Learn more


In most cases, cystitis is caused by the appearance of a strain of Escherichia coli in the bladder coming from the intestine. The urinary microbiota is also modified in cases of infection.

Excessive hygiene is a risk factor

Cystitis affects 30% of women over the course of their life. Risk factors include urinary tract obstruction, sexual relations, urinary catheters, neurological dysfunction, and pregnancy. An excess of intimate hygiene is also a risk factor, likely at least as common as a lack of hygiene1,2.

Bacteria of intestinal origin

The infection is of bacterial origin. The strains involved are naturally present in the intestinal microbiota, but are distinct from those that cause intestinal infections3,4Escherichia coli is the primary pathogenic agent and the strains in question are part of the “ExPEC” group (Extraintestinal Pathogenic E. Coli). Comparison of urinary microbiota in women with interstitial cystitis reveals a reduction in microbial diversity and an increase of lactobacilli compared to healthy women5.

Alternatives to antibiotics

Treatment is based on antibiotics, but the increase in antibiotic resistance is a major concern and alternatives are being sought out. Work is being done to prevent recurrences with vaginal applications or oral intake  of lactobacilli. It has proven effective for certain strains of L. rhamnosus, L. reuteri, and L. crispatus6,7,8. The level of proof, however, is too weak for clinical use6,7. Cranberry seems to be effective in preventing recurrence, but it remains to be proven9

1. Whiteside SA et al. The microbiome of the urinary tract--a role beyond infection. Nat Rev Urol 2015 ; 12 : 81-90. https://www.ncbi.nlm.nih.gov/pubmed/25600098
2. 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 ; 52 : 871-6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957746/
3. Köhler CD, Dobrindt U. What defines extraintestinal pathogenic Escherichia coli? Int J Med Microbiol 2011 ; 301 : 642-7. https://www.ncbi.nlm.nih.gov/pubmed/21982038
4. Starcic Erjavec M et al. Virulence potential for extraintestinal infections among commensal Escherichia coli isolated from healthy humans†the Trojan horse within our gut. FEMS Microbiol Lett 2015 ; 362 : fnu061. https://www.ncbi.nlm.nih.gov/pubmed/25657191
5. Siddiqui H. et al. Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiol. 2012 Sep 13;12:205. doi: 10.1186/1471-2180-12-205. https://www.ncbi.nlm.nih.gov/pubmed/22974186. 
6. Beerepoot MA et al. Nonantibiotic prophylaxis for recurrent urinary tract infections: a systematic review and meta-analysis of randomized controlled trials. J Urol 2013 ; 190 : 1981-9. https://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0059210/
7. Reid G et al. Oral use of Lactobacillus rhamnosus GR-1 and L. fermentum RC-14 significantly alters vaginal flora: randomized, placebo-controlled trial in 64 healthy women. FEMS Immunol Med Microbiol 2003 35 : 131-4. https://www.ncbi.nlm.nih.gov/pubmed/12628548.
8. Stapleton AE et al. Randomized, placebo-controlled phase 2 trial of a Lactobacillus crispatus probiotic given intravaginally for prevention of recurrent urinary tract infection. Clin Infect Dis. 2011 May;52(10):1212-7
9. Kontiokari T et al. Randomised trial of cranberry-lingonberry juice and Lactobacillus GG drink for the prevention of urinary tract infections in women. BMJ 2001 ; 322 : 1571. https://www.ncbi.nlm.nih.gov/pubmed/11431298


In its acute form, prostate inflammation, or prostatitis, is most often caused by an infection. In its chronic form, however, it more likely implies an imbalance in the urinary microbiota.

Prostatitis affects around 10% of men in the general population1. Symptoms include burning sensation and urinary frequency. Other symptoms may be present, such as pelvic, perianal, or rectal pain, and fever. 

Acute prostatitis: an infectious origin

Acute prostatitis is often caused by an infection. It can be sexually transmitted (like chlamydia or gonorrhea) but most often it is caused by enterobacteria, with Escherichia coli implicated in 80% of cases1

Microbiota involved in chronic forms

The origin of chronic prostatitis is less clear; bacteria are rarely succesfully isolated and the disease could be multifactorial. The etiology comes simultaneously from infectious and inflammatory factors as well as stress. All three play a significant role in interactions between the microbiota and the body2. In patients, correlations between symptoms, severity of pain and dysbiosis of the intestinal microbiota have been found when compared with healthy subjects2. The urinary microbiota is also disrupted, with an overrepresentation of Burkholderia cenocepacia3 and Clostridia4. Modification of the urinary microbiota via antibiotic treatment may be the cause of chronic prostatitis5. These observations suggest that identifying these bacteria could be useful to establish a diagnosis, while modulating them could be used for treatment2

Chronic forms sometimes difficult to treat

Acute prostatitis is treated with simple antibiotics6. Treatment for chronic forms is more difficult, and sometimes requires a multidisciplinary approach given the more complex etiology2. Probiotic options to rebalance the urinary microbiota are still at an extremely preliminary stage.

1. Nickel JC et al.  Prevalence of prostatitis-like symptoms in a population based study using the National Institutes of Health chronic prostatitis symptom index. J Urol 2001 ; 165 (3) : 842-5 https://www.ncbi.nlm.nih.gov/pubmed/11176483
2. Arora HC et al. Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. Ann Transl Med. 2017 Jan;5(2):30 https://www.ncbi.nlm.nih.gov/pubmed/28217695
3. Nickel JC et al. Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network. J Urol. 2015 Jul;194(1):127-35 https://www.ncbi.nlm.nih.gov/pubmed/25596358
4. Shoskes DA 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, 2016; 92: 26-32. http://www.goldjournal.net/article/S0090-4295(16)00267-3/abstract
5. Amarenco G. Microbiote urinaire et troubles mictionnels. Prog Urol 2015; 25,11:625-27. http://www.urofrance.org/nc/science-et-recherche/base-bibliographique/article/html/microbiote-urinaire-et-troubles-mictionnels.html
6. SPILF 2014.  Mise au point. Diagnostic et antibiothérapie des infections urinaires bactériennes communautaires de l’adulte. http://www.infectiologie.com/UserFiles/File/medias/Recos/2014-infections_urinaires-long.pdf


  • Rheumatoid arthritis

  • Cutaneous

  • Cardiovascular pathologies

  • Pulmonary pathologies

  • Allergics

  • Gyneco

  • Psychiatric and Neurodegenerative


Enter your email address to subscribe to our Newsletter.

BMI overview

The Biocodex Microbiota Institute: an international leader in microbiota


Choose the language in which you wish to receive the newsletter