunately, we do not know for sure what a healthy microbiota looks like exactly and maybe there are many variations of a healthy or a sick microbiota.

But diversity is important. Reduced diversity has been associated with different disease states [2].

If we think of the microbiota as an ecosystem it makes sense that diversity is important. We can observe in nature that the health of an ecosystem depends on all the species in the ecosystem. Take one species away and the ecosystem may collapse (for example, take away a predator and its prey will overgrow and potentially destroy other members of the ecosystem, like certain plants).

The same applies to the microbiome – some species may be killed off (by antimicrobials for example), allowing other species to overgrow.

Too much of one thing is hardly ever good. Therefore, one species that might normally be harmless could start causing issues when overgrown.

Balance is Key

The problem is that current UTI testing does not identify all cases of infections, or we might not even know about all potential species causing infections yet.

Therefore, many cases of IC may just be missed infections or an imbalance in microbes.

What can we do to help?

  • Putting in good microbes (fermented foods, beneficial bacteria supplements)
  • Stop disrupting the microbiome (unhealthy diet and lifestyle, antimicrobials, stress)
  • Feed the good bugs (fibre!)

Do you suffer from IC and expect and imbalance in your bladder microbiota? What have you done about it? Let me know in the comments!

Pin it for later:


Peter Sidaway Changes in urinary microbiota correlate with IC/BPS Nature Reviews Urology | Published online 1 Mar 2017

  1. Abernethy et al Urinary Microbiome and Cytokine Levels in Women With Interstitial Cystitis OBSTETRICS & GYNECOLOGY VOL. 129, NO. 3, MARCH 2017
  2. Siddiqui, Huma et al. “Alterations of Microbiota in Urine from Women with Interstitial Cystitis.” BMC Microbiology 12 (2012): 205. PMC. Web. 4 Feb. 2018.
  3. Darbro, Benjamin W., Brian K. Petroelje, and Gary V. Doern. “Lactobacillus Delbrueckii as the Cause of Urinary Tract Infection .” Journal of Clinical Microbiology 47.1 (2009): 275–277. PMC. Web. 4 Feb. 2018.


  • Reply


    March 11, 2018

    I’d like to try fermented foods to try to help my microbiome, but they’re known to trigger IC flares. Are there any fermented foods that are safe for IC?

    • Reply


      March 11, 2018

      Hi Chelsea, fermented foods can trigger IC flares in people with mast cell issues, as the bacteria produce histamine. If you don’t have mast cell issues, then fermented foods should be fine. For people with mast cell (histamine) issues, D-lactate free beneficial bacteria supplements or soil strain bacteria supplements could be an option as these don’t produce histamine.

  • Reply

    Charlotte Staggs

    November 28, 2020

    What specific fermented foods are recommended? Do fermented foods not contain a high degree of acid?

    • Reply


      November 28, 2020

      Sauerkraut, kimchi, kvass, kombucha, kefir etc could all be beneficial, but it is very individual. Yes, fermentation causes acidity, so people with problems around acidic foods may not tolerate them. In this case, beneficial bacteria supplements may be better tolerated.

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