Multi-site microbiota alteration is a hallmark of kidney stone formation

The roles of bacteria on urolithiasis progression and associated compounds

As a common urological disease, the formation of urinary tract stones involves multiple factors, including genetics, the environment, dietary habits, and bacterial species (e.g., Proteus mirabilis and Escherichia coli). Previous studies have demonstrated that P. mirabilis primarily contributes to infectious urinary calculus formation by producing urease, an enzyme that breaks down urea into ammonia and carbon dioxide, thereby altering the urinary pH and promoting crystal formation and growth. In contrast, calcium oxalate (CaOx) stones are the main type of kidney stones, and the most common bacteria in CaOx stones are E. coli. Intriguingly, E. coli can also facilitate stone formation via flagellin and other virulence factors, which induce renal epithelial cell injury and increase crystal adhesion and aggregation. These bacteria play complex and multidimensional roles in the formation of urinary tract stones, necessitating further research to elucidate their underlying mechanisms. Here, we summarise the roles of common urinary tract bacteria, particularly P. mirabilis and E. coli, in forming urinary tract stones, aiming to enhance our understanding of urolithiasis exploration in the future.

Balancing Stone Prevention and Kidney Function: A Therapeutic Dilemma

Managing nephrolithiasis in chronic kidney disease (CKD) poses a therapeutic challenge: preventing stone recurrence while preserving kidney function. Standard urological interventions and preventive strategies, such as high fluid intake, thiazides, and potassium citrate, cut recurrence by 50-60% in healthy kidneys but risk fluid overload, hyperkalemia, and diminished efficacy in CKD as glomerular filtration rate (GFR) declines. Often, stone prevention and CKD care are addressed separately, leaving clinicians without unified guidance for this rising patient group. This review explores the bidirectional relationship between nephrolithiasis and CKD, integrating pathophysiology and therapeutic strategies into a practical, decision-oriented framework. It offers tailored interventions based on GFR category, stone type, and comorbid conditions, emphasizing the potential for dual-purpose therapies. Going beyond previous reviews, it connects clinical practice with existing research gaps, offering tools to balance outcomes and guide future studies.

Assessing microbiota in vivo: debugging with medical imaging

The microbiota is integral to human health and has been mostly characterized through various ex vivo 'omic'-based approaches. To better understand the real-time function and impact of the microbiota, in vivo molecular imaging is required. With technologies such as positron emission tomography (PET), magnetic resonance imaging (MRI), and computed tomography (CT), insight into microbiological processes may be coupled to in vivo information. Noninvasive imaging enables longitudinal tracking of microbes and their components in real time; mapping of microbiota biodistribution, persistence and migration; and simultaneous monitoring of host physiological responses. The development of molecular imaging for clinical translation is an interdisciplinary science, with broad implications for deeper understanding of host-microbe interactions and the role(s) of the microbiome in health and disease.

Genetic Links between Gastrointestinal Disorders and Kidney Stone Disease: Insights from a Genome-Wide Cross-Trait Analysis

Key Points

Positive genetic links and shared genetic architecture exist between gastrointestinal disorders and kidney stone disease. Ion homeostasis and response to vitamin D bridge two types of disorders. Genetically predicted irritable bowel syndrome, gastroesophageal reflux, and Crohn's disease were associated with higher risk of kidney stone disease.

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, peptic ulcer disease, inflammatory bowel disease and its subtypes, irritable bowel syndrome, and diverticular disease (N =311,254–720,199). Their overall genetic correlations were first estimated. We then detected the shared genetic architecture, including pleiotropic single nucleotide polymorphisms, loci, genes, and biological processes, through cross-trait analyses. In addition, bidirectional Mendelian randomization 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 single nucleotide polymorphisms, and 33 of which were pleiotropic loci shared by the two disorders. Gene-level analyses revealed eight pleiotropic causal genes, primarily enriched in biological pathways involving ion homeostasis and response to vitamin D. In the Mendelian randomization analysis, we detected causal effects from gastroesophageal reflux disease, irritable bowel syndrome, 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.

Rapid and accurate testing for urinary tract infection: new clothes for the emperor

SUMMARYUrinary tract infection (UTI) is among the most common infections in clinical practice. In some cases, if left untreated, it can lead to pyelonephritis and urosepsis. In other cases, UTI resolves without treatment. Clinical diagnosis is typically based on patient symptoms and/or urinalysis, including urine dipsticks. The standard urine culture method is sometimes employed to identify the suspected urinary pathogen (uropathogen) and/or guide antimicrobial choice, but results are rarely available before 24 h. The standard urine culture method also misses fastidious, anaerobic, and slow-growing uropathogens and rarely reports polymicrobial infections. The unexplained combination of negative urine cultures with persistent urinary tract symptoms is distressing to both patients and clinicians. Given the broad appreciation of the advantages provided by rapid testing (e.g., for COVID-19 or influenza A), a rapid, accurate diagnostic test is needed to deliver timely treatment to patients seeking care for UTI that optimizes antibiotic stewardship. Herein, we discuss progress being made toward an accessible, timely (i.e., within hours), accurate assay with results that are clinically useful for the treating clinician within the timeframe of the infection (i.e., the growth rate of the pathogen(s)). New and emerging uropathogens often overlooked by current diagnostic techniques are also reviewed.

Interconnected microbiomes-insights and innovations in female urogenital health

The paradigm that the vaginal microbiota is a protective gateway for the urinary and reproductive systems has endured for more than a century and driven decades of probiotic research. Evidence robustly supports the notion that healthy urogenital microbiomes are predominantly colonized by lactobacilli, particularly Lactobacillus crispatus, which can acidify the local environment and protect against urogynecologic pathogen colonization. However, recent studies are beginning to delve deeper into the intricate mechanistic interactions connecting the microbiome, its diverse functional potential, host immunity, pathogens, and the development of urogenital diseases. Leveraging these emerging insights alongside past successes presents promising opportunities for future therapies aimed at enhancing the management of conditions such as bacterial vaginosis, urinary tract infections, bladder pain, urinary incontinence, and beyond.

TSST-1 promotes colonization of Staphylococcus aureus within the vaginal tract by activation of CD8+ T cells

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.IMPORTANCEToxic 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.

Lifestyle Factors and the Microbiome in Urolithiasis: A Narrative Review

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.

Self-Reported Symptoms of Obstructive Sleep Apnea are Associated with Increased Risk of Kidney Stones: A Cross-Sectional Study from NHANES 2015-2020

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.

The Role of the Gut Microbiome in Kidney Stone Disease

Microbiome dysbiosis is closely related to the etiology of kidney stone disease (KSD) and influences a multitude of pathways. Due to our knowledge gaps on this topic, it is still unclear if microbiome interventions can be translated to demonstrate clinical efficacy. Current evidence suggests that the enhancement of butyrate-producing pathways should be the next step for KSD research. While we are not yet at a point where we can make clinical recommendations for KSD, there are many simple dietary or supplement-based approaches that could be applied in the future for prophylaxis or treatment of KSD.

Unraveling the association of bacteria and urinary stones in patients with urolithiasis: an update review article

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.

Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing

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.

Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease

Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.