Urinary Microbiome: Yin and Yang of the Urinary Tract

Abstract

The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.

Keywords: disease; health; infection; microbiome; sequencing; urinary tract.

Figure 1

Microbial identification methods for urine samples. Bacteria in urine samples can be identified by different methods: culture-based methods (standard urine culture or enhanced quantitative urine culture (EQUC)) or sequencing-based methods (amplicon sequencing or shotgun sequencing).

Figure 2

Collection methods for urine samples. Urine samples can be collected by different methods: collection of spontaneous midstream urine, catheterization with an intermittent or permanent catheter or suprapubic aspiration from the bladder. Differences between these methods lie in the grade of possible bacterial contamination from other areas such as the urethra, the skin or the genital apparatus, and the grade of invasion in each technique. The number of arrows indicates the grade of contamination depending on the collection method used.

Figure 3

Comparison between urinary, vaginal and gut bacterial communities. (A) Phyla relative abundance in urinary (Modena et al., 2017), vaginal (Diop et al., 2019) and gut microbiota (Morand et al., 2019). (B) Venn diagram showing overlapping species between urinary (Morand et al., 2019), gut (Morand et al., 2019) and vaginal (Diop et al., 2019) microbiota.

Figure 4

Risks factors for urinary tract infections related to the microbiota. UTIs may be influenced by different risk factors related to microbial communities: alterations in the urinary microbiota (either an increase in uropathogens or a decrease in commensal bacteria) (Thomas-White et al., 2018a), alterations in the intestinal microbiota (increase in uropathogens in the intestinal reservoir) (Magruder et al., 2019) and increasing age, which is related to a decrease in estrogen levels in women and fluctuations in abundance of Lactobacillus (Thomas-White et al., 2018a).