Urinary Microbiota-Are We Ready for Prime Time? A Literature Review of Study Methods' Critical Steps in Avoiding Contamination and Minimizing Biased Results

Exploring a Complex Interplay: Kidney-Gut Axis in Pediatric Chronic Kidney Disease

The human intestinal microbiota is a highly intricate structure with a crucial role in promoting health and preventing disease. It consists of diverse microbial communities that inhabit the gut and contribute to essential functions such as food digestion, nutrient synthesis, and immune system development. The composition and function of the gut microbiota are influenced by a variety of factors, including diet, host genetics, and environmental features. In pediatric patients, the gut microbiota is particularly dynamic and vulnerable to disruption from endogenous and exogenous factors. Recent research has focused on understanding the interaction between the gut and kidneys. In individuals with chronic kidney disease, there is often a significant disturbance in the gut microbiota. This imbalance can be attributed to factors like increased levels of harmful toxins from the gut entering the bloodstream, inflammation, and oxidative stress. This review looks at what is known about the link between a child's gut-kidney axis, how dysbiosis, or an imbalance in the microbiome, affects chronic kidney disease, and what treatments, both pharmaceutical and non-pharmaceutical, are available for this condition.

Menopausal Changes in the Microbiome-A Review Focused on the Genitourinary Microbiome

A balanced interaction between the host and its microbiome is crucial to health. Research regarding the significance of the gut and vaginal microbiomes in female health is substantial. However, less data regarding the urinary microbiome are available. Interactions between the gut, vaginal, and urinary microbiomes are also currently being researched. Hormone-induced dysbiosis after menopause is believed to have effects on physical changes and health consequences. Postmenopausal changes in the gut microbiome are associated with increased short-chain fatty acids and hydrogen sulfide levels. Increased vaginal pH caused by reduced estrogen alters the vaginal microbiome, resulting in reduced levels of Lactobacillus. Such changes influence the vaginal structure and functions, contributing to the onset of genitourinary syndrome of menopause. A dysbiosis of the urinary microbiome is associated with urgency and urinary incontinence and also related to interstitial cystitis/bladder pain syndrome and neuropathic bladder. As these diseases commonly affect postmenopausal women, hormone-induced changes in the microbiome may play a role. Menopause increases the alpha diversity of the urinary microbiome and lowers the percentage of Lactobacillus in urine, and such changes precede recurrent cystitis. More research regarding the effects of changes in the urinary microbiome due to menopause on urinary tract diseases is needed.

The role of microbiome: a novel insight into urolithiasis

Urolithiasis, referred to as the formation of stones in the urinary tract, is a common disease with growing prevalence and high recurrence rate worldwide. Although researchers have endeavoured to explore the mechanism of urinary stone formation for novel effective therapeutic and preventative measures, the exact aetiology and pathogenesis remain unclear. Propelled by sequencing technologies and culturomics, great advances have been made in understanding the pivotal contribution of the human microbiome to urolithiasis. Indeed, there are diverse and abundant microbes interacting with the host in the urinary tract, overturning the dogma that urinary system, and urine are sterile. The urinary microbiome of stone formers was clearly distinct from healthy individuals. Besides, dysbiosis of the intestinal microbiome appears to be involved in stone formation through the gut-kidney axis. Thus, the human microbiome has potential significant implications for the aetiology of urolithiasis, providing a novel insight into diagnostic, therapeutic, and prognostic strategies. Herein, we review and summarize the landmark microbiome studies in urolithiasis and identify therapeutic implications, challenges, and future perspectives in this rapidly evolving field. To conclude, a new front has opened with the evidence for a microbial role in stone formation, offering potential applications in the prevention, and treatment of urolithiasis.

Microbiota Ecosystem in Recurrent Cystitis and the Immunological Microenvironment of Urothelium

Urinary tract infections (UTIs) represent one of the most frequent low genital tract diseases in the female population. When UTIs occur with a frequency of at least three times per year or two times in the last six month, we speak of recurrent UTI (rUTI) and up to 70% of women will have rUTI within 1 year. It was previously thought that antibiotic resistance was principally responsible for the recurrence of UTIs, but nowadays new diagnostic technologies have shown the role of microbiota in the pathophysiology of these diseases. Much research has been conducted on the role of gut microbiome in the development of rUTI, while little is known yet about vaginal and urinary microbiome and the possible immunological and microscopical mechanisms through which they trigger symptoms. New discoveries and clinical perspectives are arising, and they all agree that a personalized, multi-modal approach, treating vaginal and urinary dysbiosis, may reduce rUTIs more successfully.

Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for male urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. Systematic comparisons of their performance indicate V1V2 hypervariable regions better assess the taxa commonly present in male urine samples, suggesting V1V2 amplicon sequencing is more suitable for male urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future male urinary microbiota studies.

Does the microbiota spectrum of prostate secretion affect the clinical status of patients with chronic bacterial prostatitis?

OBJECTIVE

To explore the influence of the microbiota of prostate secretion on the clinical status of patients with chronic bacterial prostatitis.

METHODS

This was an observational, single-center, comparative study. We evaluated the survey cards of 230 outpatients aged 18-45 years with a history of prostatitis from 2012 to 2019. As a result, 170 outpatients were selected for the study. All patients underwent an assessment of symptoms using International Prostate Symptom Score-quality of life, National Institutes of Health-Chronic Prostatitis Symptom Index, International Index of Erectile Function, pain visual analog scale. A bacteriological study (after the Meares-Stamey test) of post-massage urine was carried out on an extended media set. The following parameters were determined in each patient: leukocyturia and bacteriuria, serum testosterone and total prostate-specific antigen levels. Uroflowmetry, transrectal prostate ultrasound with color duplex mapping and ejaculate analysis were also carried out.

RESULTS

Aerobic-anaerobic bacterial associations were identified in all patients. Three comparison groups were identified depending on the microbiota's spectrum (in post-massage urine): aerobes prevailed in group 1 (n = 67), anaerobes prevailed in group 2 (n = 33), and the levels of aerobic and anaerobic bacteriuria were higher than ≥10³  colony-forming units per mL in group 3 (n = 70). It was found that the severity of clinical symptoms (urination disorders, sexual dysfunction etc.) of chronic bacterial prostatitis, laboratory and instrumental changes (testosterone, prostate-specific antigen, prostate volume etc.) in groups 2 and 3 were significantly higher than in group 1.

CONCLUSION

In patients with chronic bacterial prostatitis, a predominance of anaerobes or a combination of aerobes and anaerobes in a titer of ≥10³  colony-forming units per mL in post-massage urine is associated with worse clinical status.

Polymicrobial interactions in the urinary tract: is the enemy of my enemy my friend?

The vast majority of research pertaining to urinary tract infection has focused on a single pathogen in isolation, and predominantly Escherichia coli. However, polymicrobial urine colonization and infection are prevalent in several patient populations, including individuals with urinary catheters. The progression from asymptomatic colonization to symptomatic infection and severe disease is likely shaped by interactions between traditional pathogens as well as constituents of the normal urinary microbiota. Recent studies have begun to experimentally dissect the contribution of polymicrobial interactions to disease outcomes in the urinary tract, including their role in development of antimicrobial-resistant biofilm communities, modulating the innate immune response, tissue damage, and sepsis. This review aims to summarize the epidemiology of polymicrobial urine colonization, provide an overview of common urinary tract pathogens, and present key microbe-microbe and host-microbe interactions that influence infection progression, persistence, and severity.

The Role of Gut, Vaginal, and Urinary Microbiome in Urinary Tract Infections: From Bench to Bedside

The current paradigm of urinary tract infection (UTI) pathogenesis takes into account the contamination of the periurethral space by specific uropathogens residing in the gut, which is followed by urethral colonization and pathogen ascension to the urinary bladder. Consequently, studying the relationship between gut microbiota and the subsequent development of bacteriuria and UTI represents an important field of research. However, the well-established diagnostic and therapeutic paradigm for urinary tract infections (UTIs) has come into question with the discovery of a multifaceted, symbiotic microbiome in the healthy urogenital tract. More specifically, emerging data suggest that vaginal dysbiosis may result in Escherichia coli colonization and prompt recurrent UTIs, while urinary microbiome perturbations may precede the development of UTIs and other pathologic conditions of the urinary system. The question is whether these findings can be exploited for risk reduction and treatment purposes. This review aimed to appraise the three aforementioned specific microbiomes regarding their potential influence on UTI development by focusing on the recent studies in the field and assessing the potential linkages between these different niches, as well as evaluating the state of translational research for novel therapeutic and preventative approaches.

Voided Urinary Microbiota Is Stable Over Time but Impacted by Post Void Storage

Background: New sensitive techniques have revealed a thriving bacterial community in the human urinary tract, challenging the perception that urine in healthy humans is sterile. While the functional role of this urinary microbiota is unknown, dysbiosis has been linked to urgency urinary incontinence and risk of urinary tract infections. When comparing studies, it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether collection and storage conditions had any impact on the urinary microbial composition. Results: For comparison of different storage conditions, midstream urine was collected from five healthy adult female donors and analyzed by 16S rRNA gene sequencing. Samples stored at -80 and -20°C, but not 4°C, were found to be comparable to freshly handled voided urine. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in 19 healthy donors, including four women, five men, five girls, and five boys. Apart from two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of voided urinary microbiota was found to be effectively maintained by freezing, but not storage at 4°C. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys. Together our study supports present methodologies that can be used in future studies investigating the urinary microbiota.