Urinary Tract Virome as an Urgent Target for Metagenomics

Abstract

Virome—a part of a microbiome—is a term used to describe all viruses found in the specific organism or system. Recently, as new technologies emerged, it has been confirmed that kidneys and the lower urinary tract are colonized not only by the previously described viruses, but also completely novel species. Viruses can be both pathogenic and protective, as they often carry important virulence factors, while at the same time represent anti-inflammatory functions. This paper aims to show and compare the viral species detected in various, specific clinical conditions. Because of the unique characteristics of viruses, new sequencing techniques and databases had to be developed to conduct research on the urinary virome. The dynamic development of research on the human microbiome suggests that the detailed studies on the urinary system virome will provide answers to many questions about the risk factors for civilization, cancer, and autoimmune diseases.

The Impact of Human Microbiotas in Hematopoietic Stem Cell and Organ Transplantation

“…Overall, much remains to be understood about the viromes of the different human microbiotas. Furthermore, since bacteriophages are the most prevalent component of the human virome, deciphering the complex bacteriophage–bacteria interaction dynamics of the different microbiotas may galvanize the development of bacteriophage cocktails, which can supplement or, in some cases, replace existing antibiotic therapy in immunosuppressed patients ( 186 ).…”

“…The discovery of exotic microbiotas such as the renal microbiota directly contradicts the traditional overestimates of the sterility of various human organ systems. The urinary bladder and, consequently, urine were also once considered to be sterile in healthy individuals but have since been demonstrated to host the urobiome (the urinary microbiota), the alterations in which have been associated with different urinary pathologies ( 179 , 181 , 186 , 207 ). Emerging evidence across multiple domains is indicative of the existence of numerous complex microbiotas in various locations of the body that are in constant bidirectional crosstalk with each other as well as our organ systems.…”

The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder

“…Among them, most frequently detected viruses in urinary tract are human polyomavirus type 1 (BK Virus) and 2 (JC Virus), both of which are mainly studied in immunocompromised patients, such as kidney and bone marrow transplant recipients (Jhang et al, 2018). Meanwhile, both JC and BK are double-stranded DNA viruses and belong to polyomavirus (Salabura et al, 2021). Detection of JC Virus is reported in recent studies of urinary diseases such as lower urinary tract symptoms (LUTS) and OAB, but its relationships with urinary bacteria and OAB symptoms require further research (Garretto et al, 2018;Thomas et al, 2021).…”

“…Additionally, human papillomavirus, adenovirus, and cytomegalovirus infections have been associated with LUTS (Paduch, 2007;Brubaker et al, 2021). Although urinary tract infections (UTIs) are mainly caused by bacteria such as Escherichia coli and viral infections are rare pathogens, viral infections of the urinary tract are linked to considerable morbidity and distress, including increased mortality in immunocompromised patients (Khonsari et al, 2021;Salabura et al, 2021). However, there is an important link between bacteria and viruses, such as increased antibiotic resistance in UTI patients, which leads to an increase in the global medical burden, and bacteriophages, as the most abundant group of human viruses, can be used as a feasible treatment for UTI (Behzadi et al, 2020;Ahmadi, 2021).…”

“…Next-generation sequencing (NGS) of bacterial 16S rRNA is widely applied in clinical pathogen detection including urology (Derosa et al, 2020;Salabura et al, 2021). One such application is the unbiased next-generation metagenomic sequencing (mNGS), which overcomes the limitations of current diagnostic tests and allows untargeted, cultureindependent pathogen detection directly from clinical samples (Neugent et al, 2020).…”