Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition

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.

Survey of the infant male urobiome and genomic analysis of Actinotignum spp

The urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of enhanced culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Cesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum spp., a bacterial genus that has been associated with urinary tract infections in older male adults. Herein, we isolate and sequence 9 distinct strains of Actinotignum spp. enhancing the genomic knowledge surrounding this genus and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.

MicroEXPERT: Microbiome profiling platform with cross-study metagenome-wide association analysis functionality

The framework of the MicroEXPERT platform. Our Platform was composed of five modules. Data management module: Users upload raw data and metadata to the system using a guided workflow. Data processing module: Uploaded data is processed to generate taxonomical distribution and functional composition results. Metagenome-wide association studies module (MWAS): Various methods, including biomarker analysis, PCA, co-occurrence networks, and sample classification, are employed using metadata. Data search module: Users can query nucleotide sequences to retrieve information in the MicroEXPERT database. Data visualization module: Visualization tools are used to illustrate the metagenome analysis results.

The emerging role of the urinary microbiome in benign noninfectious urological conditions: an up-to-date systematic review

PURPOSE

The goal of this systematic review was to examine the current literature on the urinary microbiome and its associations with noninfectious, nonmalignant, urologic diseases. Secondarily, we aimed to describe the most common bioinformatics used to analyze the urinary microbiome.

METHODS

A comprehensive literature search of Ovid MEDLINE using the keywords "microbiota" AND "prostatic hyperplasia," "microbiota" AND "urinary bladder, overactive," "microbiota" AND "pelvic pain," and "microbiota" AND "urolithiasis" OR "nephrolithiasis" OR "urinary calculi" AND "calcium oxalate" was performed to identify relevant clinical microbiome studies associated with noninfectious benign urological conditions published from 2010 to 2022. We included human studies that evaluated the urinary, stone, or semen microbiota, or any combination of the above-mentioned locations.

RESULTS

A total of 25 human studies met the inclusion criteria: 4 on benign prostatic hyperplasia (BPH), 9 on overactive bladder (OAB), 8 on calcium oxalate stones, and 4 on chronic pelvic pain syndrome (CPPS). Specific taxonomic profiles in the urine microbiome were associated with each pathology, and evaluation of alpha- and beta-diversity and relative abundance was accounted for most of the studies. Symptom prevalence and severity were also analyzed and showed associations with specific microbes.

CONCLUSION

The study of the urogenital microbiome is rapidly expanding in urology. Noninfectious benign urogenital diseases, such as BPH, calcium oxalate stones, CPPS, and OAB were found to be associated with specific microbial taxonomies. Further research with larger study populations is necessary to solidify the knowledge of the urine microbiome in these conditions and to facilitate the creation of microbiome-based diagnostic and therapeutic approaches.

Vitamins as regulators of calcium-containing kidney stones - new perspectives on the role of the gut microbiome

Calcium-based kidney stone disease is a highly prevalent and morbid condition, with an often complicated and multifactorial aetiology. An abundance of research on the role of specific vitamins (B6, C and D) in stone formation exists, but no consensus has been reached on how these vitamins influence stone disease. As a consequence of emerging research on the role of the gut microbiota in urolithiasis, previous notions on the contribution of these vitamins to urolithiasis are being reconsidered in the field, and investigation into previously overlooked vitamins (A, E and K) was expanded. Understanding how the microbiota influences host vitamin regulation could help to determine the role of vitamins in stone disease.

Urinary microbiome differences between lichen sclerosus induced and non-lichen sclerosus induced urethral stricture disease

OBJECTIVE

To describe differences in the urinary microbiome of patients with pathologically confirmed lichen sclerosus (LS) urethral stricture disease (USD) vs non-lichen sclerosus (non-LS) USD pre- and post-operatively.

METHODS

Patients were pre-operatively identified and prospectively followed, all underwent surgical repair and had tissue samples obtained to make a pathological diagnosis of LS. Pre- and post-operative urine samples were collected. Bacterial genomic DNA was extracted. Alpha and beta diversity measurements were calculated and compared. A zero-inflated negative binomial model was utilized to compare taxa abundances between disease status and surgery status.

RESULTS

Urine samples were obtained from both cohorts, 69 samples in total: 36 samples were obtained pre-operatively and 33 samples were obtained post-operatively. Ten patients provided both a pre-operative and post-operative urine sample. Twenty-six patients had pathological evidence of LS and 33 patients did not. There was a statistically significant difference in alpha diversity between the pre-operative urine samples of patients with non-LS USD and LS USD, (p = 0.01). There was no significant difference in alpha diversity within post-operative urine samples between patients with non-LS USD and LS USD, (p = 0.1). A significant difference was observed in Weighed UniFrac distances with respect to disease and operative status, (p = 0.001 and 0.002).

CONCLUSIONS

LS USD have significant alterations in diversity and differential abundance of urine microbiota compared to non-LS USD controls. These findings could be used to guide further investigations into the role of the urinary microbiome in LS USD pathogenesis, severity of presentation, and stricture recurrence.

Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease

Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear. Delineating the contribution of rare and common phylotypes to urinary stone disease is important for the development of bacteriotherapies to promote urologic health. Methods: The objectives of the current report were to conduct a metaanalysis of 16S rRNA datasets derived from the kidney stone, stool, and urine samples of participants with or without urinary stone disease. To delineate the impact of rare and common phylotypes, metaanalyses were conducted by first separating rare and common taxa determined by both the frequency and abundance of amplicon sequence variants. Results: Consistent with previous analyses, we found that gut, upper urinary, and lower urinary tract microbiomes were all unique. Rare phylotypes comprised the majority of species observed in all sample types, with kidney stones exhibiting the greatest bias toward rarity, followed by urine and stool. Both rare and common fractions contributed significantly to the differences observed between sample types and health disparity. Furthermore, the rare and common fractions were taxonomically unique across all sample types. A total of 222 and 320 unique rare phylotypes from urine and stool samples were found to be significantly associated with USD. A co-occurrence correlation analysis revealed that rare phylotypes are most important for microbiome structure in stones, followed by urine and stool. Discussion: Collectively, the results indicate that rare phylotypes may be important for the pathophysiology of USD, particularly in the kidney stone matrix, which is inherently a very low microbial biomass niche that can have implications for the diagnosis and treatment of kidney stones. Further studies are needed to investigate the functional significance of rare phylotypes in kidney stone pathogenesis.

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.

Defining the Infant Male Urobiome and Moving Towards Mechanisms in Urobiome Research

The urinary bladder harbors a community of microbes termed the urobiome, which remains understudied. In this study, we present the urobiome of healthy infant males from samples collected by transurethral catheterization. Using a combination of extended culture and amplicon sequencing, we identify several common bacterial genera that can be further investigated for their effects on urinary health across the lifespan. Many genera were shared between all samples suggesting a consistent urobiome composition among this cohort. We note that, for this cohort, early life exposures including mode of birth (vaginal vs. Caesarean section), or prior antibiotic exposure did not influence urobiome composition. In addition, we report the isolation of culturable bacteria from the bladders of these infant males, including Actinotignum schaalii, a bacterial species that has been associated with urinary tract infection in older male adults. Herein, we isolate and sequence 9 distinct strains of A. schaalii enhancing the genomic knowledge surrounding this species and opening avenues for delineating the microbiology of this urobiome constituent. Furthermore, we present a framework for using the combination of culture-dependent and sequencing methodologies for uncovering mechanisms in the urobiome.

Update on the Effect of the Urinary Microbiome on Urolithiasis

Microbiota are ecological communities of commensal, symbiotic, and pathogenic microorganisms. The microbiome could be involved in kidney stone formation through hyperoxaluria and calcium oxalate supersaturation, biofilm formation and aggregation, and urothelial injury. Bacteria bind to calcium oxalate crystals, which causes pyelonephritis and leads to changes in nephrons to form Randall's plaque. The urinary tract microbiome, but not the gut microbiome, can be distinguished between cohorts with urinary stone disease (USD) and those without a history of the disease. In the urine microbiome, the role is known of urease-producing bacteria (Proteus mirabilis, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, Providencia stuartii, Serratia marcescens, and Morganella morganii) in stone formation. Calcium oxalate crystals were generated in the presence of two uropathogenic bacteria (Escherichia coli and K. pneumoniae). Non-uropathogenic bacteria (S. aureus and Streptococcus pneumoniae) exhibit calcium oxalate lithogenic effects. The taxa Lactobacilli and Enterobacteriaceae best distinguished the healthy cohort from the USD cohort, respectively. Standardization is needed in urine microbiome research for urolithiasis. Inadequate standardization and design of urinary microbiome research on urolithiasis have hampered the generalizability of results and diminished their impact on clinical practice.

Fifty years of basic and clinical renal stone research: have we achieved major breakthroughs? A debate

PURPOSE OF REVIEW

After 50 years of basic and clinical renal stone research, it is appropriate to evaluate whether breakthroughs have been achieved and if so, how they may be harnessed to combat stone disease therapeutically and prophylactically.

RECENT FINDINGS

Regarding stone therapeutics and prophylaxis, recent innovative studies are sparse. Researchers have resorted to publishing articles derived from data mining. Stone incidence and prevalence have increased during the past 50 years, suggesting the absence of any major breakthroughs. However, new sciences and technologies have created fresh opportunities. Information technology stores huge epidemiological databases leading to identification of new risk factors. Genetic coding has prompted identification of monogenic diseases associated with urolithiasis. Genome-wide association studies in combination with epigenomics, transcriptomics, proteomics, and metabolomics are providing new insights. High-throughput and culture-independent techniques promise to define the impact of microbiome on stone formation while artificial intelligent techniques contribute to diagnosis and prediction of treatment outcomes. These technologies, as well as those which are advancing surgical treatment of stones represent major breakthroughs in stone research.

SUMMARY

Although efforts to cure stones have not yielded major breakthroughs, technological advances have improved surgical management of this disease and represent significant headway in applied stone research.

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.

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.

Screening out key compounds of Glechomae Herba for antiurolithic activity and quality control based on spectrum-effect relationships coupled with UPLC-QDA

Glechomae Herba (GH) has been widely used in the treatment of urolithiasis, especially kidney stones, in China and Southeast Asia. Pharmacological studies have suggested that the antioxidant property of GH contributes to its anticalculus effect. CaSR is one of the main locations of kidney stones, and the mechanism of action of CaSR inhibitors in the treatment of kidney stones is similar to that of GH. However, until now, the antiurolithic chemical compounds in GH and their interaction with CaSR remain unknown. In our study, we revealed the interaction between the active compounds in GH and the active compounds in CaSR inhibitors by using spectrum-effect relationship analysis, pharmacodynamics, and molecular docking techniques. The results showed ten common peaks from the fingerprints of GH extracts from different regions. Pharmacological experiments showed that GH could significantly treat renal tissue lesions. Chlorogenic acid (CA), rosmarinic acid (RA), P5, luteolin, apigenin, and P9 were screened after the analysis of spectrum-effect relationships. In vitro validation experiments showed that all the screened compounds had inhibitory effects on the development of kidney stones in our model. The molecular docking results showed that the above compounds could be docked with CaSR in a natural state, and the docking score was less than 7. This work constructs a general model for the combination of UPLC-QDA and antiurolithic drugs, studies the spectrum-effect relationship of GH, and provides a new possibility for the development of new antiurolithic drugs.

Interaction Between Diet and Microbiota in the Pathophysiology of Alzheimer's Disease: Focus on Polyphenols and Dietary Fibers

Animal studies increasingly indicate that the gut microbiota composition and function can be involved in the pathophysiology and progression of Alzheimer's disease (AD) at multiple levels. However, few studies have investigated this putative gut-brain axis in human beings, and none of them considered diet as a determinant of intestinal microbiota composition. Epidemiological studies highlight that a high intake of fruit and vegetables, such as that typical of the Mediterranean diet, can modulate AD progression. Thus, nutritional interventions are being increasingly studied as a possible non-pharmacological strategy to slow down the progression of AD. In particular, polyphenols and fibers represent the nutritional compounds with the higher potential of counterbalancing the pathophysiological mechanisms of dementia due to their antioxidant, anti-inflammatory, and anti-apoptotic properties. These actions are mediated by the gut microbiota, that can transform polyphenols and fibers into biologically active compounds including, among others, phenyl-γ-valerolactones, urolithins, butyrate, and other short-chain fatty acids. In this review, the complex mechanisms linking nutrition, gut microbiota composition, and pathophysiology of cognitive decline in AD are discussed, with a particular focus on the role of polyphenols and fibers. The gaps between pre-clinical and clinical studies are particularly emphasized, as well as the urgent need for studies comprehensively evaluating the link between nutrition, microbiome, and clinical aspects of AD.

Antibiotic Sensitivity of Proteus mirabilis Urinary Tract Infection in Patients with Urinary Calculi

BACKGROUND

The study's objective was to determine Proteus mirabilis susceptibility in individuals with urinary tract infections and stones to antibiotics and prescribe optimal antimicrobial treatment.

METHODS

Nonrepetitive Proteus mirabilis strains were isolated from urine specimens obtained from 317 patients diagnosed with urinary stones from January, 2018, to December, 2021. A VITEK mass spectrometer was used for species identification, and a VITEK-compact 2 automatic microbial system was used for the antimicrobial susceptibility test (AST). Susceptibility to imipenem and cefoperazone/sodium sulbactam was tested by the disc diffusion method (K-B method). The antibiotic sensitivity of the strains was analyzed by sex and season.

RESULTS

A total of 317 patients were reviewed: 202 females (63.7%) and 115 males (36.3%). Proteus mirabilis infections were observed during spring (21.8%, n = 69), summer (26.2%, n = 83), autumn (33.8%, n = 107), and winter (18.2%, n = 57). Proteus mirabilis infections in females were diagnosed most often during the fall (24.3%, n = 77) and during the summer in males (11.0%, n = 35) (p = 0.010). Female patients responded best to levofloxacin (p = 0.014), and male patients responded best to sulfamethoxazole (p = 0.023). Seasonal variation in antibiotic sensitivity was confirmed, with significantly higher rates in the winter for cefuroxime (p = 0.002) and sulfamethoxazole (p = 0.002). Significant seasonal increases were also found in levofloxacin sensitivity during the summer (p = 0.005).

CONCLUSIONS

Highly effective antibiotics such as cefoxitin and ceftazidime should be used empirically by considering antibiotic sensitivity changes by sex, season, and year. Regional studies should be conducted frequently.

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.