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Noonin C, Thongboonkerd V. Beneficial roles of gastrointestinal and urinary microbiomes in kidney stone prevention via their oxalate-degrading ability and beyond. Microbiol Res 2024; 282:127663. [PMID: 38422861 DOI: 10.1016/j.micres.2024.127663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/11/2024] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
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.
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Affiliation(s)
- Chadanat Noonin
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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2
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Li X, Tang Y, Xu Z, Lin H, Wei S, Sheng J, Hu L, Wang S, Zhao Y, Li Z, Fu C, Gu Y, Wei Q, Liu F, Feng N, Chen W. Impact of coexisting type 2 diabetes mellitus on the urinary microbiota of kidney stone patients. PeerJ 2024; 12:e16920. [PMID: 38426133 PMCID: PMC10903351 DOI: 10.7717/peerj.16920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024] Open
Abstract
Objectives Type 2 diabetes mellitus (T2DM) commonly complicates kidney stone disease (KSD). Our objective is to investigate the variations in the urinary microbiota between individuals with KSD alone and those with KSD plus T2DM. This exploration could have implications for disease diagnosis and treatment strategies. Methods During lithotripsy, a ureterscope was employed, and 1 mL of urine was collected from the renal pelvis after bladder disinfection. Sequencing targeting the V3-V4 hypervariable region was performed using the 16S rRNA and Illumina Novaseq platform. Results The Shannon index showed a significant decrease in the KSD plus T2DM group compared to the KSD-only group (false discovery rate = 0.041). Principal Coordinate Analysis (PCoA) demonstrated a distinct bacterial community in the KSD plus T2DM group compared to the KSD-only group (false discovery rate = 0.027). The abundance of Sphingomonas, Corynebacterium, and Lactobacillus was significantly higher in the KSD plus T2DM group than in the KSD-only group (false discovery rate < 0.05). Furthermore, Enhydrobacter, Chryseobacterium, and Allobaculum were positively correlated with fasting blood glucose and HbA1c values (P < 0.05). Conclusions The urinary microbiota in the renal pelvis exhibits differences between patients with KSD plus T2DM and those with KSD alone. Further studies employing animal models are necessary to validate these distinctions, potentially paving the way for therapeutic developments based on the urinary microbiota.
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Affiliation(s)
- Xiang Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yifan Tang
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Zhenyi Xu
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Hao Lin
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Shichao Wei
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Jiayi Sheng
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Lei Hu
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Shiyu Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yu Zhao
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zhi Li
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Chaowei Fu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yifeng Gu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Qun Wei
- Department of Surgical Oncology, Institute of Clinical Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Weiguo Chen
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
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Reasoner SA, Flores V, Van Horn G, Morales G, Peard LM, Abelson B, Manuel C, Lee J, Baker B, Williams T, Schmitz JE, Clayton DB, Hadjifrangiskou M. Survey of the infant male urobiome and genomic analysis of Actinotignum spp. NPJ Biofilms Microbiomes 2023; 9:91. [PMID: 38040700 PMCID: PMC10692110 DOI: 10.1038/s41522-023-00457-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/10/2023] [Indexed: 12/03/2023] Open
Abstract
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.
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Affiliation(s)
- Seth A Reasoner
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Viktor Flores
- Division of Pediatric Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gerald Van Horn
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Personalized Microbiology (CPMi), Vanderbilt University Medical Center, Nashville, TN, USA
| | - Grace Morales
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leslie M Peard
- Division of Pediatric Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin Abelson
- Division of Pediatric Urology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Pediatric Urology, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Carmila Manuel
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jessica Lee
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bailey Baker
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy Williams
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan E Schmitz
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Personalized Microbiology (CPMi), Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Douglass B Clayton
- Division of Pediatric Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Center for Personalized Microbiology (CPMi), Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA.
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4
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Yang Y, Miao L, Lu Y, Wang S. The genetics of urinary microbiome, an exploration of the trigger in calcium oxalate stone. Front Genet 2023; 14:1260278. [PMID: 37854058 PMCID: PMC10579592 DOI: 10.3389/fgene.2023.1260278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
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.
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Affiliation(s)
| | | | - Yuchao Lu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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5
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Hong SY, Miao LT, Zhang JQ, Wang SG. Identification of Two Clusters in Renal Pelvis Urobiome of Unilateral Stone Formers Using 2bRAD-M. Microorganisms 2023; 11:2276. [PMID: 37764120 PMCID: PMC10534321 DOI: 10.3390/microorganisms11092276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Urolithiasis is a common urological disease with increasing incidence and a high recurrence rate, whose etiology is not fully understood. The application of sequencing and culturomics has revealed that urolithiasis is closely related to the urinary microbiome (urobiome), shedding new light on the pathogenesis of stone formation. In this study, we recruited 30 patients with unilateral stones and collected their renal pelvis urine from both sides. Then, we performed 2bRAD-M, a novel sequencing technique that provides precise microbial identification at the species level, to characterize the renal pelvis urobiome of unilateral stone formers in the both sides. We first found that the urobiome in the stone side could be divided into two clusters (Stone1 and Stone2) based on distance algorithms. Stone2 harbored higher microbial richness and diversity compared to Stone1. The genera Cupriavidus and Sphingomonas were overrepresented in Stone1, whereas Acinetobacter and Pseudomonas were overrepresented in Stone2. Meanwhile, differential species were identified between Stone1 and Stone2. We further constructed a random forest model to discriminate two clusters which achieved a powerful diagnostic potential. Moreover, the urobiome of the non-stone side (Control1/2) was compared with that of the stone side (Stone1/2). Stone1 and Control1 showed different microbial community distributions, while Stone2 was similar to Control2 based on diversity analysis. We also identified differentially abundant species among all groups. We assumed that there might be different mechanisms of how microbiota contribute to stone formation in two clusters. Our findings might assist in the selection of suitable medical treatments for urolithiasis.
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Affiliation(s)
| | | | - Jia-Qiao Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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Hong SY, Xia QD, Yang YY, Li C, Zhang JQ, Xu JZ, Qin BL, Xun Y, Wang SG. The role of microbiome: a novel insight into urolithiasis. Crit Rev Microbiol 2023; 49:177-196. [PMID: 35776498 DOI: 10.1080/1040841x.2022.2045899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
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.
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Affiliation(s)
- Sen-Yuan Hong
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Qi-Dong Xia
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yuan-Yuan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Cong Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jia-Qiao Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jin-Zhou Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Bao-Long Qin
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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Galán-Llopis JA, Sánchez-Pellicer P, Navarro-López V. Role of microbiome in kidney stone disease. Curr Opin Urol 2023; 33:84-89. [PMID: 36210763 DOI: 10.1097/mou.0000000000001051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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.
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Affiliation(s)
- Juan A Galán-Llopis
- Department of Urology, General University Hospital Dr Balmis; Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante
| | - Pedro Sánchez-Pellicer
- MiBioPath Research Group, Department of Clinical Medicine, Health Sciencies Faculty, Catholic University of Murcia, Murcia
| | - Vicente Navarro-López
- MiBioPath Research Group, Department of Clinical Medicine, Health Sciencies Faculty, Catholic University of Murcia, Murcia; Infectious Diseases Unit, University Hospital of Vinalopó-Fisabio, Elche, Spain
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Reid G. Perspective: microbial interventions in the urinary tract. MICROBIOME RESEARCH REPORTS 2023; 2:3. [PMID: 38045610 PMCID: PMC10688806 DOI: 10.20517/mrr.2022.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/14/2023] [Indexed: 12/05/2023]
Abstract
Despite multiple advances in medicine, the management of urinary tract infections (UTIs) in women has remained stalled for decades. To prevent the development of symptomatic recurrences, low-dose antibiotics are the mainstay, while alternative approaches have been attempted with limited success. The use of probiotics was first considered forty years ago, and while some promising studies have been published, additional evidence in larger patient groups is needed to recommend specific strains as a primary preventive regimen. Overall, the role of beneficial microbes in reducing the risk of UTI and other urological diseases, such as urolithiasis, remains a target for researchers. The aim of this perspective is to offer a viewpoint on the status of this approach and recommendations for how to develop novel probiotic therapies.
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Affiliation(s)
- Gregor Reid
- Canadian R&D Centre for Human Microbiome and Probiotics, Lawson Health Research Institute, London, Ontario N6A 4V2, Canada
- Departments of Microbiology and Immunology, and Surgery, Western University, London, Ontario N6A 3K7, Canada
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Hong SY, Yang YY, Xu JZ, Xia QD, Wang SG, Xun Y. The renal pelvis urobiome in the unilateral kidney stone patients revealed by 2bRAD-M. J Transl Med 2022; 20:431. [PMID: 36153619 PMCID: PMC9509602 DOI: 10.1186/s12967-022-03639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/14/2022] [Indexed: 11/27/2022] Open
Abstract
Background The pathogenesis of kidney stone disease (KSD) is not fully understood, and potential contributing factors remain to be explored. Several studies have revealed that the urinary microbiome (urobiome) of stone formers was distinct from that of healthy individuals using 16S rRNA gene sequencing, most of which only provided microbial identification at the genus level. 2bRAD sequencing for Microbiome (2bRAD-M) is a novel sequencing technique that enables accurate characterization of the low-biomass microbiome at the species resolution. We aimed to apply 2bRAD-M to profile the renal pelvis urobiome of unilateral kidney stone patients and compared the urobiome with and without stone(s). Method A total of 30 patients with unilateral stones were recruited, and their renal pelvis urine from both sides was collected. A ureteroscope was inserted into the renal pelvis with stone(s) and a ureteral catheter was placed into the ureteroscope to collect renal pelvis urine. This procedure was repeated again with new devices to collect the urine of the other side. 2bRAD-M was performed to characterize the renal pelvis urobiome of unilateral stone formers to explore whether microbial differences existed between the stone side and the non-stone side. Results The microbial community composition of the stone side was similar to that of the non-stone side. Paired comparison showed that Corynebacterium was increased and Prevotella and Lactobacillus were decreased in the stone side. Four species (Prevotella bivia, Lactobacillus iners, Corynebacterium aurimucosum, and Pseudomonas sp_286) were overrepresented in the non-stone side. 24 differential taxa were also identified between two groups by linear discriminant analysis effect size (LEfSe). Extensive and close connections among genera and species were observed in the correlation analysis. Moreover, a random forest classifier was constructed using specific enriched species, which can distinguish the stone side from the non-stone side with an accuracy of 71.2%. Conclusion This first 2bRAD-M microbiome survey gave an important hint towards the potential role of urinary dysbiosis in KSD and provided a better understanding of mechanism of stone formation. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03639-6.
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The Bladder Microbiome, Metabolome, Cytokines, and Phenotypes in Patients with Systemic Lupus Erythematosus. Microbiol Spectr 2022; 10:e0021222. [PMID: 35913213 PMCID: PMC9620774 DOI: 10.1128/spectrum.00212-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Emerging studies reveal unique bacterial communities in the human bladder, with alteration of composition associated to disease states. Systemic lupus erythematosus (SLE) is a complex autoimmune disease that is characterized by frequent impairment of the kidney. Here, we explored the bladder microbiome, metabolome, and cytokine profiles in SLE patients, as well as correlations between microbiome and metabolome, cytokines, and disease profiles. We recruited a group of 50 SLE patients and 50 individually matched asymptomatic controls. We used transurethral catheterization to collect urine samples, 16S rRNA gene sequencing to profile bladder microbiomes, and liquid chromatography-tandem mass spectrometry to perform untargeted metabolomic profiling. Compared to controls, SLE patients possessed unique bladder microbial communities and increased alpha diversity. These differences were accompanied by differences in urinary metabolomes, cytokines, and patients’ disease profiles. The SLE-enriched genera, including Bacteroides, were positively correlated with several SLE-enriched metabolites, including olopatadine. The SLE-depleted genera, such as Pseudomonas, were negatively correlated to SLE-depleted cytokines, including interleukin-8. Alteration of the bladder microbiome was associated with disease profile. For example, the genera Megamonas and Phocaeicola were negatively correlated with serum complement component 3, and Streptococcus was positively correlated with IgG. Our present study reveals associations between the bladder microbiome and the urinary metabolome, cytokines, and disease phenotypes. Our results could help identify biomarkers for SLE. IMPORTANCE Contrary to dogma, the human urinary bladder possesses its own unique bacterial community with alteration of composition associated with disease states. Systemic lupus erythematosus (SLE) is a complex autoimmune disease often characterized by kidney impairment. Here, we explored the bladder microbiome, metabolome, and cytokine profiles in SLE patients, as well as correlations between the microbiome and metabolome, cytokines, and disease profiles. Compared to controls, SLE patients possessed a unique bladder microbial community and elevated alpha diversity. These differences were accompanied by differences in bladder metabolomes, cytokines, and patients’ disease profiles. SLE-enriched genera were positively correlated with several SLE-enriched metabolites. SLE-depleted genera were negatively correlated to SLE-depleted cytokines. Alteration of the bladder microbiome was associated with disease profile. Thus, our study reveals associations between the bladder microbiome and the bladder metabolome, cytokines, and disease phenotypes. These results could help identify biomarkers for SLE.
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