1
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Fu C, Zhang Y, Liang L, Lin H, Shan K, Liu F, Feng N. The microbiota in patients with interstitial cystitis/bladder pain syndrome: a systematic review. BJU Int 2024. [PMID: 38890150 DOI: 10.1111/bju.16439] [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] [Indexed: 06/20/2024]
Abstract
OBJECTIVE To comprehensively review and critically assess the literature on microbiota differences between patients with interstitial cystitis (IC)/bladder pain syndrome (BPS) and normal controls and to provide clinical practice guidelines. MATERIALS AND METHODS In this systematic review, we evaluated previous research on microbiota disparities between IC/BPS and normal controls, as well as distinctions among IC/BPS subgroups. A comprehensive literature search was conducted across PubMed/MEDLINE, EMBASE, Web of Science, and the Cochrane Central Register of Controlled Trials. Relevant studies were shortlisted based on predetermined inclusion and exclusion criteria, followed by quality assessment. The primary focus was identifying specific taxonomic variations among these cohorts. RESULTS A total of 12 studies met the selection criteria. Discrepancies were adjudicated by a third reviewer. The Newcastle-Ottawa Scale was used to assess study quality. Predominantly, the studies focused on disparities in urine microbiota between IC/BPS patients and normal controls, with one study examining gut microbiota differences between the groups, and two studies exploring vaginal microbiota distinctions. Unfortunately, analyses of discrepancies in other microbiota were limited. Our findings revealed evidence of distinct bacterial abundance variations, particularly involving Lactobacillus, alongside variations in specific metabolites among IC/BPS patients compared to controls. CONCLUSIONS Currently, there is evidence suggesting significant variations in the diversity and species composition of the urinary microbiota between individuals diagnosed with IC/BPS and control groups. In the foreseeable future, urologists should consider urine microbiota dysbiosis as a potential aetiology for IC, with potential clinical implications for diagnosis and treatment.
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Affiliation(s)
- Chaowei Fu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuwei Zhang
- Nantong University Medical School, Nantong, China
| | - Linghui Liang
- Department of Urology, Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Hao Lin
- Department of Urology, Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Kai Shan
- School of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
| | - Ninghan Feng
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
- Department of Urology, Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
- Nantong University Medical School, Nantong, China
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3
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Jeries LM, Sysoeva TA, Karstens L, Kelly MS. Synthesis of current pediatric urinary microbiome research. Front Pediatr 2024; 12:1396408. [PMID: 38957777 PMCID: PMC11217333 DOI: 10.3389/fped.2024.1396408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
The human urinary bladder hosts a complex microbial community of low biomass referred to as the urobiome. While the composition of the urobiome has been investigated in adults for over a decade now, only a few studies have considered the presence and composition of the urobiome in children. It is critical to explore how the urobiome develops throughout the life span and how it changes in the presence of various health conditions. Therefore, we set to review the available data on pediatric urobiome composition and its development with age and disease. In addition, we focused on identifying and reporting specific gaps in our knowledge of the pediatric urobiome that we hope will be addressed by future studies in this swiftly developing field with fast-improving methods and consensus.
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Affiliation(s)
- Layla M. Jeries
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Tatyana A. Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Maryellen S. Kelly
- Division of Healthcare of Women and Children, School of Nursing, Duke University, Durham, NC, United States
- Department of Urology, Duke University Hospital, Durham, NC, United States
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4
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Jendraszak M, Skibińska I, Kotwicka M, Andrusiewicz M. The elusive male microbiome: revealing the link between the genital microbiota and fertility. Critical review and future perspectives. Crit Rev Clin Lab Sci 2024:1-29. [PMID: 38523477 DOI: 10.1080/10408363.2024.2331489] [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: 12/15/2023] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
There is a growing focus on understanding the role of the male microbiome in fertility issues. Although research on the bacterial communities within the male reproductive system is in its initial phases, recent discoveries highlight notable variations in the microbiome's composition and abundance across distinct anatomical regions like the skin, foreskin, urethra, and coronary sulcus. To assess the relationship between male genitourinary microbiome and reproduction, we queried various databases, including MEDLINE (available via PubMed), SCOPUS, and Web of Science to obtain evidence-based data. The literature search was conducted using the following terms "gut/intestines microbiome," "genitourinary system microbiome," "microbiome and female/male infertility," "external genital tract microbiome," "internal genital tract microbiome," and "semen microbiome." Fifty-one relevant papers were analyzed, and eleven were strictly semen quality or male fertility related. The male microbiome, especially in the accessory glands like the prostate, seminal vesicles, and bulbourethral glands, has garnered significant interest because of its potential link to male fertility and reproduction. Studies have also found differences in bacterial diversity present in the testicular tissue of normozoospermic men compared to azoospermic suggesting a possible role of bacterial dysbiosis and reproduction. Correlation between the bacterial taxa in the genital microbiota of sexual partners has also been found, and sexual activity can influence the composition of the urogenital microbiota. Exploring the microbial world within the male reproductive system and its influence on fertility opens doors to developing ways to prevent, diagnose, and treat infertility. The present work emphasizes the importance of using consistent methods, conducting long-term studies, and deepening our understanding of how the reproductive tract microbiome works. This helps make research comparable, pinpoint potential interventions, and smoothly apply microbiome insights to real-world clinical practices.
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Affiliation(s)
- Magdalena Jendraszak
- Chair and Department of Cell Biology, Poznan University of Medical Sciences, Poznań, Poland
| | - Izabela Skibińska
- Chair and Department of Cell Biology, Poznan University of Medical Sciences, Poznań, Poland
| | - Małgorzata Kotwicka
- Chair and Department of Cell Biology, Poznan University of Medical Sciences, Poznań, Poland
| | - Mirosław Andrusiewicz
- Chair and Department of Cell Biology, Poznan University of Medical Sciences, Poznań, Poland
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5
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Tamborino F, Cicchetti R, Mascitti M, Litterio G, Orsini A, Ferretti S, Basconi M, De Palma A, Ferro M, Marchioni M, Schips L. Pathophysiology and Main Molecular Mechanisms of Urinary Stone Formation and Recurrence. Int J Mol Sci 2024; 25:3075. [PMID: 38474319 DOI: 10.3390/ijms25053075] [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: 12/22/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Kidney stone disease (KSD) is one of the most common urological diseases. The incidence of kidney stones has increased dramatically in the last few decades. Kidney stones are mineral deposits in the calyces or the pelvis, free or attached to the renal papillae. They contain crystals and organic components, and they are made when urine is supersaturated with minerals. Calcium-containing stones are the most common, with calcium oxalate as the main component of most stones. However, many of these form on a calcium phosphate matrix called Randall's plaque, which is found on the surface of the kidney papilla. The etiology is multifactorial, and the recurrence rate is as high as 50% within 5 years after the first stone onset. There is a great need for recurrence prevention that requires a better understanding of the mechanisms involved in stone formation to facilitate the development of more effective drugs. This review aims to understand the pathophysiology and the main molecular mechanisms known to date to prevent recurrences, which requires behavioral and nutritional interventions, as well as pharmacological treatments that are specific to the type of stone.
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Affiliation(s)
- Flavia Tamborino
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Rossella Cicchetti
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Marco Mascitti
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Giulio Litterio
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Angelo Orsini
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Simone Ferretti
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Martina Basconi
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Antonio De Palma
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 20141 Milan, Italy
| | - Michele Marchioni
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
| | - Luigi Schips
- Department of Medical Oral and Biotechnological Science, Università degli Studi "G. d'Annunzio" of Chieti, 66100 Chieti, Italy
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6
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Carnes MU, Siddiqui NY, Karstens L, Gantz MG, Dinwiddie DL, Sung VW, Bradley M, Brubaker L, Ferrando CA, Mazloomdoost D, Richter HE, Rogers RG, Smith AL, Komesu YM. Urinary microbiome community types associated with urinary incontinence severity in women. Am J Obstet Gynecol 2024; 230:344.e1-344.e20. [PMID: 38937257 PMCID: PMC11211640 DOI: 10.1016/j.ajog.2023.10.036] [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: 06/09/2023] [Revised: 09/22/2023] [Accepted: 10/23/2023] [Indexed: 06/29/2024]
Abstract
BACKGROUND Urinary microbiome (urobiome) studies have previously reported on specific taxa and community differences in women with mixed urinary incontinence compared with controls. Therefore, a hypothesis was made that higher urinary and vaginal microbiome diversity would be associated with increased urinary incontinence severity. OBJECTIVE This study aimed to test whether specific urinary or vaginal microbiome community types are associated with urinary incontinence severity in a population of women with mixed urinary incontinence. STUDY DESIGN This planned secondary, cross-sectional analysis evaluated associations between the urinary and vaginal microbiomes and urinary incontinence severity in a subset of Effects of Surgical Treatment Enhanced With Exercise for Mixed Urinary Incontinence trial participants with urinary incontinence. Incontinence severity was measured using bladder diaries and Urinary Distress Inventory questionnaires collected at baseline. Catheterized urine samples and vaginal swabs were concurrently collected before treatment at baseline to assess the urinary and vaginal microbiomes. Of note, 16S rRNA V4 to V6 variable regions were sequenced, characterizing bacterial taxa to the genus level using the DADA2 pipeline and SILVA database. Using Dirichlet multinomial mixtures methods, samples were clustered into community types based on core taxa. Associations between community types and severity measures (Urinary Distress Inventory total scores, Urinary Distress Inventory subscale scores, and the number of urinary incontinence episodes [total, urgency, and stress] from the bladder diary) were evaluated using linear regression models adjusted for age and body mass index. In addition, alpha diversity measures for richness (total taxa numbers) and evenness (proportional distribution of taxa abundance) were analyzed for associations with urinary incontinence episodes and community type. RESULTS Overall, 6 urinary microbiome community types were identified, characterized by varying levels of common genera (Lactobacillus, Gardnerella, Prevotella, Tepidimonas, Acidovorax, Escherichia, and others). The analysis of urinary incontinence severity in 126 participants with mixed urinary incontinence identified a Lactobacillus-dominated reference group with the highest abundance of Lactobacillus (mean relative abundance of 76%). A community characterized by fewer Lactobacilli (mean relative abundance of 19%) and greater alpha diversity was associated with higher total urinary incontinence episodes (2.67 daily leaks; 95% confidence interval, 0.76-4.59; P=.007) and urgency urinary incontinence episodes (1.75 daily leaks; 95% confidence interval, 0.24-3.27; P=.02) than the reference group. No significant association was observed between community type and stress urinary incontinence episodes or Urogenital Distress Inventory total or subscores. The composition of vaginal community types and urinary community types were similar but composed of slightly different bacterial taxa. Vaginal community types were not associated with urinary incontinence severity, as measured by bladder diary or Urogenital Distress Inventory total and subscale scores. Alpha diversity indicated that greater sample richness was associated with more incontinence episodes (observed genera P=.01) in urine. Measures of evenness (Shannon and Pielou) were not associated with incontinence severity in the urinary or vaginal microbiomes. CONCLUSION In the urobiome of women with mixed urinary incontinence, a community type with fewer Lactobacilli and more diverse bacteria was associated with more severe urinary incontinence episodes (total and urgency) compared with a community type with high predominance of a single genus, Lactobacillus. Whether mixed urinary incontinence severity is due to lesser predominance of Lactobacillus, greater presence of other non-Lactobacillus genera, or the complement of bacteria consisting of urobiome community types remains to be determined.
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Affiliation(s)
- Megan U Carnes
- Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC.
| | - Nazema Y Siddiqui
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University, Durham, NC
| | - Lisa Karstens
- Division of Bioinformatics and Computational Biomedicine; Division of Urogynecology, Oregon Health & Science University, Portland, OR
| | - Marie G Gantz
- Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Darrell L Dinwiddie
- Division of Genetics, Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Vivian W Sung
- Division of Urogynecology, Department of Obstetrics and Gynecology, Warren Alpert Medical School of Brown University, Providence, RI
| | - Megan Bradley
- Division of Urogynecology, Department of Obstetrics and Gynecology, University of Pittsburgh, Pittsburgh, PA
| | - Linda Brubaker
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, San Diego, CA
| | - Cecile A Ferrando
- Center for Urogynecology and Pelvic Reconstructive Surgery, Women's Health Institute, Cleveland Clinic, Cleveland, OH
| | - Donna Mazloomdoost
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD
| | - Holly E Richter
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL
| | - Rebecca G Rogers
- Division of Urology, Department of Obstetrics and Gynecology, Albany Medical Center, Albany, NY
| | - Ariana L Smith
- Division of Urology, Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Yuko M Komesu
- Division of Urogynecology, Department of Obstetrics and Gynecology, University of New Mexico Health Sciences and Services Building, Albuquerque, NM
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7
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Balboni A, Franzo G, Bano L, Urbani L, Segatore S, Rizzardi A, Cordioli B, Cornaggia M, Terrusi A, Vasylyeva K, Dondi F, Battilani M. No viable bacterial communities reside in the urinary bladder of cats with feline idiopathic cystitis. Res Vet Sci 2024; 168:105137. [PMID: 38181480 DOI: 10.1016/j.rvsc.2024.105137] [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: 05/24/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Urinary microbial diversities have been reported in humans according to sex, age and clinical status, including painful bladder syndrome/interstitial cystitis (PBS/IC). To date, the role of the urinary microbiome in the pathogenesis of PBS/IC is debated. Feline idiopathic cystitis (FIC) is a chronic lower urinary tract disorder affecting cats with similarities to PBS/IC in women and represents an important problem in veterinary medicine as its aetiology is currently unknown. In this study, the presence of a bacterial community residing in the urinary bladder of cats with a diagnosis of FIC was investigated. Nineteen cats with clinical signs and history of FIC and without growing bacteria in standard urine culture were included and urine collected with ultrasound-guided cystocentesis. Bacterial community was investigated using a culture-dependent approach consisted of expanded quantitative urine culture techniques and a culture-independent approach consisted of 16S rRNA NGS. Several methodological practices were adopted to both avoid and detect any contamination or bias introduced by means of urine collection and processing which could be relevant due to the low microbial biomass environment of the bladder and urinary tract, including negative controls analysis. All the cats included showed no growing bacteria in the urine analysed. Although few reads were originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and negative controls, and no taxa were confidently classified as non-contaminant. The results obtained suggest the absence of viable bacteria and of bacterial DNA of urinary origin in the urinary bladder of cats with FIC.
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Affiliation(s)
- Andrea Balboni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Luca Bano
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Lorenza Urbani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Sofia Segatore
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Alessia Rizzardi
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Benedetta Cordioli
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Matteo Cornaggia
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Alessia Terrusi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Kateryna Vasylyeva
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Mara Battilani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
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8
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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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9
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Pernigoni N, Guo C, Gallagher L, Yuan W, Colucci M, Troiani M, Liu L, Maraccani L, Guccini I, Migliorini D, de Bono J, Alimonti A. The potential role of the microbiota in prostate cancer pathogenesis and treatment. Nat Rev Urol 2023; 20:706-718. [PMID: 37491512 DOI: 10.1038/s41585-023-00795-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
The human body hosts a complex and dynamic population of trillions of microorganisms - the microbiota - which influences the body in homeostasis and disease, including cancer. Several epidemiological studies have associated specific urinary and gut microbial species with increased risk of prostate cancer; however, causal mechanistic data remain elusive. Studies have associated bacterial generation of genotoxins with the occurrence of TMPRSS2-ERG gene fusions, a common, early oncogenic event during prostate carcinogenesis. A subsequent study demonstrated the role of the gut microbiota in prostate cancer endocrine resistance, which occurs, at least partially, through the generation of androgenic steroids fuelling oncogenic signalling via the androgen receptor. These studies present mechanistic evidence of how the host microbiota might be implicated in prostate carcinogenesis and tumour progression. Importantly, these findings also reveal potential avenues for the detection and treatment of prostate cancer through the profiling and modulation of the host microbiota. The latter could involve approaches such as the use of faecal microbiota transplantation, prebiotics, probiotics, postbiotics or antibiotics, which can be used independently or combined with existing treatments to reverse therapeutic resistance and improve clinical outcomes in patients with prostate cancer.
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Affiliation(s)
- Nicolò Pernigoni
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Christina Guo
- Institute of Cancer Research, London, UK
- Royal Marsden Hospital, London, UK
| | | | - Wei Yuan
- Institute of Cancer Research, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Martina Troiani
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Lei Liu
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Luisa Maraccani
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
| | - Ilaria Guccini
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Denis Migliorini
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Léman, Lausanne and Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Johann de Bono
- Institute of Cancer Research, London, UK
- Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Veneto Institute of Molecular Medicine, Padova, Italy.
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland.
- Department of Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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10
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Morańska K, Englert-Golon M, Durda-Masny M, Sajdak S, Grabowska M, Szwed A. Why Does Your Uterus Become Malignant? The Impact of the Microbiome on Endometrial Carcinogenesis. Life (Basel) 2023; 13:2269. [PMID: 38137870 PMCID: PMC10744771 DOI: 10.3390/life13122269] [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: 10/02/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
The aim of this review was to describe the uterine microbiome composition that has been analyzed so far and describe potential pathways in the carcinogenesis of the endometrium. The microbiome in the uterine environment is involved in apoptosis and proliferation during the menstruation cycle, pregnancy maintenance, and immune system support. However, bacteria in the uterus could stimulate inflammation, which when chronic results in malignancy. An altered gut microbiota initiates an inflammatory response through microorganism-associated molecular patterns, which leads to intensified steroidogenesis in the ovaries and cancers. Moreover, intestinal bacteria secreting the enzyme β-glucuronidase may increase the level of circulating estrogen and, as a result, be influential in gynecological cancers. Both the uterine and the gut microbiota play a pivotal role in immune modulation, which is why there is a demand for further investigation from both the diagnostic and the therapeutic perspectives.
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Affiliation(s)
- Katarzyna Morańska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland (A.S.)
| | - Monika Englert-Golon
- Department of Gynaecology Obstetrics and Gynaecological Oncology, Division of Gynecological Surgery, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Magdalena Durda-Masny
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland (A.S.)
| | - Stefan Sajdak
- Department of Gynaecology Obstetrics and Gynaecological Oncology, Division of Gynecological Surgery, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Marlena Grabowska
- Department of Gynaecology Obstetrics and Gynaecological Oncology, Division of Gynecological Surgery, Poznan University of Medical Sciences, 60-535 Poznan, Poland
| | - Anita Szwed
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland (A.S.)
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11
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De Maio F, Grotti G, Mariani F, Buonsenso D, Santarelli G, Bianco DM, Posteraro B, Sanguinetti M, Rendeli C. Profiling the Urobiota in a Pediatric Population with Neurogenic Bladder Secondary to Spinal Dysraphism. Int J Mol Sci 2023; 24:ijms24098261. [PMID: 37175968 PMCID: PMC10178886 DOI: 10.3390/ijms24098261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
The human bladder has been long thought to be sterile until that, only in the last decade, advances in molecular biology have shown that the human urinary tract is populated with microorganisms. The relationship between the urobiota and the development of urinary tract disorders is now of great interest. Patients with spina bifida (SB) can be born with (or develop over time) neurological deficits due to damaged nerves that originate in the lower part of the spinal cord, including the neurogenic bladder. This condition represents a predisposing factor for urinary tract infections so that the most frequently used approach to treat patients with neurogenic bladder is based on clean intermittent catheterization (CIC). In this study, we analyzed the urobiota composition in a pediatric cohort of patients with SB compared to healthy controls, as well as the urobiota characteristics based on whether patients received CIC or not.
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Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Giacomo Grotti
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Francesco Mariani
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Danilo Buonsenso
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Centro di Salute Globale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Delia Mercedes Bianco
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie-Sezione di Microbiologia, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie-Sezione di Microbiologia, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Claudia Rendeli
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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12
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Čeprnja M, Hadžić E, Oros D, Melvan E, Starcevic A, Zucko J. Current Viewpoint on Female Urogenital Microbiome-The Cause or the Consequence? Microorganisms 2023; 11:1207. [PMID: 37317181 DOI: 10.3390/microorganisms11051207] [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: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
An increasing amount of evidence implies that native microbiota is a constituent part of a healthy urinary tract (UT), making it an ecosystem on its own. What is still not clear is whether the origin of the urinary microbial community is the indirect consequence of the more abundant gut microbiota or a more distinct separation exists between these two systems. Another area of uncertainty is the existence of a link between the shifts in UT microbial composition and both the onset and persistence of cystitis symptoms. Cystitis is one of the most common reasons for antimicrobial drugs prescriptions in primary and secondary care and an important contributor to the problem of antimicrobial resistance. Despite this fact, we still have trouble distinguishing whether the primary cause of the majority of cystitis cases is a single pathogen overgrowth or a systemic disorder affecting the entire urinary microbiota. There is an increasing trend in studies monitoring changes and dynamics of UT microbiota, but this field of research is still in its infancy. Using NGS and bioinformatics, it is possible to obtain microbiota taxonomic profiles directly from urine samples, which can provide a window into microbial diversity (or the lack of) underlying each patient's cystitis symptoms. However, while microbiota refers to the living collection of microorganisms, an interchangeably used term microbiome referring to the genetic material of the microbiota is more often used in conjunction with sequencing data. It is this vast amount of sequences, which are truly "Big Data", that allow us to create models that describe interactions between different species contributing to an UT ecosystem, when coupled with machine-learning techniques. Although in a simplified predator-prey form these multi-species interaction models have the potential to further validate or disprove current beliefs; whether it is the presence or the absence of particular key players in a UT microbial ecosystem, the exact cause or consequence of the otherwise unknown etiology in the majority of cystitis cases. These insights might prove to be vital in our ongoing struggle against pathogen resistance and offer us new and promising clinical markers.
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Affiliation(s)
- Marina Čeprnja
- Biochemical Laboratory, Special Hospital Agram, Polyclinic Zagreb, 10000 Zagreb, Croatia
| | - Edin Hadžić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Damir Oros
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Ena Melvan
- Department of Biological Science, Faculty of Science, Macquarie University, Sydney, NSW 2109, Australia
| | - Antonio Starcevic
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
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13
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Toh E, Xing Y, Gao X, Jordan SJ, Batteiger TA, Batteiger BE, Van Der Pol B, Muzny CA, Gebregziabher N, Williams JA, Fortenberry LJ, Fortenberry JD, Dong Q, Nelson DE. Sexual behavior shapes male genitourinary microbiome composition. Cell Rep Med 2023; 4:100981. [PMID: 36948151 PMCID: PMC10040456 DOI: 10.1016/j.xcrm.2023.100981] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/21/2022] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbiosis is linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Most urethral specimens contain characteristic lactic acid bacteria and Corynebacterium spp. In contrast, several bacteria associated with vaginal dysbiosis were present only in specimens from men who reported vaginal intercourse. Sexual behavior, but not other evaluated behavioral, demographic, or clinical variables, strongly associated with inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a simple core microbiome that is established independent of sexual exposures but can be re-shaped by vaginal sex. Overall, the results suggest that urogenital microbiology and sexual behavior are inexorably intertwined, and show that the male urethra harbors female urogenital pathobionts.
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Affiliation(s)
- Evelyn Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yue Xing
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Xiang Gao
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Stephen J Jordan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Teresa A Batteiger
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byron E Batteiger
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Barbara Van Der Pol
- Department of Medicine, Division of Infectious Diseases, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Christina A Muzny
- Department of Medicine, Division of Infectious Diseases, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Netsanet Gebregziabher
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - James A Williams
- Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lora J Fortenberry
- Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - J Dennis Fortenberry
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qunfeng Dong
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA; Center for Biomedical Informatics, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - David E Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
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14
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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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15
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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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16
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Gong H, You X, Jin M, Meng Y, Zhang H, Yang S, Xu J. Graph neural network and multi-data heterogeneous networks for microbe-disease prediction. Front Microbiol 2022; 13:1077111. [PMID: 36620040 PMCID: PMC9814480 DOI: 10.3389/fmicb.2022.1077111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
The research on microbe association networks is greatly significant for understanding the pathogenic mechanism of microbes and promoting the application of microbes in precision medicine. In this paper, we studied the prediction of microbe-disease associations based on multi-data biological network and graph neural network algorithm. The HMDAD database provided a dataset that included 39 diseases, 292 microbes, and 450 known microbe-disease associations. We proposed a Microbe-Disease Heterogeneous Network according to the microbe similarity network, disease similarity network, and known microbe-disease associations. Furthermore, we integrated the network into the graph convolutional neural network algorithm and developed the GCNN4Micro-Dis model to predict microbe-disease associations. Finally, the performance of the GCNN4Micro-Dis model was evaluated via 5-fold cross-validation. We randomly divided all known microbe-disease association data into five groups. The results showed that the average AUC value and standard deviation were 0.8954 ± 0.0030. Our model had good predictive power and can help identify new microbe-disease associations. In addition, we compared GCNN4Micro-Dis with three advanced methods to predict microbe-disease associations, KATZHMDA, BiRWHMDA, and LRLSHMDA. The results showed that our method had better prediction performance than the other three methods. Furthermore, we selected breast cancer as a case study and found the top 12 microbes related to breast cancer from the intestinal flora of patients, which further verified the model's accuracy.
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Affiliation(s)
- Houwu Gong
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China,Academy of Military Sciences, Beijing, China
| | - Xiong You
- Center of Rehabilitation Diagnosis and Treatment, Hunan Provincial Rehabilitation Hospital, Changsha, China
| | - Min Jin
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China,*Correspondence: Min Jin, ✉
| | - Yajie Meng
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China
| | - Hanxue Zhang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Shuaishuai Yang
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Junlin Xu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China,Junlin Xu, ✉
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17
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Abstract
The knowledge of bacterial species diversity within the female urinary microbiome (FUM) is essential for understanding the role of the FUM in urinary tract health and disease. This study aimed to characterize the bacterial species diversity of the FUM of asymptomatic reproductive-age European women by combining extended culturomics and long-read sequencing of the near-full-length 16S rRNA gene. A total of 297 bacterial species (median of 53 species/sample) were identified, yet only 22% of the species were detected by both culture and sequencing methods. Recently recognized Gardnerella, Lactobacillus, and Limosilactobacillus species and 5 new putative Corynebacterium species were identified by culturomics, while anaerobic species (e.g., 11 Peptoniphilus spp.) were mostly detected by amplicon sequencing. Notably, there was not a single species common to all samples, although members of the genus Lactobacillus were detected in all. Lactobacillus crispatus, Lactobacillus iners, and Lactobacillus mulieris were observed in high relative abundance in several samples, as well as other species (e.g., Streptococcus agalactiae, Fannyhessea vaginae, Gardnerella vaginalis, Gardnerella swidsinskii), while low-abundance members (e.g., Finegoldia magna) were often more prevalent. A moderate correlation (Mantel test; r = 0.5) between community structure types captured by culturomics and amplicon sequencing was observed, highlighting the benefit of combining both methodologies. This study provided a detailed FUM structure at the species level, which is critical to unveil the potential relationship between specific microbiome members and urinary diseases/disorders. Moreover, the different capacity to characterize microbiome profiles of culturomic and amplicon sequencing is described, providing valuable insights for further urinary microbiome studies. IMPORTANCE The bacterial species diversity within the female urinary microbiome (FUM) has been insufficiently characterized. This study demonstrated that complementarity between optimized culture-dependent and -independent approaches is highly beneficial for comprehensive FUM species profiling by detecting higher FUM species diversity than previously reported, including identification of unreported species belonging to the genera Lactobacillus, Limosilactobacillus, and Latilactobacillus and putative novel Corynebacterium species. Although some species were present in high relative abundance, low-abundance members were more prevalent. FUM classification into community structure types demonstrated high interindividual differences in urinary microbiome composition among asymptomatic women. We also report moderate correlation between culture-dependent and -independent derived data-highlighting drawbacks of each methodological approach. Our findings suggest that FUM bacterial diversity reported from previous studies may be underestimated. Finally, our results contribute to the fundamental knowledge of the FUM required for further exploration of the urinary microbiome role in urinary tract diseases.
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18
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Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL, De Nisco NJ. Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome. Cell Rep Med 2022; 3:100753. [PMID: 36182683 PMCID: PMC9588997 DOI: 10.1016/j.xcrm.2022.100753] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/28/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022]
Abstract
Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary environment. However, changes in the urogenital microbiome underlying rUTI susceptibility are unknown. Here, we perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility. We identify candidate taxonomic biomarkers of rUTI susceptibility in postmenopausal women and an enrichment of lactobacilli in postmenopausal women taking estrogen hormone therapy. We find robust correlations between Bifidobacterium and Lactobacillus and urinary estrogens in women without urinary tract infection (UTI) history. Functional analyses reveal distinct metabolic and antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, we find that ARGs are enriched in the urogenital microbiomes of women with rUTI history independent of current UTI status. Our data suggest that rUTI and estrogen shape the urogenital microbiome in postmenopausal women.
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Affiliation(s)
- Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neha V Hulyalkar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kevin C Lutz
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Vivian H Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Jorge L Fuentes
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cong Zhang
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Amber Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Belle M Sharon
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Amy Kuprasertkul
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda P Arute
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Tahmineh Ebrahimzadeh
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Nitya Natesan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, TX, USA; Advanced Environmental Research Institute, The University of North Texas, Denton, TX, USA
| | - Qiwei Li
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Philippe E Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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19
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Abstract
Nongonococcal urethritis (NGU) is a common genital tract syndrome in men, and up to 50% of cases are considered idiopathic, i.e., no etiological agent is identified. This poses challenges for clinicians in the diagnosis and treatment of NGU and often results in antibiotic misuse and overuse. Therefore, to identify potential infectious causes of urethritis and inform clinical management of urethritis cases, we characterized and compared the urethral microbiota of men with and without idiopathic urethritis. Participants were derived from a case-control study that examined viral and bacterial pathogens and sexual practices associated with NGU. Men with NGU who tested negative for established causes of NGU (Chlamydia trachomatis, Mycoplasma genitalium, Trichomonas vaginalis, adenoviruses, herpes simplex virus [HSV]-1, and/or HSV-2) were classified as idiopathic cases, and the controls were men reporting no current urethral symptoms. Men provided a urine sample that was used to characterize the urethral microbiota using 16S rRNA gene sequencing. Bacterial taxa associated with idiopathic urethritis were identified using analysis of compositions of microbiomes with bias correction. When stratified by sex of sexual partner, we found that the abundance of Haemophilus influenzae was significantly increased in men who have sex with men with idiopathic urethritis, and the abundance of Corynebacterium was significantly increased in men who have sex with women with idiopathic urethritis. Other taxa, including Ureaplasma, Staphylococcus haemolyticus, Streptococcus pyogenes, Escherichia, and Streptococcus pneumoniae/pseudopneumoniae, dominated the urethral microbiota of idiopathic urethritis cases but not controls, suggesting that these organisms may also contribute to urethritis. Importantly, the taxa we identified represent biologically plausible causes of urethritis and should be prioritized for future study.
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20
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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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21
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The Oncobiome in Gastroenteric and Genitourinary Cancers. Int J Mol Sci 2022; 23:ijms23179664. [PMID: 36077063 PMCID: PMC9456244 DOI: 10.3390/ijms23179664] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Early evidence suggests a strong association of microorganisms with several human cancers, and great efforts have been made to understand the pathophysiology underlying microbial carcinogenesis. Bacterial dysbiosis causes epithelial barrier failure, immune dysregulation and/or genotoxicity and, consequently, creates a tumor-permissive microenvironment. The majority of the bacteria in our body reside in the gastrointestinal tract, known as gut microbiota, which represents a complex and delicate ecosystem. Gut microbes can reach the pancreas, stomach and colon via the bloodstream. Oral bacterial translocations can also occur. In the stomach, pancreas and colon, low microbial diversity is associated with cancer, in particular with a bad prognosis. The urogenital tract also harbors unique microbiota, distinct from the gut microbiota, which might have a role in the urinary and female/male reproductive cancers’ pathogenesis. In healthy women, the majority of bacteria reside in the vagina and cervix and unlike other mucosal sites, the vaginal microbiota exhibits low microbial diversity. Genital dysbiosis might have an active role in the development and/or progression of gynecological malignancies through mechanisms including modulation of oestrogen metabolism. Urinary dysbiosis may influence the pathogenesis of bladder cancer and prostate cancer in males. Modulation of the microbiome via pre, pro and postbiotics, fecal or vaginal microbiota transplantation and engineering bacteria might prove useful in improving cancer treatment response and quality of life. Elucidating the complex host-microbiome interactions will result in prevention and therapeutic efficacy interventions.
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22
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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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Maślak E, Miśta W, Złoch M, Błońska D, Pomastowski P, Monedeiro F, Buszewski B, Mrochem-Kwarciak J, Bojarska K, Gabryś D. A New Approach to Imaging and Rapid Microbiome Identification for Prostate Cancer Patients Undergoing Radiotherapy. Biomedicines 2022; 10:biomedicines10081806. [PMID: 36009352 PMCID: PMC9405325 DOI: 10.3390/biomedicines10081806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Little is known about the impact of urinary microflora, in particular, its effects on side effects after radiotherapy. The use of mass spectrometry identification method (MALDI) may bring a new look at the issue of the composition and significance of the urinary microbiome. This study aimed to use the mass spectrometry identification method (MALDI) to identify the microbiome of urine samples collected from 50 irradiated prostate cancer patients. (2) Methods: Blood and urine samples were collected before gold marker implantation, at the start and last day of radiotherapy, 1, 4 months after. Patients do not always collect the urine from the midstream; therefore, samples were collected from the first void and midstream in 12 patients for MALDI analysis; in the remaining 38 patients—from the midstream void for MALDI and biochemical analysis. (3) Results: Microorganisms were present in 140/181 urine samples. We found 33 different species 3G(−) and 30G(+). The most frequently isolated strains were: Staphylococcus haemolyticus, Staphylococcus epidermidis, Staphylococcus hominis, Enterococcus faecalis, and Micrococcus luteus. When comparing the type of urine samples, bacteria were more common in samples from the first-void urine than from the midstream one. The absence of bacteria was found in 12.2% of samples from the first-void urine and in 24.7% from the midstream. There was no difference in the total incidence of species between streams (p = 0.85). Before fiducial implantation, the total number of detected bacterial species was significantly higher in comparison to the end of radiotherapy (p = 0.038), indicating that the administered therapy resulted in depleting the local microbiome. One month after radiotherapy, an increase in the number of isolated bacteria was observed. The number of bacterial species in urine did not correlate with blood parameters. The presence of leukocytes (p = 0.013) and proteins (p = 0.004) in urine was related to a greater variety of bacteria found in urine specimens. (4) Conclusions: We obtained a similar spectrum of bacteria from the initial and middle urine streams. We also showed that there is a change in bacteria species affected by the treatment of prostate cancer patients, with both antibiotics before gold fiducial implantation and radiotherapy.
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Affiliation(s)
- Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Wioletta Miśta
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland;
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Dominika Błońska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Fernanda Monedeiro
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
| | - Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str., 87-100 Toruń, Poland; (E.M.); (M.Z.); (D.B.); (P.P.); (F.M.); (B.B.)
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Jolanta Mrochem-Kwarciak
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland; (J.M.-K.); (K.B.)
| | - Katarzyna Bojarska
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland; (J.M.-K.); (K.B.)
| | - Dorota Gabryś
- Radiotherapy Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeże Armii Krajowej 15 Str., 44-102 Gliwice, Poland;
- Correspondence: ; Tel.: +48-32-278-80-51
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Heidrich V, Inoue LT, Asprino PF, Bettoni F, Mariotti ACH, Bastos DA, Jardim DLF, Arap MA, Camargo AA. Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling. Front Cell Infect Microbiol 2022; 12:862338. [PMID: 35531325 PMCID: PMC9069555 DOI: 10.3389/fcimb.2022.862338] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/29/2022] [Indexed: 12/04/2022] Open
Abstract
Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for male urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. Systematic comparisons of their performance indicate V1V2 hypervariable regions better assess the taxa commonly present in male urine samples, suggesting V1V2 amplicon sequencing is more suitable for male urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future male urinary microbiota studies.
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Affiliation(s)
- Vitor Heidrich
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Lilian T. Inoue
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Paula F. Asprino
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Fabiana Bettoni
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Diogo A. Bastos
- Centro de Oncologia, Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Marco A. Arap
- Departamento de Urologia, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Anamaria A. Camargo
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- *Correspondence: Anamaria A. Camargo,
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Kloping YP, Hakim L. Prostate Cancer Microbiome: A Narrative Review of What We Know So Far. CURRENT CLINICAL MICROBIOLOGY REPORTS 2022. [DOI: 10.1007/s40588-022-00178-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nardos R, Leung ET, Dahl EM, Davin S, Asquith M, Gregory WT, Karstens L. Network-Based Differences in the Vaginal and Bladder Microbial Communities Between Women With and Without Urgency Urinary Incontinence. Front Cell Infect Microbiol 2022; 12:759156. [PMID: 35402312 PMCID: PMC8988226 DOI: 10.3389/fcimb.2022.759156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Background Little is known about the relationship of proximal urogenital microbiomes in the bladder and the vagina and how this contributes to bladder health. In this study, we use a microbial ecology and network framework to understand the dynamics of interactions/co-occurrences of bacteria in the bladder and vagina in women with and without urgency urinary incontinence (UUI). Methods We collected vaginal swabs and catheterized urine specimens from 20 women with UUI (cases) and 30 women without UUI (controls). We sequenced the V4 region of the bacterial 16S rRNA gene and evaluated using alpha and beta diversity metrics. We used microbial network analysis to detect interactions in the microbiome and the betweenness centrality measure to identify central bacteria in the microbial network. Bacteria exhibiting maximum betweenness centrality are considered central to the microbe-wide networks and likely maintain the overall microbial network structure. Results There were no significant differences in the vaginal or bladder microbiomes between cases and controls using alpha and beta diversity. Silhouette metric analysis identified two distinct microbiome clusters in both the bladder and vagina. One cluster was dominated by Lactobacillus genus while the other was more diverse. Network-based analyses demonstrated that vaginal and bladder microbial networks were different between cases and controls. In the vagina, there were similar numbers of genera and subgroup clusters in each network for cases and controls. However, cases tend to have more unique bacterial co-occurrences. While Bacteroides and Lactobacillus were the central bacteria with the highest betweenness centrality in controls, Aerococcus had the highest centrality in cases and correlated with bacteria commonly associated with bacterial vaginosis. In the bladder, cases have less than half as many network clusters compared to controls. Lactobacillus was the central bacteria in both groups but associated with several known uropathogens in cases. The number of shared bacterial genera between the bladder and the vagina differed between cases and controls, with cases having larger overlap (43%) compared to controls (29%). Conclusion Our study shows overlaps in microbial communities of bladder and vagina, with higher overlap in cases. We also identified differences in the bacteria that are central to the overall community structure.
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Affiliation(s)
- Rahel Nardos
- Division of Urogynecology, Oregon Health and Science University, Portland, OR, United States
- Division of Female Pelvic Medicine and Reconstructive Surgery, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Rahel Nardos,
| | - Eric T. Leung
- Division of Bioinformatics and Computational Biomedicine, Oregon Health and Science University, Portland, OR, United States
| | - Erin M. Dahl
- Division of Bioinformatics and Computational Biomedicine, Oregon Health and Science University, Portland, OR, United States
| | - Sean Davin
- Division of Arthritis and Rheumatology, Oregon Health and Science University, Portland, OR, United States
| | - Mark Asquith
- Division of Arthritis and Rheumatology, Oregon Health and Science University, Portland, OR, United States
| | - W. Thomas Gregory
- Division of Urogynecology, Oregon Health and Science University, Portland, OR, United States
| | - Lisa Karstens
- Division of Urogynecology, Oregon Health and Science University, Portland, OR, United States
- Division of Bioinformatics and Computational Biomedicine, Oregon Health and Science University, Portland, OR, United States
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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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Zarei A, Javid H, Sanjarian S, Senemar S, Zarei H. Metagenomics studies for the diagnosis and treatment of prostate cancer. Prostate 2022; 82:289-297. [PMID: 34855234 DOI: 10.1002/pros.24276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 12/19/2022]
Abstract
AIM Mutation occurs in the prostate cell genes, leading to abnormal prostate proliferation and ultimately cancer. Prostate cancer (PC) is one of the most common cancers amongst men, and its prevalence worldwide increases relative to men's age. About 16% of the world's cancers are the result of microbes in the human body. Impaired population balance of symbiosis microbes in the human reproductive system is linked to PC development. DISCUSSION With the advent of metagenomics science, the genome sequence of the microbiota of the human body has been unveiled. Therefore, it is now possible to identify a higher range of microbiome changes in PC tissue via the Next Generation Technique, which will have positive consequences in personalized medicine. In this review, we intend to question the role of metagenomics studies in the diagnosis and treatment of PC. CONCLUSION The microbial imbalance in the men's genital tract might have an effect on prostate health. Based on next-generation sequencing-generated data, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes are the nine frequent phyla detected in a PC sample, which might be involved in inducing mutation in the prostate cells that cause cancer.
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Affiliation(s)
- Ali Zarei
- Department of Human Genetics, Iranian Academic Center for Education, Culture and Research (ACECR)-Fars Branch Institute for Human Genetics Research, Shiraz, Iran
| | - Hossein Javid
- Department of Human Genetics, Iranian Academic Center for Education, Culture and Research (ACECR)-Fars Branch Institute for Human Genetics Research, Shiraz, Iran
| | - Sara Sanjarian
- Department of Human Genetics, Iranian Academic Center for Education, Culture and Research (ACECR)-Fars Branch Institute for Human Genetics Research, Shiraz, Iran
| | - Sara Senemar
- Department of Human Genetics, Iranian Academic Center for Education, Culture and Research (ACECR)-Fars Branch Institute for Human Genetics Research, Shiraz, Iran
| | - Hanieh Zarei
- Department of Physical Therapy, School of Rehabilitation Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Biehl LM, Farowski F, Hilpert C, Nowag A, Kretzschmar A, Jazmati N, Tsakmaklis A, Wieters I, Khodamoradi Y, Wisplinghoff H, Vehreschild MJGT. Longitudinal variability in the urinary microbiota of healthy premenopausal women and the relation to neighboring microbial communities: A pilot study. PLoS One 2022; 17:e0262095. [PMID: 35030190 PMCID: PMC8759677 DOI: 10.1371/journal.pone.0262095] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022] Open
Abstract
Background The understanding of longitudinal changes in the urinary microbiota of healthy women and its relation to intestinal microbiota is limited. Methods From a cohort of 15 premenopausal women without known urogenital disease or current symptoms, we collected catheter urine (CU), vaginal and periurethral swabs, and fecal samples on four visits over six months. Additionally, ten participants provided CU and midstream urine (MU) to assess comparability. Urine was subjected to expanded culture. 16S rRNA gene sequencing was performed on all urine, fecal, and selected vaginal and periurethral samples. Sequence reads were processed (DADA2 pipeline) and analyzed using QIIME 2 and R. Results Relative abundances of urinary microbiota were variable over 6–18 months. The degree of intraindividual variability of urinary microbiota was higher than that found in fecal samples. Still, nearly half of the observed beta diversity of all urine samples could be attributed to differences between volunteers (R2 = 0.48, p = 0.001). After stratification by volunteer, time since last sexual intercourse was shown to be a factor significantly contributing to beta diversity (R2 = 0.14, p = 0.001). We observed a close relatedness of urogenital microbial habitats and a clear distinction from intestinal microbiota in the overall betadiversity analysis. Microbiota compositions derived from MU differed only slightly from CU compositions. Within this analysis of low-biomass samples, we identified contaminating sequences potentially stemming from sequencing reagents. Conclusions Results from our longitudinal cohort study confirmed the presence of a rather variable individual urinary microbiota in premenopausal women. These findings from catheter urine complement previous observations on temporal dynamics in voided urine. The higher intraindividual variability of urinary microbiota as compared to fecal microbiota will be a challenge for future studies investigating associations with urogenital diseases and aiming at identifying pathogenic microbiota signatures.
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Affiliation(s)
- Lena M. Biehl
- Faculty of Medicine and University Hospital of Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Bonn-Cologne, Germany
| | - Fedja Farowski
- Faculty of Medicine and University Hospital of Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Bonn-Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Catharina Hilpert
- Faculty of Medicine and University Hospital of Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
| | - Angela Nowag
- Wisplinghoff laboratories, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | | | - Nathalie Jazmati
- Wisplinghoff laboratories, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Anastasia Tsakmaklis
- Faculty of Medicine and University Hospital of Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
| | - Imke Wieters
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Hilmar Wisplinghoff
- Wisplinghoff laboratories, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- Institute for Virology and Medical Microbiology, Witten/Herdecke University, Witten, Germany
| | - Maria J. G. T. Vehreschild
- Faculty of Medicine and University Hospital of Cologne, Department I of Internal Medicine, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Bonn-Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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Kawalec A, Zwolińska D. Emerging Role of Microbiome in the Prevention of Urinary Tract Infections in Children. Int J Mol Sci 2022; 23:870. [PMID: 35055056 PMCID: PMC8775962 DOI: 10.3390/ijms23020870] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
The microbiome of the urinary tract plays a significant role in maintaining health through the impact on bladder homeostasis. Urobiome is of great importance in maintaining the urothelial integrity and preventing urinary tract infection (UTI), as well as promoting local immune function. Dysbiosis in this area has been linked to an increased risk of UTIs, nephrolithiasis, and dysfunction of the lower urinary tract. However, the number of studies in the pediatric population is limited, thus the characteristic of the urobiome in children, its role in a child's health, and pediatric urologic diseases are not completely understood. This review aims to characterize the healthy urobiome in children, the role of dysbiosis in urinary tract infection, and to summarize the strategies to modification and reshape disease-prone microbiomes in pediatric patients with recurrent urinary tract infections.
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Affiliation(s)
- Anna Kawalec
- Clinic of Pediatric Nephrology, University Hospital, 50-556 Wroclaw, Poland
| | - Danuta Zwolińska
- Department of Pediatric Nephrology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
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RICHTER HOLLYE, CARNES MEGANU, KOMESU YUKOM, LUKACZ EMILYS, ARYA LILY, BRADLEY MEGAN, ROGERS REBECCAG, SUNG VIVIANW, SIDDIQUI NAZEMAY, CARPER BENJAMIN, MAZLOOMDOOST DONNA, DINWIDDIE DARRYL, GANTZ MARIEG. Association between the urogenital microbiome and surgical treatment response in women undergoing midurethral sling operation for mixed urinary incontinence. Am J Obstet Gynecol 2022; 226:93.e1-93.e15. [PMID: 34297969 PMCID: PMC8748268 DOI: 10.1016/j.ajog.2021.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND The urogenital microbiome is associated with urgency and mixed urinary incontinence symptoms and differential treatment responses to pharmacotherapy for urgency urinary incontinence. OBJECTIVE This study aimed to describe whether the preoperative urinary and vaginal microbiomes were associated with surgical treatment responses at 12 months after a midurethral sling operation in women with mixed urinary incontinence. STUDY DESIGN This cohort study compared the preoperative microbiome compositions of urine and vaginal samples from a subset of women undergoing a midurethral sling operation in the Effects of Surgical Treatment Enhanced With Exercise for Mixed Urinary Incontinence trial (NCT01959347) and compared the microbiota in women who were surgical responders vs surgical nonresponders. Twelve-month objective response was defined as a ≥70% reduction from baseline urinary incontinence episodes on a 3-day diary. Subjective response was defined as a change from baseline in the Urogenital Distress Inventory scores. Bacterial abundance and beta diversity were assessed using 16S ribosomal RNA sequencing. The primary differential abundance analysis described predominant bacterial operational taxonomic units associated with responders vs nonresponders using unadjusted and age-adjusted linear models. RESULTS Objective nonresponders (n=28) compared with responders (n=72) were older (58.5±10.7 vs 51.6±10.2 years) and more likely postmenopausal without hormone use (odds ratio, 6.4; 95% confidence interval, 1.8-22.6). Vaginal and urinary microbiota beta diversities were associated with age (P<.05) for both responders and nonresponders. Overall, predominant operational taxonomic units (genera) were Lactobacillus, Gardnerella, Tepidimonas, Escherichia, Streptococcus, and Prevotella. Operational taxonomic units from baseline urine samples were not significantly associated (P threshold=.05) with surgical treatment responses. A greater abundance of baseline vaginal Lactobacillus was associated with an objective response (P=.04) and Prevotella with an objective nonresponse (P=.01). Adjusting for age, only a greater abundance of baseline vaginal Prevotella was associated with an objective nonresponse (P=.01). Moreover, less abundant vaginal operational taxonomic units were associated with objective and subjective responses and persistent urinary incontinence symptoms (P<.05). CONCLUSION Women meeting a 70% reduction of urinary incontinence treatment episodes (objective responders) had greater vaginal Lactobacillus at the time of the surgical procedure; however, controlling for age diminished this association. Women not meeting a 70% reduction of urinary incontinence episodes 1 year after a midurethral sling operation had greater vaginal Prevotella at the time of the midurethral sling operation. Further research is needed to determine whether therapy altering the vaginal microbiome may impact surgical treatment responses in women with mixed urinary incontinence.
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Affiliation(s)
- HOLLY E. RICHTER
- Obstetrics & Gynecology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - MEGAN U. CARNES
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, United States
| | - YUKO M. KOMESU
- Obstetrics & Gynecology, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - EMILY S. LUKACZ
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, San Diego, CA, United States
| | - LILY ARYA
- Obstetrics & Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - MEGAN BRADLEY
- Obstetrics & Gynecology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - REBECCA G. ROGERS
- Obstetrics & Gynecology, Dell Medical School University of Texas Austin, Austin TX, United States
| | - VIVIAN W. SUNG
- Obstetrics & Gynecology, Alpert Medical School of Brown University, Providence, RI, United States
| | | | - BENJAMIN CARPER
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, United States
| | - DONNA MAZLOOMDOOST
- Gynecologic Health and Disease Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) National Institutes of Health (NIH), Bethesda, MD, United States
| | - DARRYL DINWIDDIE
- Pediatrics, Clinical Translational Science Center, University of New Mexico Health Sciences, Albuquerque, NM, United States
| | - MARIE G. GANTZ
- Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, United States
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Jayalath S, Magana-Arachchi D. Dysbiosis of the Human Urinary Microbiome and its Association to Diseases Affecting the Urinary System. Indian J Microbiol 2021; 62:153-166. [DOI: 10.1007/s12088-021-00991-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022] Open
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Shoemaker R, Kim J. Urobiome: An outlook on the metagenome of urological diseases. Investig Clin Urol 2021; 62:611-622. [PMID: 34729961 PMCID: PMC8566783 DOI: 10.4111/icu.20210312] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/09/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
The urinary tract likely plays a role in the development of various urinary diseases due to the recently recognized notion that urine is not sterile. In this mini review, we summarize the current literature regarding the urinary microbiome and mycobiome and its relationship to various urinary diseases. It has been recently discovered that the healthy urinary tract contains a host of microorganisms, creating a urinary microbiome. The relative abundance and type of bacteria varies, but generally, deviations in the standard microbiome are observed in individuals with urologic diseases, such as bladder cancer, benign prostatic hyperplasia, urgency urinary incontinence, overactive bladder syndrome, interstitial cystitis, bladder pain syndrome, and urinary tract infections. However, whether this change is causative, or correlative has yet to be determined. In summary, the urinary tract hosts a complex microbiome. Changes in this microbiome may be indicative of urologic diseases and can be tracked to predict, prevent, and treat them in individuals. However, current analytical and sampling collection methods may present limitations to the development in the understanding of the urinary microbiome and its relationship with various urinary diseases. Further research on the differences between healthy and diseased microbiomes, the long-term effects of antibiotic treatments on the urobiome, and the effect of the urinary mycobiome on general health will be important in developing a comprehensive understanding of the urinary microbiome and its relationship to the human body.
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Affiliation(s)
- Rachel Shoemaker
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jayoung Kim
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, University of California, Los Angeles, CA, USA.,Department of Urology, Gachon University College of Medicine, Incheon, Korea.
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Hoffman C, Siddiqui NY, Fields I, Gregory WT, Simon HM, Mooney MA, Wolfe AJ, Karstens L. Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing. mSystems 2021; 6:e0051821. [PMID: 34519534 PMCID: PMC8547459 DOI: 10.1128/msystems.00518-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023] Open
Abstract
The human bladder contains bacteria, even in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing. However, the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA amplicon sequencing is commonly used to identify bacteria in urinary specimens, but it is typically restricted to genus-level identification. Our primary aim here was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA amplicon sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a reference database, a 16S rRNA gene variable region, and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible and that the reference database chosen is the most important component, followed by the 16S variable region sequenced. IMPORTANCE Accurate species-level identification from culture-independent techniques is of importance for microbial niches that are less well characterized, such as that of the bladder. 16S rRNA amplicon sequencing, a common culture-independent way to identify bacteria, is often critiqued for lacking species-level resolution. Here, we extensively evaluate classification schemes for species-level bacterial annotation of 16S amplicon data from bladder bacteria. Our results show that the proper choice of taxonomic database and variable region of the 16S rRNA gene sequence makes species level identification possible. We also show that this improvement can be achieved through the more careful application of existing methods and resources. Species-level information may deepen our understanding of associations between bacteria in the bladder and bladder conditions such as lower urinary tract symptoms and urinary tract infections.
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Affiliation(s)
- Carter Hoffman
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Nazema Y. Siddiqui
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina, USA
| | - Ian Fields
- Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - W. Thomas Gregory
- Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Michael A. Mooney
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Lisa Karstens
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
- Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
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Abstract
The introduction of next generation sequencing techniques has enabled the characterization of the urinary tract microbiome, which resulted in the rejection of the long-held notion of urinary bladder sterility. Since the discovery and confirmation of the human bladder microbiome, an increasing number of studies have defined this microbial community and understand better its relationship to urinary pathologies. The composition of microbial communities in the urinary tract is linked to a variety of urinary diseases. The purpose of this review is to provide an overview of current information about the urinary microbiome and diseases as well as the development of novel treatment methods.
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Brubaker L, Gourdine JPF, Siddiqui NY, Holland A, Halverson T, Limeria R, Pride D, Ackerman L, Forster CS, Jacobs KM, Thomas-White KJ, Putonti C, Dong Q, Weinstein M, Lukacz ES, Karstens L, Wolfe AJ. Forming Consensus To Advance Urobiome Research. mSystems 2021; 6:e0137120. [PMID: 34282932 PMCID: PMC8409733 DOI: 10.1128/msystems.01371-20] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good. This consensus document, developed by a group of expert investigators currently engaged in urobiome research (UROBIOME 2020 conference participants), aims to promote standardization and advances in this field by the adoption of common core research practices. We propose a standardized nomenclature as well as considerations for specimen collection, preservation, storage, and processing. Best practices for urobiome study design include our proposal for standard metadata elements as part of core metadata collection. Although it is impractical to follow fixed analytical procedures when analyzing urobiome data, we propose guidelines to document and report data originating from urobiome studies. We offer this first consensus document with every expectation of subsequent revision as our field progresses.
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Affiliation(s)
- Linda Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, California, USA
| | - Jean-Philippe F. Gourdine
- Oregon Clinical & Translational Research Institute (OCTRI), Oregon Health & Science University, Portland, Oregon, USA
| | - Nazema Y. Siddiqui
- Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Duke University, Durham, North Carolina, USA
| | - Amanda Holland
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Thomas Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Roberto Limeria
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, San Diego, California, USA
- Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Lenore Ackerman
- Department of Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, Los Angeles, Los Angeles, California, USA
| | - Catherine S. Forster
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kristin M. Jacobs
- Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Rush University, Chicago, Illinois, USA
| | - Krystal J. Thomas-White
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine Putonti
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Qunfeng Dong
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Center for Biomedical Informatics, Loyola University Chicago, Chicago, Illinois, USA
| | - Michael Weinstein
- Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA
- Zymo Research, Irvine, California, USA
| | - Emily S. Lukacz
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, California, USA
| | - Lisa Karstens
- Department of Clinical Epidemiology and Medical Informatics, Oregon Health & Science University, Portland, Oregon, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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37
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Ozer MS, Yildiz HA, Incir C, Deger MD, Bozkurt O, Ergor G, Tuncok Y, Esen N, Esen AA. Urinary microbiota; Which non-ınvasive urine collection method should we use? Int J Clin Pract 2021; 75:e14193. [PMID: 33797158 DOI: 10.1111/ijcp.14193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/27/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE The aim of this study is to establish the optimal non-invasive urine sample collection method for the microbiota studies. METHODOLOGY Twelve men with bladder carcinoma underwent first voided and midstream urine collection. Urine samples were analysed using V3-V4 regions of bacterial 16s ribosomal RNAs. Bacterial groups with relative abundance above 1% were analysed in first voided urine and midstream urine samples at phylum, class, order and family level. At the genus level, all of the identified bacterial groups' relative abundances were analysed. The statistical significance (P < .05) of differences between first voided and midstream urine sample microbiota was evaluated using the Wilcoxon test. RESULTS According to the analysis, 8 phyla, 14 class, 23 orders, 39 families and 29 different genera were identified in the first voided and the midstream urine samples. Statistical differences were not identified between first voided and midstream urine samples of all bacteria groups except the Clostridiales at order level (p:0.04) and Clostridia at class level (P: .04). CONCLUSIONS Either first voided or midstream urine samples can be used in urinary microbiota studies as we determined that there is no statistically significant difference between them regarding the results of 16s ribosomal RNA analysis.
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Affiliation(s)
- Muhammed Selcuk Ozer
- Department of Urology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | | | - Canet Incir
- Department of Medical Pharmacology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Muslim Dogan Deger
- Department of Urology, Edirne Sultan 1. Murat State Hospital, Edirne, Turkey
| | - Ozan Bozkurt
- Department of Urology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Gul Ergor
- Department of Public Health, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Yesim Tuncok
- Department of Medical Pharmacology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Nuran Esen
- Department of Microbiology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Ahmet Adil Esen
- Department of Urology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
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Jones-Freeman B, Chonwerawong M, Marcelino VR, Deshpande AV, Forster SC, Starkey MR. The microbiome and host mucosal interactions in urinary tract diseases. Mucosal Immunol 2021; 14:779-792. [PMID: 33542492 DOI: 10.1038/s41385-020-00372-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.
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Affiliation(s)
- Bernadette Jones-Freeman
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Aniruddh V Deshpande
- Priority Research Centre GrowUpWell, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia.,Department of Pediatric Urology and Surgery, John Hunter Children's Hospital, New Lambton Heights, NSW, Australia.,Urology Unit, Department of Pediatric Surgery, Children's Hospital at Westmead, Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Malcolm R Starkey
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Priority Research Centre GrowUpWell, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia.
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Molina NM, Plaza-Díaz J, Vilchez-Vargas R, Sola-Leyva A, Vargas E, Mendoza-Tesarik R, Galán-Lázaro M, Mendoza-Ladrón de Guevara N, Tesarik J, Altmäe S. Assessing the testicular sperm microbiome: a low-biomass site with abundant contamination. Reprod Biomed Online 2021; 43:523-531. [PMID: 34344601 DOI: 10.1016/j.rbmo.2021.06.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/19/2021] [Accepted: 06/22/2021] [Indexed: 12/31/2022]
Abstract
RESEARCH QUESTION The semen harbours a diverse range of microorganisms. The origin of the seminal microbes, however, has not yet been established. Do testicular spermatozoa harbour microbes and could they potentially contribute to the seminal microbiome composition? DESIGN The study included 24 samples, comprising a total of 307 testicular maturing spermatozoa. A high-throughput sequencing method targeting V3 and V4 regions of 16S rRNA gene was applied. A series of negative controls together with stringent in-silico decontamination methods were analysed. RESULTS Between 50 and 70% of all the detected bacterial reads accounted for contamination in the testicular sperm samples. After stringent decontamination, Blautia (P = 0.04), Cellulosibacter (P = 0.02), Clostridium XIVa (P = 0.01), Clostridium XIVb (P = 0.04), Clostridium XVIII (P = 0.02), Collinsella (P = 0.005), Prevotella (P = 0.04), Prolixibacter (P = 0.02), Robinsoniella (P = 0.04), and Wandonia (P = 0.04) genera demonstrated statistically significant abundance among immature spermatozoa. CONCLUSIONS Our results indicate that the human testicle harbours potential bacterial signature, though in a low-biomass, and could contribute to the seminal microbiome composition. Further, applying stringent decontamination methods is crucial for analysing microbiome in low-biomass site.
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Affiliation(s)
- Nerea M Molina
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Julio Plaza-Díaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain; University of Granada, Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, Granada 18071, Spain; Institute of Nutrition and Food Technology (INYTA), 'José Mataix Verdú' Biomedical Research Centre (CIBM), University of Granada, Granada 18016, Spain; Children's Hospital of Eastern Ontario Research Institute, Ottawa ON K1H 8L1, Canada
| | - Ramiro Vilchez-Vargas
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto von Guericke University Hospital Magdeburg, Magdeburg 39120, Germany
| | - Alberto Sola-Leyva
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Eva Vargas
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen 23071, Spain
| | | | - Maribel Galán-Lázaro
- MARGen Clinic, Molecular Assisted Reproduction and Genetics, Granada 18006, Spain
| | | | - Jan Tesarik
- MARGen Clinic, Molecular Assisted Reproduction and Genetics, Granada 18006, Spain
| | - Signe Altmäe
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Sciences, Granada 18071, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain; Competence Centre on Health Technologies, Tartu 50410, Estonia.
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Parente G, Gargano T, Pavia S, Cordola C, Vastano M, Baccelli F, Gallotta G, Bruni L, Corvaglia A, Lima M. Pyelonephritis in Pediatric Uropathic Patients: Differences from Community-Acquired Ones and Therapeutic Protocol Considerations. A 10-Year Single-Center Retrospective Study. CHILDREN-BASEL 2021; 8:children8060436. [PMID: 34071019 PMCID: PMC8224700 DOI: 10.3390/children8060436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022]
Abstract
Pyelonephritis (PN) represents an important cause of morbidity in the pediatric population, especially in uropathic patients. The aim of the study is to demonstrate differences between PNs of uropathic patients and PNs acquired in community in terms of uropathogens involved and antibiotic sensitivity; moreover, to identify a proper empiric therapeutic strategy. A retrospective study was conducted on antibiograms on urine cultures from PNs in vesicoureteral reflux (VUR) patients admitted to pediatric surgery department and from PNs in not VUR patients admitted to Pediatric Emergency Unit between 2010 and 2020. We recorded 58 PNs in 33 patients affected by VUR and 112 PNs in the not VUR group. The mean age of not VUR patients at the PN episode was 1.3 ± 2.6 years (range: 20 days of life–3 years), and almost all the urine cultures, 111 (99.1%), isolated Gram-negative bacteria and rarely, 1 (0.9%), Gram-positive bacteria. The Gram-negative uropathogens isolated were Escherichia coli (97%), Proteus mirabilis (2%), and Klebsiella spp. (1%). The only Gram-positive bacteria isolated was an Enterococcus faecalis. As regards the antibiograms, 96% of not VUR PNs responded to beta-lactams, 99% to aminoglycosides, and 80% to sulfonamides. For the VUR group, mean age was 3.0 years ± 3.0 years (range: 9 days of life–11 years) and mean number of episodes per patient was 2.0 ± 1.0 (range: 1–5); 83% of PNs were by Gram-negatives bacteria vs. 17% by Gram-positive: the most important Gram-negative bacteria were Pseudomonas aeruginosa (44%), Escherichia coli (27%), and Klebsiella spp. (12%), while Enterococcus spp. determined 90% of Gram-positive UTIs. Regimen ampicillin/ceftazidime (success rate: 72.0%) was compared to ampicillin/amikacin (success rate of 83.0%): no statistically significant difference was found (p = 0.09). The pathogens of PNs in uropathic patients are different from those of community-acquired PNs, and clinicians should be aware of their peculiar antibiotic susceptibility. An empiric therapy based on the association ampicillin + ceftazidime is therefore suggested.
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Affiliation(s)
- Giovanni Parente
- Pediatric Surgery Department, IRCCS Sant’Orsola-Malpighi University Hospital, via Massarenti 11, 40138 Bologna, Italy; (T.G.); (S.P.); (C.C.); (M.V.); (M.L.)
- Correspondence:
| | - Tommaso Gargano
- Pediatric Surgery Department, IRCCS Sant’Orsola-Malpighi University Hospital, via Massarenti 11, 40138 Bologna, Italy; (T.G.); (S.P.); (C.C.); (M.V.); (M.L.)
| | - Stefania Pavia
- Pediatric Surgery Department, IRCCS Sant’Orsola-Malpighi University Hospital, via Massarenti 11, 40138 Bologna, Italy; (T.G.); (S.P.); (C.C.); (M.V.); (M.L.)
| | - Chiara Cordola
- Pediatric Surgery Department, IRCCS Sant’Orsola-Malpighi University Hospital, via Massarenti 11, 40138 Bologna, Italy; (T.G.); (S.P.); (C.C.); (M.V.); (M.L.)
| | - Marzia Vastano
- Pediatric Surgery Department, IRCCS Sant’Orsola-Malpighi University Hospital, via Massarenti 11, 40138 Bologna, Italy; (T.G.); (S.P.); (C.C.); (M.V.); (M.L.)
| | - Francesco Baccelli
- Specialty School of Paediatrics, Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (F.B.); (G.G.); (L.B.)
| | - Giulia Gallotta
- Specialty School of Paediatrics, Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (F.B.); (G.G.); (L.B.)
| | - Laura Bruni
- Specialty School of Paediatrics, Alma Mater Studiorum—University of Bologna, 40138 Bologna, Italy; (F.B.); (G.G.); (L.B.)
| | - Adelaide Corvaglia
- School of Medicine, Alma Mater Studiorum—University of Bologna, 40126 Bologna, Italy;
| | - Mario Lima
- Pediatric Surgery Department, IRCCS Sant’Orsola-Malpighi University Hospital, via Massarenti 11, 40138 Bologna, Italy; (T.G.); (S.P.); (C.C.); (M.V.); (M.L.)
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41
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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: 90] [Impact Index Per Article: 30.0] [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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42
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Abstract
Ureteral stents are commonly used medical devices that harbor a unique and patient-specific microbial community. This protocol describes an optimized procedure for high-quality DNA extraction from both urine and ureteral stent samples for the purpose of downstream microbiota characterization by amplicon sequencing. Detailed instruction is provided for 16S rRNA gene V4 region sequencing with the Illumina platform, which enables accurate and reproducible microbiota profiling of low bacterial abundance urine and stent samples. For complete details on the use and execution of this protocol, please refer to Al et al. (2020). The urinary tract harbors low-abundance microbiota capable of influencing health Traditional sample preparation yields variable results vulnerable to contamination Protocol optimizes urological specimen processing for 16S rRNA amplicon sequencing The method ensures high-quality, reproducible urological microbiota data generation
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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
| | - 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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43
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Benchmarking DNA isolation kits used in analyses of the urinary microbiome. Sci Rep 2021; 11:6186. [PMID: 33731788 PMCID: PMC7969918 DOI: 10.1038/s41598-021-85482-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 03/02/2021] [Indexed: 12/22/2022] Open
Abstract
The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
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44
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Ceprnja M, Oros D, Melvan E, Svetlicic E, Skrlin J, Barisic K, Starcevic L, Zucko J, Starcevic A. Modeling of Urinary Microbiota Associated With Cystitis. Front Cell Infect Microbiol 2021; 11:643638. [PMID: 33796485 PMCID: PMC8008076 DOI: 10.3389/fcimb.2021.643638] [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] [Received: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 01/04/2023] Open
Abstract
A decade ago, when the Human Microbiome Project was starting, urinary tract (UT) was not included because the bladder and urine were considered to be sterile. Today, we are presented with evidence that healthy UT possesses native microbiota and any major event disrupting its “equilibrium” can impact the host also. This dysbiosis often leads to cystitis symptoms, which is the most frequent lower UT complaint, especially among women. Cystitis is one of the most common causes of antimicrobial drugs prescriptions in primary and secondary care and an important contributor to the problem of antimicrobial resistance. Despite this fact, we still have trouble distinguishing whether the primary cause of majority of cystitis cases is a single pathogen overgrowth, or a systemic disorder affecting entire UT microbiota. There are relatively few studies monitoring changes and dynamics of UT microbiota in cystitis patients, making this field of research still an unknown. In this study variations to the UT microbiota of cystitis patients were identified and microbial dynamics has been modeled. The microbial genetic profile of urine samples from 28 patients was analyzed by 16S rDNA Illumina sequencing and bioinformatics analysis. One patient with bacterial cystitis symptoms was prescribed therapy based on national guideline recommendations on antibacterial treatment of urinary tract infections (UTI) and UT microbiota change was monitored by 16S rDNA sequencing on 24 h basis during the entire therapy duration. The results of sequencing implied that a particular class of bacteria is associated with majority of cystitis cases in this study. The contributing role of this class of bacteria – Gammaproteobacteria, was further predicted by generalized Lotka-Volterra modeling (gLVM). Longitudinal microbiota insight obtained from a single patient under prescribed antimicrobial therapy revealed rapid and extensive changes in microbial composition and emphasized the need for current guidelines revision in regards to therapy duration. Models based on gLVM indicated protective role of two taxonomic classes of bacteria, Actinobacteria and Bacteroidia class, which appear to actively suppress pathogen overgrowth.
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Affiliation(s)
- Marina Ceprnja
- Biochemical Laboratory, Special Hospital Agram, Polyclinic Zagreb, Zagreb, Croatia.,Department of Medical Biochemistry and Hematology, Faculty of Pharmacy and Biochemistry, Zagreb University, Zagreb, Croatia
| | - Damir Oros
- Laboratory for Bioinformatics, Faculty of Food Technology and Biotechnology, Zagreb University, Zagreb, Croatia
| | - Ena Melvan
- Laboratory for Bioinformatics, Faculty of Food Technology and Biotechnology, Zagreb University, Zagreb, Croatia.,Department of Biological Science, Faculty of Science, Macquarie University, Sydney, NSW, Australia
| | - Ema Svetlicic
- Laboratory for Bioinformatics, Faculty of Food Technology and Biotechnology, Zagreb University, Zagreb, Croatia
| | - Jasenka Skrlin
- Department for Clinical Microbiology and Hospital Infection, University Hospital Dubrava, Zagreb, Croatia
| | - Karmela Barisic
- Department of Medical Biochemistry and Hematology, Faculty of Pharmacy and Biochemistry, Zagreb University, Zagreb, Croatia
| | - Lucija Starcevic
- Laboratory for Bioinformatics, Faculty of Food Technology and Biotechnology, Zagreb University, Zagreb, Croatia
| | - Jurica Zucko
- Laboratory for Bioinformatics, Faculty of Food Technology and Biotechnology, Zagreb University, Zagreb, Croatia
| | - Antonio Starcevic
- Laboratory for Bioinformatics, Faculty of Food Technology and Biotechnology, Zagreb University, Zagreb, Croatia
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45
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Yoo JJ, Shin HB, Song JS, Kim M, Yun J, Kim Z, Lee YM, Lee SW, Lee KW, Kim WB, Ryu CB, Park SW, Park SK, Song HY, Kim YH. Urinary Microbiome Characteristics in Female Patients with Acute Uncomplicated Cystitis and Recurrent Cystitis. J Clin Med 2021; 10:jcm10051097. [PMID: 33807946 PMCID: PMC7961880 DOI: 10.3390/jcm10051097] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
Traditionally, the diagnostic mainstay of recurrent urinary tract infection has been urinary culture. However, the causative uropathogen of recurrent cystitis has not been well established. Urine DNA next-generation sequencing (NGS) can provide additional information on these infections. Herein, we compared urine NGS results and urine cultures in patients with acute uncomplicated cystitis (AUC) and recurrent cystitis (RC), and evaluated the difference in microbiome patterns in the NGS results. Patients who underwent urine culture and NGS due to AUC or RC were retrospectively reviewed. All urine samples were collected via a transurethral catheter and studied utilizing a type of NGS called 16S ribosomal RNA gene amplification and sequencing. The sensitivity of urine NGS was significantly higher than that of conventional urine culture (69.0% vs. 16.7%, p < 0.05). The detection rate of urine NGS was slightly lower in the RC group than in the AUC group (67.7% vs. 72.7%). Microbiome diversity was significantly higher in the RC group compared to the AUC group (p = 0.007), and the microbiome composition was significantly different between the AUC and RC groups. In the urine NGS results, Pseudomonas, Acinetobacter, and Enterobacteriaceae were found in the AUC group, and Sphingomonas, Staphylococcus, Streptococcus, and Rothia spp. were detected in the RC group. Urine NGS can significantly increase the diagnostic sensitivity compared to traditional urine culture methods, especially in RC patients. AUC and RC patients had significant differences in bacterial diversity and patterns. Therefore, recurrent cystitis might be approached from a different perspective.
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Affiliation(s)
- Jeong-Ju Yoo
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (J.-J.Y.); (J.Y.); (C.B.R.); (S.-W.P.); (S.K.P.)
| | - Hee Bong Shin
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea;
| | - Ju Sun Song
- GC Genome, Green Cross Laboratories, Department of Laboratory Medicine, Yongin 16924, Korea; (J.S.S.); (M.K.)
| | - Minjung Kim
- GC Genome, Green Cross Laboratories, Department of Laboratory Medicine, Yongin 16924, Korea; (J.S.S.); (M.K.)
| | - Jina Yun
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (J.-J.Y.); (J.Y.); (C.B.R.); (S.-W.P.); (S.K.P.)
| | - Zisun Kim
- Department of Surgery, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea;
| | - Yoo Min Lee
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea;
| | - Sang Wook Lee
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (S.W.L.); (K.W.L.); (W.b.K.)
| | - Kwang Woo Lee
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (S.W.L.); (K.W.L.); (W.b.K.)
| | - Woong bin Kim
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (S.W.L.); (K.W.L.); (W.b.K.)
| | - Chang Beom Ryu
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (J.-J.Y.); (J.Y.); (C.B.R.); (S.-W.P.); (S.K.P.)
| | - Sung-Woo Park
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (J.-J.Y.); (J.Y.); (C.B.R.); (S.-W.P.); (S.K.P.)
| | - Seong Kyu Park
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (J.-J.Y.); (J.Y.); (C.B.R.); (S.-W.P.); (S.K.P.)
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Korea;
| | - Young Ho Kim
- Department of Urology, Soonchunhyang University Bucheon Hospital, Bucheon 14584, Korea; (S.W.L.); (K.W.L.); (W.b.K.)
- Correspondence: ; Tel.: +82-32-621-5463
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46
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Ksiezarek M, Ugarcina-Perovic S, Rocha J, Grosso F, Peixe L. Long-term stability of the urogenital microbiota of asymptomatic European women. BMC Microbiol 2021; 21:64. [PMID: 33632119 PMCID: PMC7905919 DOI: 10.1186/s12866-021-02123-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Background To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates’ identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM. Results Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5–39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found. A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1–41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance. Conclusions Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals. Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract. This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02123-3.
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Affiliation(s)
- Magdalena Ksiezarek
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Svetlana Ugarcina-Perovic
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Joana Rocha
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal.
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47
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Molina NM, Sola-Leyva A, Haahr T, Aghajanova L, Laudanski P, Castilla JA, Altmäe S. Analysing endometrial microbiome: methodological considerations and recommendations for good practice. Hum Reprod 2021; 36:859-879. [DOI: 10.1093/humrep/deab009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
There is growing evidence that the upper female genital tract is not sterile, harbouring its own microbial communities. However, the significance and the potential effect of endometrial microorganisms on reproductive functions remain to be fully elucidated. Analysing the endometrial microbiome, the microbes and their genetic material present in the endometrium, is an emerging area of study. The initial studies suggest it is associated with poor reproductive outcomes and with different gynaecological pathologies. Nevertheless, studying a low-biomass microbial niche as is endometrium, the challenge is to conduct well-designed and well-controlled experiments in order to avoid and adjust for the risk of contamination, especially from the lower genital tract. Herein, we aim to highlight methodological considerations and propose good practice recommendations for future endometrial microbiome studies.
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Affiliation(s)
- Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Thor Haahr
- The Fertility Clinic, Skive Regional Hospital, Skive 7800, Denmark
| | - Lusine Aghajanova
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford School of Medicine, Sunnyvale, CA 94087, USA
| | - Piotr Laudanski
- Department of Obstetrics and Gynecology, Medical University of Warsaw, Warsaw 02-015, Poland
| | - Jose Antonio Castilla
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, Granada 18012, Spain
- CEIFER Biobanco—NextClinics, Granada 18004, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Competence Centre on Health Technologies, Tartu 50410, Estonia
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48
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Qin J, Shi X, Xu J, Yuan S, Zheng B, Zhang E, Huang G, Li G, Jiang G, Gao S, Tian C, Guo R, Fu Z, Huang Q, Yang R, Zhang W, Li S, Wu S. Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals. Front Microbiol 2021; 12:673969. [PMID: 34489882 PMCID: PMC8417382 DOI: 10.3389/fmicb.2021.673969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/27/2021] [Indexed: 02/05/2023] Open
Abstract
Accumulated evidence shows that complex microbial communities resides in the healthy human urinary tract and can change in urological disorders. However, there lacks a comprehensive profiling of the genitourinary microbiota in healthy cohort. Here, we performed 16S rRNA gene sequencing of midstream urine specimens from 1,172 middle-aged and elderly healthy individuals. The core microbiota included 6 dominant genera (mean relative abundance >5%), including Prevotella, Streptococcus, Lactobacillus, Gardnerella, Escherichia-Shigella, and Veillonella, and 131 low-abundance genera (0.01-5%), displaying a distinct microbiome profiles to that of host-matched gut microbiota. The composition and diversity of genitourinary microbiome (GM) were distinct between genders and may fluctuate with ages. Several urotypes were identified by the stratification of microbiome profiles, which were mainly dominated by the six most predominant genera. The prevalence of urotypes was disparate between genders, and the male sample additionally harbored other urotypes dominated by Acinetobacter, Corynebacterium, Staphylococcus, or Sphingomonas. Peptoniphilus, Ezakiella, and Porphyromonas were co-occurred and co-abundant, and they may play crucial roles as keystone genera and be associated with increased microbial diversity. Our results delineated the microbial structure and diversity landscape of the GM in healthy middle-aged and elderly adults and provided insights into the influence of gender and age to it.
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Affiliation(s)
- Junjie Qin
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, China
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Xulian Shi
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Junming Xu
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, China
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Simin Yuan
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Bo Zheng
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, China
| | - Enpu Zhang
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Guixiao Huang
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Guo Li
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Ganggang Jiang
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Shan Gao
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Cheng Tian
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Ruochun Guo
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Zhicong Fu
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Qingru Huang
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Rentao Yang
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Wenyong Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Shenghui Li
- Department of Human Microbiome, Promegene Institute, Shenzhen, China
| | - Song Wu
- Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, China
- Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Song Wu,
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49
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Chen C, Hao L, Wei W, Li F, Song L, Zhang X, Dai J, Jie Z, Li J, Song X, Wang Z, Zhang Z, Zeng L, Du H, Tang H, Zhang T, Yang H, Wang J, Brix S, Kristiansen K, Xu X, Wu R, Jia H. The female urinary microbiota in relation to the reproductive tract microbiota. GIGABYTE 2020; 2020:gigabyte9. [PMID: 36824591 PMCID: PMC9632005 DOI: 10.46471/gigabyte.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/26/2020] [Indexed: 11/09/2022] Open
Abstract
Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the female reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.
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Affiliation(s)
- Chen Chen
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China,Department of Biology, Ole MaalØes Vej 5, University of Copenhagen, Copenhagen, Denmark
| | - Lilan Hao
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Weixia Wei
- Peking University Shenzhen Hospital, Shenzhen 518036, China,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, PR China
| | - Fei Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liju Song
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiaowei Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Juanjuan Dai
- Peking University Shenzhen Hospital, Shenzhen 518036, China,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, PR China
| | - Zhuye Jie
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | - Jiandong Li
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | | | | | - Zhe Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Liping Zeng
- Peking University Shenzhen Hospital, Shenzhen 518036, China,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, PR China
| | - Hui Du
- Peking University Shenzhen Hospital, Shenzhen 518036, China,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, PR China
| | - Huiru Tang
- Peking University Shenzhen Hospital, Shenzhen 518036, China,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, PR China
| | - Tao Zhang
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China,Department of Biology, Ole MaalØes Vej 5, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China
| | - Ruifang Wu
- Peking University Shenzhen Hospital, Shenzhen 518036, China,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, PR China, Corresponding authors. E-mail: ;
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen 518083, China,China National Genebank, BGI-Shenzhen, Shenzhen 518120, China,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China,Macau University of Science and Technology, Taipa, Macau 999078, China, Corresponding authors. E-mail: ;
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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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