Profiling the urinary microbiome in men with calcium-based kidney stones.
Ontology highlight
ABSTRACT:
SUBMITTER: Xie J
PROVIDER: S-EPMC7049185 | biostudies-literature | 2020 Feb
REPOSITORIES: biostudies-literature
Publications
Profiling the urinary microbiome in men with calcium-based kidney stones.
Xie Jing J Huang Jian-Sheng JS Huang Xiang-Jiang XJ Peng Jun-Ming JM Yu Zhou Z Yuan Ye-Qing YQ Xiao Ke-Feng KF Guo Ji-Nan JN
BMC microbiology 20200228 1
<h4>Background</h4>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.<h4>Results</h4>The diversity of the urinary microbiota in kidney stone pati ...[more]
Similar Datasets
Project description:Urinary Microbiome From Patients With Kidney Stones Raw Sequence Reads
| PRJNA516685 | ENA
Project description:BACKGROUND:The long-held notion that, without urinary tract or circulatory infection, bladder urine and blood are sterile biofluids has been disproven. There have been no previous reports on the kidney pelvis urinary microbiome after bladder disinfection in kidney stone patients. This study aimed to determine whether a kidney pelvis urinary microbiome is present after eliminating the influence of the bladder urinary microbiome, whether the microbiome composition is different in patients with stone kidney pelvis (SKP) and non-stone kidney pelvis (NSKP), and the correlation between SKP and patient clinical characteristics. RESULTS:Comparisons of bacterial diversity and community structure exhibited that urine in bladder was similar to SKP and NSKP. However, the comparisons showed that urine samples were different from blood. The most common operational taxonomic units were shared by all three types of urine samples. Corynebacterium was significantly higher in SKP compared to NSKP. Several bacteria were associated with patient characteristics, including Lactobacillus, which was positively correlated with fasting blood glucose, and Prevotella was negatively correlated with BMI. Lactobacillus was significantly higher in SKP compared to blood but not in NSKP compared to blood. CONCLUSIONS:The composition of the kidney pelvis urinary microbiome after disinfection of the bladder and its similarity to the bladder microbiome indicate that bladder urine can be used to replace kidney pelvis urine in microbiome research. Additionally, the comparison of SKP and NSKP and clinical associations suggest that the occurrence of kidney stones is responsible for the SKP urinary microbiome.
| S-EPMC7643416 | biostudies-literature
Project description:Calcium nephrolithiasis may be considered as a complex disease having multiple pathogenetic mechanisms and characterized by various clinical manifestations. Both genetic and environmental factors may increase susceptibility to calcium stones; therefore, it is crucial to characterize the patient phenotype to distinguish homogeneous groups of stone formers. Family and twin studies have shown that the stone transmission pattern is not mendelian, but complex and polygenic. In these studies, heritability of calcium stones was calculated around 50%Calcium-sensing receptor (CaSR) is mostly expressed in the parathyroid glands and in renal tubules. It regulates the PTH secretion according to the serum calcium concentration. In the kidney, it modulates electrolyte and water excretion regulating the function of different tubular segments. In particular, CaSR reduces passive and active calcium reabsorption in distal tubules, increases phosphate reabsorption in proximal tubules and stimulates proton and water excretion in collecting ducts. Therefore, it is a candidate gene for calcium nephrolithiasis.In a case-control study we found an association between the normocitraturic stone formers and two SNPs of CaSR, located near the promoters region (rs7652589 and rs1501899). This result was replicated in patients with primary hyperparathyroidism, comparing patients with or without kidney stones. Bioinformatic analysis suggested that the minor alleles at these polymorphisms were able to modify the binding sites of specific transcription factors and, consequently, CaSR expression.Our studies suggest that CaSR is one of the candidate genes explaining individual predisposition to calcium nephrolithiasis. Stone formation may be favored by an altered CaSR expression in kidney medulla involving the normal balance among calcium, phosphate, protons and water excretion.
| S-EPMC3339356 | biostudies-literature
Project description:OBJECTIVE:Inflammation plays a leading role in the pathogenesis of nephrolithiasis. The association of the dietary inflammatory index (DII) with urinary lithogenic factors is unclear. This study aimed to evaluate the relation of DII to urinary risk factors of kidney stones formation. RESULTS:Of 264 participants, 61.4% (n?=?162), 72% (n?=?190), 74.6% (n?=?197), 68.6% (n?=?181), and 80.3% (n?=?212) had hyperoxaluria, hypercreatininuria, hypercalciuria, hyperuricosuria, hypocitraturia, respectively. There was a significant increasing trajectory in urinary calcium, uric acid, and creatinine as well as a decreasing trend in urinary citrate across tertiles of DII score (all P?=??0.001). After multivariate adjustment for energy intake, age, physical activity and body mass index, high DII scores were associated with elevated odds of having hypercreatininuria (OR?=?2.80, 95%CI: 1.10-7.12, Ptrend?=?0.04), hypercalciuria (OR?=?7.44, 95%CI: 2.62-21.14, Ptrend???0.001), hyperuricosuria (OR?=?2.22, 95%CI: 1.001-4.95, Ptrend?=?0.05), and hypocitraturia (OR?=?5.84, 95%CI: 2.14-15.91, Ptrend???0.001). No association was identified between DII and hyperoxaluria.
| S-EPMC7414556 | biostudies-literature
Project description: Not available
| S-EPMC8207319 | biostudies-literature
Project description:PURPOSE:Studies demonstrating bacterial DNA and cultivable bacteria in urine samples have challenged the clinical dogma that urine is sterile. Furthermore, studies now indicate that dysbiosis of the urinary microbiome is associated with pathological conditions. We propose that the urinary microbiome may influence chronic inflammation observed in the prostate, leading to prostate cancer development and progression. Therefore, we profiled the urinary microbiome in men with positive vs negative biopsies for prostate cancer. MATERIALS AND METHODS:Urine was collected from men prior to biopsy for prostate cancer. DNA was extracted from urine pellet samples and subjected to bacterial 16S rDNA Illumina® sequencing and 16S rDNA quantitative polymerase chain reaction. We determined the association between bacterial species and the presence or absence of cancer, cancer grade, and type and degree of prostate inflammation. RESULTS:Urine samples revealed diverse bacterial populations. There were no significant differences in ? or ? diversity and no clear hierarchical clustering of benign or cancer samples. We identified a cluster of pro-inflammatory bacteria previously implicated in urogenital infections in a subset of samples. Many species, including known uropathogens, were significantly and differentially abundant among cancer and benign samples, in low vs higher grade cancers and in relation to prostate inflammation type and degree. CONCLUSIONS:To our knowledge we report the most comprehensive study to date of the male urinary microbiome and its relationship to prostate cancer. Our results suggest a prevalence of pro-inflammatory bacteria and uropathogens in the urinary tract of men with prostate cancer.
| S-EPMC5937117 | biostudies-literature
Project description:Calcium oxalate kidney stones contain low amounts of proteins, some of which have been implicated in progression or prevention of kidney stone formation. To gain insights into the pathophysiology of urolithiasis, we have characterized protein components of calcium oxalate kidney stones by proteomic approaches. Proteins extracted from kidney stones showed highly heterogeneous migration patterns in gel electrophoresis as reported. This was likely to be mainly due to proteolytic degradation and protein-protein crosslinking of Tamm-Horsfall protein and prothrombin. Protein profiles of calcium oxalate kidney stones were obtained by in-solution protease digestion followed by nanoLC-MALDI-tandem mass spectrometry, which resulted in identification of a total of 92 proteins in stones from 9 urolithiasis patients. Further analysis showed that protein species and their relative amounts were highly variable among individual stones. Although proteins such as prothrombin, osteopontin, calgranulin A and calgranulin B were found in most stones tested, some samples had high contents of prothrombin and osteopontin, while others had high contents of calgranulins. In addition, calgranulin-rich stones had various neutrophil-enriched proteins such as myeloperoxidase and lactotransferrin. These proteomic profiles of individual kidney stones suggest that multiple systems composed of different groups of proteins including leucocyte-derived ones are differently involved in pathogenesis of individual kidney stones depending on situations.
| S-EPMC3706363 | biostudies-literature
Project description:Background:Urolithiasis is the process of stone formation in the urinary tract. Its etiology is only partly known, and efficient therapeutic approaches are currently lacking. Metabolomics is increasingly used in biomarkers discovery for its ability to identify mediators of relevant (patho)physiological processes. Amino acids may be involved in kidney stone formation. The aim of the present study was to investigate the presence of an amino acid signature in stone former urine through a targeted metabolomic approach. Methods:A panel of 35 amino acids and derivatives was assessed in urines from 15 stone former patients and 12 healthy subjects by UPLC-MS. Partial Least Squares Discriminant Analysis (PLS-DA) was used to define amino acid profiles of cases and controls. Results and Discussion. Our approach led to the definition of a specific amino acid fingerprint in people with kidney stones. A urinary amino acid profile of stone formers was characterized by lower levels of ?-aminobutyric acid, asparagine, ethanolamine, isoleucine, methionine, phenylalanine, serine, tryptophan, and valine. Metabolomic analysis may lend insights into the pathophysiology of urolithiasis and allow tracking this prevalent condition over time.
| S-EPMC7345965 | biostudies-literature
Project description:Idiopathic hypercalciuria is a frequent defect in calcium kidney stone formers that is associated with high intestinal calcium absorption and osteopenia. Characteristics distinguishing hypercalciuric stone formers from hypercalciuric patients without kidney stone history (HNSFs) are unknown and were explored in our study.We compared 172 hypercalciuric stone formers with 36 HNSFs retrospectively selected from patients referred to outpatient clinics of the San Raffaele Hospital in Milan from 1998 to 2003. Calcium metabolism and lumbar bone mineral density were analyzed in these patients. A strontium oral load test was performed: strontium was measured in 240-minute urine and serum 30, 60, and 240 minutes after strontium ingestion; serum strontium concentration-time curve and renal strontium clearance were evaluated to estimate absorption and excretion of divalent cations.Serum strontium concentration-time curve (P<0.001) and strontium clearance (4.9±1.3 versus 3.5±2.7 ml/min; P<0.001) were higher in hypercalciuric stone formers than HNSFs, respectively. The serum strontium-time curve was also higher in hypercalciuric stone formers with low bone mineral density (n=42) than in hypercalciuric stone formers with normal bone mineral density (n=130; P=0.03) and HNSFs with low (n=22; P=0.01) or normal bone mineral density (n=14; P=0.02). Strontium clearance was greater in hypercalciuric stone formers with normal bone mineral density (5.3±3.4 ml/min) than in hypercalciuric stone formers and HNSFs with low bone mineral density (3.6±2.5 and 3.1±2.5 ml/min, respectively; P=0.03). Multivariate regression analyses displayed that strontium absorption at 30 minutes was positively associated calcium excretion (P=0.03) and negatively associated with lumbar bone mineral density z score (P=0.001) in hypercalciuric stone formers; furthermore, hypercalciuric patients in the highest quartile of strontium absorption had increased stone production risk (odds ratio, 5.06; 95% confidence interval, 1.2 to 20.9; P=0.03).High calcium absorption in duodenum and jejunum may expose hypercalciuric patients to the risk of stones because of increased postprandial calcium concentrations in urine and tubular fluid. High calcium absorption may identify patients at risk of bone loss among stone formers.
| S-EPMC4974885 | biostudies-other
Project description:BackgroundIn Japan, the incidence of kidney stones has increased markedly in recent decades. Major causes of kidney stones remain unclear, and limited data are available on the relationship between overweight/obesity and the incidence of kidney stones. We therefore evaluated body mass index (BMI) and the incidence of kidney stones in Japanese men.MethodsOf the workers at a gas company, 5984 males aged 20-40 years underwent a medical examination in 1985 (baseline). This study includes 4074 of the men, who were free of kidney stones at baseline and underwent a second medical examination performed between April 2004 and March 2005. BMI was calculated from measured height and weight in 1985, and men were categorized into tertiles. The development of kidney stones during follow-up was based on self-reports from questionnaires at the second medical examination.ResultsThe average duration of follow-up was 19 years, with 258 participants developing kidney stones during this period. Using the lowest BMI (1st tertile) group as a reference, the hazard ratios (95% confidence intervals [CIs]) for the 2nd and 3rd BMI tertiles were: 1.26 (95% CI, 0.92-1.73) and 1.44 (95% CI, 1.06-1.96), respectively (P for trend = 0.019). After additionally adjusting for potential confounders, such as age, systolic blood pressure, cardiorespiratory fitness, cigarette smoking, and alcohol consumption, the hazard ratios were 1.28 (95% CI, 0.93-1.76) and 1.41 (95% CI, 1.02-1.97), respectively (P for trend = 0.041).ConclusionsThese results suggest that increased BMI is a risk factor for kidney stones in Japanese men.
| S-EPMC4773489 | biostudies-literature