The genitourinary microbiome refers to the aggregate of bacteria, archaea, and fungi that may colonize the human genital and urinary tract.
Some microbiome analyses also include any viruses and protists present.
This term encompasses both the human urinary microbiome (urobiome), as well as the genital microbiome, and is a subset of the human microbiome.
Of the genitourinary microbiome, only the vaginal microbiome has been thoroughly characterized.
Next-generation sequencing has allowed researchers to use 16S ribosomal RNA to identify organisms present in asymptomatic or healthy individuals.
There is a long-standing misnomer that urine that does not grow colony-forming units (CFUs) in standard microbiological cultures.
There is now evidence to support colonization of the female bladder as well as the male lower urinary tract.
Perturbations in the genitourinary microbiome could have implications for patients with urinary tract infections (UTIs), sexually transmitted infections (STIs), interstitial cystitis and chronic prostatitis.
Urinary microbiome:
In both males and females, Bacillota, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria make up the general phyla of the human urinary microbiome.
Firmicutes/Bacillota and Bacteroidetes account for about 74% of the urinary microbiome.
Studies up until 2018 found the general bacterial species composition of the urinary microbiome to consist of primarily Lactobacillus, Gardnerella, and Streptococcus.
however, the genitourinary microbiome was notably excluded from analysis.
Gender and age disparities
There is a higher prevalence of organisms in females corresponding with healthy vaginal flora.
The urinary microbiome changes with age, possibly due to changes in hormones, diet, and metabolism.
Women tend to have a decrease in Lactobacillus abundance after menopause, suggesting hormones may affect microbiome composition.
The most common disease-causing organisms in urinary tract infections are Escherichia coli, Enterococcus faecalis, Klebsiella species, Pseudomonas aeruginosa, Proteus species and Streptococcus species.
Many of these species are represented in the urobiome.
Factors that influence the makeup and proportions of organisms in the urobiome include age, gender, and diet.
Molecular studies suggests that non-culturable or slow-growing organisms may be present in urine samples and not identified due to the limitations of standard microbiological culture parameters.
Uncontaminated urine samples are difficult to obtain without bladder catheterization due to the proximity of the urinary system to genitals and the GI tract.
A single genitourinary microbiome community does not exist.
The vaginal microbiome has been thoroughly characterized.
Organisms belonging to the vaginal flora may be seen in urine cultures due to contamination or collection method.
The most abundant organisms in the vaginal microbiome are Lactobacilli, which do not grow in standard microbiological urine cultures.
Some common organisms from this genus found in the vaginal microbiome include L. crispatus, L. iners, L. jensenii, and L. gasseri.
Characterization of the microbiome of the internal male reproductive system has not been performed.
Males were not previously known to have a genital microbiome due to the connection to the urinary system, but research no longer supports sterility of the urethra and/or bladder in males or females.
Disturbances in the microbiome may affect the occurrence or severity of sexually transmitted infections.
Antibiotics are administered to treat an overgrowth of disease-causing bacteria, affecting the microbiome.
Decreasing relative abundance of the genital or urinary microbiome can lead to recurrent urinary tract infections and yeast infections in the vagina.
Lactobacilli typically prevent overgrowth of Candida species in the vagina.
Chronic antibiotic use can lead to the formation of antibiotic-resistant organisms and contribute to the incidence of polymicrobial urinary tract infections.