Figure - available from: Microbiome
This content is subject to copyright. Terms and conditions apply.
Phylogeny and differentially abundant gut microbiota taxa. A A maximum-likelihood phylogenetic tree of dereplicated genomes from the gut microbiota. The outermost grey bars represent the overall prevalence of the taxonomic bin. Orange and purple dots in the second layer denote taxonomic bins that were significantly more abundant in SF or HC, respectively (Benjamini–Hochberg corrected Wilcoxon test (P < 0.1) and effect size >|0.5|). Tree branches are coloured by phylum. B Average relative phylum abundance bar plot of HC and SF cohorts. Each vertical bar represents the average relative abundance within the cohort, coloured by phylum. C Effect sizes of taxa are coloured by cohort of enrichment and labelled where taxonomic information is available. Coloured species were significantly different by Benjamini–Hochberg corrected Wilcoxon test (P < 0.1) and effect size >|0.5|
Source publication
Background
Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified...
Similar publications
Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great...
Citations
... In a recent study, next-generation sequencing was utilized to examine 18 CaOx stones; the results showed that 7 stones contained bacterial 16S rRNA and human host nonribosomal DNA fragments, while fungal amplicon sequences were detected in 9 stones [19]. This identification of living microorganisms within the matrix of CaOx stones provides further evidence that the formation of kidney stones may occur through pathological biomineralization [25]. Pathological biomineraliza-tion of CaOx kidney stones arises from various microbial activities that affect the urinary supersaturation state, catalyze mineral precipitation, facilitate nucleation, and promote crystal growth and aggregation [5,21,25]. ...
... This identification of living microorganisms within the matrix of CaOx stones provides further evidence that the formation of kidney stones may occur through pathological biomineralization [25]. Pathological biomineraliza-tion of CaOx kidney stones arises from various microbial activities that affect the urinary supersaturation state, catalyze mineral precipitation, facilitate nucleation, and promote crystal growth and aggregation [5,21,25]. Several groups have suggested the existence of a kidney stone microbiome which may contribute to nephrolithiasis, while others have implicated the gut and urinary microbiomes [25,26]. nucleation, and promote crystal growth and aggregation [5,21,26]. ...
... Pathological biomineraliza-tion of CaOx kidney stones arises from various microbial activities that affect the urinary supersaturation state, catalyze mineral precipitation, facilitate nucleation, and promote crystal growth and aggregation [5,21,25]. Several groups have suggested the existence of a kidney stone microbiome which may contribute to nephrolithiasis, while others have implicated the gut and urinary microbiomes [25,26]. nucleation, and promote crystal growth and aggregation [5,21,26]. ...
Kidney stone disease affects 12% of the global population with a prevalence that continues to increase. It is recurrent in up to 50% of patients within 5 years and is associated with major health concerns including coronary artery disease and chronic kidney disease. Thus, kidney stones pose a substantial health and economic burden. However, despite kidney stone disease being one of the oldest known and most common diseases worldwide, our understanding of the mechanisms underlying stone formation is lacking. Moreover, recent data have raised questions about the efficacy of currently used therapeutic options for calcium oxalate stones, which account for 75% of all kidney stones. Development of new therapeutics for the successful prevention and management of this disease will require improved understanding of the causes of kidney stones. Recent advancements have shed light on the nuanced contribution of diet, environment and genetics as well as the more fundamental roles of calcium oxalate crystallization, Randall’s plaque formation, inflammation and even a possible contribution of the recently discovered urinary microbiome. This review provides a comprehensive overview of our current understanding of kidney stone pathogenesis and identifies new frontiers and remaining gaps in our knowledge of this disease.
... Regarding the urine samples, rare taxa such as Actinomyces, Corynebacterium, Sphingomonas, Anaerococcus, and Bacteroides, and common taxa such as Corynebacterium were found to be enriched in the controls, and common taxa such as Anaerococcus and Corynebacterium were abundant in the patient group. Recently, Al et al. published the results of their study, which focused on the microbiome perturbations found in the stool, urine, stone material, and, additionally, in the saliva of stone formers [91]. Eighty-three stone formers were recruited along with thirty controls, and their biological material was analyzed by 16S rRNA gene sequencing (for urine and saliva samples), and whole shotgun metagenomic sequencing (for stool samples). ...
Urolithiasis represents one of the most common urologic diseases, and its incidence demonstrates, globally, an increasing trend. The application of preventive measures is an established strategy to reduce urolithiasis-related morbidity, and it is based mostly on the adaptation of lifestyle factors and pharmacotherapy. Furthermore, other research areas demonstrate promising results, such as the research on the microbiome. In the current review, we searched for the latest data on lifestyle–based prevention and microbiome alterations in urolithiasis patients. The majority of the proposed lifestyle measures are already included in the urological guidelines, while additional factors, such as vitamin D supplementation, seem to have a putative positive effect. From the microbiome studies, several microbial composition patterns and metabolic pathways demonstrated an inhibiting or promoting role in lithogenesis. Up to the present, stone prevention has not shown satisfying results, which suggests that lifestyle measures are not adequate. Moreover, microbiome studies are prone to bias, since microbes are strongly affected by numerous clinical factors, while the analysis procedures are not standardized yet. Analysis standardization and data pooling from extensive registration of clinical and microbiome data are essential steps in order to improve the existing prevention strategy with targeted microbiome manipulations.
... For microbiome analysis, tissue sections from the internal vaginal tract were extracted with the Qiagen DNeasy Powersoil Pro kit as previously described (46). Extracted DNA was stored at −20°C until PCR amplification. ...
Toxic shock syndrome toxin-1 (TSST-1) is a superantigen produced by Staphylococcus aureus and is the determinant of menstrual toxic shock syndrome (mTSS); however, the impact of TSST-1 on the vaginal environment beyond mTSS is not understood. Herein, we assessed how TSST-1 affects vaginal colonization by S. aureus, host inflammatory responses, and changes in microbial communities within the murine vagina. We demonstrated that TSST-1 induced a CD8⁺ T-cell-dependent inflammatory response in 24 h that correlated with S. aureus persistence within the vaginal tract. This increase was due to superantigen-dependent T-cell activation that triggered a change in microbial composition within the vaginal tract. Altogether, this study demonstrates that within the vaginal tract, TSST-1 modulates the vaginal microbiota to favor the survival of S. aureus in the absence of mTSS.
IMPORTANCE
Toxic shock syndrome toxin-1 (TSST-1) is a superantigen toxin produced from Staphylococcus aureus that causes the menstrual form of toxic shock syndrome. This research demonstrates that TSST-1 also has a wider function within the vaginal tract than previously expected. We show that TSST-1, by activating CD8⁺ T cells, induces an inflammatory environment that modifies the vaginal microbiota to favor colonization by S. aureus. These are important findings as S. aureus can colonize the human vaginal tract efficiently and subsequently trigger dysbiosis within the microbial communities leading to several adverse outcomes such as decreased fertility, increased risks for sexually transmitted diseases, and issues related to pregnancy and birth.
... 1 Multiple factors, including dietary patterns and microbiota alterations, are widely reported to influence stone formation. 4,5 These factors also contribute to the pathogenesis and progression of gastrointestinal disorders. 6 Meanwhile, a recent genome-wide association study (GWAS) showed strong genetic correlations between KSD and digestive diseases, and the duodenum and colonic mucosa were found to include cell types relevant to KSD. 1 All the above suggested the existence of the gut-kidney axis in KSD physiopathology, indicating potential links and shared genetic etiology between KSD and gastrointestinal diseases. ...
Background
Epidemiological associations between kidney stone disease (KSD) and gastrointestinal disorders have been reported, and intestinal homeostasis plays a critical role in stone formation. However, the underlying intrinsic link is not adequately understood. This study aims to investigate the genetic associations between these two types of diseases.
Methods
We obtained summary statistics from large-scale genome-wide association studies of KSD and gastrointestinal diseases, including gastroesophageal reflux disease (GERD), peptic ulcer disease, inflammatory bowel disease and its subtypes, irritable bowel syndrome (IBS) and diverticular disease ( N = 311,254 to 720,199). Their overall genetic correlations were first estimated. We then detected the shared genetic architecture, including pleiotropic single nucleotide polymorphisms (SNPs), loci, genes and biological processes, through cross-trait analyses. In addition, bidirectional Mendelian randomization (MR) analysis was performed to look for their causal relationships.
Results
We found significantly positive genetic correlations between KSD and all five gastrointestinal diseases. The cross-trait analysis identified 3184 potential pleiotropic SNPs, and 33 of which were pleiotropic loci shared by the two disorders. Gene-level analyses revealed 8 pleiotropic causal genes, primarily enriched in biological pathways involving ion homeostasis and response to vitamin D. In the MR analysis, we detected causal effects from GERD, IBS and Crohn’s disease to KSD, while no reverse causality was observed.
Conclusions
Our study demonstrated the positive genetic links between KSD and gastrointestinal diseases and reported pleiotropic variants, loci, and genes, implicating potential biological mechanisms in the pathogenesis of stone disease. These findings further support the role of the gut-kidney axis and provide a genetic basis for the prevention, coregulation and treatment of these diseases.
... Al et al compared the gut, oral, and urinary microbiota of 30 healthy controls and 83 stone formers and suggested that multisite microbiota alterations may serve as effective indicators of kidney stone development. 22 Mechanistically, oxalate-degrading bacteria, including Oxalobacter formigenes, have been shown to reduce the formation of kidney stones by promoting degradation and modulating the function of the oxalate transporter SLC26A6. 9,23 Short-chain fatty acids, a common group of microbiota-derived metabolites, may also affect kidney stone formation via oxalate transporter modulation and GPR43-dependent immune regulation. ...
Objective
To investigate whether self-reported symptoms of obstructive sleep apnea (OSA), including snoring, snorting/stopping breathing, and sleepiness, are associated with increased risk of kidney stones.
Methods
This cross-sectional study was conducted based on the 2015–2020 National Health and Nutrition Examination Survey (NHANES). Self-reported symptoms of OSA and history of kidney stones were diagnosed via questionnaires. Multivariable logistic regression was used to determine the associations between self-reported symptoms of OSA and kidney stones. Subgroup analyses and interaction tests were performed to address this issue further.
Results
A total of 9,973 participants were enrolled, and the prevalence of kidney stones was 10.76%. Although no significant association was observed between frequent snoring and kidney stones after covariate adjustments (OR 1.033, 95% CI 0.726, 1.469 p = 0.850), frequent snorting/stopping breathing was associated with a greater risk of kidney stones after covariate adjustments (OR 1.655, 95% CI 1.262, 2.172, p = 0.002). Participants who often or almost always felt sleepy also had a greater risk of kidney stones after covariate adjustment (OR 1.651, 95% CI 1.222, 2.229; p = 0.004). The interaction tests suggested that marital status (p = 0.015) and smoking status (p < 0.001) significantly interacted with the association between snorting/stopping breathing and kidney stones.
Conclusion
Self-reported frequent snorting/stopping breathing and sleepiness may be associated with increased risk of kidney stones. Although these findings may emphasize prevention of kidney stones in these people, further research was still needed to verify our results.
... These beneficial bacteria may compete with stoneforming pathogens for resources or produce metabolites that inhibit crystal formation. Understanding the complex interplay between the urinary microbiome and urinary stone disease could lead to novel therapeutic approaches, such as probiotics or targeted antimicrobial treatments, aimed at restoring microbial balance and preventing stone formation (54,63). ...
Urinary stone disease (USD) is a prevalent urological condition, ranking as one of the most common urinary tract disorders globally. Various risk factors influence the formation of kidney stones, and recent research indicates a rising prevalence of urolithiasis worldwide, particularly in developing countries. While the morbidity associated with urinary stones has decreased in recent years, long-term complications such as stone recurrence, kidney failure, and uremia continue to burden patients. Understanding the etiologies of urolithiasis, including the role of bacteria, is crucial as they can contribute to stone recurrence. The incidence of urinary tract infection (UTI) stones can be attributed to specific infectious risk factors, socio-demographic factors, and comorbid metabolic disorders. This review article explores the emerging evidence suggesting the involvement of bacteria in USD. It discusses the potential role of microorganisms in non-infection stones and highlights the association between UTIs and urolithiasis. Furthermore, it surveys the relationship between kidney stones and recurrent UTIs and the formation of bacterial biofilms in UTIs. Considering various risk factors, including biochemical stone analysis and the presence of bacteria, is essential for treating patients with infectious stones optimally. This review aims to provide an updated understanding of the association between bacteria and urinary stones in patients with urolithiasis, shedding light on the pathophysiology of urinary stone formation, urinary stone characteristics, and the urinary microbiome in urinary stones.
... Microbial diversity plays a crucial role in maintaining the stability and ecological functions of the intestinal ecosystem. In this study, third-generation sequencing technology showed that the bacterial richness and diversity in kidney stone patients was significantly lower than that in healthy participants which is consistent with previous research [20,21] indicating that such alterations can destabilize the gut ecosystem and impair its function, leading to disease conditions [22]. Similarly, the bacterial species composition and abundance were strikingly different between kidney stone patients and healthy participants. ...
The critical role of the human gut microbiota in kidney stone formation remains largely unknown, due to the low taxonomic resolution of previous sequencing technologies. Therefore, this study aimed to explore the gut microbiota using high-throughput sequencing to provide valuable insights and identify potential bacterial species and metabolite roles involved in kidney stone formation. The overall gut bacterial community and its potential functions in healthy participants and patients were examined using PacBio sequencing targeting the full-length 16S rRNA gene, coupled with stone and statistical analyses. Most kidney stones comprised calcium oxalate and calcium phosphate (75%), pure calcium oxalate (20%), and calcium phosphate and magnesium phosphate (5%), with higher content of Ca (130,510.5 ± 108,362.7 ppm) followed by P (18,746.4 ± 23,341.2 ppm). The microbial community structure was found to be weaker in patients’ kidney stone samples, followed by patients’ stool samples, than in healthy participants’ stool samples. The most abundant bacterial species in kidney stone samples was uncultured Morganella, whereas that in patient and healthy participant stool samples was Bacteroides vulgatus. Similarly, Akkermansia muciniphila was significantly enriched in patient stool samples at the species level, whereas Bacteroides plebeius was significantly enriched in kidney stone samples than that in healthy participant stool samples. Three microbial metabolic pathways, TCA cycle, fatty acid oxidation, and urea cycle, were significantly enriched in kidney stone patients compared to healthy participants. Inferring bacteria at the species level revealed key players in kidney stone formation, enhancing the clinical relevance of gut microbiota.
... Также с помощью секвенирования выявлено, что наиболее распространенными родами в образцах мочи и камней были Escherichia (29,7%), Lactobacillus (12,8%), Staphylococcus (10,3%), Gardnerella (7,3%) и Streptococcus (7,3%) [38]. При исследовании камней почки было определено, что доминирующими бактериями являлись Gardnerella sp., Megasphaera sp., A. omnicolens, Atopobium sp., Sneathia sp. ...
... При исследовании камней почки было определено, что доминирующими бактериями являлись Gardnerella sp., Megasphaera sp., A. omnicolens, Atopobium sp., Sneathia sp. и Prevotella sp., а в моче преобладали Lactobacillus jensenii [38]. При исследовании образцов мочи показано, что большую часть составляли бактерии типов Proteobacteria и Firmicutes [8]. ...
In recent years, there has been an upward trend in the urolithiasis incidence worldwide and an increase in the recurrence of stone formation. Urolithiasis prevalence rates range from 1% to 20%. In some countries, there is an increase in rates up to 37%. Stones are classified into those caused by infections, non infectious causes, and genetic diseases. Alteration in urine microbiome plays a significant role in the infection stone formation. Our objective was to review the current literature on the role of bacteria in the formation of kidney concrements. The gained knowledge could be used to explore new possibilities and improve the understanding of stone formation. We analyzed articles on the composition of the urine microbiome and kidney stones.
... This discovery has led investigators to question the role microbes may play in nephrolithiasis. Jeremy P. Burton, Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, Canada, and his team provided a unified assessment of the bacterial contribution to kidney stones by systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC) [2] .. This study demonstrated that independent of diet, the microbiome in stone formers is altered at multiple anatomical sites (Fig.2). This study demonstrated that independent of diet, the microbiome in stone formers is altered at multiple anatomical sites. ...
Background
Kidney stones are a common urologic disorder that imposes a significant burden on global public health. This study aimed to determine the association between oral microbiome diversity and kidney stones.
Methods
The data for this study came from the National Health and Nutrition Examination Survey 2009–2012 survey cycle. Use of alpha diversity to assess oral microbiome diversity. Multivariate logistic regression modeling was used to assess the association between different alpha-diversity indicators and kidney stones. Subgroup analyses and interaction tests were used to assess the stability of the association between alpha-diversity and kidney stones. Restricted cubic spline plots were used to assess non-linear associations and dose-response relationships.
Results
The study included 5,870 eligible participants with a mean age of 43.74 years at baseline. After adjusting for all covariates, the observed oral microbiome diversity was significantly negatively associated with the risk of kidney stones (P < 0.05). Subgroup analyses showed that oral microbiome diversity was negatively associated with the risk of kidney stones in certain populations, particularly among those aged 40–60 years, men, obese, with moderate to high cardiovascular health scores, smokers, and those without hypertension. Restricted cubic spline analysis suggested a significant non-linear negative correlation between the Shannon and Simpson diversity indices and the risk of kidney stones (p for non-linear < 0.05). Since our study was a cross-sectional design, the main limitation was the inability to prove causality.
Conclusions
In this study, we found an inverse relationship between oral microbiome diversity and kidney stone risk observed in alpha diversity. This reveals the complexity of host-microbiome interactions, and further mechanistic studies are necessary to elucidate these complex roles in the future.
