1
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the phylogenetic diversity of human bladder bacterial isolates. Genome Biol 2024; 25:75. [PMID: 38515176 PMCID: PMC10958879 DOI: 10.1186/s13059-024-03216-8] [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: 10/02/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. CONCLUSIONS This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Present address: Division of Nutritional Science, Cornell University, Ithaca, NY, 14850, USA
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Baylie R Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Alan J Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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Grygorcewicz B, Gliźniewicz M, Jabłońska J, Augustyniak A, Olszewska P, Wojciuk B, Miłek D, Serwin N, Czajkowski A, Cecerska-Heryć E, Rakoczy R, Cymbaluk-Płoska A. Bacteriophage-based approach for treatment of urinary tract infections: a quick outlook. APMIS 2024; 132:81-93. [PMID: 38031200 DOI: 10.1111/apm.13362] [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: 06/29/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections affecting millions worldwide. The increasing emergence of antibiotic-resistant bacteria has become a serious concern in managing UTIs. Therefore, there is a growing interest in using bacteriophages as an alternative or adjunct therapy for UTIs. Bacteriophages are viruses that infect and kill bacteria, making them a promising tool for treating UTIs caused by antibiotic-resistant bacteria. This article provides a quick outlook on using bacteriophages to treat UTIs. We summarize the current understanding of the biology of bacteriophages, the challenges associated with developing phage-based therapies, and the promising results of several case reports and clinical trials. We also highlight the potential of phage therapy as a valuable tool in the fight against antibiotic-resistant UTIs. This quick outlook on a bacteriophage-based approach for treating UTIs offers a timely and informative summary of the current research in this field.
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Affiliation(s)
- Bartłomiej Grygorcewicz
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Marta Gliźniewicz
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Joanna Jabłońska
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Adrian Augustyniak
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
- Chair of Building Materials and Construction Chemistry, Technische Universität Berlin, Germany, Berlin, Germany
- Institute of Biology, University of Szczecin, Szczecin, Poland
| | - Patrycja Olszewska
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bartosz Wojciuk
- Department of Immunology Diagnostics, Chair of Microbiology, Immunology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Dominika Miłek
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Natalia Serwin
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Artur Czajkowski
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Elżbieta Cecerska-Heryć
- Faculty of Pharmacy, Medical Biotechnology and Laboratory Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Rafał Rakoczy
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Szczecin, Poland
| | - Aneta Cymbaluk-Płoska
- Department of Reconstructive Surgery and Gynecological Oncology, Pomeranian Medical University in Szczecin, Szczecin, Poland
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3
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Elsayed NS, Wolfe AJ, Burk RD. Urine microbiome in individuals with an impaired immune system. Front Cell Infect Microbiol 2024; 13:1308665. [PMID: 38274734 PMCID: PMC10808152 DOI: 10.3389/fcimb.2023.1308665] [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: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
With the advent of next generation sequencing, it is now appreciated that human urine is not sterile. Recent investigations of the urinary microbiome (urobiome) have provided insights into several urological diseases. Urobiome dysbiosis, defined as non-optimal urine microbiome composition, has been observed in many disorders; however, it is not clear whether this dysbiosis is the cause of urinary tract disorders or a consequence. In addition, immunologically altered disorders are associated with higher rates of urinary tract infections. These disorders include immunoproliferative and immunodeficiency diseases, cancer, and immunosuppressant therapy in transplant recipients. In this review, we examine the current state of knowledge of the urobiome in immunologically altered diseases, its composition and metabolomic consequences. We conclude that more data are required to describe the urobiome in immune altered states, knowledge that could facilitate understanding the role of the urobiome and its pathophysiological effects on urinary tract infections and other disorders of the urinary tract.
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Affiliation(s)
- Noha S. Elsayed
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Departments of Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, United States
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4
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Montelongo Hernandez C, Putonti C, Wolfe AJ. Urinary Plasmids Reduce Permissivity to Coliphage Infection. Microbiol Spectr 2023; 11:e0130923. [PMID: 37409956 PMCID: PMC10433841 DOI: 10.1128/spectrum.01309-23] [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: 03/26/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. While urinary Escherichia coli strains associated with urinary tract infection (UTI) and their phages have been catalogued for the urobiome, bacterium-plasmid-phage interactions have yet to be explored. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were predicted in 47 of 67 urinary E. coli isolates, and most of these plasmids carried genes that encode toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Urinary E. coli plasmids, from urinary microbiota strains UMB0928 and UMB1284, were conjugated into E. coli K-12 strains. These transconjugants included genes for antibiotic resistance and virulence, and they decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Plasmids in one transconjugant were maintained in E. coli K-12 for up to 10 days in the absence of antibiotic resistance selection; this included the maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli strains could play a role in coliphage dynamics and the maintenance of antibiotic resistance in urinary E. coli. IMPORTANCE The urinary tract contains a resident microbial community called the urinary microbiota or urobiota. Evidence exists that it is associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. Bacterium-plasmid-phage interactions have been studied primarily in laboratory settings and are yet to be thoroughly tested in complex communities. This is especially true of the urinary tract, where the bacterial genetic determinants of phage infection are not well understood. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Urinary E. coli plasmids, encoding antibiotic resistance and transferred by conjugation into naive laboratory E. coli K-12 strains, decreased permissivity to coliphage infection. We propose a model by which urinary plasmids present in urinary E. coli strains could help to decrease phage infection susceptibility and maintain the antibiotic resistance of urinary E. coli. This has consequences for phage therapy, which could inadvertently select for plasmids that encode antibiotic resistance.
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Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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5
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541916. [PMID: 37292924 PMCID: PMC10245883 DOI: 10.1101/2023.05.23.541916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Baylie R. Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
- Department of Biology, Loyola University Chicago, Chicago, IL 60660
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
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6
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Crum E, Merchant Z, Ene A, Miller-Ensminger T, Johnson G, Wolfe AJ, Putonti C. Coliphages of the human urinary microbiota. PLoS One 2023; 18:e0283930. [PMID: 37053131 PMCID: PMC10101464 DOI: 10.1371/journal.pone.0283930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.
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Affiliation(s)
- Elias Crum
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Zubia Merchant
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Taylor Miller-Ensminger
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
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Sun Q, Li L, Zhou H, Wu Y, Gao Y, Wu B, Qiu Y, Zhou Z, Song Q, Zhao J, Wu P. The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder. Front Microbiol 2022; 13:984234. [PMID: 36212847 PMCID: PMC9537457 DOI: 10.3389/fmicb.2022.984234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 11/15/2022] Open
Abstract
Although it is known that changes in bacterial components of the urinary microbiome are associated with overactive bladder (OAB), the specific role of viruses is still insufficiently investigated. The aim of the present study is to evaluate the role of urinary viruses in woman with OAB, and analyze the potential relationship between viruses, bacteria and disease. Catheterized urine samples were collected from 55 women with OAB and 18 control individuals. OAB patients fulfilling the following criteria were considered eligible for this study: female, 18 years of age or older; presented with classic OAB symptoms defined by the International Continence Society; and OAB Symptom Score (OABSS) total score ≥ 3 points and question 3 (urgency) score ≥ 2 points. Based on results of metagenomic next-generation sequencing (mNGS), all participants were divided into virus-infected and virus-uninfected groups for analysis. The results of mNGS showed that the diversity of the OAB group was lower than that of the control group when focused on bacterial sequences, which was consistent with our previous study. According to the questionnaire filled out by the patients, OABSS and 8-item OAB questionnaire, female OAB patients who had viruses detected in their urine had more severe symptoms. In parallel, John Cunningham virus (mainly subtype 7 and subtype 2) was the most frequently detected virus in urine. Correlation analysis indicated that risk factors for virus infection in OAB patients include age, habit of holding urine and pelvic surgery history. Given our preliminary data, viral infection can aggravate OAB severity and affect the composition of bacterial. Further research is required to explain how viral infections can aggravate OAB patient symptoms and cause bacterial changes.
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Affiliation(s)
- Qi Sun
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Leqian Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Zhou
- Department of Hospital Infection Management, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Wu
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Yubo Gao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bingyi Wu
- Medical Research Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yifeng Qiu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhipeng Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qixiang Song
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Qixiang Song,
| | - Jie Zhao
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Jie Zhao,
| | - Peng Wu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Peng Wu,
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8
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Pallares-Mendez R, Cervantes-Miranda DE, Gonzalez-Colmenero AD, Ochoa-Arvizo MA, Gutierrez-Gonzalez A. A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections - A Review. Curr Urol Rep 2022; 23:235-244. [PMID: 36053406 DOI: 10.1007/s11934-022-01108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Greater availability of sequencing methods has broadened the knowledge of the urinary microbiome in an environment previously believed to be sterile. This review discusses internal and external influences that promote either a balance or a dysbiosis of the urinary tract and the future perspectives in understanding lower urinary tract infections. RECENT FINDINGS Efforts have been made to identify a "core" urinary microbiome in which Firmicutes and Bacteroidetes account for most of the bacterial representations. A shift to a Proteobacteria-dominant representation shapes the fingerprint of the infectious urinary microbiome; furthermore, the virome and the mycobiome are important modulators of the urinary microbiome, which have been recently explored to determine their role in the health-disease process of the lower urinary tract. A disturbance of bacterial representation and diversity triggers a transition from health to disease; conversely, a functional cooperative interplay between the host and microbiome allows for basic metabolic and immune functions to take place.
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Affiliation(s)
- Rigoberto Pallares-Mendez
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico.
| | - Daniel E Cervantes-Miranda
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | | | - Mario A Ochoa-Arvizo
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Adrian Gutierrez-Gonzalez
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
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9
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Yu SH, Jung SI. The Potential Role of Urinary Microbiome in Benign Prostate Hyperplasia/Lower Urinary Tract Symptoms. Diagnostics (Basel) 2022; 12:diagnostics12081862. [PMID: 36010213 PMCID: PMC9406308 DOI: 10.3390/diagnostics12081862] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
Historically, urine in the urinary tract was considered “sterile” based primarily on culture-dependent methods of bacterial detection. Rapidly developing sequencing methods and analytical techniques have detected bacterial deoxyribonucleic acid and live bacteria in urine, improving our ability to understand the urinary tract microbiome. Recently, many studies have revealed evidence of a microbial presence in human urine in the absence of clinical infections. In women, fascinating evidence associates urinary tract microbiota with lower urinary tract symptoms (LUTS). However, the association between urinary tract microbiota and men with LUTS, particularly those with benign prostate hyperplasia (BPH), has not been established. In addition, the identification of the proinflammatory cytokines and pathogens responsible for the clinical progression of BPH is still underway. This review article aimed to address microbiome-related evidence for BPH. Further studies are required for a comprehensive understanding of the relationship between the urogenital microbiome and BPH pathogenesis to facilitate the development of preventive and therapeutic approaches for male LUTS.
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10
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virMine 2.0: Identifying Viral Sequences in Microbial Communities. Microbiol Resour Announc 2022; 11:e0010722. [PMID: 35499341 PMCID: PMC9119091 DOI: 10.1128/mra.00107-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present virMine 2.0, the next generation of the virMine software tool. virMine 2.0 uses an exclusion technique to remove nonviral data from sequencing reads and scores the remaining data based on relatedness to viral elements, eliminating the sole dependency on homology identification.
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11
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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 DOI: 10.1007/s00240-022-01314-5] [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: 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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12
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. The Urinary Microbiome and Biological Therapeutics: Novel Therapies For Urinary Tract Infections. Microbiol Res 2022; 259:127010. [DOI: 10.1016/j.micres.2022.127010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022]
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Adu-Oppong B, Thänert R, Wallace MA, Burnham CAD, Dantas G. Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. MICROBIOME 2022; 10:6. [PMID: 35039079 PMCID: PMC8762997 DOI: 10.1186/s40168-021-01204-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/30/2021] [Indexed: 06/10/2023]
Abstract
BACKGROUND The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota. RESULTS The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as 'insignificant', 'contaminated', or 'no-growth' by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae. CONCLUSION Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract.
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Affiliation(s)
- Boahemaa Adu-Oppong
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri USA
| | - Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri USA
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri USA
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri USA
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Montelongo Hernandez C, Putonti C, Wolfe AJ. Characterizing Plasmids in Bacteria Species Relevant to Urinary Health. Microbiol Spectr 2021; 9:e0094221. [PMID: 34937183 PMCID: PMC8694116 DOI: 10.1128/spectrum.00942-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The urinary tract has a microbial community (the urinary microbiota or urobiota) that has been associated with human health. Whole genome sequencing of bacteria is a powerful tool, allowing investigation of the genomic content of the urobiota, also called the urinary microbiome (urobiome). Bacterial plasmids are a significant component of the urobiome yet are understudied. Because plasmids can be vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. In this project, we sought plasmids in 11 clinically relevant urinary species: Aerococcus urinae, Corynebacterium amycolatum, Enterococcus faecalis, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Lactobacillus gasseri, Lactobacillus jensenii, Staphylococcus epidermidis, Streptococcus anginosus, and Streptococcus mitis. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in other species sequenced thus far. Some identified plasmidic assemblies were predicted to have putative virulence and/or antibiotic resistance genes, although the majority of their annotated coding regions were of unknown predicted function. In this study, we report on plasmids from urinary species as a first step to understanding the role of plasmids in the bacterial urobiota. IMPORTANCE The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids. Because plasmids are vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. Currently, urobiota plasmids are understudied. Here, we sought plasmids in 11 clinically relevant urinary species. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in the other 6 species. We identified putative virulence and/or antibiotic resistance genes in some of the plasmidic assemblies, but most of their annotated coding regions were of unknown function. This is a first step to understanding the role of plasmids in the bacterial urobiota.
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Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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15
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Salabura A, Łuniewski A, Kucharska M, Myszak D, Dołęgowska B, Ciechanowski K, Kędzierska-Kapuza K, Wojciuk B. Urinary Tract Virome as an Urgent Target for Metagenomics. Life (Basel) 2021; 11:life11111264. [PMID: 34833140 PMCID: PMC8618529 DOI: 10.3390/life11111264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022] Open
Abstract
Virome—a part of a microbiome—is a term used to describe all viruses found in the specific organism or system. Recently, as new technologies emerged, it has been confirmed that kidneys and the lower urinary tract are colonized not only by the previously described viruses, but also completely novel species. Viruses can be both pathogenic and protective, as they often carry important virulence factors, while at the same time represent anti-inflammatory functions. This paper aims to show and compare the viral species detected in various, specific clinical conditions. Because of the unique characteristics of viruses, new sequencing techniques and databases had to be developed to conduct research on the urinary virome. The dynamic development of research on the human microbiome suggests that the detailed studies on the urinary system virome will provide answers to many questions about the risk factors for civilization, cancer, and autoimmune diseases.
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Affiliation(s)
- Agata Salabura
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland;
- Correspondence: ; Tel.: +48-664-477-450
| | - Aleksander Łuniewski
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Maria Kucharska
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Denis Myszak
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Barbara Dołęgowska
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
| | - Kazimierz Ciechanowski
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland;
| | - Karolina Kędzierska-Kapuza
- Center of Postgraduate Medical Education in Warsaw, Department of Gastroenterological Surgery and Transplantology, 137 Wołoska St., 02-507 Warsaw, Poland;
| | - Bartosz Wojciuk
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.Ł.); (M.K.); (D.M.); (B.D.); (B.W.)
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16
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Podlacha M, Grabowski Ł, Kosznik-Kawśnicka K, Zdrojewska K, Stasiłojć M, Węgrzyn G, Węgrzyn A. Interactions of Bacteriophages with Animal and Human Organisms-Safety Issues in the Light of Phage Therapy. Int J Mol Sci 2021; 22:8937. [PMID: 34445641 PMCID: PMC8396182 DOI: 10.3390/ijms22168937] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages are viruses infecting bacterial cells. Since there is a lack of specific receptors for bacteriophages on eukaryotic cells, these viruses were for a long time considered to be neutral to animals and humans. However, studies of recent years provided clear evidence that bacteriophages can interact with eukaryotic cells, significantly influencing the functions of tissues, organs, and systems of mammals, including humans. In this review article, we summarize and discuss recent discoveries in the field of interactions of phages with animal and human organisms. Possibilities of penetration of bacteriophages into eukaryotic cells, tissues, and organs are discussed, and evidence of the effects of phages on functions of the immune system, respiratory system, central nervous system, gastrointestinal system, urinary tract, and reproductive system are presented and discussed. Modulations of cancer cells by bacteriophages are indicated. Direct and indirect effects of virulent and temperate phages are discussed. We conclude that interactions of bacteriophages with animal and human organisms are robust, and they must be taken under consideration when using these viruses in medicine, especially in phage therapy, and in biotechnological applications.
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Affiliation(s)
- Magdalena Podlacha
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (Ł.G.); (K.K.-K.)
| | - Katarzyna Kosznik-Kawśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (Ł.G.); (K.K.-K.)
| | - Karolina Zdrojewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Małgorzata Stasiłojć
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.P.); (K.Z.); (M.S.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland; (Ł.G.); (K.K.-K.)
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17
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Mormando R, Wolfe AJ, Putonti C. Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets. Viruses 2021; 13:v13061041. [PMID: 34072839 PMCID: PMC8230216 DOI: 10.3390/v13061041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.
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Affiliation(s)
- Rita Mormando
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
- Correspondence:
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18
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Prezioso C, Van Ghelue M, Pietropaolo V, Moens U. Detection of Quebec Polyomavirus DNA in Samples from Different Patient Groups. Microorganisms 2021; 9:microorganisms9051082. [PMID: 34070030 PMCID: PMC8158138 DOI: 10.3390/microorganisms9051082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Polyomaviruses infect many species, including humans. So far, 15 polyomaviruses have been described in humans, but it remains to be established whether all of these are genuine human polyomaviruses. The most recent polyomavirus to be detected in a person is Quebec polyomavirus (QPyV), which was identified in a metagenomic analysis of a stool sample from an 85-year-old hospitalized man. We used PCR to investigate the presence of QPyV DNA in urine samples from systemic lupus erythematosus (SLE) patients (67 patients; 135 samples), multiple sclerosis patients (n = 35), HIV-positive patients (n = 66) and pregnant women (n = 65). Moreover, cerebrospinal fluid from patients with suspected neurological diseases (n = 63), nasopharyngeal aspirates from patients (n = 80) with respiratory symptoms and plasma samples from HIV-positive patients (n = 65) were examined. QPyV DNA was found in urine from 11 (16.4%), 10 (15.4%) and 5 (14.3%) SLE patients, pregnant women, and multiple sclerosis patients, respectively. No QPyV DNA could be detected in the other samples. Alignment with the only available QPyV sequence in the GenBank revealed amino acid substitutions in the HI-loop of capsid protein VP1 in 6/28 of the isolates. Our results show that QPyV viruria can occur, but whether it may cause clinical symptoms in the patients remains to be determined.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
- IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-degenerative Pathologies, 00163 Rome, Italy
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, 9038 Tromsø, Norway;
- Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
- Correspondence: (V.P.); (U.M.)
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
- Correspondence: (V.P.); (U.M.)
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19
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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: 83] [Impact Index Per Article: 27.7] [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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20
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Brubaker L, Putonti C, Dong Q, Wolfe AJ. The human urobiome. Mamm Genome 2021; 32:232-238. [PMID: 33651197 DOI: 10.1007/s00335-021-09862-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.
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Affiliation(s)
- L Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - C Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Q Dong
- Department of Medicine and Center for Biomedical Informatics, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60089, USA.
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21
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Żaczek M, Weber-Dąbrowska B, Międzybrodzki R, Górski A. Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications. Microorganisms 2020; 8:microorganisms8111802. [PMID: 33212807 PMCID: PMC7696197 DOI: 10.3390/microorganisms8111802] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022] Open
Abstract
Recent metagenomic analyses imply an immense abundance of phages in the human body. Samples collected from different sites (lungs, skin, oral cavity, intestines, ascitic fluid, and urine) reveal a generally greater number of phage particles than that of eukaryotic viruses. The presence of phages in those tissues and fluids reflects the paths they must overcome in the human body, but may also relate to the health statuses of individuals. Besides shaping bacterial metabolism and community structure, the role of phages circulating in body fluids has not been fully understood yet. The lack of relevant reports is especially visible with regard to the human urobiome. Certainly, phage presence and the role they have to fulfill in the human urinary tract raises questions on potential therapeutic connotations. Urinary tract infections (UTIs) are among the most common bacterial infections in humans and their treatment poses a difficult therapeutic dilemma. Despite effective antibiotic therapy, these infections tend to recur. In this review, we summarized the recent data on phage presence in the human urinary tract and its possible implications for health and disease.
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Affiliation(s)
- Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ż.); (B.W.-D.); (R.M.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Infant Jesus Hospital, Medical University of Warsaw, 02-005 Warsaw, Poland
- Correspondence:
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22
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Abreu IN, Cortinhas JM, Dos Santos MB, Queiroz MAF, da Silva ANMR, Cayres-Vallinoto IMV, Vallinoto ACR. Detection of Human polyomavirus 2 (HPyV2) in oyster samples in northern Brazil. Virol J 2020; 17:85. [PMID: 32590993 PMCID: PMC7318511 DOI: 10.1186/s12985-020-01360-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/23/2020] [Indexed: 01/14/2023] Open
Abstract
Background Human polyomavirus 2 (HPyV2 or JCPyV) is persistent in the environment due to its excretion in urine and feces; it is detected in samples of wastewater, surface water and drinking water. A lack of basic sanitation and sewage collection results in the presence of this virus in food, especially in oysters, since they are bioaccumulators and are consumed in their natural form, thus posing a risk to human health. Methods This study investigated the frequency of HPyV2 in samples of oysters marketed in northeastern Pará State, Brazil, and optimized a real-time PCR (qPCR) protocol for the detection of an endogenous oyster control. A total of 217 oysters in 22 pools from five municipalities in the state of Pará were analyzed. Samples underwent dissection and total maceration of oyster tissue using a viral concentration technique, followed by DNA extraction with phenol-chloroform and amplification of the VP1 region for molecular detection via qPCR. Results HPyV2 was detected in 18.2% (4/22) of the pooled samples, with frequencies of 25, 20, 20 and 16% in the municipalities of Salinópolis, Augusto Corrêa, São Caetano de Odivelas and Curuçá, respectively. Notably, the sample pool from the municipality of Bragança did not have detectable HPyV2 and this was the only sampled location with a water treatment station. In this study, Crassostrea genus-specific primers (AFL52 ribosomal RNA gene) of oyster were developed for use as an endogenous control in the qPCR analysis, which will be useful for future studies. Conclusions The detection of HPyV2 in oyster samples commercialized in the state of Pará shows the circulation of this virus in the studied municipalities. Thus, it is necessary to implement measures for improving sewage collection and basic sanitation to avoid contamination of water and food with HPyV2.
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Affiliation(s)
- Isabella Nogueira Abreu
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Virologia, Belém, Pará, 66075-110, Brazil.,Instituto Evandro Chagas, Seção de Virologia, Ananindeua, Pará, 67030-000, Brazil
| | - Jacqueline Monteiro Cortinhas
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Virologia, Belém, Pará, 66075-110, Brazil
| | - Mike Barbosa Dos Santos
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Virologia, Belém, Pará, 66075-110, Brazil
| | - Maria Alice Freitas Queiroz
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Laboratório de Virologia, Belém, Pará, 66075-110, Brazil
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23
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Abstract
The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.
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24
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Ackerman AL, Chai TC. The Bladder is Not Sterile: an Update on the Urinary Microbiome. CURRENT BLADDER DYSFUNCTION REPORTS 2019; 14:331-341. [PMID: 32612735 DOI: 10.1007/s11884-019-00543-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose of Review The article discusses (1) techniques used to study bacterial urinary microbiota; (2) existence of non-bacterial urinary microbiota; (3) associations between changes in urinary microbiota and various benign lower urinary tract disorders. Recent Findings Urine harbors a diverse microbial community that resides within it. A multitude of studies have identified differences in these communities associated with urologic conditions, suggesting that microbial communities may maintain normal bladder homeostasis. Technological advances in analytic approaches have improved our understanding of the urinary microbiome. The choice of urine sampling method (voided, catheterized, or aspirated) will significantly influence microbiome findings. Sex and age highly influence urinary microbiota; in addition to rigorous inclusion criteria, microbial studies must be sufficiently powered to overcome the substantial interindividual variability of urinary microbiota. Regardless of these complicating factors, studies have identified microbial patterns correlating with both urologic diagnoses and treatment responses. Summary Without a clear understanding of the variability of and exogenous influences on the urinary microbiota in the absence of disease, it has been challenging to reveal the microbial patterns responsible for disease pathophysiology. Host mechanisms in response to the urinary microbiome are also poorly understood. Additional research can address whether the manipulation of urinary microbiota will benefit lower urinary tract health.
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Affiliation(s)
- A Lenore Ackerman
- Cedars-Sinai Medical Center, 99 N. La Cienega Blvd. Suite M102, Beverly Hills, CA 90211, USA
| | - Toby C Chai
- Boston Medical Center, Boston University School of Medicine, 725 Albany St., Suite 3B, Shapiro Building, Boston, MA 02118, USA
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25
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Jung CE, Chopyk J, Shin JH, Lukacz ES, Brubaker L, Schwanemann LK, Knight R, Wolfe AJ, Pride DT. Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome. Sci Rep 2019; 9:13409. [PMID: 31527753 PMCID: PMC6746804 DOI: 10.1038/s41598-019-49823-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
Standardized conditions for collection, preservation and storage of urine for microbiome research have not been established. We aimed to identify the effects of the use of preservative AssayAssure® (AA), and the effects of storage time and temperatures on reproducibility of urine microbiome results. We sequenced the V3-4 segment of the 16S rRNA gene to characterize the bacterial community in the urine of a cohort of women. Each woman provided a single voided urine sample, which was divided into aliquots and stored with and without AA, at three different temperatures (room temperature [RT], 4 °C, or -20 °C), and for various time periods up to 4 days. There were significant microbiome differences in urine specimens stored with and without AA at all temperatures, but the most significant differences were observed in alpha diversity (estimated number of taxa) at RT. Specimens preserved at 4 °C and -20 °C for up to 4 days with or without AA had no significant alpha diversity differences. However, significant alpha diversity differences were observed in samples stored without AA at RT. Generally, there was greater microbiome preservation with AA than without AA at all time points and temperatures, although not all results were statistically significant. Addition of AA preservative, shorter storage times, and colder temperatures are most favorable for urinary microbiome reproducibility.
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Affiliation(s)
- Carrie E Jung
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, 92093, USA
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, CA, 92093, USA
| | - Ji Hyun Shin
- Department of Pathology, University of California, San Diego, CA, 92093, USA
| | - Emily S Lukacz
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, 92093, USA
| | - Linda Brubaker
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, 92093, USA
| | - Leila K Schwanemann
- Department of Pathology, University of California, San Diego, CA, 92093, USA
| | - Rob Knight
- Departments of Pediatrics, Bioengineering, and Computer Science and Engineering, University of California, San Diego, 92093, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 601534, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, CA, 92093, USA.
- Department of Medicine, University of California, San Diego, CA, 92093, USA.
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26
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Bajic P, Dornbier RA, Doshi CP, Wolfe AJ, Farooq AV, Bresler L. Implications of the Genitourinary Microbiota in Prostatic Disease. Curr Urol Rep 2019; 20:34. [PMID: 31104156 DOI: 10.1007/s11934-019-0904-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW To summarize recent investigation into associations between the genitourinary microbiota and prostatic disease. RECENT FINDINGS The genitourinary tract is not sterile. There are microbial communities (microbiota) in each niche of the genitourinary tract including the bladder, prostate, and urethra, which have been the subject of increasing scientific interest. Investigators have utilized several unique methods to study them, resulting in a highly heterogeneous body of literature. To characterize these genitourinary microbiota, diverse clinical specimens have been analyzed, including urine obtained by various techniques, seminal fluid, expressed prostatic secretions, and prostatic tissue. Recent studies have attempted to associate the microbiota detected from these samples with urologic disease and have implicated the genitourinary microbiota in many common conditions, including benign prostatic hyperplasia (BPH), prostate cancer, and chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). In this review, we summarize the recent literature pertaining to the genitourinary microbiota and its relationship to the pathophysiology and management of three common prostatic conditions: BPH, prostate cancer, and CP/CPPS.
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Affiliation(s)
- Petar Bajic
- Department of Urology, Loyola University Chicago Stritch School of Medicine, 2160 South First Ave. Building 54, Room 23A, Maywood, IL, 60153, USA.
| | - Ryan A Dornbier
- Department of Urology, Loyola University Chicago Stritch School of Medicine, 2160 South First Ave. Building 54, Room 23A, Maywood, IL, 60153, USA
| | - Chirag P Doshi
- Department of Urology, Loyola University Chicago Stritch School of Medicine, 2160 South First Ave. Building 54, Room 23A, Maywood, IL, 60153, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, 2160 South First Ave. CTRE Building, Room 224, Maywood, IL, 60153, USA
| | - Ahmer V Farooq
- Department of Urology, Loyola University Chicago Stritch School of Medicine, 2160 South First Ave. Building 54, Room 23A, Maywood, IL, 60153, USA
| | - Larissa Bresler
- Department of Urology, Loyola University Chicago Stritch School of Medicine, 2160 South First Ave. Building 54, Room 23A, Maywood, IL, 60153, USA
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27
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Garretto A, Hatzopoulos T, Putonti C. virMine: automated detection of viral sequences from complex metagenomic samples. PeerJ 2019; 7:e6695. [PMID: 30993039 PMCID: PMC6462185 DOI: 10.7717/peerj.6695] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/26/2019] [Indexed: 12/29/2022] Open
Abstract
Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.
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Affiliation(s)
- Andrea Garretto
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America
| | - Thomas Hatzopoulos
- Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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28
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Johnson G, Wolfe AJ, Putonti C. Characterization of the ϕCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota. Access Microbiol 2019; 1. [PMID: 32864566 PMCID: PMC7454045 DOI: 10.1099/acmi.0.000002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37,152 bp genome that closely resembles the temperate P. aeruginosa phage ϕCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby's genome was queried against publicly available bacterial sequences identifying 44 other ϕCTX-like prophages. These prophages are integrated within the genomes of P. aeruginosa strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate ϕCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.
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Affiliation(s)
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL USA.,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA.,Department of Biology, Loyola University Chicago, Chicago, IL USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL USA
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