Urogenital Microbiota- Normal Flora of Urinary and Vaginal Tract

Normal floras are the microorganisms (bacteria and fungi) that are constantly present in the skin and mucous membrane of every human in a relatively stable manner, either for a particular period or throughout life, without causing any disease/infection in a healthy individual. It is amazing fact that only 10% of cells in our body is a human cell, and 90% is microbial cells. About 10¹³ human cells are present in the average human body, while about 10¹⁴ bacterial cells are routinely present as normal flora.

The upper urinary tract (kidney, ureter) posterior urethra, and bladder are normally sterile and do not contain any normal flora. Similarly, internal organs of the genital system like the testes, ovary, fallopian tube, and inner uterus are sterile. The anterior urethra of both males and females contains normal flora. Females have a comparatively higher concentration and diversity of urogenital flora. The vagina of females harbors lots of normal flora which is highly influenced by puberty and age.

List of Normal Flora in Urethra (Urinary Tract)

List of Normal Flora in Vaginal Tract

Bacteria are the main flora found in the vaginal tract. Their number and species diversity totally depend on age, hormonal level, pH, and menstrual cycle. 

Gram +ve and Gram -ve Bacteria of Urogenital Microbiota

Staphylococcus epidermidis

• Gram-positive
• Catalase-positive
• Coagulase-negative Staphylococcus 
• Facultative anaerobic cocci bacteria 
• Family –   Staphylococcaceae 
• Characteristic grape-like clusters under a microscope 

It is normally present in human skin. From the skin of the area around the urethral opening, it migrates to the anterior urethral tract and resides there as normal flora. Its presence in a urine culture is regarded as contamination and their growth of less than 10⁴ CFU/mL of urine is non-significant. 

At puberty, the pH of the vaginal tract drops increasing the load of S. epidermidis in the vagina.  

E. coli

• Gram-negative 
• Rod-shaped 
• Lactose fermenting 
• Facultatively anaerobic 
• Mesophilic coliform bacteria
• Family – Enterobacteriaceae
• Genus – Escherichia  

Non-pathogenic E. coli strains (strains other than uropathogenic E. coli strains) are reported as normal flora occasionally in about 10 – 30% of people. 

Neisseria spp.

• Gram-negative 
• Aerobic or facultative anaerobic 
• Cocci (and diplococci) 
• Betaproteobacteria 
• Family –  Neisseriaceae 

It is commensal to the nasopharynx and sometimes they are found in the mucosal lining of the vaginal tract.

N. lactamica, N. bacilliformis, N. polysaccharea are commonly reported commensal species of Neisseria in the urogenital tract. They are reported as normal flora only in very a few populations, about 10 – 30% of people.

Proteus spp.

• Gram-negative 
• Rod-shaped 
• Aerobic and facultative anaerobic 
• Motile bacteria 
• Family Enterobacteriaceae 
• Best known for their swarming colonies

Non-pathogenic strains of Proteus spp. are reported in about 10 – 30% of healthy females as commensal in the vagina and cervix.  

Mycobacterium smegmatis

• Gram-positive (Acid-fast bacilli), 
• rod-shaped, 
• aerobic 
• Actinobacteria 
• Family Mycobacteriaceae 
• Characteristic mycolic acid content in cell-wall making them acid-fast 

M. smegmatis is reported as the normal flora of the urethra. 

Corynebacterium spp.

• Gram-positive 
• Rod-shaped (club-shaped) 
• Aerobic bacteria 
• Family –   Corynebacteriaceae  

Several corynebacteria like C. coyleae, C. aurimucosum, C. amycolatum , C. xerosis, etc. microflora of the urogenital tract. In the vaginal tract, they are reported at puberty when pH drops.  

Lactobacillus spp.

• Gram-positive 
• Rod-shaped 
• Microaerophilic, 
• Non-sporing bacteria 
• Family Lactobacillaceae

It is an important normal flora of the female genital system. 

Lactobacillus is the major genus predominant in the female vagina. It is found in all stages of females; prepuberty, puberty, and postpuberty stages. L. acidophilus is the major species present in the vagina. These bacteria increase the acidity of the vagina and prevent from colonization of pathogenic bacteria. 

L. fermentum, L. casei, L. cellobiosus are other common normal flora.   

Viridans Streptococci

• Gram-positive 
• Anaerobic and facultative anaerobic 
• Catalase-negative 
• Cocci bacteria 
• Family – Streptococcaceae 
• Characteristic arrangement in the form of a chain of spheres

Viridans Streptococci is a group of commensal Streptococci producing alpha-hemolytic colonies in blood agar.  They are commensals of the oral cavity, the gastrointestinal and genitourinary tracts. They are present in the vaginal tract of females at the puberty stage.  

Micrococcus spp.

• Gram-positive 
• Mostly non-motile (few species are motile) 
• Strictly aerobic 
• Cocci in clusters 
• Family – Micrococcaceae

Micrococcus spp. is present in the vaginal tract before puberty and after menopause.  

Peptostreptococcus spp.

• Gram-positive 
• Motile 
• Anaerobic 
• Non-sporing 
• Cocci bacteria 
• Family – Peptostreptococcaceae 

They are the commensals of the vagina, urinary tracts, skin, and GI tract. 

P. anaerobius, P. asaccharolyticus, and P. magnus are species commonly identified as normal microflora in the lower reproductive tract of females. 

Gardnerella vaginalis

• Gram stain variable 
• Non-motile 
• Non-sporing 
• Facultatively anaerobic 
• Coccobacilli 
• Family – Bifidobacteriaceae

 G. vaginalis is normal flora in the vagina of many young adult females. 

Actinobaculum schaalii

• Gram-positive 
• Rod-shaped
• Facultative anaerobic 
• Actinobacteria 
• Family –  Actinomycetaceae 

It is a commensal flora of the human genitourinary tract.

Other Normal Flora of Urogenital Microbiota

Candida spp.

Candida is a genus of yeasts in the Saccharomycetes class. It is present in the vagina in about 30% of females as normal vaginal flora. C. albicans is the most common species, while C. krusei, C. glabrata, C. dubliniesis are occasionally found species.

References

1. Subadh Chandra Parija. Textbook of Microbiology and Immunology. 2^nd edition. Elsevier, a division of Reed Elsevier India Private Limited. ISBN: 978-81-312-2810-4. 
2. Davis CP. Normal Flora. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 6. Available from: https://www.ncbi.nlm.nih.gov/books/NBK7617/?msclkid=9b4b3be8ce7511ec86f02a1257a4cbbb
3. Normal flora: Introduction, types, beneficial and harmful effects (universe84a.com)
4. Normal flora of genitourinary tract – Online Biology Notes
5. Normal Human Microbiota Definition, Types, Advantages and Disadvantages. (microbiologynote.com)
6. The Normal Bacterial Flora of Humans (textbookofbacteriology.net)
7. Willén, M., Holst, E., Myhre, E. B., & Olsson, A. M. (1996). The bacterial flora of the genitourinary tract in healthy fertile men. Scandinavian journal of urology and nephrology, 30(5), 387–393. https://doi.org/10.3109/00365599609181315
8. Lee E, Anjum F. Staphylococcus Epidermidis. [Updated 2021 Dec 8]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2022 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK563240/?msclkid=feaf3730ce7f11ecab40bc5aafcf21d0
9. Liu, G., Tang, C. M., & Exley, R. M. (2015). Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus. Microbiology (Reading, England), 161(7), 1297–1312. https://doi.org/10.1099/mic.0.000086
10. Tlaskalová-Hogenová, H., Stepánková, R., Hudcovic, T., Tucková, L., Cukrowska, B., Lodinová-Zádníková, R., Kozáková, H., Rossmann, P., Bártová, J., Sokol, D., Funda, D. P., Borovská, D., Reháková, Z., Sinkora, J., Hofman, J., Drastich, P., & Kokesová, A. (2004). Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases. Immunology letters, 93(2-3), 97–108. https://doi.org/10.1016/j.imlet.2004.02.005
11. Catlin B. W. (1992). Gardnerella vaginalis: characteristics, clinical considerations, and controversies. Clinical microbiology reviews, 5(3), 213–237. https://doi.org/10.1128/CMR.5.3.213
12. Ryan KJ; Ray CG, eds. (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. ISBN 0-8385-8529-9.
13. Cattoir V. (2012). Actinobaculum schaalii: review of an emerging uropathogen. The Journal of infection, 64(3), 260–267. https://doi.org/10.1016/j.jinf.2011.12.009
14. Olsen, Anne & Andersen, Pernille & Bank, Steffen & Søby, Karen & Lund, Lars & Prag, Jørgen. (2013). Actinobaculum schaalii , a commensal of the urogenital area. BJU international. 112. 10.1111/j.1464-410X.2012.11739.x.