The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease

Potassium sodium hydrogen citrate intervention on gut microbiota and clinical features in uric acid stone patients

The high recurrence rate of renal uric acid stone (UAS) poses a significant challenge for urologists, and potassium sodium hydrogen citrate (PSHC) has been proven to be an effective oral dissolution drug. However, no studies have investigated the impact of PSHC on gut microbiota and its metabolites during stone dissolution therapy. We prospectively recruited 37 UAS patients and 40 healthy subjects, of which 12 patients completed a 3-month pharmacological intervention. Fasting vein blood was extracted and mid-stream urine was retained for biochemical testing. Fecal samples were collected for 16S ribosomal RNA (rRNA) gene sequencing and short chain fatty acids (SCFAs) content determination. UAS patients exhibited comorbidities such as obesity, hypertension, gout, and dyslipidemia. The richness and diversity of the gut microbiota were significantly decreased in UAS patients, Bacteroides and Fusobacterium were dominant genera while Subdoligranulum and Bifidobacterium were poorly enriched. After PSHC intervention, there was a significant reduction in stone size accompanied by decreased serum uric acid and increased urinary pH levels. The abundance of pathogenic bacterium Fusobacterium was significantly downregulated following the intervention, whereas there was an upregulation observed in SCFA-producing bacteria Lachnoclostridium and Parasutterella, leading to a significant elevation in butyric acid content. Functions related to fatty acid synthesis and amino acid metabolism within the microbiota showed upregulation following PSHC intervention. The correlation analysis revealed a positive association between stone pathogenic bacteria abundance and clinical factors for stone formation, while a negative correlation with SCFAs contents. Our preliminary study revealed that alterations in gut microbiota and metabolites were the crucial physiological adaptation to PSHC intervention. Targeted regulation of microbiota and SCFA holds promise for enhancing drug therapy efficacy and preventing stone recurrence. KEY POINTS: • Bacteroides and Fusobacterium were identified as dominant genera for UAS patients • After PSHC intervention, Fusobacterium decreased and butyric acid content increased • The microbiota increased capacity for fatty acid synthesis after PSHC intervention.

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.

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.

Beneficial roles of gastrointestinal and urinary microbiomes in kidney stone prevention via their oxalate-degrading ability and beyond

Formation of calcium oxalate (CaOx) crystal, the most common composition in kidney stones, occurs following supersaturation of calcium and oxalate ions in the urine. In addition to endogenous source, another main source of calcium and oxalate ions is dietary intake. In the intestinal lumen, calcium can bind with oxalate to form precipitates to be eliminated with feces. High intake of oxalate-rich foods, inappropriate amount of daily calcium intake, defective intestinal transporters for oxalate secretion and absorption, and gastrointestinal (GI) malabsorption (i.e., from gastric bypass surgery) can enhance intestinal oxalate absorption, thereby increasing urinary oxalate level and risk of kidney stone disease (KSD). The GI microbiome rich with oxalate-degrading bacteria can reduce intestinal oxalate absorption and urinary oxalate level. In addition to the oxalate-degrading ability, the GI microbiome also affects expression of oxalate transporters and net intestinal oxalate transport, cholesterol level, and short-chain fatty acids (SCFAs) production, leading to lower KSD risk. Recent evidence also shows beneficial effects of urinary microbiome in KSD prevention. This review summarizes the current knowledge on the aforementioned aspects. Potential benefits of the GI and urinary microbiomes as probiotics for KSD prevention are emphasized. Finally, challenges and future perspectives of probiotic treatment in KSD are discussed.

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.

Analysis of Dietary Patterns Associated with Kidney Stone Disease Based on Data-Driven Approaches: A Case-Control Study in Shanghai

The main objective of this study was to analyze dietary patterns using data-driven approaches and to explore preventive or risk dietary factors for kidney stone disease (KSD). A case-control matching study was conducted in adults (n = 6396) from a suburb of Shanghai. A food frequency questionnaire was used to assess the consumption of various types of food, and B-ultrasound was used to identify kidney stones. Principal component analysis and regression were used to generate dietary patterns and further explore the relationship between dietary patterns and KSD. LASSO regression and post-selection inference were used to identify food groups most associated with KSD. Among males, the "balanced but no-sugary-beverages pattern" (OR = 0.78, p < 0.05) and the "nuts and pickles pattern" (OR = 0.84, p < 0.05) were protective dietary patterns. Among females, "high vegetables and low-sugary-beverages pattern" (OR = 0.83, p < 0.05) and "high-crustaceans and low-vegetables pattern" (OR = 0.79, p < 0.05) were protective dietary patterns, while the "comprehensive pattern with a preference for meat" (OR = 1.06, p < 0.05) and "sugary beverages pattern" (OR = 1.16, p < 0.05) were risk dietary patterns. We further inferred that sugary beverages (p < 0.05) were risk factors and pickles (p < 0.05) and crustaceans (p < 0.05) were protective factors.

Differential oral and gut microbial structure related to systemic metabolism in kidney stone patients

OBJECTIVES

To investigate the role of the oral and gut microbiome related to systemic metabolism and clinical parameters in various types of kidney stone disease.

PATIENTS AND METHODS

We conducted a case-control study by analyzing 16S rRNA and untargeted metabolomics profiling of 76 fecal, 68 saliva, 73 urine, and 43 serum samples from 76 participants aged 18-75 years old. The participants included 15 patients with uric acid stones, 41 patients with calcium oxalate stones, and 20 healthy controls. Correlations among microbiome, metabolism, and clinical parameters were identified through Spearman's correlation analysis. (Clinical trial No. ChiCTR2200055316).

RESULTS

Patients with uric acid stones exhibited reduced richness and diversity in their microbiome, as well as altered composition in both oral and gut microbiome. Furthermore, their fecal samples showed lower relative abundances of Bacteroides and Lachnospiraceae, while their saliva samples showed higher relative abundances of Porphyromonas and Neisseria. Predicted KEGG metabolism pathways, including amino acid and fatty acid metabolisms, were significantly altered in subjects with uric acid stones. Oral, gut microbiota, and metabolism were also associated with low water intake and urine pH. The area under the curve (AUC) of the specific microbiota and metabolite prediction models was over 0.85.

CONCLUSION

The structure and composition of the oral and gut microbiome in different types of kidney stone disease, the correlations between oral and gut microbiome, and the associations among oral and gut microbiota, systemic metabolism and clinical parameters imply an important role that the oral and gut microbiome may play in kidney stone disease.

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

BACKGROUND

Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD.

RESULTS

Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism.

CONCLUSIONS

We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.

Enteroendocrine cells and gut hormones as potential targets in the crossroad of the gut-kidney axis communication

Recent studies suggest that disruptions in intestinal homeostasis, such as changes in gut microbiota composition, infection, and inflammatory-related gut diseases, can be associated with kidney diseases. For instance, genomic investigations highlight how susceptibility genes linked to IgA nephropathy are also correlated with the risk of inflammatory bowel disease. Conversely, investigations demonstrate that the use of short-chain fatty acids, produced through fermentation by intestinal bacteria, protects kidney function in models of acute and chronic kidney diseases. Thus, the dialogue between the gut and kidney seems to be crucial in maintaining their proper function, although the factors governing this crosstalk are still emerging as the field evolves. In recent years, a series of studies have highlighted the significance of enteroendocrine cells (EECs) which are part of the secretory lineage of the gut epithelial cells, as important components in gut-kidney crosstalk. EECs are distributed throughout the epithelial layer and release more than 20 hormones in response to microenvironment stimuli. Interestingly, some of these hormones and/or their pathways such as Glucagon-Like Peptide 1 (GLP-1), GLP-2, gastrin, and somatostatin have been shown to exert renoprotective effects. Therefore, the present review explores the role of EECs and their hormones as regulators of gut-kidney crosstalk and their potential impact on kidney diseases. This comprehensive exploration underscores the substantial contribution of EEC hormones in mediating gut-kidney communication and their promising potential for the treatment of kidney diseases.

The genetics of urinary microbiome, an exploration of the trigger in calcium oxalate stone

Background: Kidney stone disease is a global disease; however, it has not been totally understood. Calcium oxalate (CaOx) stone is the dominant type of kidney stone, and the potential factors involved in its formation are yet to be explored. Clinically, we found that the CaOx stones in patients were mainly unilateral; therefore, systemic factors cannot explain them, although some local factors must be involved. Urinary microbiota is involved in stone formation. Therefore, this study aimed to explore the association between the urinary microbiota and CaOx stones and provide insight into the medical treatment and prevention of CaOx stones. Methods: Sixteen pelvic urine samples were collected from the stone and non-stone sides of patients with unilateral CaOx stones following strict criteria. The 16S rRNA gene sequencing was performed on each pair of pelvic urine samples at the species level. Many bioinformatic analyses were conducted to explore the potential factors affecting CaOx stone formation. Results: Although no statistically significant difference was found between the overall microbiota of the pelvis urine from the two sides. Many biologically distinct taxa were observed, including many bacteria found in previous studies, like Proteobacteria, Actinobacteria, Firmicute and Enterobacter cloacae and so on. What's more, despite these common bacteria, our current study added to these bacterial communities with additional identification of Deinococcus-Thermus, Coriobacteriia, Porphyromonas and Ralstonia. To predict the functions of these microbiota, Kyoto Encyclopedia for Genes and Genomes and MetaCyc analysis were conducted and immunometabolism might be an important pathway. Moreover, a random forest predictor was constructed to distinguish the stone side from the non-stone side, with an accuracy of 62.5%. Conclusion: Our research profiled the microbiome in the pelvis urine from both the stone and non-stone sides of patients with unilateral CaOx stones, provided insight into the dominant role of urinary dysbiosis in CaOx stones formation. Furthermore, this study also predicted the potential crosstalk among urinary microbiota, immunometabolism, and CaOx stones.

Oxalate (dys)Metabolism: Person-to-Person Variability, Kidney and Cardiometabolic Toxicity

Oxalate is a metabolic end-product whose systemic concentrations are highly variable among individuals. Genetic (primary hyperoxaluria) and non-genetic (e.g., diet, microbiota, renal and metabolic disease) reasons underlie elevated plasma concentrations and tissue accumulation of oxalate, which is toxic to the body. A classic example is the triad of primary hyperoxaluria, nephrolithiasis, and kidney injury. Lessons learned from this example suggest further investigation of other putative factors associated with oxalate dysmetabolism, namely the identification of precursors (glyoxylate, aromatic amino acids, glyoxal and vitamin C), the regulation of the endogenous pathways that produce oxalate, or the microbiota's contribution to oxalate systemic availability. The association between secondary nephrolithiasis and cardiovascular and metabolic diseases (hypertension, type 2 diabetes, and obesity) inspired the authors to perform this comprehensive review about oxalate dysmetabolism and its relation to cardiometabolic toxicity. This perspective may offer something substantial that helps advance understanding of effective management and draws attention to the novel class of treatments available in clinical practice.

The altered composition of gut microbiota and biochemical features as well as dietary patterns in a southern Chinese population with recurrent renal calcium oxalate stones

The correlation among gut microbiota, biochemical features, and dietary patterns in recurrent stone formers has been inadequately investigated in the Chinese population. Forty-two patients with calcium oxalate stones (CaOxS group), including 34 recurrent stone formers (RS group), and 40 nonstone healthy subjects (NS group) from Changshu Hospital Affiliated with Soochow University, were prospectively recruited. Food frequency questionnaires were completed by participants, fasting vein blood was extracted, 24-h urine was collected for biochemical detection, and fecal samples were gathered for 16S ribosomal RNA (rRNA) gene sequencing. BMI; serum levels of triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), magnesium, and creatinine; and urine levels of magnesium in stone formers were significantly different from those of controls, and RS patients showed significantly low serum phosphate and high urine phosphate levels. Celery, bamboo shoots, and pickled food were the favored foods of local stone formers. Patients with recurrent stones had altered microbiota composition, with Escherichia, Fusobacterium, and Epulopiscium being the predominant pathogenic genera. The gut microbiota in RS patients had stronger functions in fatty acid and amino acid degradation but weaker functions in their biosynthesis. The pathogenic genera were positively correlated with BMI; serum levels of TGs and creatinine; urine levels of calcium, phosphate, and uric acid (UA); and celery, bamboo shoots, and pickled food intake. The abundance of Escherichia and Fusobacterium and the levels of serum magnesium and creatinine were the most relevant factors associated with stone recurrence and could be validated as biomarkers of recurrence. Our research provides a novel prevention strategy for the recurrence of renal calcium oxalate stones in the Han Chinese population of southern China.

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.

Butyric acid inhibits oxidative stress and inflammation injury in calcium oxalate nephrolithiasis by targeting CYP2C9

This study investigates the mechanism by which butyric acid can protect against calcium oxalate (CaOx) nephrolithiasis. To do so, a rat model was used with 0.75% ethylene glycol administration to induce CaOx crystal formation. Histological and von Kossa staining revealed calcium deposits and renal injury, while dihydroethidium fluorescence staining was used to detect reactive oxygen species (ROS) levels. Flow cytometry and TUNEL assays were used to assess apoptosis, respectively. Treatment with sodium butyrate (NaB) was found to partially reverse the oxidative stress, inflammation, and apoptosis associated with CaOx crystallization in the kidney. In addition, in HK-2 cells, NaB reversed the decreased cell viability, increased ROS levels and apoptosis damage caused by oxalate exposure. Network pharmacology was employed to predict the target genes of butyric acid, CYP2C9. Subsequently, NaB was found to significantly reduce CYP2C9 levels in vivo and in vitro, and inhibition of CYP2C9 by Sulfaphenazole (a specific CYP2C9 inhibitor), was able to reduce ROS levels, inflammation injury, and apoptosis in oxalate-induced HK-2 cells. Collectively, these findings suggest that butyric acid may inhibit oxidative stress and reduce inflammation injury in CaOx nephrolithiasis by suppressing CYP2C9.

Exploring the characteristics of gut microbiome in patients of Southern Fujian with hypocitraturia urolithiasis and constructing clinical diagnostic models

PURPOSE

Hypocitraturia is an important cause of urolithiasis. Exploring the characteristics of the gut microbiome (GMB) of hypocitriuria urolithiasis (HCU) patients can provide new ideas for the treatment and prevention of urolithiasis.

METHODS

The 24 h urinary citric acid excretion of 19 urolithiasis patients was measured, and patients were divided into the HCU group and the normal citrate urolithiasis (NCU) group. The 16 s ribosomal RNA (rRNA) was used to detect GMB composition differences and construct operational taxonomic units (OTUs) coexistence networks. The key bacterial community was determined by Lefse analysis, Metastats analysis and RandomForest analysis. Redundancy analysis (RDA) and Pearson correlation analysis visualized the correlation between key OTUs and clinical features and then established the disease diagnosis model of microbial-clinical indicators. Finally, PICRUSt2 was used to explore the metabolic pathway of related GMB in HCU patients.

RESULTS

The alpha diversity of GMB in HCU group was increased and Beta diversity analysis suggested significant differences between HCU and NCU groups, which was related to renal function damage and urinary tract infection. Ruminococcaceae_ge and Turicibacter are the characteristic bacterial groups of HCU. Correlation analysis showed that the characteristic bacterial groups were significantly associated with various clinical features. Based on this, the diagnostic models of microbiome-clinical indicators in HCU patients were constructed with the areas under the curve (AUC) of 0.923 and 0.897, respectively. Genetic and metabolic processes of HCU are affected by changes in GMB abundance.

CONCLUSION

GMB disorder may be involved in the occurrence and clinical characteristics of HCU by influencing genetic and metabolic pathways. The new microbiome-clinical indicator diagnostic model is effective.

Oxalate as a potent promoter of kidney stone formation

Kidney stones are among the most prevalent urological diseases, with a high incidence and recurrence rate. Treating kidney stones has been greatly improved by the development of various minimally invasive techniques. Currently, stone treatment is relatively mature. However, most current treatment methods are limited to stones and cannot effectively reduce their incidence and recurrence. Therefore, preventing disease occurrence, development, and recurrence after treatment, has become an urgent issue. The etiology and pathogenesis of stone formation are key factors in resolving this issue. More than 80% of kidney stones are calcium oxalate stones. Several studies have studied the formation mechanism of stones from the metabolism of urinary calcium, but there are few studies on oxalate, which plays an equally important role in stone formation. Oxalate and calcium play equally important roles in calcium oxalate stones, whereas the metabolism and excretion disorders of oxalate play a crucial role in their occurrence. Therefore, starting from the relationship between renal calculi and oxalate metabolism, this work reviews the occurrence of renal calculi, oxalate absorption, metabolism, and excretion mechanisms, focusing on the key role of SLC26A6 in oxalate excretion and the regulatory mechanism of SLC26A6 in oxalate transport. This review provides some new clues for the mechanism of kidney stones from the perspective of oxalate to improve the understanding of the role of oxalate in the formation of kidney stones and to provide suggestions for reducing the incidence and recurrence rate of kidney stones.

Untargeted and targeted metabolomics reveal bile acid profile changes in rats with ethylene glycol-induced calcium oxalate nephrolithiasis

Calcium oxalate (CaOx) nephrolithiasis is a prevalent disorder linked to metabolism. Examining metabolic alterations could potentially give an initial understanding of the origins of CaOx nephrolithiasis. This study aims to determine gut metabolic biomarkers differentiating CaOx nephrolithiasis utilizing untargeted and targeted metabolomics. CaOx nephrolithiasis model rats were built by 1% ethylene glycol administration. Histologic staining and renal function measurement revealed the presence of crystals in the lumen of the renal tubules, the renal injury and interstitial fibrosis in CaOx rats, demonstrating that the models of CaOx were established successfully. Hematoxylin & eosin (H&E) staining showed that CaOx group had inflammation and damage in the ileal tissue. Immunofluorescence and PCR results displayed that the tight junction proteins, ZO-1 and Occludin levels were decreased in the ileal tissues of the CaOx group. The untargeted metabolomic analysis revealed that 269 gut metabolites were differentially expressed between the CaOx group and the control group. Meanwhile, bile secretion, the main metabolic pathway in CaOx nephrolithiasis, was identified. Following, five significant bile acid metabolites were selected utilizing the targeted bile acid metabolomics, including Hyodeoxycholic acid (HDCA), Glycohyodeoxycholic acid (GHDCA), Nor-Deoxycholic Acid, omega-muricholic acid, and Taurolithocholic acid. Among these metabolites, HDCA and GHDCA presented the highest predictive accuracy with AUC = 1 to distinguish the CaOx group from the control group. As a result of network pharmacology, target genes of HDCA and GHDCA in CaOx nephrolithiasis were enriched in oxidative stress and apoptosis pathways. Conclusively, our study provides insight into bile acids metabolic changes related to CaOx nephrolithiasis. Although alterations in biochemical pathways indicate a complex pathology in CaOx rats, bile acid changes may serve as biomarkers of CaOx nephrolithiasis.

Causal relationship in gut microbiota and upper urinary urolithiasis using Mendelian randomization

Background

Several reports in recent years have found an association between gut microbiota and upper urinary urolithiasis. However, the causal relationship between them remains to be clarified.

Methods

Genetic variation is used as a tool in Mendelian randomization for inference of whether exposure factors have a causal effect on disease outcomes. We selected summary statistics from a large genome-wide association study of the gut microbiome published by the MiBioGen consortium with a sample size of 18,340 as an exposure factor and upper urinary urolithiasis data from FinnGen GWAS with 4,969 calculi cases and 213,445 controls as a disease outcome. Then, a two-sample Mendelian randomization analysis was performed by applying inverse variance-weighted, MR-Egger, maximum likelihood, and weighted median. In addition, heterogeneity and horizontal pleiotropy were excluded by sensitivity analysis.

Results

IVW results confirmed that class Deltaproteobacteria (OR = 0.814, 95% CI: 0.666-0.995, P = 0.045), order NB1n (OR = 0.833, 95% CI: 0.737-0.940, P = 3.15 × 10^-3), family Clostridiaceae1 (OR = 0.729, 95% CI: 0.581-0.916, P = 6.61 × 10^-3), genus Barnesiella (OR = 0.695, 95% CI: 0.551-0.877, P = 2.20 × 10^-3), genus Clostridium sensu_stricto_1 (OR = 0.777, 95% CI: 0.612-0.986, P = 0.0380), genus Flavonifractor (OR = 0.711, 95% CI: 0.536-0.944, P = 0.0181), genus Hungatella (OR = 0.829, 95% CI: 0.690-0.995, P = 0.0444), and genus Oscillospira (OR = 0.758, 95% CI: 0.577-0.996, P = 0.0464) had a protective effect on upper urinary urolithiasis, while Eubacterium xylanophilum (OR =1.26, 95% CI: 1.010-1.566, P = 0.0423) had the opposite effect. Sensitivity analysis did not find outlier SNPs.

Conclusion

In summary, a causal relationship was found between several genera and upper urinary urolithiasis. However, we still need further randomized controlled trials to validate.

The role of microbiome: a novel insight into urolithiasis

Urolithiasis, referred to as the formation of stones in the urinary tract, is a common disease with growing prevalence and high recurrence rate worldwide. Although researchers have endeavoured to explore the mechanism of urinary stone formation for novel effective therapeutic and preventative measures, the exact aetiology and pathogenesis remain unclear. Propelled by sequencing technologies and culturomics, great advances have been made in understanding the pivotal contribution of the human microbiome to urolithiasis. Indeed, there are diverse and abundant microbes interacting with the host in the urinary tract, overturning the dogma that urinary system, and urine are sterile. The urinary microbiome of stone formers was clearly distinct from healthy individuals. Besides, dysbiosis of the intestinal microbiome appears to be involved in stone formation through the gut-kidney axis. Thus, the human microbiome has potential significant implications for the aetiology of urolithiasis, providing a novel insight into diagnostic, therapeutic, and prognostic strategies. Herein, we review and summarize the landmark microbiome studies in urolithiasis and identify therapeutic implications, challenges, and future perspectives in this rapidly evolving field. To conclude, a new front has opened with the evidence for a microbial role in stone formation, offering potential applications in the prevention, and treatment of urolithiasis.

Role of microbiome in kidney stone disease

PURPOSE OF REVIEW

The process of renal stone formation is complex, multifactorial, and variable depending on the type of stone. The microbiome, whether by direct or indirect action, is a factor that both promotes the formation and protects from developing of renal stones. It is a highly variable factor due to the great interindividual and intraindividual variability that it presents. In recent years, with the incorporation of nonculture-based techniques such as the high-throughput sequencing of 16S rRNA bacterian gene, both intestinal and urinary microbiota have been deeply studied in various diseases such as the kidney stone disease.

RECENT FINDINGS

This review has examined the new insights on the influence of the intestinal and urinary microbiome in nephrolithiasis disease and its usefulness as a diagnostic and prognostic tool, highlighting its contribution to the pathogenesis, its ability to modulate it and to influence disease development.

SUMMARY

The incidence of urolithiasis has been increasing considerably. These patients represent a significant expense for national health systems. With the knowledge of the influence of the urobiome and intestinal microbiota on the urolithiasis, it could be possible to modulate it to interrupt its development.

Microbiome in urological diseases: Axis crosstalk and bladder disorders

Since the identification of the human urinary microbiome, numerous studies have characterized this microbial community and improved our knowledge of its association with urinary diseases. This association between urinary diseases and microbiota is not confined to the urinary microbiota; it is interconnected with the microbiota of other organs. The gastrointestinal, vaginal, kidney, and bladder microbiota all affect urinary diseases because they work with their respective organs to control the growth and operation of the immune, metabolic, and nervous systems through dynamic bidirectional communication along the bladder-centered axis. Therefore, disturbances in the microbial communities may result in the emergence of urinary diseases. In this review, we describe the increasing and intriguing evidence of complicated and critical relationships that may contribute to the development and progression of urinary diseases through disruption of the microbiota in various organs.

The Urinary Microbiome; Axis Crosstalk and Short-Chain Fatty Acid

Our knowledge that "urine is sterile" is no longer accepted after the development of a next-generation sequencing (NGS) test. Using NGS, microbiota in the human body were discovered, and it is expected that this will improve our understanding of human diseases. However, the mechanism involved in the effect of the microbiome on diseases is still poorly understood. Associations of gut microbiome with diseases have been recently reported. Based on such associations, bladder-gut-brain axis, gut-bladder axis, gut-vagina-bladder axis, and gut-kidney axis as novel mechanisms of action of the microbiome have been suggested. Each axis can influence the development and progression of disease through interactions. In these interactions, metabolites of the microbiome including short-chain fatty acids (SCFA) and the inflammasome play an important role. Inflammasomes are multiprotein oligomers that can initiate inflammatory responses. Inflammasomes can trigger inflammation and pyroptosis and ultimately contribute to disease development. SCFAs play an important role in immune cell migration, cytokine production, and maintenance of cellular homeostasis. Associations of inflammasomes with systemic diseases such as obesity and insulin resistance have been reported. The roles of inflammasomes and SCFAs in kidney, bladder, and prostate diseases have also been revealed recently.

Mechanisms of the intestinal and urinary microbiome in kidney stone disease

Kidney stone disease affects ~10% of the global population and the incidence continues to rise owing to the associated global increase in the incidence of medical conditions associated with kidney stone disease including, for example, those comprising the metabolic syndrome. Considering that the intestinal microbiome has a substantial influence on host metabolism, that evidence has suggested that the intestinal microbiome might have a role in maintaining oxalate homeostasis and kidney stone disease is unsurprising. In addition, the discovery that urine is not sterile but, like other sites of the human body, harbours commensal bacterial species that collectively form a urinary microbiome, is an additional factor that might influence the induction of crystal formation and stone growth directly in the kidney. Collectively, the microbiomes of the host could influence kidney stone disease at multiple levels, including intestinal oxalate absorption and direct crystal formation in the kidneys.

Possibilities and limitations of using low biomass samples for urologic disease and microbiome research

With the dogma of sterile urine no longer held as truth, numerous studies have implicated distinct changes in microbial diversity and composition to diseased subgroups in both benign and malignant urological diseases, ranging from overactive bladder to bladder and prostate cancer. Further facilitated by novel and effective techniques of urine culture and sequencing, analysis of the genitourinary microbiome holds high potential to identify biomarkers for disease and prognosis. However, the low biomass of samples included in microbiome studies of the urinary tract challenge researchers to draw definitive conclusions, confounded by technical and procedural considerations that must be addressed. Lack of samples and adequate true negative controls can lead to overestimation of microbial influence with clinical relevance. As such, results from currently available studies and assessment of their limitations required a thorough understanding. The purpose of this narrative review was to summarize notable microbiome studies in the field of urology with a focus on significant findings and limitations of study design. Methodological considerations in future research are also discussed.

Risks of Carotid Artery Stenosis and Atherosclerotic Cardiovascular Disease in Patients with Calcium Kidney Stone: Assessment of Systemic Inflammatory Biomarkers

(1) Background: To assess the clinical significance of preoperative inflammatory biomarkers combined with atherosclerotic cardiovascular disease (ASCVD) risk score to evaluate carotid artery stenosis in patients with calcium kidney stones; (2) Methods: We conducted a prospective observational case-control study, enrolling 74 patients with calcium kidney stones and 66 age- and sex-matched healthy controls. We calculated the inflammatory biomarkers including the neutrophil-lymphocyte ratio (NLR), monocyte-lymphocyte ratio (MLR), and systemic inflammation response index (SIRI). An ultrasound of the carotid arteries was performed on all participants to identify the severity of the stenosis; (3) Results: All inflammatory biomarkers and the severity of carotid artery stenosis were higher in the calcium kidney stone group than in controls. After stratification of ASCVD, inflammatory biomarkers and carotid artery stenosis severity were still significantly higher in the calcium kidney stone group. Multivariate analyses showed that calcium kidney stones significantly increased the risk of ASCVD and carotid artery stenosis. In multivariate linear logistic regression analyses, calcium kidney stone and ASCVD score had a significant association with carotid artery occlusion, but SIRI did not; (4) Conclusions: Calcium kidney stone is associated with higher levels of inflammatory biomarkers and carotid artery stenosis. Calcium kidney stone is associated with higher levels of inflammatory biomarkers and carotid artery stenosis.

Cocoa seeds and chocolate products interaction with gut microbiota; mining microbial and functional biomarkers from mechanistic studies, clinical trials and 16S rRNA amplicon sequencing

In recent years, gut microbiome has evolved as a focal point of interest with growing recognition that a well-balanced gut microbiota is highly relevant to an individual's health status. The present review provides a mechanistic insight on the effects of cocoa chemicals on the gut microbiome and further reveals in silico biomarkers, taxonomic and functional features that distinguish gut microbiome of cocoa consumers and controls by using 16S rRNA gene sequencing data. The polyphenols in cocoa can change the gut microbiota either by inhibiting the growth of pathogenic bacteria in the gut such as Clostridium perfringens or by increasing the growth of beneficial microbiota in the gut such as Lactobacillus and Bifidobacterium. This paper demonstrates the holistic effect of gut microbiota on cocoa chemicals and how it impacts human health. We present herein the first comprehensive review and analysis of how raw and roasted cocoa and its products can specifically influence gut homeostasis, and likewise, how microbiota metabolizes cocoa chemicals. In addition to that, our 16S rRNA amplicon sequencing analysis revealed that the flavone and flavonols metabolism, aminobenzoate degradation and fatty acid elongation pathways represent the three most important signatures of microbial functions associated with cocoa consumption.

Short-chain fatty acid: An updated review on signaling, metabolism, and therapeutic effects

Fatty acids are good energy sources (9 kcal per gram) that aerobic tissues can use except for the brain (glucose is an alternative source). Apart from the energy source, fatty acids are necessary for cell signaling, learning-related memory, modulating gene expression, and functioning as cytokine precursors. Short-chain fatty acids (SCFAs) are saturated fatty acids arranged as a straight chain consisting minimum of 6 carbon atoms. SCFAs possess various beneficial effects like improving metabolic function, inhibiting insulin resistance, and ameliorating immune dysfunction. In this review, we discussed the biogenesis, absorption, and transport of SCFA. SCFAs can act as signaling molecules by stimulating G protein-coupled receptors (GPCRs) and suppressing histone deacetylases (HDACs). The role of SCFA on glucose metabolism, fatty acid metabolism, and its effect on the immune system is also reviewed with updated details. SCFA possess anticancer, anti-diabetic, and hepatoprotective effects. Additionally, the association of protective effects of SCFA against brain-related diseases, kidney diseases, cardiovascular damage, and inflammatory bowel diseases were also reviewed. Nanotherapy is a branch of nanotechnology that employs nanoparticles at the nanoscale level to treat various ailments with enhanced drug stability, solubility, and minimal side effects. The SCFA functions as drug carriers, and nanoparticles were also discussed. Still, much research was not focused on this area. SCFA functions in host gene expression through inhibition of HDAC inhibition. However, the study has to be focused on the molecular mechanism of SCFA against various diseases that still need to be investigated.

Urinary Microbial and Metabolomic Profiles in Kidney Stone Disease

Background

Kidney stones or nephrolithiasis is a chronic metabolic disease characterized by renal colic and hematuria. Currently, a pathogenetic mechanism resulting in kidney stone formation remains elusive. We performed a multi-omic study investigating urinary microbial compositions and metabolic alterations during nephrolithiasis.

Method

Urine samples from healthy and individuals with nephrolithiasis were collected for 16S rRNA gene sequencing and liquid chromatography-mass spectroscopy. Microbiome and metabolome profiles were analyzed individually and combined to construct interactome networks by bioinformatic analysis.

Results

Distinct urinary microbiome profiles were determined in nephrolithiasis patients compared with controls. Thirty-nine differentially abundant taxa between controls and nephrolithiasis patients were identified, and Streptococcus showed the most significant enrichment in nephrolithiasis patients. We also observed significantly different microbial compositions between female and male nephrolithiasis patients. The metabolomic analysis identified 112 metabolites that were differentially expressed. Two significantly enriched metabolic pathways, including biosynthesis of unsaturated fatty acids and tryptophan metabolism, were also identified in nephrolithiasis patients. Four potentially diagnostic metabolites were also identified, including trans-3-hydroxycotinine, pyroglutamic acid, O-desmethylnaproxen, and FAHFA (16:0/18:2), and could function as biomarkers for the early diagnosis of nephrolithiasis. We also identified three metabolites that contributed to kidney stone size. Finally, our integrative analysis of the urinary tract microbiome and metabolome identified distinctly different network characteristics between the two groups.

Conclusions

Our study has characterized important profiles and correlations among urinary tract microbiomes and metabolomes in nephrolithiasis patients for the first time. These results shed new light on the pathogenesis of nephrolithiasis and could provide early clinical biomarkers for diagnosing the disease.

Association of Gut Microbiota and Biochemical Features in a Chinese Population With Renal Uric Acid Stone

Previous studies suggest that patients with nephrolithiasis exhibit dysbiosis in their gut microbiota, but those studies were conducted in calcium oxalate stone patients. We aimed to explore the association of gut microbiota and biochemical features of renal uric acid stone (UAS) patients in a Chinese population and identify the related bacteria that may affect the pathopoiesis of UAS. A case-control study of 117 patients with UAS, 123 patients with gout, and 135 healthy controls were included from January 2014 to October 2020. For each subject, data on demographics, biochemical parameters of blood and urine were analyzed. Fifteen patients with gout, 16 patients with UAS, 17 UAS patients with gout, and 17 healthy subjects were enrolled and provided fecal samples. The characteristics of gut microbiota were explored by using 16S ribosomal RNA (rRNA) gene sequencing and analyzed by using a combination of software mother and R. Hyperuricemia was the main risk factor for the development of gout and UAS. Obesity, dyslipidemia, and aciduria were unique risk factors for UAS patients. The richness, diversity, and relative abundance of dominant bacteria at the phylum and genus levels of gut microbiota in UAS patients were significantly distinct from other subjects. Abundance of Bacteroides and Fusobacterium was significantly positively correlated with the serum uric acid (UA) level of UAS patients. Fusobacteria was involved in the metabolism and degradation of certain short-chain fatty acids, amino acids, and sugars in pathopoiesis of UAS, and inhibited their synthesis pathways. Fusobacteria may be related to the pathogenesis of UAS, and this finding contributes to the personalized treatment of UAS from the perspective of maintaining micro-ecological equilibrium in gut.

Lactiplantibacillus plantarum J-15 reduced calcium oxalate kidney stones by regulating intestinal microbiota, metabolism, and inflammation in rats

The prevention role of Lactiplantibacillus plantarum against the formation of kidney stones has been increasingly recognized; its mechanism, however, has mainly been focused on inhibiting the inflammation in the colon in the gastrointestinal (GI) system, and the intestinal metabolites from microflora have not been revealed fully with regarding to the stone formation. In this study, we investigated the effect of L. plantarum J-15 on kidney stone formation in renal calcium oxalate (CaOx) rats induced by ethylene glycol and monitored the changes of intestinal microflora and their metabolites detected by 16S rRNA sequencing and widely targeted analysis, followed by the evaluation of the intestinal barrier function and inflammation levels in the colon, blood and kidney. The results showed that L. plantarum J-15 effectively reduced renal crystallization and urinary oxalic acid. Ten microbial genera, including anti-inflammatory and SCFAs-related Faecalibaculum, were enriched in the J-15 treatment group. There are 136 metabolites from 11 categories significantly different in the J-15 supplementation group compared with CaOx model rats, most of which were enriched in the amino acid metabolic and secondary bile acid pathways. The expression of intestinal tight junction protein Occludin and the concentration of pro-inflammatory cytokines and prostaglandin were decreased in the intestine, which further reduced the translocated lipopolysaccharide and inflammation levels in the blood upon J-15 treatment. Thus, the inflammation and injury in the kidney might be alleviated by downregulating TLR4/NF-κB/COX-2 signaling pathway. It suggested that L. plantarum J-15 might reduce kidney stone formation by restoring intestinal microflora and metabolic disorder, protecting intestinal barrier function, and alleviating inflammation. This finding provides new insights into the therapies for renal stones.

Domestic Environment and Gut Microbiota: Lessons from Pet Dogs

Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota–host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.

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.

The Intestinal Microbiota and Metabolites in the Gut-Kidney-Heart Axis of Chronic Kidney Disease

Emerging evidences demonstrate the involvement of gut microbiota in the progression of chronic kidney disease (CKD) and CKD-associated complications including cardiovascular disease (CVD) and intestinal dysfunction. In this review, we discuss the interactions between the gut, kidney and heart in CKD state, and elucidate the significant role of intestinal microbiota in the gut-kidney-heart axis hypothesis for the pathophysiological mechanisms of these diseases, during which process mitochondria may serve as a potential therapeutic target. Dysregulation of this axis will lead to a vicious circle, contributing to CKD progression. Recent studies suggest novel therapies targeting gut microbiota in the gut-kidney-heart axis, including dietary intervention, probiotics, prebiotics, genetically engineered bacteria, fecal microbiota transplantation, bacterial metabolites modulation, antibiotics, conventional drugs and traditional Chinese medicine. Further, the identification of specific microbial communities and their corresponding pathophysiological metabolites and the illumination of the gut-kidney-heart axis may contribute to innovative basic research, clinical trials and therapeutic strategies against CKD progression and uremic complications in CKD patients.

Gut microbiota and the prevalence and incidence of renal stones

The role of the gut microbiome in the development of renal stone diseases has not been well characterized. This study focused on the taxonomic and functional profiles of gut microbiomes according to the prevalence and incidence of nephrolithiasis. Stool samples from 915 Korean adults were collected at baseline. Participants were followed for a median of 4.0 years. We evaluated the biodiversity of the gut microbiota and taxonomic profiles associated with nephrolithiasis status, using 16S rRNA gene sequencing. Nephrolithiasis status was categorized into three groups: control (no-stone at both baseline and follow-up visits), incidental nephrolithiasis, and prevalent nephrolithiasis. Compared to the control and incidental nephrolithiasis, the prevalent nephrolithiasis showed a reduced evenness in alpha diversity. Nephrolithiasis was associated with a reduced abundance of some key taxa involved in short-chain fatty acid production. Moreover, the abundance of Bifidobacterium, which possess oxalate-degrading ability, was higher in the control. Conversely, there was no significant difference in the bacterial composition between the incidental and prevalent nephrolithiasis. In our study with repeated nephrolithiasis measurements, prevalent renal stones were associated with an altered gut microbiota composition compared to the control. Besides the known oxalate degradation pathway, other functional pathways inferred in this study require further investigation.

Identification of Resolvin D1 and Protectin D1 as Potential Therapeutic Agents for Treating Kidney Stones

Intrarenal calcium oxalate (CaOx) crystals induce renal tubular epithelial cell (TEC) inflammatory and oxidative injury. This study is aimed at exploring potential therapeutic lipid components in kidney stones because lipids are involved in the development of several diseases and indicate the risk of kidney stones. Serum specimens were collected from 35 kidney stone patients and 35 normal controls. The lipid components in serum were measured, and differences were analyzed. The documented biological importance was comprehensively reviewed to identify lipids that differed significantly between the two groups to find potential agents associated with kidney stones. CaOx nephrocalcinosis mouse model was established to examine the therapeutic effects of specific lipids on CaOx deposition and CaOx-induced oxidative renal injury. Several lipids with significantly different levels were present in the serum of patients with stones and normal controls. Resolvin D1 (RvD1) (4.93-fold change, P < 0.001) and protectin D1 (PD1) (5.06-fold change, P < 0.001) were significantly decreased in the serum of patients with kidney stones, and an integrative review suggested that these factors might be associated with inflammatory responses, which is a crucial mechanism associated with stone damage. The administration of RvD1 and PD1 significantly inhibited kidney CaOx deposition and suppressed CaOx-induced renal tubular cell inflammatory injury and necrosis in a CaOx nephrocalcinosis mouse model. Furthermore, RvD1 and PD1 facilitated the expression of the oxidative indicator superoxide dismutase 2 (SOD2), inhibited NADPH oxidase 2 (NOX2) expression, and diminished intracellular reactive oxygen species (ROS) levels. This study preliminarily elucidated the role of lipids in kidney stones. The inhibitory effects of RvD1 and PD1 on oxidative damage induced by CaOx deposition provide a promising perspective for kidney stone treatment strategies.

Trimethylamine N-oxide promotes hyperoxaluria-induced calcium oxalate deposition and kidney injury by activating autophagy

Calcium oxalate (CaOx) is the most common component of kidney stones. Oxidative stress, inflammation and autophagy-induced cell death are the major causes of CaOx crystal deposition and CaOx crystal deposition can further lead to kidney injury. Trimethylamine N-oxide (TMAO), a gut microbiota-derived metabolite, plays an important role in the pathogenesis of many diseases, such as atherosclerosis, diabetes and chronic kidney disease, but the effect of TMAO on hyperoxaluria-induced CaOx crystal deposition and kidney injury remains unknown. We hypothesize that TMAO aggravates CaOx crystal deposition via promoting CaOx-mediated cell death. C57Bl/6 mice were given high-oxalate diet as a model of hyperoxaluria. TMAO was provided via drinking water. Serum TMAO levels increased 15 days after CaOx treatment (6.30 ± 0.17 μmol/L vs. 34.65 ± 8.95 μmol/L). High-oxalate diet induced inflammation, CaOx deposition and kidney injury, which TMAO aggravated. In accordance, TMAO intensified high-oxalate diet induced oxidative stress, autophagy and apoptosis. Moreover, TMAO enhanced CaOx crystal adhesion to HK-2 cells and reduced cell viability (from 88.9 ± 1.6% to 75.0 ± 2.7%). Protein kinase R-like endoplasmic reticulum kinase (PERK) may mediate these TMAO effects, as TMAO promoted PERK phosphorylation. Consistently, PERK knockdown alleviated TMAO-evoked CaOx-autophagy, apoptosis and oxidative stress in HK-2 cells. In conclusion, TMAO can aggravate hyperoxaluria-induced kidney injury by triggering the PERK/ROS pathway, which enhances autophagy, apoptosis and inflammation, and facilitates CaOx crystal deposition in renal tubular cells.

Low-Dose Interleukin-2 Altered Gut Microbiota and Ameliorated Collagen-Induced Arthritis

Purpose

Low-dose interleukin-2 (ld-IL-2) has been shown to regulate the balance between effector T and regulatory T (Treg) cells and has been used in several clinical trials to treat autoimmune diseases including rheumatoid arthritis (RA). In this study, we investigated the effects of ld-IL-2 on collagen-induced arthritis (CIA) in mice.

Methods

Arthritis severity in CIA mice was measured using the arthritis index (AI), radiographs, and hematoxylin and eosin staining. Cytokines were detected using enzyme-linked immunosorbent assay. Gut microbiota alterations and short-chain fatty acid production were analyzed through 16S rRNA sequencing and gas chromatography.

Results

The AI scores of CIA mice treated with ld-IL-2 were significantly lower compared to the model group, which significantly reduced the severity of arthritis. Ld-IL-2 also altered the gut microbiota in CIA mice. The diversity, composition, and dominant species of gut microbiota were altered by ld-IL-2 treatment. Ld-IL-2 also increased short-chain fatty acid levels. There was a strong correlation between ld-IL-2 treatment and improved gut microbiota.

Conclusion

Ld-IL-2 significantly ameliorated joint inflammation and bone damage and improved gut microbial dysbiosis in CIA, indicating that it may be a promising therapy for RA patients.

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.

Identifying Two Novel Clusters in Calcium Oxalate Stones With Urinary Tract Infection Using 16S rDNA Sequencing

Urinary stones and urinary tract infection (UTI) are the most common diseases in urology and they are characterized by high incidence and high recurrence rate in China. Previous studies have shown that urinary stones are closely associated with gut or urine microbiota. Calcium oxalate stones are the most common type of urinary stones. However, the profile of urinary tract microorganisms of calcium oxalate stones with UTI is not clear. In this research, we firstly found two novel clusters in patients with calcium oxalate stones (OA) that were associated with the WBC/HP (white blood cells per high-power field) level in urine. Two clusters in the OA group (OA1 and OA2) were distinguished by the key microbiota Firmicutes and Enterobacteriaceae. We found that Enterobacteriaceae enriched in OA1 cluster was positively correlated with several infection-related pathways and negatively correlated with a few antibiotics-related pathways. Meantime, some probiotics with higher abundance in OA2 cluster such as Bifidobacterium were positively correlated with antibiotics-related pathways, and some common pathogens with higher abundance in OA2 cluster such as Enterococcus were positively correlated with infection-related pathways. Therefore, we speculated that as a sub-type of OA disease, OA1 was caused by Enterobacteriaceae and the lack of probiotics compared with OA2 cluster. Moreover, we also sequenced urine samples of healthy individuals (CK), patients with UTI (I), patients with uric acid stones (UA), and patients with infection stones (IS). We identified the differentially abundant taxa among all groups. We hope the findings will be helpful for clinical treatment and diagnosis of urinary 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.

Probiotic Lactiplantibacillus plantarum N-1 could prevent ethylene glycol-induced kidney stones by regulating gut microbiota and enhancing intestinal barrier function

Defective permeability barrier is considered to be an incentive of hyperuricemia, however, the link between them has not been proven. Here, we evaluated the potential preventive effects of Lactiplantibacillus plantarum N-1 (LPN1) on gut microbiota and intestinal barrier function in rats with hyperoxaluria-induced kidney stones. Male rats were supplied with 1% ethylene glycol (EG) dissolved in drinking water for 4 weeks to develop hyperoxaluria, and some of them were administered with LPN1 for 4 weeks before EG treatment as a preventive intervention. We found that EG not only resulted hyperoxaluria and kidney stone formation, but also promoted the intestinal inflammation, elevated intestinal permeability, and gut microbiota disorders. Supplementation of LPN1 inhibited the renal crystalline deposits through reducing urinary oxalic acid and renal osteopontin and CD44 expression and improved EG-induced intestinal inflammation and barrier function by decreasing the serum LPS and TLR4/NF-κB signaling and up-regulating tight junction Claudin-2 in the colon, as well as increasing the production of short-chain fatty acid (SCFAs) and the abundance of beneficial SCFAs-producing bacteria, mainly from the families of Lachnospiraceae and Ruminococcaceae. Probiotic LPN1 could prevent EG-induced hyperoxaluria by regulating gut microbiota and enhancing intestinal barrier function.

Short Chain Fatty Acids Prevent Glyoxylate-Induced Calcium Oxalate Stones by GPR43-Dependent Immunomodulatory Mechanism

Calcium oxalate (CaOx) stones are the most common type of kidney stones and are associated with high recurrence, short chain fatty acids (SCFAs), and inflammation. However, it remains uncertain whether SCFAs affect the formation of CaOx stones through immunomodulation. We first performed mass cytometry (CyTOF) and RNA sequencing on kidney immune cells with glyoxylate-induced CaOx crystals (to elucidate the landscape of the associated immune cell population) and explored the role of SCFAs in renal CaOx stone formation through immunomodulation. We identified 29 distinct immune cell subtypes in kidneys with CaOx crystals, where CX3CR1+CD24- macrophages significantly decreased and GR1+ neutrophils significantly increased. In accordance with the CyTOF data, RNA sequencing showed that most genes involved were related to monocytes and neutrophils. SCFAs reduced kidney CaOx crystals by increasing the frequency of CX3CR1+CD24- macrophages and decreasing GR1+ neutrophil infiltration in kidneys with CaOx crystals, which was dependent on the gut microbiota. GPR43 knockdown by transduction with adeno-associated virus inhibited the alleviation of crystal formation and immunomodulatory effects in the kidney, due to SCFAs. Moreover, CX3CR1+CD24- macrophages regulated GR1+ neutrophils via GPR43. Our results demonstrated a unique trilateral relationship among SCFAs, immune cells, and the kidneys during CaOx formation. These findings suggest that future immunotherapies may be used to prevent kidney stones using SCFAs.

Renal Sensing of Bacterial Metabolites in the Gut-kidney Axis

Seminal works have now revealed the gut microbiota is connected with several diseases, including renal disorders. The balance between optimal and dysregulated host-microbiota interactions has completely changed our understanding of immunity and inflammation. Kidney injury is associated with accumulation of uremic toxins in the intestine, augmented intestinal permeability, and systemic inflammation. Intestinal bacteria can signal through innate receptors and induce immune cell activation in the lamina propria and release of inflammatory mediators into the bloodstream. But the gut microbiota can also modulate immune functions through soluble products as short-chain fatty acids (SCFAs). The three most common SCFAs are propionate, butyrate, and acetate, which can signal through specific G-protein coupled receptors (GPCRs), such as GPR43, GPR41, and GPR109a, expressed on the surface of epithelial, myeloid, endothelial, and immune cells, among others. The triggered signaling can change cell metabolism, immune cell activation, and cell death. In this study, we reviewed the gut-kidney axis, how kidney cells can sense SCFAs, and its implication in kidney diseases.