The impact of microbiome in urological diseases: a systematic review

Engineered microorganisms: A new direction in kidney stone prevention and treatment

Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.

Alterations in urinary microbiota composition in urolithiasis patients: insights from 16S rRNA gene sequencing

Objectives

To investigate the urinary microbiota composition in urolithiasis patients compared to healthy controls and to identify potential microbial markers and their association with clinical parameters.

Methods

A total of 66 samples, comprising 45 from urolithiasis patients and 21 from healthy controls, were analyzed. 16S rRNA gene sequencing was employed to determine the microbiota composition. Various statistical and bioinformatics tools, including ANOVA, PCoA, and LEfSe, were utilized to analyze the sequencing data and identify significant differences in microbial abundance.

Results

No significant demographic differences were observed between the two groups. Post-quality control, clean tags ranged from 60,979 to 68,736. Significant differences in α-diversity were observed between the two groups. β-diversity analysis revealed distinct clustering of the urinary microbiota in urolithiasis patients and controls. Notably, Ruminococcaceae was predominant in urolithiasis samples, while Proteobacteria was more prevalent in healthy samples. Lactobacillus was significantly overrepresented in samples from healthy females.

Conclusion

The urinary microbiota composition in urolithiasis patients is distinct from that of healthy controls. Specific microbial taxa, such as Ruminococcaceae and Proteobacteria, could serve as potential biomarkers for urolithiasis. The findings pave the way for further exploration of the role of microbiota in urolithiasis and the development of microbiome-based therapeutic strategies.

Profiling the Urobiota in a Pediatric Population with Neurogenic Bladder Secondary to Spinal Dysraphism

The human bladder has been long thought to be sterile until that, only in the last decade, advances in molecular biology have shown that the human urinary tract is populated with microorganisms. The relationship between the urobiota and the development of urinary tract disorders is now of great interest. Patients with spina bifida (SB) can be born with (or develop over time) neurological deficits due to damaged nerves that originate in the lower part of the spinal cord, including the neurogenic bladder. This condition represents a predisposing factor for urinary tract infections so that the most frequently used approach to treat patients with neurogenic bladder is based on clean intermittent catheterization (CIC). In this study, we analyzed the urobiota composition in a pediatric cohort of patients with SB compared to healthy controls, as well as the urobiota characteristics based on whether patients received CIC or not.

Role of microbiome and its metabolite, short chain fatty acid in prostate cancer

The microbiome which is an assembly of all microbes living inside our bodies performs a major role in maintaining human health and wellness. It has been found that the imbalance of the microbiome can cause various diseases in humans. Similarly, there is growing evidence that the microbiome largely affects a person's chance of contracting certain cancers and how the disease develops and progresses. Studies have shown that about 15% to 20% of all cancers are caused by microbial pathogens. The prevalence of prostate cancer, which is increasing rapidly in Korea, is related to lifestyle including diet. These diets can alter the gut microbial composition, and the effect of the microbiome on prostate cancer development can be estimated. However, the microbiome associated with prostate cancer has been reported differently according to race. This means that the metabolite rather than the specific microbiome will be important. Short chain fatty acids, metabolites of the microbiome, plays an important role in the action mechanism of the microbiome. Short chain fatty acids play roles such as immunomodulation and inhibition of histone deacetylase. Here, we examined the most up-to-date literature featuring the effects of the microbiome on the risk and pathogenesis of prostate cancer.

Emerging Role of Microbiome in the Prevention of Urinary Tract Infections in Children

The microbiome of the urinary tract plays a significant role in maintaining health through the impact on bladder homeostasis. Urobiome is of great importance in maintaining the urothelial integrity and preventing urinary tract infection (UTI), as well as promoting local immune function. Dysbiosis in this area has been linked to an increased risk of UTIs, nephrolithiasis, and dysfunction of the lower urinary tract. However, the number of studies in the pediatric population is limited, thus the characteristic of the urobiome in children, its role in a child's health, and pediatric urologic diseases are not completely understood. This review aims to characterize the healthy urobiome in children, the role of dysbiosis in urinary tract infection, and to summarize the strategies to modification and reshape disease-prone microbiomes in pediatric patients with recurrent urinary tract infections.

Monitoring of distribution of antibiotic-resistant strains of microorganisms in patients with dysbiosis of the urogenital tract

Currently, the problem of the development of resistance to drugs among microorganisms that colonize the urogenital system is becoming especially relevant due to broadly distributed dysbiotic conditions of the reproductive system of men and women. Therefore, there should be constant monitoring of the qualitative and quantitative composition of microbiota of the urogential tract and determination of the levels of antibiotic-resistance of strains of conditionally pathogenic microorganisms in the reproductive system of various layers of the population. We monitored 774,375 people of various age and sex – patients of the independent diagnostic laboratory INVITRO in the city Dnipro in 2017–2019. Among the examined people, 640,783 of the patients were diagnosed with the development of dysbiotic disorders, accounting for 82.7% of the total amount of the applications for medical help. According to the results of identification of the range of dysbiotic conditions of the urogenital system of patients of different ages and sexes, we determined the dominating role of facultative anaerobes in the development of dysbiotic impairments caused by colonizations by large numbers of conditionally-pathogenic microorganisms: in women, Gardnerella accounted for 86.1%, Staphylococcus – 63.2%, Streptococcus – 54.1%, Candida – 69.3%; in men, Streptococcus were found in 83.0%, Staphylococcus – 79.4%, Corynebacterium – 54.2% and Candida – 37.6% of the cases. Share of obligate anaerobes was also quite large: women were diagnosed with Prevotella in 59.7%, Peptostreptococcus in 53.2%, Fusobacterium in 45.4% of the cases cases; men were observed to have Peptostreptococcus 62.4%, Clostridium in 54.3%, Bacteroides in 32.5% of the cases. We determined high parameters of frequency of diagnosing antibiotic-resistant isolates of conditionally pathogenic microorganisms that circulate in the urogenital tract of patients with dysbiotic impairments, belonging to the following families: Mycoplasmataceae – 78.6%, Enterobacteriaceae – 56.0% and genera – Staphylococcus – 76.1%, Gardnerella – 24.3%, Corynebacterium – 21.2%. The research revealed increase in the frequency of detection of strains of urapathogenic bacteria resistant to the applied antibiotic preparations in 2018–2019 compared with the data of 2017: increases of 10.3% and 6.4% in representatives of family Mycoplasmataceae resistant to ciprofloxacin and ofloxacin respectively, 4.8% and 4.0% in Enterobacteriaceae resistant to chloramphenicol and ampicillin respectively, and 8.9% in the genus Staphylococcus resistant to vancomycin.

The microbiome in urological diseases

Due to the rapid development of next-generation sequencing, it has become possible to obtain information on the sequences of all genes in a specific microbiome. The detection of bacteria in patients with no urinary tract infections indicated that the dogma that “urine is sterile” was false, leading to active research regarding the roles of the urinary microbiome in the human urinary tract. Here, we present a review of the current literature regarding the role of the microbiome in urology.

Profiling the urinary microbiome in men with calcium-based kidney stones

Background

The dogma that urine is sterile in healthy individuals has been overturned by recent studies applying molecular-based methods. Mounting evidences indicate that dysbiosis of the urinary microbiota is associated with several urological diseases. In this study, we aimed to investigate the urinary microbiome of male patients with calcium-based kidney stones and compare it with those of healthy individuals.

Results

The diversity of the urinary microbiota in kidney stone patients was significantly lower than that of healthy controls based on the Shannon and Simpson index (P < 0.001 for both indices). The urinary microbiota structure also significantly differed between kidney stone patients and healthy controls (ANOSIM, R = 0.11, P < 0.001). Differential representation of inflammation associated bacteria (e.g., Acinetobacter) and several enriched functional pathways were identified in the urine of kidney stones patients. Meanwhile, we found the species diversity, overall composition of microbiota and predicted functional pathways were similar between bladder urine and renal pelvis urine in kidney stone patients.

Conclusions

A marked dysbiosis of urinary microbiota in male patients with calcium-based kidney stones was observed, which may be helpful to interpret the association between bacteria and calcium-based kidney stones.