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Xie J, Zhang XQ, Guo JN, Yuan Q, Xiao KF, Yuan YQ. The urinary microbiota composition and functionality of calcium oxalate stone formers. Front Cell Infect Microbiol 2024; 14:1394955. [PMID: 38912208 PMCID: PMC11190077 DOI: 10.3389/fcimb.2024.1394955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/29/2024] [Indexed: 06/25/2024] Open
Abstract
Background Accumulated evidences indicate that dysbiosis of the urinary microbiota is associated with kidney stone formation. In the present study, we aimed to investigate the urinary microbiota composition and functionality of patients with calcium oxalate stones and compare it with those of healthy individuals. Method We collected bladder urine samples from 68 adult patients with calcium oxalate stones and 54 age-matched healthy controls by transurethral catheterization. 16S rRNA gene and shotgun sequencing were utilized to characterize the urinary microbiota and functionality associated with calcium oxalate stones. Results After further exclusion, a total of 100 subjects was finally included and analyzed. The diversity of the urinary microbiota in calcium oxalate stone patients was not significantly different from that of healthy controls. However, the urinary microbiota structure of calcium oxalate stone formers significantly differed from that of healthy controls (PERMANOVA, r = 0.026, P = 0.019). Differential representation of bacteria (e.g., Bifidobacterium) and several enriched functional pathways (e.g., threonine biosynthesis) were identified in the urine of calcium oxalate stone patients. Conclusion Our results showed significantly different urinary microbiota structure and several enriched functional pathways in calcium oxalate stone patients, which provide new insight into the pathogenesis of calcium oxalate stones.
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Affiliation(s)
- Jing Xie
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Xue-qi Zhang
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Ji-nan Guo
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Qian Yuan
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Ke-feng Xiao
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Ye-qing Yuan
- Department of Urology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Shenzhen Engineering and Technology Center of Minimally Invasive Urology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
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Wan W, Wu W, Amier Y, Li X, Yang J, Huang Y, Xun Y, Yu X. Engineered microorganisms: A new direction in kidney stone prevention and treatment. Synth Syst Biotechnol 2024; 9:294-303. [PMID: 38510204 PMCID: PMC10950756 DOI: 10.1016/j.synbio.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Numerous studies have shown that intestinal and urinary tract flora are closely related to the formation of kidney stones. The removal of probiotics represented by lactic acid bacteria and the colonization of pathogenic bacteria can directly or indirectly promote the occurrence of kidney stones. However, currently existing natural probiotics have limitations. Synthetic biology is an emerging discipline in which cells or living organisms are genetically designed and modified to have biological functions that meet human needs, or even create new biological systems, and has now become a research hotspot in various fields. Using synthetic biology approaches of microbial engineering and biological redesign to enable probiotic bacteria to acquire new phenotypes or heterologous protein expression capabilities is an important part of synthetic biology research. Synthetic biology modification of microorganisms in the gut and urinary tract can effectively inhibit the development of kidney stones by a range of means, including direct degradation of metabolites that promote stone production or indirect regulation of flora homeostasis. This article reviews the research status of engineered microorganisms in the prevention and treatment of kidney stones, to provide a new and effective idea for the prevention and treatment of kidney stones.
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Affiliation(s)
- Wenlong Wan
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Weisong Wu
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yirixiatijiang Amier
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xianmiao Li
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Junyi Yang
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yisheng Huang
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yang Xun
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiao Yu
- Department of Urology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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Joubran P, Roux FA, Serino M, Deschamps JY. Gut and Urinary Microbiota in Cats with Kidney Stones. Microorganisms 2024; 12:1098. [PMID: 38930480 PMCID: PMC11205531 DOI: 10.3390/microorganisms12061098] [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: 04/23/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
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.
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Affiliation(s)
- Patrick Joubran
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
| | - Françoise A. Roux
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
- Emergency and Critical Care Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France
| | - Matteo Serino
- IRSD, Institut de Recherche en Santé Digestive, Institut National de la Santé et de la Recherche Médicale (INSERM) U1220, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse III-Paul Sabatier (UPS), CS 60039, 31 024 Toulouse, France
| | - Jack-Yves Deschamps
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
- Emergency and Critical Care Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France
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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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Wu K, Li Y, Ma K, Zhao W, Yao Z, Zheng Z, Sun F, Mu X, Liu Z, Zheng J. The microbiota and renal cell carcinoma. Cell Oncol (Dordr) 2024; 47:397-413. [PMID: 37878209 DOI: 10.1007/s13402-023-00876-9] [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] [Accepted: 09/16/2023] [Indexed: 10/26/2023] Open
Abstract
Renal cell carcinoma (RCC) accounts for about 2% of cancer diagnoses and deaths worldwide. Recent studies emphasized the critical involvement of microbial populations in RCC from oncogenesis, tumor growth, and response to anticancer therapy. Microorganisms have been shown to be involved in various renal physiological and pathological processes by influencing the immune system function, metabolism of the host and pharmaceutical reactions. These findings have extended our understanding and provided more possibilities for the diagnostic or therapeutic development of microbiota, which could function as screening, prognostic, and predictive biomarkers, or be manipulated to prevent RCC progression, boost anticancer drug efficacy and lessen the side effects of therapy. This review aims to present an overview of the roles of microbiota in RCC, including pertinent mechanisms in microbiota-related carcinogenesis, the potential use of the microbiota as RCC biomarkers, and the possibility of modifying the microbiota for RCC prevention or treatment. According to these scientific findings, the clinical translation of microbiota is expected to improve the diagnosis and treatment of RCC.
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Affiliation(s)
- Ke Wu
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaorong Li
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kangli Ma
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiguang Zhao
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhixian Yao
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhong Zheng
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Sun
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingyu Mu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihong Liu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Junhua Zheng
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Araujo R, Merino-Ribas A, Pereira L, Campos J, Silva N, Alencastre IS, Pestana M, Sampaio-Maia B. The urogenital microbiome in chronic kidney disease patients on peritoneal dialysis. Nefrologia 2024; 44:194-203. [PMID: 38697697 DOI: 10.1016/j.nefroe.2024.04.004] [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: 03/10/2023] [Accepted: 08/27/2023] [Indexed: 05/05/2024] Open
Abstract
INTRODUCTION AND OBJECTIVES Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters. MATERIALS AND METHODS Mid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3-V4 region of the bacterial 16S rRNA gene. Correlations with the patients' clinical data and inflammatory profile were performed. RESULTS CKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14. CONCLUSIONS Our results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.
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Affiliation(s)
- Ricardo Araujo
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.
| | - Ana Merino-Ribas
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; Nephrology Department, Hospital Universitari de Girona Doctor Josep Trueta, Girona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luciano Pereira
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; Nephrology Department, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Joana Campos
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Nádia Silva
- Nephrology Department, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Inês Soares Alencastre
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Manuel Pestana
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; Nephrology Department, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Benedita Sampaio-Maia
- Nephrology & Infectious Diseases R&D Group, i3S - Instituto de Investigação e Inovação em Saúde, INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal; Faculdade de Medicina Dentária, Universidade do Porto, Porto, Portugal
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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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Bowie KR, Garzotto M, Orwoll E, Karstens L. BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571758. [PMID: 38168244 PMCID: PMC10760175 DOI: 10.1101/2023.12.14.571758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.
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Affiliation(s)
- Kate R Bowie
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark Garzotto
- School of Medicine, Oregon Health & Science University, Portland, OR, USA
- Portland VA Medical Center, Portland, Oregon, USA
| | - Eric Orwoll
- Division of Endocrinology, Diabetes, and Clinical Nutrition, Oregon Health & Science University, Portland, Oregon, USA
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
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Werneburg GT, Adler A, Khooblall P, Wood HM, Gill BC, Vij SC, Angermeier KW, Lundy SD, Miller AW, Bajic P. Penile prostheses harbor biofilms driven by individual variability and manufacturer even in the absence of clinical infection. J Sex Med 2023; 20:1431-1439. [PMID: 37837552 DOI: 10.1093/jsxmed/qdad124] [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: 06/05/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Culture-based studies have shown that penile prostheses harbor biofilms in the presence and absence of infection, but these findings have not been adequately validated using contemporary microbiome analytic techniques. AIM The study sought to characterize microbial biofilms of indwelling penile prosthesis devices according to patient factors, device components, manufacturer, and infection status. METHODS Upon penile prostheses surgical explantation, device biofilms were extracted, sonicated, and characterized using shotgun metagenomics and culture-based approaches. Device components were also analyzed using scanning electron microscopy. OUTCOMES Outcomes included the presence or absence of biofilms, alpha and beta diversity, specific microbes identified and the presence of biofilm, and antibiotic resistance genes on each prosthesis component. RESULTS The average age of participants from whom devices were explanted was 61 ± 11 years, and 9 (45%) of 20 had a diagnosis of diabetes mellitus. Seventeen devices were noninfected, and 3 were associated with clinical infection. Mean device indwelling time prior to explant was 5.1 ± 5.1 years. All analyzed components from 20 devices had detectable microbial biofilms, both in the presence and absence of infection. Scanning electron microscopy corroborated the presence of biofilms across device components. Significant differences between viruses, prokaryotes, and metabolic pathways were identified between individual patients, device manufacturers, and infection status. Mobiluncus curtisii was enriched in manufacturer A device biofilms relative to manufacturer B device biofilms. Bordetella bronchialis, Methylomicrobium alcaliphilum, Pseudoxanthomonas suwonensis, and Porphyrobacter sp. were enriched in manufacturer B devices relative to manufacturer A devices. The most abundant bacterial phyla were the Proteobacteria, Actinobacteria, and Firmicutes. Glycogenesis, the process of glycogen synthesis, was among the predominant metabolic pathways detected across device components. Beta diversity of bacteria, viruses, protozoa, and pathways did not differ among device components. CLINICAL IMPLICATIONS All components of all penile prostheses removed from infected and noninfected patients have biofilms. The significance of biofilms on noninfected devices remains unknown and merits further investigation. STRENGTHS AND LIMITATIONS Strengths include the multipronged approach to characterize biofilms and being the first study to include all components of penile prostheses in tandem. Limitations include the relatively few number of infected devices in the series, a relatively small subset of devices included in shotgun metagenomics analysis, and the lack of anaerobic and other expanded conditions for culture. CONCLUSION Penile prosthesis biofilms are apparent in the presence and absence of infection, and the composition of biofilms was driven primarily by device manufacturer, individual variability, and infection, while being less impacted by device component.
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Affiliation(s)
- Glenn T Werneburg
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Ava Adler
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Prajit Khooblall
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Hadley M Wood
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Bradley C Gill
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Sarah C Vij
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Kenneth W Angermeier
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Scott D Lundy
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Aaron W Miller
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
| | - Petar Bajic
- Department of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, United States
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10
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He SK, Wang JH, Li T, Yin S, Cui JW, Xiao YF, Tang Y, Wang J, Bai YJ. Sleep and circadian rhythm disturbance in kidney stone disease: a narrative review. Front Endocrinol (Lausanne) 2023; 14:1293685. [PMID: 38089624 PMCID: PMC10711275 DOI: 10.3389/fendo.2023.1293685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
The circadian rhythm generated by circadian clock genes functions as an internal timing system. Since the circadian rhythm controls abundant physiological processes, the circadian rhythm evolved in organisms is salient for adaptation to environmental change. A disturbed circadian rhythm is a trigger for numerous pathological events. Recently, accumulated data have indicated that kidney stone disease (KSD) is related to circadian rhythm disturbance. However, the mechanism between them has not been fully elucidated. In this narrative review, we summarized existing evidence to illustrate the possible association between circadian rhythm disturbance and KSD based on the epidemiological studies and risk factors that are linked to circadian rhythm disturbance and discuss some chronotherapies for KSD. In summary, KSD is associated with systemic disorders. Metabolic syndrome, inflammatory bowel disease, and microbiome dysbiosis are the major risk factors supported by sufficient data to cause KSD in patients with circadian rhythm disturbance, while others including hypertension, vitamin D deficiency, parathyroid gland dysfunction, and renal tubular damage/dysfunction need further investigation. Then, some chronotherapies for KSD were confirmed to be effective, but the molecular mechanism is still unclear.
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Affiliation(s)
- Si-Ke He
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jia-Hao Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Li
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shan Yin
- Department of Urology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jian-Wei Cui
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yun-Fei Xiao
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yin Tang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yun-Jin Bai
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
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11
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Al KF, Joris BR, Daisley BA, Chmiel JA, Bjazevic J, Reid G, Gloor GB, Denstedt JD, Razvi H, Burton JP. Multi-site microbiota alteration is a hallmark of kidney stone formation. MICROBIOME 2023; 11:263. [PMID: 38007438 PMCID: PMC10675928 DOI: 10.1186/s40168-023-01703-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/17/2023] [Indexed: 11/27/2023]
Abstract
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.
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Affiliation(s)
- Kait F Al
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Benjamin R Joris
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Brendan A Daisley
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada
| | - John A Chmiel
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jennifer Bjazevic
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregor Reid
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregory B Gloor
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - John D Denstedt
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Jeremy P Burton
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
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12
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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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13
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Kumar A, Estes Bright LM, Garren MRS, Manuel J, Shome A, Handa H. Chemical Modification of Tiopronin for Dual Management of Cystinuria and Associated Bacterial Infections. ACS APPLIED MATERIALS & INTERFACES 2023; 15:43332-43344. [PMID: 37671841 PMCID: PMC10520916 DOI: 10.1021/acsami.3c07160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023]
Abstract
Cystinuria is an inherited autosomal recessive disease of the kidneys of recurring nature that contributes to frequent urinary tract infections due to bacterial growth and biofilm formation surrounding the stone microenvironment. In the past, commonly used strategies for managing cystinuria involved the use of (a) cystine crystal growth inhibitors such as l-cystine dimethyl ester and lipoic acid, and (b) thiol-based small molecules such as N-(2-mercaptopropionyl) glycine, commonly known as tiopronin, that reduce the formation of cystine crystals by reacting with excess cystine and generating more soluble disulfide compounds. However, there is a dearth of simplistic chemical approaches that have focused on the dual treatment of cystinuria and the associated microbial infections. This work strategically exploited a single chemical approach to develop a nitric oxide (NO)-releasing therapeutic compound, S-nitroso-2-mercaptopropionyl glycine (tiopronin-NO), for the dual management of cystine stone formation and the related bacterial infections. The results successfully demonstrated that (a) the antibacterial activity of NO rendered tiopronin-NO effective against the stone microenvironment inhabitants, Escherichia coli and Pseudomonas aeruginosa, and (b) tiopronin-NO retained the ability to undergo disulfide exchange with cystine while being reported to be safe against canine kidney and mouse fibroblast cells. Thus, the synthesis of such a facile molecule aimed at the dual management of cystinuria and related infections is unprecedented in the literature.
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Affiliation(s)
- Anil Kumar
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Lori M. Estes Bright
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Mark Richard Stephen Garren
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - James Manuel
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Arpita Shome
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Hitesh Handa
- School
of Chemical Materials and Biomedical Engineering, University of Georgia, Athens, Georgia 30602, United States
- Pharmaceutical
and Biomedical Sciences Department, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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14
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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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15
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Thongprayoon C, Vaughan LE, Barreto EF, Mehta RA, Koo K, Schulte PJ, Lieske JC, Rule AD. Outpatient Antibiotic Use is Not Associated with an Increased Risk of First-Time Symptomatic Kidney Stones. J Am Soc Nephrol 2023; 34:1399-1408. [PMID: 37184480 PMCID: PMC10400106 DOI: 10.1681/asn.0000000000000155] [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: 01/15/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
SIGNIFICANCE STATEMENT Antibiotics modify human microbiomes and may contribute to kidney stone risk. In a population-based case-control study using 1247 chart-validated first-time symptomatic kidney stone formers and 4024 age- and sex-matched controls, the risk of kidney stones was transiently higher during the first year after antibiotic use. However, this risk was no longer evident after adjustment for comorbidities and excluding participants with prior urinary symptoms. Findings were consistent across antibiotic classes and the number of antibiotic courses received. This suggests that antibiotics are not important risk factors of kidney stones. Rather, kidney stones when they initially cause urinary symptoms are under-recognized, resulting in antibiotic use before a formal diagnosis of kidney stones ( i.e. , reverse causality). BACKGROUND Antibiotics modify gastrointestinal and urinary microbiomes, which may contribute to kidney stone formation. This study examined whether an increased risk of a first-time symptomatic kidney stone episode follows antibiotic use. METHODS A population-based case-control study surveyed 1247 chart-validated first-time symptomatic kidney stone formers with a documented obstructing or passed stone (cases) in Olmsted County, Minnesota, from 2008 to 2013 and 4024 age- and sex-matched controls. All prescriptions for outpatient oral antibiotic use within 5 years before the onset of symptomatic stone for the cases and their matched controls were identified. Conditional logistic regression estimated the odds ratio (OR) of a first-time symptomatic kidney stone across time after antibiotic use. Analyses were also performed after excluding cases and controls with prior urinary tract infection or hematuria because urinary symptoms resulting in antibiotic prescription could have been warranted because of undiagnosed kidney stones. RESULTS The risk of a symptomatic kidney stone was only increased during the 1-year period after antibiotic use (unadjusted OR, 1.31; P = 0.001), and this risk was attenuated after adjustment for comorbidities (OR, 1.16; P = 0.08). After excluding cases and controls with prior urinary symptoms, there was no increased risk of a symptomatic kidney stone during the 1-year period after antibiotic use (unadjusted OR, 1.04; P = 0.70). Findings were consistent across antibiotic classes and the number of antibiotic courses received. CONCLUSIONS The increased risk of a first-time symptomatic kidney stone with antibiotic use seems largely due to both comorbidities and prescription of antibiotics for urinary symptoms. Under-recognition of kidney stones that initially cause urinary symptoms resulting in antibiotic use may explain much of the perceived stone risk with antibiotics ( i.e. , reverse causality).
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Affiliation(s)
| | - Lisa E. Vaughan
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | | | - Ramila A. Mehta
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - Kevin Koo
- Department of Urology, Mayo Clinic, Rochester, Minnesota
| | - Phillip J. Schulte
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, Minnesota
| | - John C. Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew D. Rule
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
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16
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Khan SR, Canales BK. Proposal for pathogenesis-based treatment options to reduce calcium oxalate stone recurrence. Asian J Urol 2023; 10:246-257. [PMID: 37538166 PMCID: PMC10394280 DOI: 10.1016/j.ajur.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/02/2022] [Accepted: 01/18/2023] [Indexed: 08/05/2023] Open
Abstract
Objective Prevalence of kidney stone disease continues to increase globally with recurrence rates between 30% and 50% despite technological and scientific advances. Reduction in recurrence would improve patient outcomes and reduce cost and stone morbidities. Our objective was to review results of experimental studies performed to determine the efficacy of readily available compounds that can be used to prevent recurrence. Methods All relevant literature up to October 2020, listed in PubMed is reviewed. Results Clinical guidelines endorse the use of evidence-based medications, such as alkaline agents and thiazides, to reduce urinary mineral supersaturation and recurrence. However, there may be additional steps during stone pathogenesis where medications could moderate stone risk. Idiopathic calcium oxalate stones grow attached to Randall's plaques or plugs. Results of clinical and experimental studies suggest involvement of reactive oxygen species and oxidative stress in the formation of both the plaques and plugs. The renin-angiotensin-aldosterone system (RAAS), nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, mitochondria, and NOD-like receptor pyrin domain containing-3 (NLRP3) inflammasome have all been implicated at specific steps during stone pathogenesis in animal models. Conclusion In addition to supersaturation-reducing therapies, the use of anti-oxidants, free radical scavengers, and inhibitors of NADPH oxidase, NLRP3 inflammasome, and RAAS may prove beneficial for stone prevention. Compounds such as statins and angiotensin converting enzyme inhibitors are already in use as therapeutics for hypertension and cardio-vascular disease and have previously shown to reduce calcium oxalate nephrolithiasis in rats. Although clinical evidence for their use in stone prevention in humans is limited, experimental data support they be considered along with standard evidence-based medications and clinical expertise when patients are being counselled for stone prevention.
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Affiliation(s)
- Saeed R. Khan
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
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17
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Yang JW, Wan S, Li KP, Chen SY, Yang L. Gut and urinary microbiota: the causes and potential treatment measures of renal cell carcinoma. Front Immunol 2023; 14:1188520. [PMID: 37441065 PMCID: PMC10333567 DOI: 10.3389/fimmu.2023.1188520] [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: 03/17/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Mounting evidence suggests that the gut microbiota plays a crucial role in the development and treatment of various cancers. Recent research on the urinary microbiota challenges the long-standing belief that urine is sterile, as urinary microbiota has been implicated in the development of bladder and prostate cancers, similar to the role of gut microbiota in cancer development. Although the precise involvement of microbiota in the proliferation and differentiation of renal cell carcinoma (RCC) remains unclear, dysbiosis is considered one possible mechanism by which microbiota may contribute to RCC development and treatment. This review summarizes potential mechanisms by which gut microbiota may contribute to the development of RCC, and provides evidence for the involvement of urinary microbiota in RCC. We also explore the role of gut microbiota in RCC treatment and propose that the composition of gut microbiota could serve as a predictive marker for the potential efficacy of immune checkpoint inhibitors (ICIs) in RCC patients. Additionally, evidence suggests that modulating the abundance and distribution of microbiota can enhance the therapeutic effects of drugs, suggesting that microbiota may serve as a promising adjuvant therapy for RCC. Overall, we believe that further investigation into the gut and urinary microbiome of RCC patients could yield valuable insights and strategies for the prevention and personalized treatment of RCC.
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Affiliation(s)
| | | | | | | | - Li Yang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
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18
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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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19
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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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20
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Choi HW, Lee KW, Kim YH. Microbiome in urological diseases: Axis crosstalk and bladder disorders. Investig Clin Urol 2023; 64:126-139. [PMID: 36882171 PMCID: PMC9995957 DOI: 10.4111/icu.20220357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/29/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
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.
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Affiliation(s)
- Hae Woong Choi
- Division of Life Sciences, Korea University, Seoul, Korea
| | - Kwang Woo Lee
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Young Ho Kim
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon, Korea.
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21
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Miller AW, Penniston KL, Fitzpatrick K, Agudelo J, Tasian G, Lange D. Mechanisms of the intestinal and urinary microbiome in kidney stone disease. Nat Rev Urol 2022; 19:695-707. [PMID: 36127409 PMCID: PMC11234243 DOI: 10.1038/s41585-022-00647-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2022] [Indexed: 02/08/2023]
Abstract
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.
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Affiliation(s)
- Aaron W Miller
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Kristina L Penniston
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kate Fitzpatrick
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - José Agudelo
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gregory Tasian
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dirk Lange
- The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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22
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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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Gao H, Lin J, Xiong F, Yu Z, Pan S, Huang Y. Urinary Microbial and Metabolomic Profiles in Kidney Stone Disease. Front Cell Infect Microbiol 2022; 12:953392. [PMID: 36132987 PMCID: PMC9484321 DOI: 10.3389/fcimb.2022.953392] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundKidney 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.MethodUrine 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.ResultsDistinct 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.ConclusionsOur 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.
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Affiliation(s)
- Hong Gao
- Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, China
| | - Jiaqiong Lin
- Affiliated Dongguan Maternal and Child Healthcare Hospital, Southern Medical University, Dongguan, China
| | - Fu Xiong
- Department of Medical Genetics/Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zuhu Yu
- Shenzhen Hospital, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shilei Pan
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yuxin Huang, ; Shilei Pan,
| | - Yuxin Huang
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Yuxin Huang, ; Shilei Pan,
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24
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Friedrich V, Choi HW. The Urinary Microbiome: Role in Bladder Cancer and Treatment. Diagnostics (Basel) 2022; 12:diagnostics12092068. [PMID: 36140470 PMCID: PMC9497549 DOI: 10.3390/diagnostics12092068] [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: 07/22/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
Commensal microbes have increasingly been found to be involved in the development and progression of cancer. The recent discovery of the urinary microbiome bolstered the notion that microbes might play a role in bladder cancer. Although microbial involvement in bladder neoplastic transformation and metastatic progression, except schisto somiasis, has not been established, accumulating research suggests that dysbiosis of the urinary microbiome can produce a chronically inflammatory urothelial microenvironment and lead to bladder cancer. In this review, we describe how the urinary microbiome might facilitate the development of bladder cancer by altering the host immune system and the kind of cytokines that are directly involved in these responses. We investigated the therapeutic possibilities of modulating the urinary microbiome, including immune checkpoint therapy. The responsiveness of patients to intravesical Bacillus Calmette-Guerin therapy was evaluated with respect to microbiome composition. We conclude by noting that the application of microbes to orchestrate the inflammatory response in the bladder may facilitate the development of treatments for bladder cancer.
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25
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Cole E, Shaikh N, Forster CS. The pediatric urobiome in genitourinary conditions: a narrative review. Pediatr Nephrol 2022; 37:1443-1452. [PMID: 34654953 DOI: 10.1007/s00467-021-05274-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 12/19/2022]
Abstract
The microbial ecosystem within the bladder that can be measured within the urine, or urobiome, is an emerging field of study with little published data regarding children. However, investigations into urobiome research have the potential to significantly impact the understanding of the pathophysiology of genitourinary conditions, as well as potentially identify novel therapeutics. Therefore, both researchers and clinicians should be aware of pediatric urobiome research. The purpose of this review is to highlight the literature around urobiome research in urinary tract infections, nephrolithiasis, and neurogenic bladder; comment on pediatric-specific considerations when reading and interpreting the urobiome literature; and to identify new potential areas of research.
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Affiliation(s)
- Elisabeth Cole
- Department of Pediatrics, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Catherine S Forster
- Department of Pediatrics, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
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26
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Kachroo N, Monga M, Miller AW. Comparative functional analysis of the urinary tract microbiome for individuals with or without calcium oxalate calculi. Urolithiasis 2022; 50:303-317. [PMID: 35234986 PMCID: PMC11247624 DOI: 10.1007/s00240-022-01314-5] [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: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 11/30/2022]
Abstract
Individuals with urinary stone disease (USD) exhibit dysbiosis in the urinary tract and the loss of Lactobacillus that promote urinary tract health. However, the microbial metabolic functions that differentiate individuals with USD from healthy individuals are unknown. The objective of the current study was to determine the microbial functions across prokaryotic, viral, fungal, and protozoan domains that are associated with calcium oxalate (CaOx) stone formers through comparative shotgun metagenomics of midstream, voided urine samples for a small number of patients (n = 5 CaOx stone formers, n = 5 healthy controls). Results revealed that CaOx stone formers had reduced levels of genes associated with oxalate metabolism, as well as transmembrane transport, proteolysis, and oxidation-reduction processes. From 17 draft genomes extracted from the data and > 42,000 full length reference genomes, genes enriched in the Control group mapped overwhelming to Lactobacillus crispatus and those associated with CaOx mapped to Pseudomonas aeruginosa and Burkholderia sp. The microbial functions that differentiated the clinical cohorts are associated with known mechanisms of stone formation. While the prokaryotes most differentiated the CaOx and Control groups, a diverse, trans-domain microbiome was apparent. While our sample numbers were small, results corroborate previous studies and suggest specific microbial metabolic pathways in the urinary tract that modulate stone formation. Future studies that target these metabolic pathways as well as the influence of viruses, fungi, and protozoa on urinary tract physiology is warranted.
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Affiliation(s)
- Naveen Kachroo
- Department of Urology, Henry Ford Health System, Detroit, MI, USA
| | - Manoj Monga
- Department of Urology, University of California San Diego, San Diego, CA, USA
| | - Aaron W Miller
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
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27
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The Urobiome and Its Role in Overactive Bladder. Int Neurourol J 2022; 26:190-200. [PMID: 35468617 PMCID: PMC9537439 DOI: 10.5213/inj.2244016.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Urine is no longer considered to be sterile. After the existence of the microbiome was revealed through metagenomic analysis using next-generation sequencing, the relationship between characteristics of the microbiome and diseases have been studied and published in various journals. A microbiome exists in the urinary tract and is associated with urinary tract infection, malignancy of the genitourinary tract, and lower urinary tract symptoms. Based on the urine sampling method, sampling site, culture method, and sex, the characteristics of the microbiome vary. Most of the Lactobacillus species are identified mainly in women, and various other species are identified in men. These microorganisms can cause or prevent various diseases. Variations in the microbiome are seen in those with and without disease, and an asymptomatic status does not indicate the absence of microbes. This microbiome has been implicated in a variety of lower urinary tract symptoms and diseases, in particular, overactive bladder. The microbiome differs between patients with urgency and urge urinary incontinence and healthy individuals. There are many aspects of the microbiome yet to be studied in relation to other lower urinary tract symptoms.
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28
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Gao S, Chao Y, Li N, Li H, Zhao H, Liu X, Chen W, Dong X. An Integrated Proteomics and Metabolomics Strategy for the Mechanism of Calcium Oxalate Crystal-Induced Kidney Injury. Front Med (Lausanne) 2022; 9:805356. [PMID: 35308536 PMCID: PMC8927618 DOI: 10.3389/fmed.2022.805356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Renal fibrosis is the pathological repair reaction of the kidney to chronic injury, which is an important process of chronic kidney disease (CKD) progressing to end-stage renal failure. Nephrolithiasis is one of the most common renal diseases, with waist and abdomen pain, hematuria, urinary tract infection, and other clinical symptoms, which can increase the risk of renal fibrosis. Oxalate crystal-induced kidney injury is an early stage of nephrolithiasis; it is of great significance to explore the mechanism for the prevention and treatment of nephrolithiasis. A rodent model of calcium oxalate (CaOx) crystal-induced kidney injury was used in the present study, and a network analysis method combining proteomics and metabolomics was conducted to reveal the mechanism of crystal kidney injury and to provide potential targets for the intervention of nephrolithiasis. Using the metabolomics method based on the UHPLC-Q/TOF-MS platform and the iTRAQ quantitative proteomics method, we screened a total of 244 metabolites and 886 proteins from the kidney tissues that had significant changes in the Crystal group compared with that in the Control group. Then, the ingenuity pathway analysis (IPA) was applied to construct a protein-to-metabolic regulatory network by correlating and integrating differential metabolites and proteins. The results showed that CaOx crystals could induce inflammatory reactions and oxidative stress through Akt, ERK1/2, and P38 MAPK pathways and affect amino acid metabolism and fatty acid β-oxidation to result in kidney injury, thus providing an important direction for the early prevention and treatment of nephrolithiasis.
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Affiliation(s)
- Songyan Gao
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Yufan Chao
- School of Medicine, Shanghai University, Shanghai, China
| | - Na Li
- School of Medicine, Shanghai University, Shanghai, China
| | - Henghui Li
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Hongxia Zhao
- School of Medicine, Shanghai University, Shanghai, China
| | - Xinru Liu
- Institute of Translational Medicine, Shanghai University, Shanghai, China
- *Correspondence: Xinru Liu
| | - Wei Chen
- Department of Nephrology, Changhai Hospital, Naval Military Medical University, Shanghai, China
- Wei Chen
| | - Xin Dong
- Institute of Translational Medicine, Shanghai University, Shanghai, China
- School of Medicine, Shanghai University, Shanghai, China
- Xin Dong
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29
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The Microbiome and Urolithiasis: Current Advancements and Future Challenges. Curr Urol Rep 2022; 23:47-56. [PMID: 35138598 DOI: 10.1007/s11934-022-01088-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW The aim of this review is to explore the effect of the microbiome on urolithiasis and explore recent advances and challenges in microbiome research for urolithiasis. RECENT FINDINGS Lack of standardization and shortcomings in study design for urinary microbiome research on urolithiasis has hampered the generalizability of results and weakened the impact of findings on clinical practice. Important study limitations include sample heterogenicity, specimen contamination, poor culture yields, and lack of shared datasets for meta-analysis. Contrary to traditional teaching, the genitourinary tract is not a sterile environment. This urinary microbiome may influence the pathogenesis of urolithiasis, although the specific mechanisms are still currently being explored. Successful investigation will depend on consistency in study design and analysis, as well as sharing data and protocols across institutions. Developing an understanding of the relationship between the urinary microbiome and urolithiasis may lead to novel approaches to mitigate stone risk.
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30
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Shen C, Zhu Q, Dong F, Wang W, Fan B, Li K, Chen J, Hu S, He Z, Li X. Identifying Two Novel Clusters in Calcium Oxalate Stones With Urinary Tract Infection Using 16S rDNA Sequencing. Front Cell Infect Microbiol 2021; 11:723781. [PMID: 34869053 PMCID: PMC8635737 DOI: 10.3389/fcimb.2021.723781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/25/2021] [Indexed: 02/01/2023] Open
Abstract
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.
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Affiliation(s)
- Chen Shen
- Departmant of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Qianhui Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fan Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- Departmant of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Bo Fan
- Departmant of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Kexin Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China.,School of Engineering Medicine, Beihang University, Beijing, China
| | - Xiancheng Li
- Departmant of Urology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
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Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition. mBio 2021; 12:e0200721. [PMID: 34372696 PMCID: PMC8406293 DOI: 10.1128/mbio.02007-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
To determine whether functionally relevant questions associated with the urinary or gut microbiome and urinary stone disease (USD) can be answered from metagenome-wide association studies (MWAS), we performed the most comprehensive meta-analysis of published clinical MWAS in USD to date, using publicly available data published prior to April 2021. Six relevant studies met inclusion criteria. For alpha-diversity, significant differences were noted between USD status, stone composition, sample type, study location, age, diet, and sex. For beta-diversity, significant differences were noted by USD status, stone composition, sample type, study location, antibiotic use (30 days and 12 months before sampling), sex, hypertension, water intake, body habitus, and age. Prevotella and Lactobacillus in the gut and urinary tract, respectively, were associated with healthy individuals, while Enterobacteriaceae was associated with USD in the urine and stones. Paradoxically, other Prevotella strains were also strongly associated with USD in the gut microbiome. When data were analyzed together, USD status, stone composition, age group, and study location were the predominant factors associated with microbiome composition. Meta-analysis showed significant microbiome differences based on USD status, stone composition, age group or study location. However, analyses were limited by a lack of public data from published studies, metadata collected, and differing study protocols. Results highlight the need for field-specific standardization of experimental protocols in terms of sample collection procedures and the anatomical niches to assess, as well as in defining clinically relevant metadata and subphenotypes such as stone composition.
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32
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Perez-Carrasco V, Soriano-Lerma A, Soriano M, Gutiérrez-Fernández J, Garcia-Salcedo JA. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front Cell Infect Microbiol 2021; 11:617002. [PMID: 34084752 PMCID: PMC8167034 DOI: 10.3389/fcimb.2021.617002] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.
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Affiliation(s)
- Virginia Perez-Carrasco
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| | - Ana Soriano-Lerma
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Department of Physiology, Faculty of Pharmacy, Institute of Nutrition and Food Technology "Jose' Mataix", University of Granada, Granada, Spain
| | - Miguel Soriano
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, Almeria, Spain
| | - José Gutiérrez-Fernández
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| | - Jose A Garcia-Salcedo
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
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33
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Kachroo N, Lange D, Penniston KL, Stern J, Tasian G, Bajic P, Wolfe AJ, Suryavanshi M, Ticinesi A, Meschi T, Monga M, Miller AW. Standardization of microbiome studies for urolithiasis: an international consensus agreement. Nat Rev Urol 2021; 18:303-311. [PMID: 33782583 PMCID: PMC8105166 DOI: 10.1038/s41585-021-00450-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2021] [Indexed: 02/01/2023]
Abstract
Numerous metagenome-wide association studies (MWAS) for urolithiasis have been published, leading to the discovery of potential interactions between the microbiome and urolithiasis. However, questions remain about the reproducibility, applicability and physiological relevance of these data owing to discrepancies in experimental technique and a lack of standardization in the field. One barrier to interpreting MWAS is that experimental biases can be introduced at every step of the experimental pipeline, including sample collection, preservation, storage, processing, sequencing, data analysis and validation. Thus, the introduction of standardized protocols that maintain the flexibility to achieve study-specific objectives is urgently required. To address this need, the first international consortium for microbiome in urinary stone disease - MICROCOSM - was created and consensus panel members were asked to participate in a consensus meeting to develop standardized protocols for microbiome studies if they had published an MWAS on urolithiasis. Study-specific protocols were revised until a consensus was reached. This consensus group generated standardized protocols, which are publicly available via a secure online server, for each step in the typical clinical microbiome-urolithiasis study pipeline. This standardization creates the benchmark for future studies to facilitate consistent interpretation of results and, collectively, to lead to effective interventions to prevent the onset of urolithiasis, and will also be useful for investigators interested in microbiome research in other urological diseases.
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Affiliation(s)
- Naveen Kachroo
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Dirk Lange
- The Stone Centre at VGH, Department of Urologic Sciences, University of British Colombia, Vancouver, BC, Canada
| | - Kristina L Penniston
- Department of Urology, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - Joshua Stern
- Department of Urology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory Tasian
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Petar Bajic
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Alan J Wolfe
- Department of Microbiology & Immunology, Loyola University Chicago, Maywood, IL, USA
| | | | - Andrea Ticinesi
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, Universitaria di Parma, Parma, Italy
| | - Manoj Monga
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Urology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Aaron W Miller
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA.
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34
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Hatakeyama S, Yoneyama T, Tobisawa Y, Yamamoto H, Ohyama C. Narrative review of urinary glycan biomarkers in prostate cancer. Transl Androl Urol 2021; 10:1850-1864. [PMID: 33968674 PMCID: PMC8100853 DOI: 10.21037/tau-20-964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PC) is the second most common cancer in men worldwide. The application of the prostate-specific antigen (PSA) test has improved the diagnosis and treatment of PC. However, the PSA test has become associated with overdiagnosis and overtreatment. Therefore, there is an unmet need for novel diagnostic, prognostic, and predictive biomarkers of PC. Urinary glycoproteins and exosomes are a potential source of PC glycan biomarkers. Urinary glycan profiling can provide noninvasive monitoring of tumor heterogeneity and aggressiveness throughout a treatment course. However, urinary glycan profiling is not popular due to technical disadvantages, such as complicated structural analysis that requires specialized expertise. The technological development of glycan analysis is a rapidly advancing field. A lectin-based microarray can detect aberrant glycoproteins in urine, including PSA glycoforms and exosomes. Glycan enrichment beads can enrich the concentration of N-linked glycans specifically. Capillary electrophoresis, liquid chromatography-tandem mass spectrometry, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry can detect glycans directory. Many studies suggest potential of urinary glycoproteins, exosomes, and glycosyltransferases as a biomarker of PC. Although further technological challenges remain, urinary glycan analysis is one of the promising approaches for cancer biomarker discovery.
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Affiliation(s)
- Shingo Hatakeyama
- Department of Advanced Blood Purification Therapy, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tohru Yoneyama
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Yuki Tobisawa
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hayato Yamamoto
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Chikara Ohyama
- Department of Advanced Blood Purification Therapy, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.,Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.,Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
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35
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Saw JJ, Sivaguru M, Wilson EM, Dong Y, Sanford RA, Fields CJ, Cregger MA, Merkel AC, Bruce WJ, Weber JR, Lieske JC, Krambeck AE, Rivera ME, Large T, Lange D, Bhattacharjee AS, Romero MF, Chia N, Fouke BW. In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis. KIDNEY360 2021; 2:298-311. [PMID: 35373025 PMCID: PMC8740987 DOI: 10.34067/kid.0006942020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/23/2020] [Indexed: 02/04/2023]
Abstract
Background Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.
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Affiliation(s)
- Jessica J. Saw
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Elena M. Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Robert A. Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Chris J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Melissa A. Cregger
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Annette C. Merkel
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - William J. Bruce
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Joseph R. Weber
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - John C. Lieske
- Department of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Amy E. Krambeck
- Department of Urology, Mayo Clinic, Rochester, Minnesota
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Marcelino E. Rivera
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Timothy Large
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dirk Lange
- The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Jack Bell Research Centre, Vancouver, British Columbia, Canada
| | - Ananda S. Bhattacharjee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Michael F. Romero
- Department of Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Nicholas Chia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Department of Urology, Mayo Clinic, Rochester, Minnesota
| | - Bruce W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois
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Zha H, Liu F, Ling Z, Chang K, Yang J, Li L. Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus. Sci Rep 2021; 11:1824. [PMID: 33469094 PMCID: PMC7815922 DOI: 10.1038/s41598-021-81507-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/07/2021] [Indexed: 02/08/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.
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Affiliation(s)
- Hua Zha
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China ,grid.9654.e0000 0004 0372 3343School of Biological Sciences, The University of Auckland, Auckland, New Zealand ,grid.9654.e0000 0004 0372 3343Institute of Marine Science, The University of Auckland, Auckland, New Zealand
| | - Fengping Liu
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China ,grid.258151.a0000 0001 0708 1323School of Medicine, Jiangnan University, Wuxi, China
| | - Zongxin Ling
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China
| | - Kevin Chang
- grid.9654.e0000 0004 0372 3343Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Jiezuan Yang
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China
| | - Lanjuan Li
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China
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Jiang S, Lu S, Chen X, Li F, Zhu C, Zheng Y, Wang X, Xu S. Dysbiosis of urine microbiota in obstructive urinary retention patients revealed by next-generation sequencing. Ann Clin Microbiol Antimicrob 2021; 20:2. [PMID: 33407528 PMCID: PMC7789751 DOI: 10.1186/s12941-020-00408-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/08/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Urinary retention (UR) is a common urinary system disease can be caused by urinary tract obstruction with numerous reasons, however, the role of urine microbes in these disorders is still poorly understood. The aim of this study was to identify the urine microbial features of two common types of obstructive UR, caused by urinary stones or urinary tract tumors, with comparison to healthy controls. METHODS Urine samples were collected from a cohort of 32 individuals with stone UR, 25 subjects with tumor UR and 25 healthy controls. The urine microbiome of all samples was analyzed using high-throughput 16S rRNA (16S ribosomal RNA) gene sequencing. RESULTS We observed dramatically increased urine microbial richness and diversity in both obstructive UR groups compared to healthy controls. Despite different origins of UR, bacteria such as Pseudomonas, Acinetobacter and Sphingomonas were enriched, while Lactobacillus, Streptococcus, Gardnerella, Prevotella and Atopobium were decreased in both UR groups in comparison with healthy controls, exhibited an approximate urine microbial community and functional characteristics of two types of obstructive UR. Furthermore, disease classifiers were constructed using specific enriched genera in UR, which can distinguish stone UR or tumor UR patients from healthy controls with an accuracy of 92.29% and 97.96%, respectively. CONCLUSION We presented comprehensive microbial landscapes of two common types of obstructive urinary retention and demonstrated that urine microbial features of these patients are significantly different from that of healthy people. The urine microbial signatures would shed light on the pathogenesis of these types of urinary retention and might be used as potential classification tools in the future.
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Affiliation(s)
- Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Saisai Lu
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Chengwei Zhu
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuancai Zheng
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Shihao Xu
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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Abstract
The prevalence of urolithiasis in humans is increasing worldwide; however, non-surgical treatment and prevention options remain limited despite decades of investigation. Most existing laboratory animal models for urolithiasis rely on highly artificial methods of stone induction and, as a result, might not be fully applicable to the study of natural stone initiation and growth. Animal models that naturally and spontaneously form uroliths are an underused resource in the study of human stone disease and offer many potential opportunities for improving insight into stone pathogenesis. These models include domestic dogs and cats, as well as a variety of other captive and wild species, such as otters, dolphins and ferrets, that form calcium oxalate, struvite, uric acid, cystine and other stone types. Improved collaboration between urologists, basic scientists and veterinarians is warranted to further our understanding of how stones form and to consider possible new preventive and therapeutic treatment options.
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39
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Liu F, Zhang N, Wu Y, Jiang P, Jiang T, Wang Y, Zhang Y, Zhai Q, Zou Y, Feng N. The pelvis urinary microbiome in patients with kidney stones and clinical associations. BMC Microbiol 2020; 20:336. [PMID: 33153435 PMCID: PMC7643416 DOI: 10.1186/s12866-020-01992-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The long-held notion that, without urinary tract or circulatory infection, bladder urine and blood are sterile biofluids has been disproven. There have been no previous reports on the kidney pelvis urinary microbiome after bladder disinfection in kidney stone patients. This study aimed to determine whether a kidney pelvis urinary microbiome is present after eliminating the influence of the bladder urinary microbiome, whether the microbiome composition is different in patients with stone kidney pelvis (SKP) and non-stone kidney pelvis (NSKP), and the correlation between SKP and patient clinical characteristics. RESULTS Comparisons of bacterial diversity and community structure exhibited that urine in bladder was similar to SKP and NSKP. However, the comparisons showed that urine samples were different from blood. The most common operational taxonomic units were shared by all three types of urine samples. Corynebacterium was significantly higher in SKP compared to NSKP. Several bacteria were associated with patient characteristics, including Lactobacillus, which was positively correlated with fasting blood glucose, and Prevotella was negatively correlated with BMI. Lactobacillus was significantly higher in SKP compared to blood but not in NSKP compared to blood. CONCLUSIONS The composition of the kidney pelvis urinary microbiome after disinfection of the bladder and its similarity to the bladder microbiome indicate that bladder urine can be used to replace kidney pelvis urine in microbiome research. Additionally, the comparison of SKP and NSKP and clinical associations suggest that the occurrence of kidney stones is responsible for the SKP urinary microbiome.
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Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China.,Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Nan Zhang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Yunhong Wu
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Peng Jiang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | | | - Yang Wang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Yuwei Zhang
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
| | - Yeqing Zou
- Basic Medical School, Jiangsu Vocational College of Medicine, Yancheng, 224000, China.
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No.2 Hospital, Nanjing Medical University, Wuxi, 214002, China.
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Commentary on "The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method". Int Neurourol J 2020; 24:182-184. [PMID: 32615682 PMCID: PMC7332816 DOI: 10.5213/inj.2040170.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
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41
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Gupta S, Singh Kanwar S. The influence of dysbiosis on kidney stones that risk up renal cell carcinoma (RCC). Semin Cancer Biol 2020; 70:134-138. [PMID: 32569823 DOI: 10.1016/j.semcancer.2020.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 01/11/2023]
Abstract
Kidney stone is a common urological condition, the prevalence and incidence of which has escalated in the last few years due to dietary habits and other related medical conditions such as obesity and diabetes mellitus. It is a chronic disease which leads to loss of kidney function(s) and nephrectomy. Chronic kidney stone disease has been shown to be associated with transitional cell carcinoma (TCC) or renal cell carcinoma (RCC) and kidney tumors have been found to be more frequent among patients with kidney stones. Although hyperoxaluria is mainly responsible for kidney stone formation, dysbiosis of the gut and urinary tract microbiome may in part contribute to kidney stone disease. Dysbiosis of the gut and urinary tract microbiome have been linked to kidney stone diseases with both gain and loss of function. The review provides a detailed study of how the variations in the microbiome of the human gut and urinary tract result in the chronic kidney stone diseases which are associated with increased papillary RCC risks.
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Affiliation(s)
- Shruti Gupta
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171 005 India.
| | - Shamsher Singh Kanwar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171 005 India.
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Cumpanas AA, Bratu OG, Bardan RT, Ferician OC, Cumpanas AD, Horhat FG, Licker M, Pricop C, Cretu OM. Urinary Microbiota-Are We Ready for Prime Time? A Literature Review of Study Methods' Critical Steps in Avoiding Contamination and Minimizing Biased Results. Diagnostics (Basel) 2020; 10:diagnostics10060343. [PMID: 32471022 PMCID: PMC7345871 DOI: 10.3390/diagnostics10060343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research.
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Affiliation(s)
- Alin Adrian Cumpanas
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Gabriel Bratu
- Department of Urology, Emergency Military Central Hospital, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Razvan Tiberiu Bardan
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Catalin Ferician
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Andrei Dragos Cumpanas
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Correspondence:
| | - Florin George Horhat
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Monica Licker
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Catalin Pricop
- Department of Urology, Gr.Tr.Popa University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Octavian Marius Cretu
- Department of Surgery, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
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