Urinary Microbiota Research Articles

The Bladder is Not Sterile: an Update on the Urinary Microbiome.

The article discusses (1) techniques used to study bacterial urinary microbiota; (2) existence of non-bacterial urinary microbiota; (3) associations between changes in urinary microbiota and various benign lower urinary tract disorders. Urine harbors a diverse microbial community that resides within it. A multitude of studies have identified differences in these communities associated with urologic conditions, suggesting that microbial communities may maintain normal bladder homeostasis. Technological advances in analytic approaches have improved our understanding of the urinary microbiome. The choice of urine sampling method (voided, catheterized, or aspirated) will significantly influence microbiome findings. Sex and age highly influence urinary microbiota; in addition to rigorous inclusion criteria, microbial studies must be sufficiently powered to overcome the substantial interindividual variability of urinary microbiota. Regardless of these complicating factors, studies have identified microbial patterns correlating with both urologic diagnoses and treatment responses. Without a clear understanding of the variability of and exogenous influences on the urinary microbiota in the absence of disease, it has been challenging to reveal the microbial patterns responsible for disease pathophysiology. Host mechanisms in response to the urinary microbiome are also poorly understood. Additional research can address whether the manipulation of urinary microbiota will benefit lower urinary tract health.

Urobiome: In Sickness and in Health.

The human microbiome has been proven to contribute to the human condition, both in health and in disease. The metagenomic approach based on next-generation sequencing has challenged the dogma of urine sterility. The human urobiome consists of bacteria and eukaryotic viruses as well as bacteriophages, which potentially represent the key factor. There have been several significant findings with respect to the urobiome in the context of urological disorders. Still, the research on the urobiome in chronic kidney disease and kidney transplantation remains underrepresented, as does research on the role of the virome in the urinary microbiota. In this review, we present recent findings on the urobiome with a particular emphasis on chronic kidney disease and post-kidney transplantation status. Challenges and opportunities arising from the research on the human urobiome will also be discussed.

942P - A differential bladder microbiota composition is associated with tumour grade in bladder cancer

BackgroundMicrobiota has been linked to the development of multiple cancers through various mechanisms. In bladder cancer (BC), preliminary studies have found alterations in the urinary microbiota of patients with urothelial carcinoma in comparison with healthy individuals. However, the bladder microbiota (BMi) has not been explored. The aims of this study were to characterize the BMi in a cohort of BC patients, to explore differences in the BMi composition between tumor (T) and normal (N) mucosa, and to identify its correlation with clinicopathologic features. MethodsA total of 58 samples obtained by cystectomy from 32 BC patients (frozen tumor tissues and normal appearing mucosa for 26 patients and 6 tumor tissues) from Hospital General de Elche Biobank (Spain) were included. DNAs isolated from bladder samples were used to perform 16S rRNA gene sequencing (V3 and V4 region). A paired-end 2×300bp cycle run on Illumina MiSeq. Ribosomal Database Project Classifier was used for taxonomical assignment. Statistical analysis was performed using Rstudio platform. Groups of data were compared using Wilcoxon test and Mann Whitney test for 26T vs 26N (paired group) and 32T vs 26N (unpaired group), respectively. ResultsThere were no statistically significant differences of diversity between T and N, but there were differences of richness between T and N at the genus level (Chao1 index, p=0.049). Globally, the most abundant phylum was Firmicutes, followed by Bacteroidetes, Proteobacteria and Actinobacteria. We found that the microbial composition differed significantly between T and N in both groups. At the phylum level, while Cyanobacteria.Chloroplast (0.74% vs 2.44%; p=0.025) was enriched in T, Actinobacteria were reduced in T. Principal component analysis based on the relative abundance of phylum (36.9% PC1 and 28.7% PC2 of explained variance) revealed a significant separation in bacterial community composition between tumor tissues associated with histological tumor grade (permanova grade =0.036). ConclusionsSignificant differences in the BMi composition associated with tumor grade were observed. Additional studies are needed to determine the role of BMi in the evolution of BC and its therapeutic implications. Legal entity responsible for the studyThe authors. FundingHas not received any funding. DisclosureAll authors have declared no conflicts of interest.

Dysbiosis signatures of the microbial profile in tissue from bladder cancer.

BackgroundTo examine the microbial profiles in parenchyma tissues in bladder cancer.MethodsTissue samples of cancerous bladder mucosa were collected from patients diagnosed with bladder cancer (22 carcinoma tissues and 12 adjacent normal tissues). The V3‐V4 region of the bacterial 16S rRNA gene was PCR amplified, followed by sequencing on an Illumina MiSeq platform. Bioinformatics analysis for microbial classification and functional assessment was performed to assess bladder microbiome diversity and variations.ResultsThe predominant phylum in both tissues was Proteobacteria. The cancerous tissues exhibited lower species richness and diversity. Beta diversity significantly differed between the cancerous and normal tissues. Lower relative abundances of the microbial genera Lactobacillus, Prevotella_9, as well as Ruminococcaceae were observed, whereas those of Cupriavidus spp., an unknown genus of family Brucellaceae, and Acinetobacter, Anoxybacillus, Escherichia‐Shigella, Geobacillus, Pelomonas, Ralstonia, and Sphingomonas were higher in the cancerous tissues. These findings indicate that these genera may be potentially utilized as biomarkers for bladder cancer. PICRUSt analysis revealed that several pathways involved in the metabolism of harmful chemical compounds were enriched in the cancer tissues, thereby providing evidence that environmental factors are strongly associated with bladder cancer etiology.ConclusionThis is the first study that has described and analyzed the dysbiotic motifs of urinary microbiota in the parenchymatous tissues of bladder cancer via 16S rRNA gene sequencing. Our results suggest that changes in the bladder microbiome may serve as biomarkers for bladder cancer, possibly assisting in disease screening and monitoring.

Influence of Storage Conditions and Preservatives on Metabolite Fingerprints in Urine.

Human urine, which is rich in metabolites, provides valuable approaches for biomarker measurement. Maintaining the stability of metabolites in urine is critical for accurate and reliable research results and subsequent interpretation. In this study, the effect of storage temperature (4, 22, and 40 °C), storage time (24 and 48 h), and use of preservatives (boric acid (BA), thymol) and para-aminobenzoic acid (PABA) on urinary metabolites in the pooled urine samples from 20 participants was systematically investigated using large-scale targeted liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomics. Statistical analysis of 158 reliably detected metabolites showed that metabolites in urine with no preservative remained stable at 4 °C for 24 and 48 h as well as at 22 °C for 24 h, but significant metabolite differences were observed in urine stored at 22 °C for 48 h and at 40 °C. The mere addition of BA caused metabolite changes. Thymol was observed to be effective in maintaining metabolite stability in urine in all the conditions designed, most likely due to the inhibitory effect of thymol on urine microbiota. Our results provide valuable urine preservation guidance during sample storage, which is essential for obtaining reliable, accurate, and reproducible analytical results from urine samples.

Unique and specific Proteobacteria diversity in urinary microbiota of tolerant kidney transplanted recipients.

Host-microbiota interactions can modulate the immune system both at local and systemic levels, with potential consequences for organ transplantation outcomes. In this study, we hypothesized that differences in the urinary microbiome following kidney transplantation would be associated with posttransplantation status: stable, minimally immunosuppressed, or tolerant. One hundred thirteen urine samples from stable (n=51), minimally immunosuppressed (n=19), and spontaneously tolerant (n=16) patients, paired with age-matched controls (n=27) were profiled and compared to each other at a taxonomic level with special interest in the immunosuppressive regimen. All comparisons and correlations were adjusted on sex and time posttransplantation. Our results highlighted a unique and specific urinary microbiota associated with spontaneous tolerance characterized by a high diversity and a clear Proteobacteria profile. Finally, we report that this profile is (1) impacted by gender, (2) inversely correlated with immunosuppressive drugs (calcineurin inhibitors and mammalian target of rapamycin inhibitors), and (3) stable in time.

Potential Role of Extracellular ATP Released by Bacteria in Bladder Infection and Contractility.

Urgency urinary incontinence (UUI) and overactive bladder (OAB) can both potentially be influenced by commensal and urinary tract infection-associated bacteria. The sensing of bladder filling involves interplay between various components of the nervous system, eventually resulting in contraction of the detrusor muscle during micturition. This study models host responses to various urogenital bacteria, first by using urothelial bladder cell lines and then with myofibroblast contraction assays. To measure responses, we examined Ca2+ influx, gene expression, and alpha smooth muscle actin deposition assays. Organisms such as Escherichia coli and Gardnerella vaginalis were found to strongly induce Ca2+ influx and contraction, whereas Lactobacillus crispatus and L. gasseri did not induce this response. Additionally, supernatants from lactobacilli impeded Ca2+ influx and contraction induced by uropathogens. Upon further investigation of factors associated with purinergic signaling pathways, the Ca2+ influx and contraction of cells correlated with the amount of extracellular ATP produced by E. coli Certain lactobacilli appear to mitigate this response by utilizing extracellular ATP or producing inhibitory compounds that may act as a receptor agonist or Ca2+ channel blocker. These findings suggest that members of the urinary microbiota may be influencing UUI or OAB.IMPORTANCE The ability of uropathogenic bacteria to release excitatory compounds, such as ATP, may act as a virulence factor to stimulate signaling pathways that could have profound effects on the urothelium, perhaps extending to the vagina. This may be countered by the ability of certain commensal urinary microbiota constituents, such as lactobacilli. Further understanding of these interactions is important for the treatment and prevention of UUI and OAB. The clinical implications may require a more targeted approach to enhance the commensal bacteria and reduce ATP release by pathogens.

Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale

BackgroundRodent models are invaluable for studying biological processes in the context of whole organisms. The reproducibility of such research is based on an assumption of metabolic similarity between experimental animals, controlled for by breeding and housing strategies that minimise genetic and environmental variation. Here, we set out to demonstrate the effect of experimental uraemia on the rat urinary metabolome and gut microbiome but found instead that the effect of vendor shipment batch was larger in both areas than that of uraemia.ResultsTwenty four Wistar rats obtained from the same commercial supplier in two separate shipment batches underwent either subtotal nephrectomy or sham procedures. All animals undergoing subtotal nephrectomy developed an expected uraemic phenotype. The urinary metabolome was studied using 1H-NMR spectroscopy and found to vary significantly between animals from different batches, with substantial differences in concentrations of a broad range of substances including lactate, acetate, glucose, amino acids, amines and benzoate derivatives. In animals from one batch, there was a complete absence of the microbiome-associated urinary metabolite hippurate, which was present in significant concentrations in animals from the other batch. These differences were so prominent that we would have drawn quite different conclusions about the effect of uraemia on urinary phenotype depending on which batch of animals we had used. Corresponding differences were seen in the gut microbiota between animals in different batches when assessed by the sequencing of 16S rRNA gene amplicons, with higher alpha diversity and different distributions of Proteobacteria subtaxa and short-chain fatty acid producing bacteria in the second batch compared to the first. Whilst we also demonstrated differences in both the urinary metabolome and gut microbiota associated with uraemia, these effects were smaller in size than those associated with shipment batch.ConclusionsThese results challenge the assumption that experimental animals obtained from the same supplier are metabolically comparable, and provide metabolomic evidence that batch-to-batch variations in the microbiome of experimental animals are significant confounders in an experimental study. We discuss strategies for reducing such variability and the need for transparency in research publications about the supply of experimental animals.

Bacteria Detected in both Urine and Open Wounds in Nursing Home Residents: a Pilot Study.

Nursing home residents are at a greater risk of developing pressure injuries that develop into an open wound, which can become colonized with bacteria. Understanding the factors that influence microbial colonization of open wounds can lead to the prevention of infections. The relationship between bacteria found in urine and those in open wounds is currently unknown. To determine if bacterial species colonizing open wounds are also found in the urine, we conducted a pilot study with nursing home residents, comparing bacterial species present in the urine with those present in wounds between the umbilicus and mid-thigh. To identify microbial species that were present in both urine and open wound at one time point in one patient, standard clinical bacteriologic culture techniques followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) were used, as well as 16S rRNA-encoding gene amplicon sequencing. We found some bacterial species detected in urine were also detected in open wounds in one individual at one time point, using both culture-dependent and -independent techniques. Bacterial species that were more often detected, using culture-dependent and -independent methods, at both sites included Enterococcus faecalis, Proteus mirabilis, Escherichia coli, and Providencia stuartii This pilot study provides evidence that bacterial species identified within the urine can also be identified in open wounds in the same patient at one point in time. Further studies are needed to investigate if these species are of the same lineage and if the urinary microbiota are able to seed colonization of open wounds below the umbilicus.IMPORTANCE Older adults, specifically those in nursing facilities, are more susceptible to developing chronic open nonhealing wounds. Chronic open nonhealing wounds severely impact an individual's quality of life and can lead to other comorbidities, such as infection. Recent evidence suggests that the open wound bacterial community can influence wound healing and repair. It is important to understand all sources of open wound contamination to improve preventative infection measures and treatment protocols. In this pilot study, we investigated if bacterial species isolated from urine can also be isolated from open wounds located between the levels of the umbilicus and mid-thigh in the same patient at the same point in time. A growing body of evidence suggests that urine can harbor a microbial community, even in asymptomatic individuals, and older adults are more prone to urinary incontinence. This is the first study to investigate bacterial species concordance between these two anatomical sites. We found, using both culture-dependent and -independent methods, that the same bacterial species can colonize both the urine and wound in one patient at one point in time. Further studies are needed to investigate if these species are of the same lineage and if the urinary microbiota are able to seed colonization of these types of open wounds.

Relationship between alterations of urinary microbiota and cultured negative lower urinary tract symptoms in female type 2 diabetes patients

BackgroundLower urinary tract symptoms (LUTS) is the most common complication of diabetes. However, the underlying pathogenesis of cultured negative LUTS (cn-LUTS) in diabetic patients has not been well understood. Numerous evidence indicates that urinary dysbiosis is related to urologic disorders. We aim to study alterations of the urinary microbiota of cn-LUTS in type 2 diabetes (T2D) patients.MethodsFemale T2D patients and controls were recruited and requested to finish the American Urological Association Symptom Index. Mid-stream urine was collected for culturing and extracting DNA. Microbial diversity and composition were analyzed by targeting to 16S rDNA. Linear discriminant analysis effect size (LEfSe) was carried out to identify significantly different bacteria.Results32 female T2D patients and 26 controls were enrolled. No significant differences in alpha diversity were observed between patients and controls. However, statistically decreased richness (ACE index and Chao 1 index, 85.52(13.75, 204.84) vs. 129.82(63.89, 280.30) and 83.86(11.00, 210.77) vs. 125.19(62.00, 251.77), P = 0.005; Observed Species, 76(10, 175) vs. 98(54, 234), P = 0.011) and decreased species diversity (Shannon index, 1.37(0.04, 3.48) vs. 2.09(0.98, 3.43), P = 0.033; Simpson index, 0.46 (0.06, 0.99) vs. 0.23(0.07, 0.64), P = 0.029) were shown in moderate-to-severe LUTS group and high Hemoglobin A1c group, respectively. A significant difference of beta diversity was found between T2D patients and controls and T2D patients with different severity of cn-LUTS as well as the different level of Hemoglobin A1c. LEfSe revealed that 10 genera (e.g., Escherichia-Shigella and Klebsiella) were increased and 7 genera were decreasing in T2D patients, 3 genera (e.g., Escherichia-Shigella and Campylobacter) were increased and 16 genera (e.g., Prevotella) were reduced in moderate-to-severe LUTS group, 2 genera (Escherichia-Shigella and Lactobacillus) were over-represented and 10 genera (e.g., Prevotella) were under-represented in high Hemoglobin A1c group. Finally, Hemoglobin A1c was found positively correlated with the total score of the American Urological Association Symptom Index (r = 0.509, P = 0.003).ConclusionsUrinary dysbiosis may be related to cn-LUTS in female T2D patients. A better understanding of urinary microbiota in the development and progression of cn-LUTS in female T2D patients was necessary. The severity of cn-LUTS was correlated to hyperglycemia and chronic hyperglycemia might induce or promote cn-LUTS by influencing urinary microbiota.

Urinary microbiota - a potential biomarker and therapeutic target for bladder cancer.

Purpose. To identify potential biomarkers and/or therapeutic targets for bladder cancer we characterized and analysed the composition of the urinary microbiota from bladder cancer and non-cancer patients.Methodology. In this study, we collected urine samples from 29 bladder cancer patients and 26 non-cancer patients. To avoid contamination and the impact of antibiotics, urine specimens were collected in a clean manner prior to antibiotic administration. Using the amplicon-based next-generation sequencing approach, the potential determinant bacteria were estimated in a between-group comparison. The results illustrated the differences in microbiota abundance among cancer and non-cancer patients and the overall number of cases carrying these bacteria.Results. We found that the urine samples contained a conserved microbiota with four phyla (Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes), which accounted for 94.4 % of bacteria in all cases. Comparing the microbiota between the bladder cancer and control group, five genera of bacteria (Streptococcus, Bifidobacterium, Lactobacillus, Veillonella and Actinomyces) existed in all samples, but with significant intergroup differences (P<0.05). The bladder cancer patients presented with a higher abundance of Actinomyces, while the other strains were enriched in the control group. A higher abundance of Actinomyces europaeus was also observed in the bladder cancer group compared to the control group.Conclusion. The samples collected from the bladder cancer patients displayed a significantly different pattern relative to those from the control group. The higher abundance of A. europaeus observed in bladder cancer patient samples also suggests that the strain may be indicative of bladder cancer. The urinary microbiota may be a potential biomarker and therapeutic target for bladder cancer.

Urine and colon microbiota in patients with recurrent uncomplicated lower urinary tract infection

Background . The prevalence of urinary tract infections (UTIs) in general and recurrent lower UTIs, in particular, constantly remains at a high level. Currently, more and more researchers are attempting to study the microbial biocenosis of the urinary tract in patients with UTIs in terms of the relationship between UTIs and patient's colon microbiota in order to detail the etiology and pathogenesis of these conditions as an insufficiently studied issue. Objectives. To study the microbiota of urine and colon, as well as significant correlations in these biotopes. Materials and methods . 169 patients with recurrent lower UTIs from the Urology Clinic and the Department of Microbiology and Virology No. 1 (Rostov State Medical University) were examined. Average age: 36.2 ± 4.7 years. Midstream urine samples for bacteriological examination was taken in accordance with the rules set out in the Clinical recommendations (2014) exactly observing the preanalytical stage. The study of the colon microbiota as well as the collection of material was carried out in accordance with the rules set forth in the industry standard (OS) OST 915000. 11.0004 - 2003, Order of the Ministry of Health of the Russian Federation No. 231 of 09/09/03. Guided by this standard, the interpretation of the results was conducted. Results' statistical processing was implemented using the SPSS version 23 package. Results. In patients with recurrent lower UTIs two significant quantitative correlation coefficients were detected. The first correlation coefficient showed inverse correlation between typical E. coli isolated from urine and Eubacterium spp. isolated from feces (r = -0.434, p = 0.009). The second correlation coefficient showed a direct correlation between the amount of Lactobacilli isolated from urine and Coalulase-negative Staphylococci (CoNS) isolated from feces, accordingly (r = -0.434, p = 0.009). When comparing the frequencies of detection of various microbiota taxa, three significant correlation coefficient were found in the loci under study: between Lactobacilli or Peptococci isolated from urine and CoNS verified in feces (PCC - 0.342, p = 0.031 and PCC - 0.341, p = 0.018, respectively), as well as between Peptococci detected in urine and Enterococci in feces (PCC - 0.349, p = 0.028). Conclusion. The data we obtained on significant correlation coefficients between microorganisms isolated from urine and colon indirectly confirm the translocation mechanism. Undoubtedly, further research is needed to study the mechanism of translocation of microorganisms from the intestines and other biotopes into the organs of the urinary system in order to understand the pathogenesis of this common group of diseases.

The microbiome of calcium-based urinary stones.

Historically, the role of bacteria in urinary stone disease (USD) has been limited to urease-producing bacteria associated with struvite stone formation. However, growing evidence has revealed bacteria associated with stones of non-struvite composition. These bacteria may be derived from either urine or from the stones themselves. Using 16S rRNA gene sequencing and an enhanced culture technique (EQUC), we identified the urine and stone microbiota of USD patients and then determined if bacteria were statistically enriched in the stones relative to the urine. From 52 patients, bladder urine and urinary stones were collected intraoperatively during ureteroscopy. Stone homogenate and urine specimens were subjected to 16S rRNA gene sequencing and EQUC. Standard Chi-squared tests were applied to determine if the relative abundance of any bacterial taxon was significantly enriched in urinary stones compared to urine. Stones were primarily calcium-based. 29/52 (55.8%) stones had bacteria detected by 16S rRNA gene sequencing. Of these, dominant bacterial taxa were enriched from 12 stones. Bacterial taxa isolated by EQUC include members of the genera Staphylococcus, Enterobacter, Escherichia, Corynebacterium, and Lactobacillus. Dominant bacterial genera were enriched compared to paired bladder urine. Differences between the stone and urine microbiota may indicate that certain bacteria contribute to USD pathophysiology. Further investigation is warranted.

Bacteriophages of the lower urinarytract.

The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.

The Urinary Microbiome and Anticancer Immunotherapy: The Potentially Hidden Role of Unculturable Microbes.

Several urinary disorders, including overactive bladder, urinary incontinence, and interstitial cystitis, are often characterized by negative urine cultures. The application of metagenomics (i.e., 16S rRNA microbial profiling or whole-genome shotgun sequencing) to urine samples has enabled the identification of previously undetected bacteria, contributing to the discovery and characterization of the urinary microbiome. The most frequent species isolated are Lactobacillus (15%), Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Although several studies are emerging in this context, the role of urinary microbiota in the pathogenesis of infections and in tumor carcinogenesis remains unclear. Furthermore, data on the activity of gut microbiota in modulating sensitivity to immune checkpoint inhibitors in advanced cancer patients suggest that the influence of urinary microbiota on tumor response to anticancer therapy should also be investigated. Moreover, its possible relationship with tumor mutational burden, which is in turn correlated with response to immunotherapy, should be the focus of future studies. Of note, the effect of antibiotics on this complex scenario seems to deserve careful consideration.

Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection.

BackgroundUrinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context.MethodsIn two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI).FindingsMethanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis.InterpretationOur results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria.FundThis study was supported by IHU Méditerranée Infection, Marseille, France.

Is there a relationship between the urine, vagina, and gut microbiota in patients with an infection of the upper urinary tract?

Introduction. Urinary tract infections of any localization are rarely considered in the context of the endogenous relationship of patient's urine microbiota and the microbiota of nearby biotopes. Nowadays, there are attempts to study the microbial interrelationships of the urinary system with nearby biotope to find fundamentally new solutions in the study of the etiology and pathogenesis of diseases, but now this problem remains almost unexplored. Purpose of the study . Analysis of the correlations between various taxa of the microbiota isolated from urine, vagina and intestines in patients with upper urinary tract infection. Materials and methods . According to the inclusion criteria, bacteriological examination of cystic urine, feces and posterior vaginal fornix discharge was performed on 60 women (18-65 years old) with acute obstructive pyelonephritis. The material was taken, transported and examined by standard methods, but with some modifications of nutrient media. Statistical calculations were performed in R "R ver 3.2" ("R Foundation for Statistical Computing", Vienna, Austria) with generally accepted significance coefficients. Results. 26 significant correlation coefficients were found in the urinary tract and the vagina when conducting a comparative correlation analysis between the microbiota taxa, and 21 in the urinary tract and intestine. Significant correlations between the general taxa were direct and a large proportion of them were in optional anaerobic microbiota. 28 significant correlation coefficients were found in most cases between aerobic and anaerobic taxa of microorganisms in the vagina and intestines. Conclusion . The obtained significant correlation coefficients between various microbiota taxa in the three studied biotopes are evidence of the relationship of these loci. However, further research is needed on the phylotyping and genotyping of the microbiota taxa of the urinary tract, vagina and intestines of patients with urinary tract infection.

Female lower urinary tract microbiota do not associate with IC/PBS symptoms: a case-controlled study.

The current etiology of interstitial cystitis/painful bladder syndrome (IC/PBS) is poorly understood and multifactorial. Recent studies suggest the female urinary microbiota (FUM) contribute to IC/PBS symptoms. This study was designed to determine if the FUM, analyzed using mid-stream voided urine samples, differs between IC/PBS patients and controls. This prospective case-controlled study compared the voided FUM of women with symptoms of urinary frequency, urgency, and bladder pain for > 6months with the voided FUM of healthy female controls without pain. Bacterial identification was performed using 16S rRNA gene sequencing and EQUC, a validated enhanced urine culture approach. Urotype was defined by a genus present at > 50% relative abundance. If no genus was present above this threshold, the urotype was classified as 'mixed.' Group comparisons were performed for urotype and diversity measures. A mid-stream voided specimen was collected from 21 IC/PBS patients and 20 asymptomatic controls. The two groups had similar demographics. Urotypes did not differ between cohorts as assessed by either EQUC or 16S rRNA gene sequencing. We detected no significant differences between cohorts by alpha diversity. Cohorts also were not distinct using principle component analysis or hierarchical clustering. Detection by EQUC of bacterial species considered uropathogenic was high in both cohorts, but detection of these uropathogenic species did not differ between groups (p = 0.10). Enhanced culture and DNA sequencing methods provide evidence that IC/PBS symptoms may not be related to differences in the FUM, at least not its bacterial components. Future larger studies are needed to confirm this preliminary finding.

VirMine: automated detection of viral sequences from complex metagenomic samples.

Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.

The Human Microbiota and Prostate Cancer: Friend or Foe?

The human microbiome is gaining increasing attention in the medical community, as knowledge on its role not only in health but also in disease development and response to therapies is expanding. Furthermore, the connection between the microbiota and cancer, especially the link between the gut microbiota and gastrointestinal tumors, is becoming clearer. The interaction between the microbiota and the response to chemotherapies and, more recently, to immunotherapy has been widely studied, and a connection between a peculiar type of microbiota and a better response to these therapies and a different incidence in toxicities has been hypothesized. As knowledge on the gut microbiota increases, interest in the residing microbial population in other systems of our body is also increasing. Consequently, the urinary microbiota is under evaluation for its possible implications in genitourinary diseases, including cancer. Prostate cancer is the most common cancer in the male population; thus, research regarding its etiology and possible factors correlated to disease progression or the response to specific therapies is thriving. This review has the purpose to recollect the current knowledge on the relationship between the human microbiota and prostate cancer.