The role of the microbiome in kidney stone formation

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.

Microbial communities, antibiotic resistance genes, and virulence factors in urinary infectious stone-associated urinary tract infections

Urinary infectious stones are challenging due to bacterial involvement, necessitating a comprehensive understanding of these conditions. Antibiotic-resistant urease-producing bacteria further complicate clinical management. In this study, analysis of urine and stone samples from urinary tract infection (UTI) patients revealed microbial shifts, gene enrichment in stones, and metabolic pathway disparities; antibiotic resistance gene trends were phylum-specific, urease-producing bacteria are at risk of acquiring AMR carried by Enterobacteriaceae under antibiotic, emphasizing potential AMR dissemination between them; Correlations of key pathogenic species in kidney stone and urine microbial communities highlight the need for targeted therapeutic strategies to manage complexities in UTIs; Stones and urine contain a variety of deleterious genes even before antibiotic use, and piperacillin/tazobactam better reduced the abundance of antibiotic resistance genes in stones and urine. The presence of diverse antibiotic resistance and virulence genes underscores challenges in clinical management and emphasizes the need for effective treatment strategies to mitigate risks associated with UTIs and urinary infectious stone formation. Ongoing research is vital for advancing knowledge and developing innovative approaches to address these urological conditions.

Navigating the microbial maze: unraveling the connection between gut microbiome and pediatric kidney and urinary tract disease

The gut microbiome is made up of trillions of bacteria, viruses, archaea, and microbes that play a significant role in the maintenance of normal physiology in humans. Recent research has highlighted the effects of the microbiome and its dysbiosis in the pathogenesis and maintenance of kidney disease, especially chronic kidney disease (CKD) and its associated cardiovascular disease. While studies have addressed the kidney-microbiome axis in adults, how dysbiosis may uniquely impact pediatric kidney disease patients is not well-established. This narrative review highlights all relevant studies focusing on the microbiome and pediatric kidney disease that were published between 7/2015 and 7/2023. This review highlights pediatric-specific considerations including growth and bone health as well as emphasizing the need for increased pediatric research. Understanding microbiome-kidney interactions may allow for novel, less invasive interventions such as dietary changes and the use of probiotics to improve preventive care and ameliorate long-term morbidity and mortality in this vulnerable population.

Gut and Urinary Microbiota in Cats with Kidney Stones

Upper urinary tract urolithiasis is an emerging disease in cats, with 98% of kidney stones composed of calcium oxalate. In humans, disturbances in the intestinal and urinary microbiota are suspected to contribute to the formation of calcium oxalate stones. We hypothesized that similar mechanisms may be at play in cats. This study examines the intestinal and urinary microbiota of nine cats with kidney stones compared to nine healthy cats before, during, and after treatment with the antibiotic cefovecin, a cephalosporin. Initially, cats with kidney stones displayed a less diverse intestinal microbiota. Antibiotic treatment reduced microbiota diversity in both groups. The absence of specific intestinal bacteria could lead to a loss of the functions these bacteria perform, such as oxalate degradation, which may contribute to the formation of calcium oxalate stones. This study confirms the presence of a distinct urobiome in cats with kidney stones, characterized by greater richness and diversity compared to healthy cats. These findings highlight the potential of microbiota modulation as a strategy to prevent renal lithiasis in cats.

Association between gut microbiota and spinal stenosis: a two-sample mendelian randomization study

Introduction

Considerable evidence has unveiled a potential correlation between gut microbiota and spinal degenerative diseases. However, only limited studies have reported the direct association between gut microbiota and spinal stenosis. Hence, in this study, we aimed to clarify this relationship using a two-sample mendelian randomization (MR) approach.

Materials and Methods

Data for two-sample MR studies was collected and summarized from genome-wide association studies (GWAS) of gut microbiota (MiBioGen, n = 13, 266) and spinal stenosis (FinnGen Biobank, 9, 169 cases and 164, 682 controls). The inverse variance-weighted meta-analysis (IVW), complemented with weighted median, MR-Egger, weighted mode, and simple mode, was used to elucidate the causality between gut microbiota and spinal stenosis. In addition, we employed mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) and the MR-Egger intercept test to assess horizontal multiplicity. Cochran's Q test to evaluate heterogeneity, and "leave-one-out" sensitivity analysis to determine the reliability of causality. Finally, an inverse MR analysis was performed to assess the reverse causality.

Results

The IVW results indicated that two gut microbial taxa, the genus Eubacterium fissicatena group and the genus Oxalobacter, have a potential causal relationship with spinal stenosis. Moreover, eight potential associations between genetic liability of the gut microbiota and spinal stenosis were implied. No significant heterogeneity of instrumental variables or horizontal pleiotropy were detected. In addition, "leave-one-out" sensitivity analysis confirmed the reliability of causality. Finally, the reverse MR analysis revealed that no proof to substantiate the discernible causative relationship between spinal stenosis and gut microbiota.

Conclusion

This analysis demonstrated a possible causal relationship between certain particular gut microbiota and the occurrence of spinal stenosis. Further studies focused on the mechanism of gut microbiota-mediated spinal stenosis can lay the groundwork for targeted prevention, monitoring, and treatment of spinal stenosis.

Causal effects of gut microbiota on the risk of urinary tract stones: A bidirectional two-sample mendelian randomization study

Background

Recent studies increasingly suggest notable changes in both the quantity and types of gut microbiota among individuals suffering from urinary tract stones. However, the causal relationship between GMB and urinary tract stone formation remains elusive, which we aim to further investigate in this research through Mendelian Randomization (MR) analysis.

Materials and methods

Single nucleotide polymorphisms (SNPs) associated with the human GMB were selected from MiBioGen International Consortium GWAS dataset. Data on urinary tract stone-related traits and associated SNPs were sourced from the IEU Open GWAS database. To investigate the causal relationships between gut microbiota and urinary tract stones, Mendelian Randomization (MR) was applied using genetic variants as instrumental variables, utilizing a bidirectional two-sample MR framework. This analysis incorporated various statistical techniques such as inverse variance weighting, weighted median analysis, MR-Egger, and the maximum likelihood method. To ensure the reliability of the findings, a range of sensitivity tests were conducted, including Cochran's Q test, the MR-Egger intercept, leave-one-out cross-validation, and examination of funnel plots.

Results

The results revealed the causal relationship between the increase in the abundance of 10 microbial taxa, including Genus-Barnesiella (IVW OR = 0.73, 95%CI 0.73-0.89, P = 2.29 × 10-3) and Genus-Flavonifractor (IVW OR = 0.69, 95%CI 0.53-0.91, P = 8.57 × 10-3), and the decreased risk of urinary tract stone formation. Conversely, the development of urinary tract stones was observed to potentially instigate alterations in the abundance of 13 microbial taxa, among which Genus-Ruminococcus torques group was notably affected (IVW OR = 1.07, 95%CI 0.64-0.98, P = 1.86 × 10-3). In this context, Genus-Clostridium sensustricto1 exhibited a bidirectional causal relationship with urinary tract stones, while the remaining significant microbial taxa demonstrated unidirectional causal effects in the two-sample MR analysis. Sensitivity analyses did not identify significant estimates of heterogeneity or pleiotropy.

Conclusion

To summarize, the results of this study suggest a likely causative link between gut microbiota and the incidence of urinary tract stones. This insight opens up potential pathways for discovering biomarkers and therapeutic targets in the management and prevention of urolithiasis. However, further in-depth research is warranted to investigate these associations.

Therapeutic effects of probiotics and herbal medications on oxalate nephrolithiasis: a mini systematic review

Background and Objectives

The majority of all kidney stone cases are oxalate urolithiasis with a high risk of recurrence. Beside its widespread occurrence, kidney stones are characterized by severe complications and high treatment costs. Probiotics and herbal medications could be forthcoming therapeutic interventions in the management of oxalate kidney stones.

Materials and Methods

The PubMed/MEDLINE database was searched for keywords "Oxalobacter formigenes" AND "Oxalate" OR "oxalate degradation" AND "Lactobacillus" OR "Bifidobacterium" OR "recombinant Lactobacillus" OR "Bacillus subtilis", and "urolithiasis" AND "herbal extract". The search returned 253 results, 38 of which were included in the review.

Results

Most of the oxalate-degrading probiotics belong to the Oxalobacter formigenes, Lactobacillus, Bifidobacterium, and Bacillus genus with a minimum dosage of 107 CFU in the form of capsules, sachets, and lyophilized powder. Oxalate concentration in media was 5-50mM with an incubation time ranging from 24h to 14 days. The majority of the studies suggested that probiotic supplementation might be useful for reducing urinary excretion of oxalate and urea and alleviation of stone formation. Different herbal extracts were used on murine models of nephrolithiasis (induced by 0.5-3% ethylene glycol) with reduction of renal inflammation and urinary parameters, and calcium oxalate crystals.

Conclusion

Several strains of probiotics and herbal extracts confer protective effects against kidney stone/nephrolithiasis, indicating their promising nature for being considered as elements of preventive / adjuvant therapeutic strategies.

The Kidney-Gut Axis as a Novel Target for Nutritional Intervention to Counteract Chronic Kidney Disease Progression

A well-balanced diet is integral for overall health, aiding in managing key risk factors for kidney damage like hypertension while supplying necessary precursors for metabolite production. Dietary choices directly influence the composition and metabolic patterns of the gut microbiota, showing promise as therapeutic tools for addressing various health conditions, including chronic kidney diseases (CKD). CKD pathogenesis involves a decline in the glomerular filtration rate and the retention of nitrogen waste, fostering gut dysbiosis and the excessive production of bacterial metabolites. These metabolites act as uremic toxins, contributing to inflammation, oxidative stress, and tissue remodeling in the kidneys. Dietary interventions hold significance in reducing oxidative stress and inflammation, potentially slowing CKD progression. Functional ingredients, nutrients, and nephroprotective phytoconstituents could modulate inflammatory pathways or impact the gut mucosa. The "gut-kidney axis" underscores the impact of gut microbes and their metabolites on health and disease, with dysbiosis serving as a triggering event in several diseases, including CKD. This review provides a comprehensive overview, focusing on the gut-liver axis, and explores well-established bioactive substances as well as specific, less-known nutraceuticals showing promise in supporting kidney health and positively influencing CKD progression.

Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity

The role of microbiota-gut-brain axis in modulating longevity remains undetermined. Here, we performed a multiomics analysis of gut metagenomics, gut metabolomics, and brain functional near-infrared spectroscopy (fNIRS) in a cohort of 164 participants, including 83 nonagenarians (NAs) and 81 non-nonagenarians (NNAs) matched with their spouses and offspring. We found that 438 metabolites were significantly different between the two groups; among them, neuroactive compounds and anti-inflammatory substances were enriched in NAs. In addition, increased levels of neuroactive metabolites in NAs were significantly associated with NA-enriched species that had three corresponding biosynthetic potentials: Enterocloster asparagiformis, Hungatella hathewayi and Oxalobacter formigenes. Further analysis showed that the altered gut microbes and metabolites were linked to the enhanced brain connectivity in NAs, including the left dorsolateral prefrontal cortex (DLPFC)-left premotor cortex (PMC), left DLPFC-right primary motor area (M1), and right inferior frontal gyrus (IFG)-right M1. Finally, we found that neuroactive metabolites, altered microbe and enhanced brain connectivity contributed to the cognitive preservation in NAs. Our findings provide a comprehensive understanding of the microbiota-gut-brain axis in a long-lived population and insights into the establishment of a microbiome and metabolite homeostasis that can benefit human longevity and cognition by enhancing functional brain connectivity.

Unlocking New Approaches to Urolithiasis Management Via Nutraceuticals

Urolithiasis, commonly known as kidney stones, is characterized by the formation of hard deposits in the urinary tract. These stones can cause severe pain and discomfort, and their management typically involves a combination of medical interventions and lifestyle modifications. According to the literature, 30% and 50% of urolithiasis cases recur. Between 9 and 12% of persons in industrialised countries are predicted to have urolithiasis at some time. Due to the high frequency of stone formation, recurrent nature, and prevalence in adults, it has a significant impact on society, the person, and the health care system. Adopting the best prophylactic measures is crucial in light of these developments to decrease the impact of urolithiasis on individuals and society. In recent years, there has been growing interest in the potential role of nutraceuticals in the management of urolithiasis. Nutraceuticals, such as herbal extracts, vitamins, minerals, and probiotics, have gained recognition for their potential in promoting urinary health and reducing the risk of urolithiasis. These compounds can aid in various ways, including inhibiting crystal formation, enhancing urine pH balance, reducing urinary calcium excretion, and supporting kidney function. Additionally, nutraceuticals can help alleviate symptoms associated with urolithiasis, such as pain and inflammation. While medical interventions remain crucial, incorporating nutraceuticals into a comprehensive management plan can offer a holistic approach to urolithiasis, improving patient outcomes and quality of life. Therefore, nutraceuticals may be a desirable choice for treating and avoiding recurring urolithiasis for patients and medical professionals. Therefore, the present study has focused on nutraceuticals' role in preventing urolithiasis.

Metabolomics analysis reveals a protective effect of hydroxycitric acid on calcium oxalate-induced kidney injury

Objectives

Prior research has indicated that hydroxycitric acid (HCA) can impede the formation of calcium oxalate (CaOx) crystals, yet the specific mechanisms underlying its therapeutic effects remain unclear. In this study, we delved into the protective effects of HCA against glyoxylate-induced renal stones in rats and sought to elucidate the underlying metabolic pathways.

Materials and Methods

Forty rats were randomly assigned to five groups: control group, model group, L-HCA-treated group, M-HCA-treated group, and H-HCA-treated group. Von Kossa staining was conducted on renal sections, and blood urea nitrogen and serum creatinine were determined by biochemical analysis. Meanwhile, body weight and urine volume were also measured. We subjected urine samples from the rats to analysis using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Next, we employed a metabolomic approach to scrutinize the metabolic profiles of each group.

Results

HCA significantly reduced blood urea nitrogen and serum creatinine, and increased body weight and urine volume. It also reduced CaOx crystal deposition. A total of 24 metabolites, exhibiting a significant reversal pattern following HCA administration, were identified as urine biomarkers indicative of HCA's preventive effects against CaOx crystal-induced renal injury. These metabolites are primarily associated with glycine, serine, and threonine metabolism; phenylalanine metabolism; tricarboxylic acid cycle; taurine and hypotaurine metabolism; and tryptophan metabolism.

Conclusion

It was demonstrated that HCA has a protective effect against CaOx crystal-induced kidney injury in rats by modulating various metabolic pathways. Additionally, results suggest that HCA holds promise as a potential clinical therapeutic drug for both the prevention and treatment of renal stones.

Current Status of Protein Biomarkers in Urolithiasis-A Review of the Recent Literature

Urolithiasis is an increasingly common clinical problem worldwide. The formation of stones is a combination of metabolic status, environmental factors, family history and many other aspects. It is important to find new ways to quickly detect and assess urolithiasis because it causes sudden, severe pain and often comes back. One way to do this is by exploring new biomarkers. Current advances in proteomic studies provide a great opportunity for breakthroughs in this field. This study focuses on protein biomarkers and their connection to kidney damage and inflammation during urolithiasis.

Popular Diets and Kidney Stones

Popular diets often influence dietary patterns, which have different implications for kidney stone risk. Despite the wide variety of popular diets, some general principles can be gleaned from investigating their potential impact on nephrolithiasis. Plant-based diets, including Dietary Approaches to Stop Hypertension, Mediterranean, flexitarian, and vegetarian diets, may protect against nephrolithiasis when they consist largely of unprocessed plant foods, while carbohydrate-restricted diets (including high-protein diets and the ketogenic diet) may raise kidney stone risk. Patients should be advised to consume a diet rich in whole plants, particularly fruits and vegetables, and minimize their consumption of animal proteins. Accompanying fruits and vegetables that are higher in oxalate content with more water and some dairy intake may also be useful. (We address the oxalate content of fruits and vegetables further below). Calcium consumption is an important component of decreasing the risk of kidney stones, as higher dietary calcium from dairy or nondairy sources is independently associated with lower kidney stone risk. Patients should also be advised to be conscious of fat intake, as fat in the intestinal lumen may complex with calcium and therefore increase urinary oxalate excretion. Finally, patients should avoid consumption of processed foods, which often contain added fructose and high sodium content, two factors that increase kidney stone risk.

Association between the gut microbiota and nonalcoholic fatty liver disease: A two-sample Mendelian randomization study

BACKGROUND

Increasing studies have shown that there is a significant association between gut microbiota and non-alcoholic fatty liver disease.

AIMS

To show the potential association between gut microbiota and non-alcoholic fatty liver disease, we performed a two-sample Mendelian randomization analysis.

METHODS

We analyzed summary statistics from genome-wide association studies of gut microbiota and non-alcoholic fatty liver disease and conducted Mendelian randomization studies to evaluate relationships between these factors.

RESULTS

Of the 211 gut microbiota taxa examined, the inverse variance weighted method identified Lactobacillaceae (OR = 0.83, 95% CI = 0.72 - 0.95, P = 0.007), Christensenellaceae (OR = 0.74, 95% CI = 0.59 - 0.92, P = 0.007), and Intestinibacter (OR = 0.85, 95% CI = 0.73 - 0.99, P = 0.035) were negatively correlated with non-alcoholic fatty liver disease. And Coriobacteriia (OR = 1.22, 95% CI = 1.01 - 1.42, P = 0.038), Actinomycetales (OR = 1.25, 95% CI = 1.02 - 1.53, P = 0.031), Oxalobacteraceae (OR = 1.10, 95% CI = 1.01 - 1.21, P = 0.036), Ruminococcaceae_UCG005 (OR = 1.18, 95% CI = 1.01 - 1.38, P = 0.033) are positively associated with non-alcoholic fatty liver disease.

CONCLUSIONS

Our study found that the abundance of certain strains was associated with the progression of nonalcoholic fatty liver disease.

The Gut-Organ Axis within the Human Body: Gut Dysbiosis and the Role of Prebiotics

The human gut microbiota (GM) is a complex microbial ecosystem that colonises the gastrointestinal tract (GIT) and is comprised of bacteria, viruses, fungi, and protozoa. The GM has a symbiotic relationship with its host that is fundamental for body homeostasis. The GM is not limited to the scope of the GIT, but there are bidirectional interactions between the GM and other organs, highlighting the concept of the "gut-organ axis". Any deviation from the normal composition of the GM, termed "microbial dysbiosis", is implicated in the pathogenesis of various diseases. Only a few studies have demonstrated a relationship between GM modifications and disease phenotypes, and it is still unknown whether an altered GM contributes to a disease or simply reflects its status. Restoration of the GM with probiotics and prebiotics has been postulated, but evidence for the effects of prebiotics is limited. Prebiotics are substrates that are "selectively utilized by host microorganisms, conferring a health benefit". This study highlights the bidirectional relationship between the gut and vital human organs and demonstrates the relationship between GM dysbiosis and the emergence of certain representative diseases. Finally, this article focuses on the potential of prebiotics as a target therapy to manipulate the GM and presents the gaps in the literature and research.

Causal relationship between kidney stones and gut microbiota contributes to the gut-kidney axis: a two-sample Mendelian randomization study

Background

Gut microbiota, particularly Oxalobacter formigenes, has been previously reported to be associated with kidney stones. However, the conflicting results from both observational and intervention studies have created substantial uncertainty regarding the contribution of Oxalobacter formigenes to the formation of kidney stone.

Methods

We employed a two-sample MR analysis to investigate the causal relationship between gut microbiota and kidney stones using GWASs summary statistics obtained from the MiBioGen and FinnGen consortia. Moreover, we conducted a reserve MR analysis to assess the direction of the causal associations between gut microbiota and kidney stones. The inverse variance weighted (IVW) approach represents the primary method of Mendelian Randomization (MR) analysis.

Results

Our analyses do not yield supportive evidence for a causal link between the genus Oxalobacter (OR = 0.99, 95% CI: 0.90-1.09, p = 0.811) and the formation of kidney stones. The order Actinomycetales (OR = 0.79, 95% CI: 0.65-0.96, p = 0.020), family Actinomycetaceae (OR = 0.79, 95% CI: 0.65-0.96, p = 0.019), family Clostridiaceae 1 (OR = 0.80, 95% CI: 0.67-0.96, p = 0.015), genus Clostridiumsensustricto 1 (OR = 0.81, 95% CI: 0.67-0.98, p = 0.030) and genus Hungatella (OR = 0.86, 95% CI: 0.74-0.99, p = 0.040) had protective effects on kidney stones, and the genus Haemophilus (OR = 1.16, 95% CI: 1.01-1.33, p = 0.032), genus Ruminococcaceae (UCG010) (OR = 1.38, 95% CI: 1.04-1.84, p = 0.028), genus Subdoligranulum (OR = 1.27, 95% CI: 1.06-1.52, p = 0.009) were risk factors for kidney stones. Differential abundance analysis provide no evidence of a association between Oxalobacter formigenes and kidney stones, and showed genus Subdoligranulum were risk factors for kidney stones. Reverse MR analysis did not indicate any causal association of kidney stones on gut microbiota. No considerable heterogeneity of instrumental variables or horizontal pleiotropy was observed.

Conclusion

Our two-sample MR study did not find any causal relationship between genus Oxalobacter and kidney stones. The association between gut microbiota and kidney stones does not solely depend on the presence of genus Oxalobacter/Oxalobacter formigenes. A more integrated approach using multiple omics platforms is needed to better understand the pathogenesis of kidney stones in the context of complex gene-environment interactions over time.

Gut microbiota in patients with kidney stones: a systematic review and meta-analysis

BACKGROUND

Mounting evidence indicates that the gut microbiome (GMB) plays an essential role in kidney stone (KS) formation. In this study, we conducted a systematic review and meta-analysis to compare the composition of gut microbiota in kidney stone patients and healthy individuals, and further understand the role of gut microbiota in nephrolithiasis.

RESULTS

Six databases were searched to find taxonomy-based comparison studies on the GMB until September 2022. Meta-analyses were performed using RevMan 5.3 to estimate the overall relative abundance of gut microbiota in KS patients and healthy subjects. Eight studies were included with 356 nephrolithiasis patients and 347 healthy subjects. The meta-analysis suggested that KS patients had a higher abundance of Bacteroides (35.11% vs 21.25%, Z = 3.56, P = 0.0004) and Escherichia_Shigella (4.39% vs 1.78%, Z = 3.23, P = 0.001), and a lower abundance of Prevotella_9 (8.41% vs 10.65%, Z = 4.49, P < 0.00001). Qualitative analysis revealed that beta-diversity was different between the two groups (P < 0.05); Ten taxa (Bacteroides, Phascolarctobacterium, Faecalibacterium, Flavobacterium, Akkermansia, Lactobacillus, Escherichia coli, Rhodobacter and Gordonia) helped the detection of kidney stones (P < 0.05); Genes or protein families of the GMB involved in oxalate degradation, glycan synthesis, and energy metabolism were altered in patients (P < 0.05).

CONCLUSIONS

There is a characteristic gut microbiota dysbiosis in kidney stone patients. Individualized therapies like microbial supplementation, probiotic or synbiotic preparations and adjusted diet patterns based on individual gut microbial characteristics of patients may be more effective in preventing stone formation and recurrence.

Metabolic changes in kidney stone disease

Kidney stone disease (KSD) is one of the earliest medical diseases known, but the mechanism of its formation and metabolic changes remain unclear. The formation of kidney stones is a extensive and complicated process, which is regulated by metabolic changes in various substances. In this manuscript, we summarized the progress of research on metabolic changes in kidney stone disease and discuss the valuable role of some new potential targets. We reviewed the influence of metabolism of some common substances on stone formation, such as the regulation of oxalate, the release of reactive oxygen species (ROS), macrophage polarization, the levels of hormones, and the alternation of other substances. New insights into changes in substance metabolism changes in kidney stone disease, as well as emerging research techniques, will provide new directions in the treatment of stones. Reviewing the great progress that has been made in this field will help to improve the understanding by urologists, nephrologists, and health care providers of the metabolic changes in kidney stone disease, and contribute to explore new metabolic targets for clinical therapy.

Zn2+ regulates human oxalate metabolism by manipulating oxalate decarboxylase to treat calcium oxalate stones

A high concentration of oxalate is associated with an increased risk of kidney calcium oxalate (CaOx) stones, and the degradation of exogenous oxalate mostly depends on oxalate-degrading enzymes from the intestinal microbiome. We found that zinc gluconate supplement to patients with CaOx kidney stones could significantly improve the abundance of oxalate metabolizing bacteria in humans through clinical experiments on patients also subjected to antibiotic treatment. The analysis of clinical samples revealed that an imbalance of Lactobacillus and oxalate decarboxylase (OxDC) was involved in the formation of CaOx kidney stones. Then, we identified that Zn²⁺ could be used as an external factor to improve the activity of OxDC and promote Lactobacillus in the intestinal flora, and this treatment achieved a therapeutic effect on rats with stones aggravated by antibiotics. Finally, by analyzing the three-dimensional structure of OxDC and completing in vitro experiments, we propose a model of the Zn²⁺-induced reduction of CaOx kidney stone symptoms in rats by increasing the metabolism of oxalate through the positive effects of Zn²⁺ on Lactobacillus and OxDC.

Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.

Kidney Stone Prevention: Is There a Role for Complementary and Alternative Medicine?

Complementary and alternative medicine (CAM) is often implemented in kidney stone patients. It consists of preparations including different ingredients, such as herbs, probiotics, and vitamins, often together with alkali, that are classified within the dietary supplementation category. The majority of dietary supplements claiming to treat or prevent kidney stones contain ingredients with conflicting or no scientific evidence to support their claims. Clinicians should advise stone formers that the effects of most supplements are unknown or unstudied in humans and that the absence of evidence does not imply absence of potential harm. Unfortunately, the CAM preparation consists of a mix of different molecules, often including alkali, with different potential mechanisms of action and, even when favorable results are reported, the role of the single molecules cannot be assessed. Despite all these concerns, CAM products remain quite popular among kidney stone patients. The scarce knowledge in this field prevents one from recommending CAM products in daily clinical practice; only a weak suggestion for their use in kidney stone patients may be reasonable.

Shockwaves and the Rolling Stones: An Overview of Pediatric Stone Disease

Urinary stone disease is a common problem in adults, with an estimated 10% to 20% lifetime risk of developing a stone and an annual incidence of almost 1%. In contrast, in children, even though the incidence appears to be increasing, urinary tract stones are a rare problem, with an estimated incidence of approximately 5 to 36 per 100,000 children. Consequently, typical complications of rare diseases, such as delayed diagnosis, lack of awareness, and specialist knowledge, as well as difficulties accessing specific treatments also affect children with stone disease. Indeed, because stone disease is such a common problem in adults, frequently, it is adult practitioners who will first be asked to manage affected children. Yet, there are unique aspects to pediatric urolithiasis such that treatment practices common in adults cannot necessarily be transferred to children. Here, we review the epidemiology, etiology, presentation, investigation, and management of pediatric stone disease; we highlight those aspects that separate its management from that in adults and make a case for a specialized, multidisciplinary approach to pediatric stone disease.

Hydration and Nephrolithiasis in Pediatric Populations: Specificities and Current Recommendations

Renal lithiasis is less frequent in children than in adults; in pediatrics, lithiasis may be caused by genetic abnormalities, infections, and complex uropathies, but the association of urological and metabolic abnormalities is not uncommon. The aim of this study is to provide a synthesis of nephrolithiasis in children and to emphasize the role of hydration in its treatment. As an etiology is reported in 50% of cases, with a genetic origin in 10 to 20%, it is proposed to systematically perform a complete metabolic assessment after the first stone in a child. Recent data in the field reported increased incidence of pediatric urolithiasis notably for calcium oxalate stones. These changes in the epidemiology of stone components may be attributable to metabolic and environmental factors, where hydration seems to play a crucial role. In case of pediatric urolithiasis, whatever its cause, it is of utmost importance to increase water intake around 2 to 3 L/m² per day on average. The objective is to obtain a urine density less than 1010 on a dipstick or below 300 mOsm/L, especially with the first morning urine. Some genetic diseases may even require a more active 24 h over-hydration, e.g., primary hyperoxaluria and cystinuria; in such cases naso-gastric tubes or G-tubes may be proposed. Tap water is adapted for children with urolithiasis, with limited ecological impact and low economical cost. For children with low calcium intake, the use of calcium-rich mineral waters may be discussed in some peculiar cases, even in case of urolithiasis. In contrast, sugar-sweetened beverages are not recommended. In conclusion, even if parents and patients sometimes have the feeling that physicians do not propose "fancy" therapeutic drugs, hydration and nutrition remain cornerstones of the management of pediatric urolithiasis.

A Comparative Study of Stone Re-Treatment after Lithotripsy

The high recurrence rate has always been a problem associated with urolithiasis. This study aimed to explore the effectiveness of single interventions, combined therapies, and surgical and nonsurgical interventions. Herein, three lithotripsy procedures—extracorporeal shock wave lithotripsy (ESWL), percutaneous nephrolithotomy (PCNL), and ureteroscopic lithotripsy (URSL)—were assessed and a retrospective cohort was selected in order to further analyze the association with several risk factors. Firstly, a population-based cohort from the Taiwan National Health Insurance Research Database (NHIRD) from 1997 to 2010 was selected. In this study, 350 lithotripsy patients who underwent re-treatment were followed up for at least six years to compare re-treatment rates, with 1400 patients without any lithotripsy treatment being used as the comparison cohort. A Cox proportional hazards regression model was applied. Our results indicate that the risk of repeat urolithiasis treatment was 1.71-fold higher in patients that received lithotripsy when compared to patients that were not treated with lithotripsy (hazard ratio (HR) 1.71; 95% confidence interval (CI) = 1.427−2.048; p < 0.001). Furthermore, a high percentage of repeated treatment was observed in the ESWL group (HR 1.60; 95% CI = 1.292−1.978; p < 0.001). Similarly, the PCNL group was also independently associated with a high chance of repeated treatment (HR 2.32; 95% CI = 1.616−3.329; p < 0.001). Furthermore, age, season, level of care, and Charlson comorbidities index (CCI) should always be taken into consideration as effect factors that are highly correlated with repeated treatment rates.

Enteral nutrition and the risk of nephrolithiasis in complex pediatric patients

PURPOSE

Medically complex, non-ambulatory children can often suffer from nephrolithiasis. The purpose of this study is to determine risk factors which are predictive for recurrent stone formation in this patient population.

MATERIAL AND METHODS

A retrospective cohort study was performed on non-ambulatory patients with cerebral palsy and/or severe developmental delay presenting to a high-volume Pediatric Stone Center from 2015 to 2019. Two 24-hour urine collections were performed as a baseline prior to pharmacotherapeutic and/or dietary intervention. Healthy stone-forming children served as a control group.

RESULTS

28 non-ambulatory subjects and 38 healthy controls were evaluated. The study group had a higher rate of bilateral nephrolithiasis but a similar history of previous surgical procedures. 89% of the non-ambulatory children were fed via a gastrostomy. The median calcium excretion was the same in both groups (3.0 mg/kg/day). The median 24-hour excretion of oxalate was significantly increased in the study group (54 vs 31 mg/1.73 m²/day, p = 0.0001). Urinary citrate and phosphorus excretions, and the supersaturations of calcium oxalate and calcium phosphate were similar between study subjects and controls. Calcium oxalate stones were noted in 57% of those with known stone composition in the study group. Enteral feeding formulas were primarily based on soy protein, a known high oxalate food.

CONCLUSIONS

Urinary oxalate excretion is significantly increased in a cohort of medically complex, non-ambulatory stone-forming children. Urinary calcium excretion was not elevated between study subjects and healthy controls. Further analysis is needed to assess if dietary intervention to limit oxalate excretion results in decreased stone formation.

Contribution of Symptomatic, Herbal Treatment Options to Antibiotic Stewardship and Microbiotic Health

Epithelial surfaces in humans are home to symbiotic microbes (i.e., microbiota) that influence the defensive function against pathogens, depending on the health of the microbiota. Healthy microbiota contribute to the well-being of their host, in general (e.g., via the gut-brain axis), and their respective anatomical site, in particular (e.g., oral, urogenital, skin, or respiratory microbiota). Despite efforts towards a more responsible use of antibiotics, they are often prescribed for uncomplicated, self-limiting infections and can have a substantial negative impact on the gut microbiota. Treatment alternatives, such as non-steroidal anti-inflammatory drugs, may also influence the microbiota; thus, they can have lasting adverse effects. Herbal drugs offer a generally safe treatment option for uncomplicated infections of the urinary or respiratory tract. Additionally, their microbiota preserving properties allow for a more appropriate therapy of uncomplicated infections, without contributing to an increase in antibiotic resistance or disturbing the gut microbiota. Here, herbal treatments may be a more appropriate therapy, with a generally favorable safety profile.

Association of dietary patterns with gut microbiota in kidney stone and non-kidney stone individuals

The dietary patterns are closely associated with gut microbiota, which has been proved associated with kidney stones. To assess the association among the dietary patterns, gut microbiota, and kidney stones, patients with calcium oxalate stones and participants without kidney stones were recruited in West China Hospital and were divided into the low nephrolithiasis risk (LNR) and high nephrolithiasis risk (HNR) dietary pattern group based on the results of food frequency questionnaires. The genomic DNA of the fecal samples were extracted for 16S ribosomal RNA gene sequencing. The non-kidney stone (NS) group comprised 39 LNR and 45 HNR individuals, while the kidney stone (KS) group consisted of 19 LNR and 50 HNR individuals. The distribution of oxalate in urine (p < 0.01) but not calcium (p = 0.741) was significantly varied among the four groups. Significant difference was found in the dietary patterns of people with KS and NS controls (X² = 5.744, p = 0.017). Forty-six discriminative bacteria were found among different dietary patterns groups in KS patients and NS controls. Not only gut bacteria such as Pseudomonas, Sphingomonas, Hydrogenoanaerobacterium, Faecalitalea, etc., but also metabolic pathways associated with inflammation, lipid, and mineral metabolism were found more abundant in KS patients with HNR dietary pattern. It is noteworthy that g__Prevotellaceae_UCG_001, g__hgcI_clade, and g__Bradyrhizobium were negatively related to water intake but instead had a positive correlation with salt and meat intake. Our study revealed that gut microbiota with significantly different abundance existed in the HNR dietary patterns compared to the LNR counterparts in both calcium oxalate KS and NS individuals. The dietary patterns may affect the prevention and management of calcium oxalate stones by regulating the homeostasis of gut microbiota.

16S rRNA gene sequencing reveals altered composition of gut microbiota in postoperative individuals with renal stones

Renal stones are a common urological disease with high prevalence and recurrence rates. Characterizing gut microbiome profiles of first‐onset renal calculi patients, both before and after surgery, may provide valuable insights and identify potential biomarkers for the disease. In this study, we explored the associations between the gut microbiome and renal stone formation using 16S ribosomal RNA (rRNA) gene sequencing. In brief, 20 patients were recruited, and information on health and eating habits within the previous 1–3 months was collected upon admission. A total of 493 operational taxonomic units (OTUs) were detected in 40 specimens, with an average of 67,888 ± 827 reads per sample. The results of OTU‐based partial least squares discriminant analysis (PLS‐DA) analysis showed differences between RS1 (fecal specimen before surgery) and RS2 (one month later after surgery) groups, with a significantly higher level of OTU7 in the RS2 group. Taxonomy‑based comparisons of the gut microbiome showed differences in the flora composition, with the prevalence of Enterobacteriales, Enterobacteriaceae, Gammaproteobacteria and Escherichia being higher in the RS2 group and the prevalence of Pseudomonadaceae, Pseudomonadales and Pseudomonas being higher in the RS1 group. Correlation analysis showed that an increased prevalence of Enterobacteriaceae, Gammaproteobacteria and Escherichia associated with a decreased level of urea, and a decreased creatinine level was correlated with an increased prevalence of Escherichia. These data strongly suggest that the gut microbiome plays an important role in kidney stone formation, and these findings may provide new insights for the prevention, diagnosis, and treatment of renal stones.

Efficacy of Super-Mini-PCNL and Ureteroscopy in Kidney Stone Sufferers and Risk Factors of Postoperative Infection

To investigate the efficacy of super-mini-PCNL (SMP) and ureteroscopy in kidney stone (KS) sufferers and learn the risk factors of postoperative infection. A retrospective analysis was performed on 180 KS sufferers who were diagnosed and treated in our hospital from May 2019 to May 2021. They were enrolled into an observation group (OG, n = 104) and a control group (CG, n = 76) based on different treatment methods. Therein, the former was treated with SMP, while the latter was treated with ureteroscopy. The operation time, blood loss, hospital stay, recent stone-free rate (one week after operation), changes of serum creatinine (SCr), blood urea nitrogen (BUN), and cystatin C (CysC) levels before and after operation and complications were compared. Those sufferers were assigned to infected and uninfected groups based on their postoperative infection. The risk factors were assessed through logistic regression, and the model formula was established. The predictive value of this model for infection was tested through RO. Compared with CG, the operation time of the OG was longer, the blood loss and hospital stay were lower (P < 0.05), and the stone-free rate was higher (P < 0.05). Renal function indexes before and after treatment (P > 0.05) and postoperative complications revealed no significant difference (P > 0.05). Logistic regression analysis manifested that preoperative urinary tract infection (OR: 4.690, 95% CI: 1.170-18.802), preoperative blood glucose level (OR: 11.188, 95% CI: 2.106-59.442), positive urine culture (OR: 10.931, 95% CI: 2.453-48.705), and infectious stones (OR: 3.951, 95% CI: 1.020-15.300) were independently related to infection. The risk prediction equation is logit(p)=-8.913+1.545 × X1+2.415 × X2+2.392 × X3+1.374 × X4, with a goodness-of-fit value of 0.545. The AUC is 0.930, so SMP is superior to ureteroscopy in KS sufferers. Preoperative urinary tract infection, preoperative blood glucose level, positive urine culture, and infectious stones are independently related to infection.

The Microbiome and Urolithiasis: Current Advancements and Future Challenges

PURPOSE OF REVIEW

The aim of this review is to explore the effect of the microbiome on urolithiasis and explore recent advances and challenges in microbiome research for urolithiasis.

RECENT FINDINGS

Lack of standardization and shortcomings in study design for urinary microbiome research on urolithiasis has hampered the generalizability of results and weakened the impact of findings on clinical practice. Important study limitations include sample heterogenicity, specimen contamination, poor culture yields, and lack of shared datasets for meta-analysis. Contrary to traditional teaching, the genitourinary tract is not a sterile environment. This urinary microbiome may influence the pathogenesis of urolithiasis, although the specific mechanisms are still currently being explored. Successful investigation will depend on consistency in study design and analysis, as well as sharing data and protocols across institutions. Developing an understanding of the relationship between the urinary microbiome and urolithiasis may lead to novel approaches to mitigate stone risk.

Synbiotic supplementation and oxalate homeostasis in rats: focus on microbiota oxalate-degrading activity

The present study aimed (i) to evaluate whether ceftriaxone treatment could affect not only intestinal oxalate-degrading bacteria number but also their total activity to degrade oxalate and influence oxalate homeostasis in rats, (ii) and to estimate the ability of commercially available inulin-contained synbiotic to restore fecal oxalate-degrading activity and ceftriaxone-induced disruption of oxalate homeostasis in rats. Twenty-eight female Wistar rats (200-300 g) were randomly divided into four groups (n = 7). Group 1 was treated with vehicle sterile water (0.1 ml, i.m., 14 days); Group 2 received synbiotic (30 mg/kg, per os, 14 days); Group 3 was treated with ceftriaxone (300 mg/kg, i.m., 7 days); Group 4 was supplemented with ceftriaxone and synbiotic. Oxalate-degrading bacteria number and their total activity, urinary and plasma oxalate concentrations were measured on days 1 and 57 after the treatment withdrawal. The redoximetric titration with KMnO₄ was adopted to evaluate the total oxalate-degrading activity in highly selective Oxalate Medium. Ceftriaxone treatment reduced total fecal oxalate-degrading activity independently on oxalate-degrading bacteria number and increased urinary and plasma oxalate concentrations. The synbiotic had higher oxalate-degrading activity vs probiotics and was able to restore fecal oxalate-degrading activity and significantly decrease urinary oxalate excretion in antibiotic-treated rats. Total fecal oxalate-degrading activity but not oxalate-degrading bacteria number should be thoroughly examined in the future to develop predictive diagnostics methods, targeted prevention and personalized treatment in kidney stone disease. Synbiotic supplementation had a beneficial effect on the total oxalate-degrading activity of gut microbiota, which resulted in decreased UOx excretion in rats.

Enterobacter cloacae: a villain in CaOx stone disease?

To explore the roles microbiome of urinary tract played in calcium oxalate stones (CaOx) formation, we collected two sides’ pelvis urine of patients with unilateral CaOx stones to set self-control to diminish the influence of systemic factors. Patients with unilateral CaOx stones were recruited in our study according to strict criteria. 16S rRNA gene sequencing was applied to every pair of pelvis urine. Bacterial genome sequencing of Enterobacter cloacae was conducted and bioinformatic analysis was applied to explore the possible pathways of Enterobacter cloacae inducing CaOx stones formation. In vivo experiments were conducted to validate our claims. Von Kossa staining, TUNEL assay and Western Blot were applied to SD rats exploring the mechanism of stone formation. We found 26 significantly different bacteria between stone sides and non-stone sides’ pelvis urine, among which Enterobacter cloacae ranked the most different. Bacterial genome sequencing of Enterobacter cloacae revealed that its virulence factors included Flagellin, LPS and Fimbrial. GO and KEGG analysis revealed it probably induced CaOx stone formation via ion binging and signaling transduction pathways. The results of animal experiments indicated that Glyoxylic Acid could promote apoptosis and crystal depositions of kidney comparing with control group while pre-injected with Enterobacter cloacae could apparently compound the effects. While Western Blot demonstrated that Glyoxylic Acid or Enterobacter cloacae could increase the expression of IL-6, Mcp-1, BMP2 and OPN in rats’ kidney, Glyoxylic Acid and Enterobacter cloacae together could aggravate these increases. These findings indicated that Enterobacter cloacae might play important roles in CaOx stones formation. However, this study is just a preliminary exploration; further studies still need to be conducted.

Acute Oxalate Nephropathy Caused by Excessive Vegetable Juicing and Concomitant Volume Depletion

Acute oxalate nephropathy (AON) induced by high dietary intake of oxalate-rich food is a rare cause of acute kidney injury and end-stage renal disease (ESRD). We describe a 68-year-old man with adequate baseline renal function who developed severe AON and ESRD. Six months earlier, he started a daily oxalate-rich fruit and vegetable juice diet high in spinach, with a calculated daily oxalate dietary intake of 1500 mg, about 10 times a typical diet. Renal biopsy showed extensive tubular oxalate deposits and acute tubular damage; the renal tissue was relatively free of chronic changes such as glomerulosclerosis, tubular atrophy, and interstitial fibrosis. A year later, he remains dialysis dependent.

Probiotics in the Prevention of the Calcium Oxalate Urolithiasis

Nephrolithiasis ranks third among urological diseases in terms of prevalence, making up about 15% of cases. The continued increase in the incidence of nephrolithiasis is most probably due to changes in eating habits (high protein, sodium, and sugar diets) and lifestyle (reduced physical activity) in all developed countries. Some 80% of all kidney stones cases are oxalate urolithiasis, which is also characterized by the highest risk of recurrence. Frequent relapses of nephrolithiasis contribute to severe complications and high treatment costs. Unfortunately, there is no known effective way to prevent urolithiasis at present. In cases of diet-related urolithiasis, dietary changes may prevent recurrence. However, in some patients, the condition is unrelated to diet; in such cases, there is evidence to support the use of stone-related medications. Interestingly, a growing body of evidence indicates the potential of the microbiome to reduce the risk of developing renal colic. Previous studies have primarily focused on the use of Oxalobacterformigenes in patients with urolithiasis. Unfortunately, this bacterium is not an ideal probiotic due to its antibiotic sensitivity and low pH. Therefore, subsequent studies sought to find bacteria which are capable of oxalate degradation, focusing on well-known probiotics including Lactobacillus and Bifidobacterium strains, Eubacterium lentum, Enterococcus faecalis, and Escherichia coli.

Oxalate Flux Across the Intestine: Contributions from Membrane Transporters

Epithelial oxalate transport is fundamental to the role occupied by the gastrointestinal (GI) tract in oxalate homeostasis. The absorption of dietary oxalate, together with its secretion into the intestine, and degradation by the gut microbiota, can all influence the excretion of this nonfunctional terminal metabolite in the urine. Knowledge of the transport mechanisms is relevant to understanding the pathophysiology of hyperoxaluria, a risk factor in kidney stone formation, for which the intestine also offers a potential means of treatment. The following discussion presents an expansive review of intestinal oxalate transport. We begin with an overview of the fate of oxalate, focusing on the sources, rates, and locations of absorption and secretion along the GI tract. We then consider the mechanisms and pathways of transport across the epithelial barrier, discussing the transcellular, and paracellular components. There is an emphasis on the membrane-bound anion transporters, in particular, those belonging to the large multifunctional Slc26 gene family, many of which are expressed throughout the GI tract, and we summarize what is currently known about their participation in oxalate transport. In the final section, we examine the physiological stimuli proposed to be involved in regulating some of these pathways, encompassing intestinal adaptations in response to chronic kidney disease, metabolic acid-base disorders, obesity, and following gastric bypass surgery. There is also an update on research into the probiotic, Oxalobacter formigenes, and the basis of its unique interaction with the gut epithelium. © 2021 American Physiological Society. Compr Physiol 11:1-41, 2021.

Short-Chain Fatty Acids Reduced Renal Calcium Oxalate Stones by Regulating the Expression of Intestinal Oxalate Transporter SLC26A6

Renal calcium oxalate (CaOx) stone is a common urologic disease with a high prevalence and recurrence rate. However, short-chain fatty acids (SCFAs) are less often reported in the prevention of urolithiasis. This study aimed to explore the effect of SCFAs on the renal CaOx stone formation and the underlying mechanisms. Ethylene glycol was used to induce renal CaOx crystals in rats. SCFAs (acetate, propionate, or butyrate) were added as supplements to the drinking water with or without antibiotics. Because intestinal oxalate transporters SLC26A6 and SLC26A3 regulate the excretion and absorption of oxalate in the intestine, we injected adeno-associated virus 9 (AAV9)-SLC26A6-shRNA (short hairpin RNA) and AAV9-SLC26A3 into the tail vein of rats to suppress SLC26A6 and overexpress SLC26A3 expression in the intestine, respectively, to explore the role of SLC26A3 and SLC26A6 (SLC26A3/6) in the reduction of renal CaOx crystals induced by SCFAs. Results showed that SCFAs reduced renal CaOx crystals and urinary oxalate levels but, however, increased the abundance of SCFA-producing bacteria and cecum SCFA levels. SCFA supplements still reduced renal crystals and urinary oxalate after gut microbiota depletion. Propionate and butyrate downregulated intestinal oxalate transporter SLC26A3 expression, while acetate and propionate upregulated SLC26A6 expression, both in vivo and in vitro. AAV9-SLC26A3 exerted a protective effect against renal crystals, while AAV9-SLC26A6-shRNA contributed to the renal crystal formation even though the SCFAs were supplemented. In conclusion, SCFAs could reduce urinary oxalate and renal CaOx stones through the oxalate transporter SLC26A6 in the intestine. SCFAs may be new supplements for preventing the formation of renal CaOx stones. IMPORTANCE Some studies found that the relative abundances of short-chain-fatty-acid (SCFA)-producing bacteria were lower in the gut microbiota of renal stone patients than healthy controls. Our previous study demonstrated that SCFAs could reduce the formation of renal calcium oxalate (CaOx) stones, but the mechanism is still unknown. In this study, we found that SCFAs (acetate, propionate, and butyrate) reduced the formation of renal calcium oxalate (CaOx) crystals and the level of urinary oxalate. Depleting gut microbiota increased the amount of renal crystals in model rats, and SCFA supplements reduced renal crystals and urinary oxalate after gut microbiota depletion. Intestinal oxalate transporter SLC26A6 was a direct target of SCFAs. Our findings suggested that SCFAs could reduce urinary oxalate and renal CaOx stones through the oxalate transporter SLC26A6 in the intestine. SCFAs may be new supplements for preventing the formation of renal CaOx stones.

The controversial association of gut and urinary microbiota with kidney stone formation

Nephrolithiasis (kidney stones) is one of the most common chronic kidney diseases that are typically more common among adult men comparing to adult women. The prevalence of this disease is increasing which is influenced by genetic and environmental factors. Kidney stones are mainly composed of calcium oxalate and urinary oxalate which is considered a dangerous factor in their formation. Besides diverse leading reasons in the progression of nephrolithiasis, the gut and urinary microbiome has been recognized as a major player in the development or prevention of it. These microbes produce metabolites that have diverse effects on host biological functions. Therefore, Changes in the composition and structure of the microbiome (dysbiosis) have been implicated in various diseases. The present review focuses on the roles of gut and urinary in kidney stone formation.

The Effect of Oxalobacter formigenes Colonization in Patients with Calcium Oxalate Renal Stones in Comparison with Healthy People in Qom: A Case-Control Study

Background: Urinary stones are a major problem world, and their incidence has increased significantly in recent years. Objectives: This study aimed to develop a simple and rapid molecular method based on PCR and qPCR assays to detect Oxalobacter formigenes (which causes oxalate degradation in intestines) in fecal samples of healthy volunteers and patients with calcium oxalate nephrolithiasis, and determine the amount of urinary oxalate in the two groups. Methods: This study was performed on urine and fecal samples of 73 patients with kidney stones and 52 healthy individuals. After DNA extraction, PCR and qPCR assays were performed on two gene regions of O. formigenes, OXC, and FRC. Also, urine oxalate was measured in the study population using biochemical methods. Results: We found that the presence of O. formigenes could reduce the risk of kidney stones and calcium oxalate stones. In fact, both FRC and OXC genes were involved in the diagnosis of O. formigenes; however, the results based on the FRC gene showed higher efficiency. In addition, the presence or absence of stones did not affect the amount of urinary excretion of oxalate, rather it is affected by diet. Conclusions: Molecular identification of O. formigenes by PCR and qPCR assays allows rapid, specific, and reproducible detection in fecal samples, which also allows immediate processing of these samples in clinical conditions.

Recent advances on the mechanisms of kidney stone formation (Review)

Kidney stone disease is one of the oldest diseases known to medicine; however, the mechanisms of stone formation and development remain largely unclear. Over the past decades, a variety of theories and strategies have been developed and utilized in the surgical management of kidney stones, as a result of recent technological advances. Observations from the authors and other research groups suggest that there are five entirely different main mechanisms for kidney stone formation. Urinary supersaturation and crystallization are the driving force for intrarenal crystal precipitation. Randall's plaques are recognized as the origin of calcium oxalate stone formation. Sex hormones may be key players in the development of nephrolithiasis and may thus be potential targets for new drugs to suppress kidney stone formation. The microbiome, including urease-producing bacteria, nanobacteria and intestinal microbiota, is likely to have a profound effect on urological health, both positive and negative, owing to its metabolic output and other contributions. Lastly, the immune response, and particularly macrophage differentiation, play crucial roles in renal calcium oxalate crystal formation. In the present study, the current knowledge for each of these five aspects of kidney stone formation is reviewed. This knowledge may be used to explore novel research opportunities and improve the understanding of the initiation and development of kidney stones for urologists, nephrologists and primary care.

Genetic Background but Not Intestinal Microbiota After Co-Housing Determines Hyperoxaluria-Related Nephrocalcinosis in Common Inbred Mouse Strains

Calcium oxalate (CaOx) crystal formation, aggregation and growth is a common cause of kidney stone disease and nephrocalcinosis-related chronic kidney disease (CKD). Genetically modified mouse strains are frequently used as an experimental tool in this context but observed phenotypes may also relate to the genetic background or intestinal microbiota. We hypothesized that the genetic background or intestinal microbiota of mice determine CaOx crystal deposition and thus the outcome of nephrocalcinosis. Indeed, Casp1^-/-, Cybb^-/- or Casp1^-/-/Cybb^-/- knockout mice on a 129/C57BL/6J (B6J) background that were fed an oxalate-rich diet for 14 days did neither encounter intrarenal CaOx crystal deposits nor nephrocalcinosis-related CKD. To test our assumption, we fed C57BL/6N (B6N), 129, B6J and Balb/c mice an oxalate-rich diet for 14 days. Only B6N mice displayed CaOx crystal deposits and developed CKD associated with tubular injury, inflammation and interstitial fibrosis. Intrarenal mRNA expression profiling of 64 known nephrocalcinosis-related genes revealed that healthy B6N mice had lower mRNA levels of uromodulin (Umod) compared to the other three strains. Feeding an oxalate-rich diet caused an increase in uromodulin protein expression and CaOx crystal deposition in the kidney as well as in urinary uromodulin excretion in B6N mice but not 129, B6J and Balb/c mice. However, backcrossing 129 mice on a B6N background resulted in a gradual increase in CaOx crystal deposits from F2 to F7, of which all B6N/129 mice from the 7^th generation developed CaOx-related nephropathy similar to B6N mice. Co-housing experiments tested for a putative role of the intestinal microbiota but B6N co-housed with 129 mice or B6N/129 (3^rd and 6^th generation) mice did not affect nephrocalcinosis. In summary, genetic background but not the intestinal microbiome account for strain-specific crystal formation and, the levels of uromodulin secretion may contribute to this phenomenon. Our results imply that only littermate controls of the identical genetic background strain are appropriate when performing knockout mouse studies in this context, while co-housing is optional.

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Background

Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis.

Methods

Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions.

Results

Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite.

Conclusions

These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

Impact of age and renal function on urine chemistry in patients with calcium oxalate kidney stones

Nephrolithiasis is associated with an increased risk of chronic kidney disease, and its incidence varies with age. However, little is known on the combined impact of aging and declining renal function on urinary risk factors for calcium oxalate stone formation. A retrospective analysis was performed on 24-h urine collections from 993 calcium oxalate stone-forming patients. We first tested for interactions between age and creatinine clearance on various urinary determinants of calcium oxalate nephrolithiasis, and then examined their separate and combined effects in univariable and multivariable analyses adjusting for demographic and biochemical covariates. We identified significant interactions between age and creatinine clearance in predicting 24-h urine pH, calcium, and citrate. In view of the small number of stone formers with low creatinine clearance, we limited further regression analyses to patients with creatinine clearance ≥ 60 mL/min. In multivariable analyses, urine citrate, oxalate, and total volume were positively correlated with age, whereas urine pH, citrate, calcium, oxalate, total volume, and RSR of calcium oxalate all significantly decreased with lower creatinine clearance. A decrease in creatinine clearance from 120 to 60 mL/min was associated with clinically significant decreases in the daily excretion rate of citrate (by 188 mg/day), calcium (by 33 mg/day), and oxalate (by 4 mg/day), and in RSR calcium oxalate (by 1.84). Age and creatinine clearance are significant and independent predictors of several urinary determinants of calcium oxalate nephrolithiasis. The impacts of aging and declining renal function should be considered during the management of calcium oxalate stone-forming patients.

Metabolome and microbiome in kidney diseases

Despite several decades of intensive research and hard work in nephrology, a void exists in the availability of markers for identifying at-risk individuals, diagnosing diseases at incipient stage, and predicting treatment response. Most of the current widely available diagnostic tools such as creatinine, urine analysis, and imaging studies are quite insensitive such that about half of the kidney function is lost before perceivable changes are observed with these tests. In addition, these parameters are affected by factors other than renal, questioning their specificity. Renal biopsy, though specific, is quite expensive, risky, and invasive. The recent surge in the knowledge of small molecules in the tissue and body fluids, "metabolomics," thanks to the Human Metabolome Database created by the Human Metabolome Project, has opened a new avenue for better understanding the disease pathogenesis and, in parallel, to identify novel biomarkers and druggable targets. Kidney, by virtue of its metabolic machinery and also being a major handler of metabolites generated by other tissues, is very much amenable to the metabolomic approach of studying its various perturbations. The gut microbiome, characterized by the Human Microbiome Project, is one of the principal players in metabolomics. Changes in metabolite profile due to alterations in gut microbiome can occur either as a cause or consequence of renal diseases. Unmasking the renal-metabolome-microbiome link has a great potential to script a new era in the diagnosis and management of renal diseases.

Gut microbiota affect the formation of calcium oxalate renal calculi caused by high daily tea consumption

Kidney stones are a common and frequently occurring disease worldwide. Stones can cause urinary tract obstruction, pain, haematuria, and other symptoms. In this study, the relationship between calcium oxalate renal calculi and gut microbiota was considered. The dietary habits of 30 patients with calcium oxalate kidney stones and 30 healthy people were investigated. The 16S rDNA sequences and short-chain fatty acids (SCFAs) in their stool samples were analysed. We identified 5 genera of the gut microbiota as biomarkers for calcium oxalate renal calculi, namely, Bacteroides, Phascolarctobacterium, Faecalibacterium, Akkermansia, and Lactobacillus, with a receiver operating characteristic (ROC) curve value of 0.871 (95% confidence interval (CI) 0.785-0.957). Phascolarctobacterium and Faecalibacterium showed a positive relationship with SCFA synthesis to reduce the risk of kidney stones. Meanwhile, according to the analysis, Lactobacillus spp. made the largest contribution (79%) to prevent kidney stones caused by tea consumption, since tea offers the great parts of oxalate in kidney stone formation. Three strains of Lactobacillus spp. were isolated from stools of a healthy person with a high level of tea consumption who did not suffer from kidney stones. All these strains survived in the colon with supplementation of high concentrations of tea and efficiently degraded oxalic acid (Ca. 50%) in an in vitro colonic simulation. Therefore, a suitable adjustment of the gut microbiota or SCFA concentration enhanced the degradation of oxalate from food, which can be applied to prevent the formation of calcium oxalate renal calculi caused by tea. KEY POINTS: • Five genera, including Lactobacillus, were identified as biomarkers for calcium oxalate renal calculi. • Lactobacillus is a potential gut bacterium associated with preventing kidney stone formation. • Isolated Lactobacillus strains have the ability to degrade oxalic acid in vitro.

The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease

The gastrointestinal (GI) microbiome of cats and dogs is increasingly recognized as a metabolically active organ inextricably linked to pet health. Food serves as a substrate for the GI microbiome of cats and dogs and plays a significant role in defining the composition and metabolism of the GI microbiome. The microbiome, in turn, facilitates the host's nutrient digestion and the production of postbiotics, which are bacterially derived compounds that can influence pet health. Consequently, pet owners have a role in shaping the microbiome of cats and dogs through the food they choose to provide. Yet, a clear understanding of the impact these food choices have on the microbiome, and thus on the overall health of the pet, is lacking. Pet foods are formulated to contain the typical nutritional building blocks of carbohydrates, proteins, and fats, but increasingly include microbiome-targeted ingredients, such as prebiotics and probiotics. Each of these categories, as well as their relative proportions in food, can affect the composition and/or function of the microbiome. Accumulating evidence suggests that dietary components may impact not only GI disease, but also allergies, oral health, weight management, diabetes, and kidney disease through changes in the GI microbiome. Until recently, the focus of microbiome research was to characterize alterations in microbiome composition in disease states, while less research effort has been devoted to understanding how changes in nutrition can influence pet health by modifying the microbiome function. This review summarizes the impact of pet food nutritional components on the composition and function of the microbiome and examines evidence for the role of nutrition in impacting host health through the microbiome in a variety of disease states. Understanding how nutrition can modulate GI microbiome composition and function may reveal new avenues for enhancing the health and resilience of cats and dogs.

The influence of dysbiosis on kidney stones that risk up renal cell carcinoma (RCC)

Kidney stone is a common urological condition, the prevalence and incidence of which has escalated in the last few years due to dietary habits and other related medical conditions such as obesity and diabetes mellitus. It is a chronic disease which leads to loss of kidney function(s) and nephrectomy. Chronic kidney stone disease has been shown to be associated with transitional cell carcinoma (TCC) or renal cell carcinoma (RCC) and kidney tumors have been found to be more frequent among patients with kidney stones. Although hyperoxaluria is mainly responsible for kidney stone formation, dysbiosis of the gut and urinary tract microbiome may in part contribute to kidney stone disease. Dysbiosis of the gut and urinary tract microbiome have been linked to kidney stone diseases with both gain and loss of function. The review provides a detailed study of how the variations in the microbiome of the human gut and urinary tract result in the chronic kidney stone diseases which are associated with increased papillary RCC risks.

The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature

Background

There is mounting evidence that individuals with kidney disease and kidney stones have an abnormal gut microbiota composition. No studies to date have summarised the evidence to categorise how the gut microbiota profile of these individuals may differ from controls. Synthesis of this evidence is essential to inform future clinical trials. This systematic review aims to characterise differences of the gut microbial community in adults with kidney disease and kidney stones, as well as to describe the functional capacity of the gut microbiota and reporting of diet as a confounder in these studies.

Methods

Included studies were those that investigated the gut microbial community in adults with kidney disease or kidney stones and compared this to the profile of controls. Six scientific databases (CINHAL, Medline, PubMed, Scopus, Web of Science and Cochrane Library), as well as selected grey literature sources, were searched. Quality assessment was undertaken independently by three authors. The system of evidence level criteria was employed to quantitatively evaluate the alteration of microbiota by strictly considering the number, methodological quality and consistency of the findings. Additional findings relating to altered functions of the gut microbiota, dietary intakes and dietary methodologies used were qualitatively summarised.

Results

Twenty-five articles met the eligibility criteria and included data from a total of 892 adults with kidney disease or kidney stones and 1400 controls. Compared to controls, adults with kidney disease had increased abundances of several microbes including Enterobacteriaceae, Streptococcaceae, Streptococcus and decreased abundances of Prevotellaceae, Prevotella, Prevotella 9 and Roseburia among other taxa. Adults with kidney stones also had an altered microbial composition with variations to Bacteroides, Lachnospiraceae NK4A136 group, Ruminiclostridium 5 group, Dorea, Enterobacter, Christensenellaceae and its genus Christensenellaceae R7 group. Differences in the functional potential of the microbial community between controls and adults with kidney disease or kidney stones were also identified. Only three of the 25 articles presented dietary data, and of these studies, only two used a valid dietary assessment method.

Conclusions

The gut microbiota profile of adults with kidney disease and kidney stones differs from controls. Future study designs should include adequate reporting of important confounders such as dietary intake to assist with interpretation of findings.