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Mofolorunsho KC, Mabaso NG, Nundlall N, Ojo AO, Cason ED, Abbai NS. Comparison of the urinary microbiome in men who have sex with men with and without Chlamydia trachomatis infection. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04930-8. [PMID: 39259456 DOI: 10.1007/s10096-024-04930-8] [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: 06/07/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024]
Abstract
PURPOSE The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis. METHODS This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform. RESULTS Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385). CONCLUSION Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM.
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Affiliation(s)
- Kehinde C Mofolorunsho
- School of Clinical Medicine Laboratory, College of Health Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Nonkululeko G Mabaso
- School of Clinical Medicine Laboratory, College of Health Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Nikita Nundlall
- School of Clinical Medicine Laboratory, College of Health Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Abidemi O Ojo
- Centre for Applied Food Sustainability and Biotechnology (CAFSaB), Central University of Technology, Bloemfontein, South Africa
| | - Errol D Cason
- Department of Animal Science, University of the Free State, Bloemfontein, South Africa
| | - Nathlee S Abbai
- School of Clinical Medicine Laboratory, College of Health Sciences, University of KwaZulu- Natal, Durban, South Africa.
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2
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Pallares-Mendez R, Brassetti A, Bove AM, Simone G. Insights into the Interplay between the Urinary Microbiome and Bladder Cancer: A Comprehensive Review. J Clin Med 2024; 13:4927. [PMID: 39201069 PMCID: PMC11355659 DOI: 10.3390/jcm13164927] [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: 07/17/2024] [Revised: 08/11/2024] [Accepted: 08/18/2024] [Indexed: 09/02/2024] Open
Abstract
New insights in the urinary microbiome have led to a better understanding being built of the shifts in bacterial representations from health to disease; these hold promise as markers for diagnosis and therapeutic responses. Although several efforts have been made to identify a "core urinary microbiome", different fingerprints have been identified in men and women that shift with age. The main bacterial groups overall include Firmicutes, Actinobacteria, Fusobacteria, and Bacteroidetes. Although patients with bladder cancer have a microbiome that is similar to that of healthy individuals, differences have been observed at the species level with Fusobacterium nucleatum and Ralstonia, and at the genus level with Cutibacterium. Different bacterial representations may influence extracellular matrix composition, affecting tumor metastatic spreading and tumorigenic metalloproteinase expression. Furthermore, gene expression affecting targets of immune therapy, such as PD-L1, has been associated with changes in bacterial representations and therapeutic response to BCG. This comprehensive review aims to examine the influence of the urinary microbiome in bladder cancer.
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Affiliation(s)
| | - Aldo Brassetti
- Department of Urology, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00128 Rome, Italy; (R.P.-M.)
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3
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Costa Silva A, Pina-Vaz T, Morgado A, Martins-Silva C, Antunes-Lopes T, Alturas Silva J. The Role of the Urobiome in Kidney Transplantation: A Systematic Review. Transplant Direct 2024; 10:e1643. [PMID: 38769976 PMCID: PMC11104728 DOI: 10.1097/txd.0000000000001643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 05/22/2024] Open
Abstract
Background The urinary microbiome, also known as the urobiome, was traditionally considered sterile. However, emerging evidence suggests its presence in the urinary tract. Urobiome dysbiosis has been associated with various urologic conditions, making it a topic of interest also in kidney transplantation. This systematic review examines the evidence of urobiome changes in kidney transplant recipients (KTRs). Methods Systematic literature searches in the PubMed and SCOPUS databases. Results Of the 770 articles identified, 8 met the inclusion criteria. The urobiome showed reduced diversity in KTRs compared with healthy controls and patients on dialysis. Proteobacteria enrichment was associated with graft stability or spontaneous tolerance in KTRs without immunological events. Kidney interstitial fibrosis and tubular atrophy were associated with changes in resident urinary microbes and increased pathogenic bacteria. Additionally, KTRs with chronic allograft dysfunction had a higher prevalence of Corynebacterium. Conclusions The review highlights the importance of studying the urobiome in KTRs and its potential impact on transplant outcomes. The field remains largely unexplored, and further research is needed to establish consistent study designs and objectives. Future studies could lead to biomarker discovery, personalized therapies, and improved outcomes and graft survival in KTRs.
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Affiliation(s)
- Alberto Costa Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Teresa Pina-Vaz
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Afonso Morgado
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Carlos Martins-Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Tiago Antunes-Lopes
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - João Alturas Silva
- Urology Department, University Hospital Center of São João, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
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4
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Li J, Li Y, Zhou L, Li C, Liu J, Liu D, Fu Y, Wang Y, Tang J, Zhou L, Tan S, Wang L. The human microbiome and benign prostatic hyperplasia: Current understandings and clinical implications. Microbiol Res 2024; 281:127596. [PMID: 38215640 DOI: 10.1016/j.micres.2023.127596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]
Abstract
The research of the human microbiome in the preceding decade has yielded novel perspectives on human health and diseases. Benign prostatic hyperplasia (BPH) is a common disease in middle-aged and elderly males, which negatively affects the life quality. Existing evidence has indicated that the human microbiome, including urinary, intra-prostate, gut, oral and blood microbiome may exert a significant impact on the natural progression of BPH. The dysbiosis of the microbiome may induce inflammation at either a local or systemic level, thereby affecting the BPH. Moreover, metabolic syndrome (MetS) caused by the microbiome can also be involved in the development of BPH. Additionally, alterations in the microbiome composition during the senility process may serve as another cause of the BPH. Here, we summarize the influence of human microbiome on BPH and explore how the microbiome is linked to BPH through inflammation, MetS, and senility. In addition, we propose promising areas of investigation and discuss the implications for advancing therapeutic approaches.
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Affiliation(s)
- Jiaren Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Youyou Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Liang Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Cheng Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jiahao Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Dingwen Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yunlong Fu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yichuan Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jin Tang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Lei Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Shuo Tan
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China.
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5
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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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6
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Kustrimovic N, Bilato G, Mortara L, Baci D. The Urinary Microbiome in Health and Disease: Relevance for Bladder Cancer. Int J Mol Sci 2024; 25:1732. [PMID: 38339010 PMCID: PMC10855347 DOI: 10.3390/ijms25031732] [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: 12/19/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Bladder cancer (BC) constitutes one of the most diagnosed types of cancer worldwide. Advancements in and new methodologies for DNA sequencing, leading to high-throughput microbiota testing, have pinpointed discrepancies in urinary microbial fingerprints between healthy individuals and patients with BC. Although several studies suggest an involvement of microbiota dysbiosis in the pathogenesis, progression, and therapeutic response to bladder cancer, an established direct causal relationship remains to be elucidated due to the lack of standardized methodologies associated with such studies. This review compiles an overview of the microbiota of the human urinary tract in healthy and diseased individuals and discusses the evidence to date on microbiome involvement and potential mechanisms by which the microbiota may contribute to the development of BC. We also explore the potential profiling of urinary microbiota as a biomarker for risk stratification, as well as the prediction of the response to intravesical therapies and immunotherapy in BC patients. Further investigation into the urinary microbiome of BC patients is imperative to unravel the complexities of the role played by host-microbe interactions in shaping wellness or disease and yield valuable insights into and strategies for the prevention and personalized treatment of BC.
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Affiliation(s)
- Natasa Kustrimovic
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy;
| | - Giorgia Bilato
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy;
| | - Lorenzo Mortara
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy;
| | - Denisa Baci
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy;
- Molecular Cardiology Laboratory, IRCCS—Policlinico San Donato, 20097 Milan, Italy
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7
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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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8
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Dickson K, Zhou J, Lehmann C. Lower Urinary Tract Inflammation and Infection: Key Microbiological and Immunological Aspects. J Clin Med 2024; 13:315. [PMID: 38256450 PMCID: PMC10816374 DOI: 10.3390/jcm13020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The urinary system, primarily responsible for the filtration of blood and waste, is affected by several infectious and inflammatory conditions. Focusing on the lower tract, this review outlines the physiological and immune landscape of the urethra and bladder, addressing key immunological and microbiological aspects of important infectious/inflammatory conditions. The conditions addressed include urethritis, interstitial cystitis/bladder pain syndrome, urinary tract infections, and urosepsis. Key aspects of each condition are addressed, including epidemiology, pathophysiology, and clinical considerations. Finally, therapeutic options are outlined, highlighting gaps in the knowledge and novel therapeutic approaches.
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Affiliation(s)
- Kayle Dickson
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada;
| | - Juan Zhou
- Department of Anesthesiology, Pain Management and Perioperative Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada;
| | - Christian Lehmann
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada;
- Department of Anesthesiology, Pain Management and Perioperative Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada;
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada
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9
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Nardelli C, Aveta A, Pandolfo SD, Tripodi L, Russo F, Imbimbo C, Castaldo G, Pastore L. Microbiome Profiling in Bladder Cancer Patients Using the First-morning Urine Sample. EUR UROL SUPPL 2024; 59:18-26. [PMID: 38298766 PMCID: PMC10829607 DOI: 10.1016/j.euros.2023.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2023] [Indexed: 02/02/2024] Open
Abstract
Background Several studies support the interplay between the urinary microbiome (ie, urobiome) and bladder cancer (BCa). Specific urinary bacteria may be responsible for chronic inflammation, which in turn promotes carcinogenesis. Different signatures of urobiome in BCa patients were identified depending on tumor type, geographical area, age, and sex. Objective We explored the urobiome in BCa patients undergoing transurethral resection of bladder tumor (TURBT), to identify possible predictive biomarkers of cancer. Design setting and participants The urobiome analysis was conducted in 48 patients (13 females) undergoing TURBT, of whom 30 with BCa (five females) and 18 with benign bladder tumor, analyzing bacterial 16S rRNA by next-generation sequencing in first-morning (FM) urine samples. Forty-three cancer-free individuals and 17 prostate cancer patients were used as controls. Outcome measurements and statistical analysis First, we identified the better urine collection procedure to perform the urobiome analysis, comparing bacterial composition between catheterized (CAT) and FM urine samples in TURBT patients. Successively, we observed a specific urobiome in BCa patients rather than controls. A combined pipeline including the DESeq2 and linear discriminant analysis effect size tests was used to identify differential urinary taxa, strictly associated with BCa patients. Results and limitations The bacterial composition of CAT and FM urine samples was comparable, so the latter was used for the following analyses. An increased abundance of Porphyromonas and Porphyromonas somerae was found in BCa patients compared with controls. This signature seems to be more related (p <0.05) to male BCa patients over 50 yr old. Owing to the low biomass of urinary microbiota, several samples were excluded from the study, reducing the number of BCa patients considered. Conclusions FM urine samples represent a manageable specimen for a urobiome analysis; P. somerae is a specific biomarker of BCa risk. Patient summary Our study showed an increased abundance of Porphyromonas and Porphyromonas somerae in male bladder cancer (BCa) patients, supporting the use of a first-morning urine sample, a less invasive and low-cost collection method, for the urobiome analysis of patients at risk of BCa.
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Affiliation(s)
- Carmela Nardelli
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Achille Aveta
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Savio Domenico Pandolfo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
- Department of Urology, University of L'Aquila, L'Aquila, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Filippo Russo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Ciro Imbimbo
- Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
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10
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Bowie KR, Garzotto M, Orwoll E, Karstens L. BMI and BPH correlate with urinary microbiome diversity and lower urinary tract symptoms in men. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571758. [PMID: 38168244 PMCID: PMC10760175 DOI: 10.1101/2023.12.14.571758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.
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Affiliation(s)
- Kate R Bowie
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark Garzotto
- School of Medicine, Oregon Health & Science University, Portland, OR, USA
- Portland VA Medical Center, Portland, Oregon, USA
| | - Eric Orwoll
- Division of Endocrinology, Diabetes, and Clinical Nutrition, Oregon Health & Science University, Portland, Oregon, USA
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
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11
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Chorbińska J, Krajewski W, Nowak Ł, Małkiewicz B, Del Giudice F, Szydełko T. Urinary Microbiome in Bladder Diseases-Review. Biomedicines 2023; 11:2816. [PMID: 37893189 PMCID: PMC10604329 DOI: 10.3390/biomedicines11102816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The microbiome is the totality of microorganisms found in a specific biological niche. It has been proven that in the human body, the microbiome is responsible for its proper functioning. Dysbiosis, i.e., a disturbance in the composition of the microbiome, may be associated with the pathogenesis of many human diseases. Until recently, studies did not focus on the microbiome of the urinary tract, because, since the 19th century, there had been a dogma that urine in healthy people is sterile. Yet, advances in molecular biology techniques have allowed this dogma to be overthrown. The use of DNA sequencing has shown that the urinary tract has its own endogenous microbiome. This discovery enabled further research on the characteristics of the urine microbiomes of healthy people, as well as on the role of the urine microbiome in the pathogenesis of many urological diseases, including bladder diseases. The aim of this review is to summarize the current knowledge on the urinary microbiome in bladder diseases and to identify potential directions for further research.
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Affiliation(s)
- Joanna Chorbińska
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Wojciech Krajewski
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Łukasz Nowak
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Bartosz Małkiewicz
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Francesco Del Giudice
- Department of Maternal Infant and Urologic Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy;
| | - Tomasz Szydełko
- University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland;
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12
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Manes A, Di Renzo T, Dodani L, Reale A, Gautiero C, Di Lauro M, Nasti G, Manco F, Muscariello E, Guida B, Tarantino G, Cataldi M. Pharmacomicrobiomics of Classical Immunosuppressant Drugs: A Systematic Review. Biomedicines 2023; 11:2562. [PMID: 37761003 PMCID: PMC10526314 DOI: 10.3390/biomedicines11092562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The clinical response to classical immunosuppressant drugs (cIMDs) is highly variable among individuals. We performed a systematic review of published evidence supporting the hypothesis that gut microorganisms may contribute to this variability by affecting cIMD pharmacokinetics, efficacy or tolerability. The evidence that these drugs affect the composition of intestinal microbiota was also reviewed. The PubMed and Scopus databases were searched using specific keywords without limits of species (human or animal) or time from publication. One thousand and fifty five published papers were retrieved in the initial database search. After screening, 50 papers were selected to be reviewed. Potential effects on cIMD pharmacokinetics, efficacy or tolerability were observed in 17/20 papers evaluating this issue, in particular with tacrolimus, cyclosporine, mycophenolic acid and corticosteroids, whereas evidence was missing for everolimus and sirolimus. Only one of the papers investigating the effect of cIMDs on the gut microbiota reported negative results while all the others showed significant changes in the relative abundance of specific intestinal bacteria. However, no unique pattern of microbiota modification was observed across the different studies. In conclusion, the available evidence supports the hypothesis that intestinal microbiota could contribute to the variability in the response to some cIMDs, whereas data are still missing for others.
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Affiliation(s)
- Annalaura Manes
- Section of Pharmacology, Department of Neuroscience, Reproductive Sciences and Dentistry, Federico II University of Naples, 80131 Naples, Italy; (A.M.); (L.D.); (F.M.)
| | - Tiziana Di Renzo
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy; (T.D.R.); (A.R.)
| | - Loreta Dodani
- Section of Pharmacology, Department of Neuroscience, Reproductive Sciences and Dentistry, Federico II University of Naples, 80131 Naples, Italy; (A.M.); (L.D.); (F.M.)
| | - Anna Reale
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy; (T.D.R.); (A.R.)
| | - Claudia Gautiero
- Physiology Nutrition Unit, Department of Clinical Medicine and Surgery, Federico II University of Naples, 80131 Naples, Italy; (C.G.); (M.D.L.); (G.N.); (B.G.)
| | - Mariastella Di Lauro
- Physiology Nutrition Unit, Department of Clinical Medicine and Surgery, Federico II University of Naples, 80131 Naples, Italy; (C.G.); (M.D.L.); (G.N.); (B.G.)
| | - Gilda Nasti
- Physiology Nutrition Unit, Department of Clinical Medicine and Surgery, Federico II University of Naples, 80131 Naples, Italy; (C.G.); (M.D.L.); (G.N.); (B.G.)
| | - Federica Manco
- Section of Pharmacology, Department of Neuroscience, Reproductive Sciences and Dentistry, Federico II University of Naples, 80131 Naples, Italy; (A.M.); (L.D.); (F.M.)
| | - Espedita Muscariello
- Nutrition Unit, Department of Prevention, Local Health Authority Napoli 3 Sud, 80059 Naples, Italy;
| | - Bruna Guida
- Physiology Nutrition Unit, Department of Clinical Medicine and Surgery, Federico II University of Naples, 80131 Naples, Italy; (C.G.); (M.D.L.); (G.N.); (B.G.)
| | - Giovanni Tarantino
- Department of Clinical Medicine and Surgery, Federico II University of Naples, 80131 Naples, Italy;
| | - Mauro Cataldi
- Section of Pharmacology, Department of Neuroscience, Reproductive Sciences and Dentistry, Federico II University of Naples, 80131 Naples, Italy; (A.M.); (L.D.); (F.M.)
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13
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Bavanandan S, Keita N. Urinary Tract Infection Prevention and Treatment. Semin Nephrol 2023; 43:151468. [PMID: 38403525 DOI: 10.1016/j.semnephrol.2023.151468] [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] [Indexed: 02/27/2024]
Abstract
Urinary tract infections are the most common bacterial infections encountered by health care professionals. In women, the lifetime incidence of urinary tract infections may be up to 40% to 50%, of whom a further 40% may have recurrent infections. Urinary tract infections are associated with significant morbidity and potential mortality-they may be complicated by frequent recurrences, kidney damage, sepsis, and preterm birth, as well as collateral damage of antimicrobial use, which includes Clostridium difficile colitis and selection of drug-resistant organisms. There are personal costs such as reduced quality of life in patients affected by recurrent urinary tract infections, and societal impacts resulting from absenteeism and health care costs. In this review, we discuss the definitions and classifications, pathogenesis, and current principles of management and prevention of urinary tract infections. Semin Nephrol 43:x-xx © 2023 Elsevier Inc. All rights reserved.
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Affiliation(s)
- Sunita Bavanandan
- Department of Nephrology, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia.
| | - Niakhaleen Keita
- Department of Nephrology, National Hospital Dalal Jamm, Dakar, Senegal.
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Jaworska MM, Pecyna P, Jaskiewicz K, Rydzanicz M, Kaluzna M, Pawlaczyk K, Ploski R, Nowak-Malczewska DM, Karolak JA, Gajecka M. Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation. Front Microbiol 2023; 14:1187625. [PMID: 37350786 PMCID: PMC10282556 DOI: 10.3389/fmicb.2023.1187625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction The development of molecular biology methods and their application in microbial research allowed the detection of many new pathogens that cause urinary tract infections (UTIs). Despite the advances of using new research techniques, the etiopathogenesis of UTIs, especially in patients undergoing dialysis and patients after kidney transplantation, is still not fully understood. Methods This study aimed to characterize and compare the composition of the bacterial element of the urinary tract microbiome between the groups of patients undergoing dialysis (n = 50) and patients after kidney transplantation (n = 50), with positive or negative urine culture, compared to healthy individuals (n = 50). Results Asymptomatic bacteriuria was observed in 30% of the urine cultures of patients undergoing dialysis and patients after kidney transplantation, with Escherichia coli as the most dominant microorganism (73%) detected with the use of classical microbiology techniques. However, differences in the bacterial composition of the urine samples between the evaluated patient groups were demonstrated using the amplicon sequencing. Finegoldia, Leptotrichia, and Corynebacterium were found to be discriminative bacteria genera in patients after dialysis and kidney transplantation compared to the control group. In addition, in all of urine samples, including those without bacteriuria in classical urine culture, many types of bacteria have been identified using 16S rRNA sequencing. Discussion The revealed microbial characteristics may form the basis in searching for new diagnostic markers in treatment of patients undergoing dialysis and patients after kidney transplantation.
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Affiliation(s)
- Marcelina M. Jaworska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Paulina Pecyna
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | | | - Malgorzata Kaluzna
- Chair and Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Krzysztof Pawlaczyk
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Poznań, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dorota M. Nowak-Malczewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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15
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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 PMCID: PMC10224287 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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16
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The Urinary Microbiome and Bladder Cancer. Life (Basel) 2023; 13:life13030812. [PMID: 36983967 PMCID: PMC10053959 DOI: 10.3390/life13030812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
Bladder cancer is the 10th most common cancer worldwide. Approximately 75% of patients with bladder cancer will present with non-muscle invasive disease. Patients are usually treated with transurethral resection of bladder tumor (TURBT), in addition to adjuvant intravesical therapy (chemotherapy or anti-cancer immunotherapy with Bacillus Calmette Guerin- BCG) for those at intermediate-risk and high-risk of recurrence and progression. For many years, urine has been thought to be “sterile”; however, advanced microbiological and molecular techniques, including 16S ribosomal RNA (16S rRNA) sequencing, have negated that previous paradigm and confirmed the presence of a urinary microbiome. The urinary microbiome has been associated with several urological diseases, including interstitial cystitis, urgency urinary incontinence, neurogenic bladder dysfunction, and others. More recently, many reports are emerging about the role of the urinary microbiome in urothelial carcinogenesis, including gender disparity in bladder cancer and responses to treatments. The urinary microbiome may serve as a biomarker that can help with risk stratification as well as prediction of the response to intravesical therapies. However, the microbiome literature has been hampered by the lack of a unified standardized methodology for sample collection, type, preservation, processing, as well as bioinformatics analysis. Herein we describe and critique the literature on the association between urinary microbiome and bladder cancer and highlight some of the future directions.
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17
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Jung HD, Cho S, Lee JY. Update on the Effect of the Urinary Microbiome on Urolithiasis. Diagnostics (Basel) 2023; 13:diagnostics13050951. [PMID: 36900094 PMCID: PMC10001284 DOI: 10.3390/diagnostics13050951] [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: 01/03/2023] [Revised: 02/03/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Microbiota are ecological communities of commensal, symbiotic, and pathogenic microorganisms. The microbiome could be involved in kidney stone formation through hyperoxaluria and calcium oxalate supersaturation, biofilm formation and aggregation, and urothelial injury. Bacteria bind to calcium oxalate crystals, which causes pyelonephritis and leads to changes in nephrons to form Randall's plaque. The urinary tract microbiome, but not the gut microbiome, can be distinguished between cohorts with urinary stone disease (USD) and those without a history of the disease. In the urine microbiome, the role is known of urease-producing bacteria (Proteus mirabilis, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, Providencia stuartii, Serratia marcescens, and Morganella morganii) in stone formation. Calcium oxalate crystals were generated in the presence of two uropathogenic bacteria (Escherichia coli and K. pneumoniae). Non-uropathogenic bacteria (S. aureus and Streptococcus pneumoniae) exhibit calcium oxalate lithogenic effects. The taxa Lactobacilli and Enterobacteriaceae best distinguished the healthy cohort from the USD cohort, respectively. Standardization is needed in urine microbiome research for urolithiasis. Inadequate standardization and design of urinary microbiome research on urolithiasis have hampered the generalizability of results and diminished their impact on clinical practice.
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Affiliation(s)
- Hae Do Jung
- Department of Urology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang 10380, Republic of Korea
| | - Seok Cho
- Department of Urology, Inje University Ilsan Paik Hospital, Inje University College of Medicine, Goyang 10380, Republic of Korea
| | - Joo Yong Lee
- Department of Urology, Severance Hospital, Urological Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Center of Evidence Based Medicine, Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
- Correspondence: ; Tel.: +82-2-2228-2320; Fax: +82-2-312-2538
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18
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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: 6] [Impact Index Per Article: 6.0] [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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19
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Tvrdá E, Ďuračka M, Benko F, Kováčik A, Lovíšek D, Gálová E, Žiarovská J, Schwarzová M, Kačániová M. Ejaculatory Abstinence Affects the Sperm Quality in Normozoospermic Men-How Does the Seminal Bacteriome Respond? Int J Mol Sci 2023; 24:ijms24043503. [PMID: 36834909 PMCID: PMC9963725 DOI: 10.3390/ijms24043503] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
This study was designed to describe bacterial profiles of ejaculates collected following a long and short ejaculatory abstinence set in the context of changes in the conventional, oxidative, and immunological characteristics of semen. Two specimens were collected in succession from normozoospermic men (n = 51) following 2 days and 2 h, respectively. Semen samples were processed and analyzed according to the World Health Organization (WHO) 2021 guidelines. Afterwards, sperm DNA fragmentation, mitochondrial function, levels of reactive oxygen species (ROS), total antioxidant capacity, and oxidative damage to sperm lipids and proteins were evaluated in each specimen. Selected cytokine levels were quantified using the ELISA method. Bacterial identification by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry revealed that samples collected following two days of abstinence presented with a higher bacterial load and diversity, and a greater prevalence of potentially uropathogenic bacteria including Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. Only staphylococci and Escherichia coli remained present in specimens obtained after 2 h of abstinence. Whilst all samples accomplished the criteria set by WHO, a significantly higher motility (p < 0.05), membrane integrity (p < 0.05), mitochondrial membrane potential (p < 0.05), and DNA integrity (p < 0.0001) were detected following 2 h of ejaculatory abstinence. On the other hand, significantly higher ROS levels (p < 0.001), protein oxidation (p < 0.001), and lipid peroxidation (p < 0.01) accompanied by significantly higher concentrations of tumor necrosis factor alpha (p < 0.05), interleukin-6 (p < 0.01), and interferon gamma (p < 0.05) were observed in specimens collected after two days of abstinence. It may be summarized that shorter ejaculatory abstinence does not compromise sperm quality in normozoospermic men, while it contributes to a decreased occurrence of bacteria in semen which is accompanied by a lower probability of damage to spermatozoa by ROS or pro-inflammatory cytokines.
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Affiliation(s)
- Eva Tvrdá
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Correspondence: ; Tel.: +421-37-641-4918
| | - Michal Ďuračka
- AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Filip Benko
- Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Anton Kováčik
- Institute of Applied Biology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Daniel Lovíšek
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 84215 Bratislava, Slovakia
| | - Eliška Gálová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Mlynská Dolina, 84215 Bratislava, Slovakia
| | - Jana Žiarovská
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Marianna Schwarzová
- Department of Fruit Science, Viticulture and Enology, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Miroslava Kačániová
- Department of Fruit Science, Viticulture and Enology, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszow, Cwiklinskiej 1, 35-601 Rzeszow, Poland
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20
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2023; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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21
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Przybyciński J, Drożdżal S, Wilk A, Dziedziejko V, Szumilas K, Pawlik A. The Effect of the Gut Microbiota on Transplanted Kidney Function. Int J Mol Sci 2023; 24:ijms24021260. [PMID: 36674775 PMCID: PMC9866452 DOI: 10.3390/ijms24021260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
The intestinal microflora is extremely important, not only in the processes of absorption, digestion and biosynthesis of vitamins, but also in shaping the immune and cognitive functions of the human body. Several studies demonstrate a correlation between microbiota composition and such events as graft rejection, kidney interstitial fibrosis, urinary tract infections, and diarrhoea or graft tolerance. Some of those changes might be directly linked with pathologies such as colonization with pathogenic bacterial strains. Gut microbiota composition also plays an important role in metabolic complications and viral infections after transplantation. From the other side, gut microbiota might induce graft tolerance by promotion of T and B regulatory cells. Graft tolerance induction is still an extremely important issue regarding transplantology and might allow the reduction or even avoidance of immunosuppressive treatment. Although there is a rising evidence of the pivotal role of gut microbiota in aspects of kidney transplantation there is still a lack of knowledge on the direct mechanisms of microbiota action. Furthermore, some of those negative effects could be reversed by probiotics of faecal microbiota trapoinsplantation. While diabetes and hypertension as well as BKV and CMV viremia are common and important complications of transplantation, both worsening the graft function and causing systemic injuries, it opens up potential clinical treatment options. As has been also suggested in the current review, some bacterial subsets exhibit protective properties. However, currently, there is a lack of evidence on pro- and prebiotic supplementation in kidney transplant patients. In the current review, we describe the effect of the microbiota on the transplanted kidney in renal transplant recipients.
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Affiliation(s)
- Jarosław Przybyciński
- Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Sylwester Drożdżal
- Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Aleksandra Wilk
- Department of Histology and Embryology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Violetta Dziedziejko
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Kamila Szumilas
- Department of Physiology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
- Correspondence:
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22
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Kleinová P, Beliančinová M, Vnučák M, Graňák K, Dedinská I. Gut microbiome and renal transplantation. VNITRNI LEKARSTVI 2023; 69:41-46. [PMID: 36931881 DOI: 10.36290/vnl.2023.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Gut microbiome research has been a surge of interest in many branches of medicine in the last decade. Our main aim is to show ability of microbes to infuence the functions of human body, especially in the immune system, and on the other hand to clarify changes in composition of gut microbiome in the post-transplantation period and their function for the long-term survival of the graft and the patient in the context of the occurrence of a wide range of complications. Kidney transplantation with the subsequent use of immunosuppressants and antibiotics affects the composition of gut microbiome. The subsequent development of dysbiosis significantly increases the risk of acute rejection, interstitial fibrosis and tubular atrophy of the graft, post-transplant diarrhoea, organ´s infections and metabolic complications such as post-transplant diabetes mellitus. Also important is the influence of the microorganisms of the gut microbiome on metabolism of immunosuppressants with the production of less effective components and the subsequent necessity of modifying their levels with a higher risk of underdosing and the occurrence of graft rejection. Support of the composition of the gut microbiome in the post-transplantation period in favor of bacteria producing short chain fatty acids (SCFA) is possible by changing of diet with predominance of fiber, the application of probiotics, prebiotics. According to available studies, it can lead to benefits in term of metabolic compensation, to the induction of donor-specific tolerance and many others, with an overall improvement in the quality of patient and graft survival.
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Dicu-Andreescu I, Penescu MN, Căpușă C, Verzan C. Chronic Kidney Disease, Urinary Tract Infections and Antibiotic Nephrotoxicity: Are There Any Relationships? MEDICINA (KAUNAS, LITHUANIA) 2022; 59:49. [PMID: 36676673 PMCID: PMC9862113 DOI: 10.3390/medicina59010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
Chronic kidney disease (CKD) has been a constant burden worldwide, with a prevalence of more than 10% of the population and with mortality reaching 1.2 million deaths and 35.8 million disability-adjusted life years (DALYs) in 2017, as it is claimed by the Global Burden of Diseases. Moreover, an increase in its prevalence is expected in the next years due to a rise in the number of people suffering from obesity, diabetes mellitus and hypertension. On the other hand, with cardiovascular morbidity and mortality showing a downward trend, maybe it is time to focus on CKD, to minimize the preventable risk factors involved in its progression toward end-stage kidney disease (ESKD) and to offer a better quality of life. Another major health burden is represented by infectious diseases, particularly urinary tract infections (UTIs), as it is considered that approximately 40-50% of women and 5% of men will have at least one episode during their lifetime. Additionally, CKD consists of a constellation of immunological and metabolical disturbances that lead to a greater risk of UTIs: increased apoptosis of lymphocytes, elevated levels of tumor necrosis factor α and interleukin 6, which lower the function of neutrophils and increased levels of uremic toxins like p-cresyl sulfate and indoxyl sulfate, which alter the adherence and migration of leukocytes to the sites of injury. Moreover, UTIs can lead to a more rapid decline of kidney function, especially in stages G3-G5 of CKD, with all the complications involved. Last, but not least, antibiotherapy is often complicated in this category of patients, as antibiotics can also negatively affect the kidneys. This review will try to focus on the particularities of the urinary microbiome, asymptomatic bacteriuria and UTIs and the subtle balance between the risks of them and the risks of antibiotherapy in the evolution of CKD.
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Affiliation(s)
- Ioana Dicu-Andreescu
- Clinical Department No 3, Internal Medicine and Nephrology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Dr. Carol Davila” Teaching Hospital of Nephrology, Nephrology Department, Cal. Grivitei No 4, Sector 1, 010731 Bucharest, Romania
| | - Mircea Niculae Penescu
- Clinical Department No 3, Internal Medicine and Nephrology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Dr. Carol Davila” Teaching Hospital of Nephrology, Nephrology Department, Cal. Grivitei No 4, Sector 1, 010731 Bucharest, Romania
| | - Cristina Căpușă
- Clinical Department No 3, Internal Medicine and Nephrology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Dr. Carol Davila” Teaching Hospital of Nephrology, Nephrology Department, Cal. Grivitei No 4, Sector 1, 010731 Bucharest, Romania
| | - Constantin Verzan
- Clinical Department No 3, Internal Medicine and Nephrology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- “Dr. Carol Davila” Teaching Hospital of Nephrology, Nephrology Department, Cal. Grivitei No 4, Sector 1, 010731 Bucharest, Romania
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Hu X, Haas JG, Lathe R. The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data. BMC Microbiol 2022; 22:317. [PMID: 36550399 PMCID: PMC9773549 DOI: 10.1186/s12866-022-02671-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life. RESULTS We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved. CONCLUSIONS This generic methodology is likely to find wide application in microbiome analysis including diagnostics.
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Affiliation(s)
- Xinyue Hu
- Program in Bioinformatics, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Jürgen G Haas
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK
| | - Richard Lathe
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK.
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Friedrich V, Choi HW. The Urinary Microbiome: Role in Bladder Cancer and Treatment. Diagnostics (Basel) 2022; 12:diagnostics12092068. [PMID: 36140470 PMCID: PMC9497549 DOI: 10.3390/diagnostics12092068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
Commensal microbes have increasingly been found to be involved in the development and progression of cancer. The recent discovery of the urinary microbiome bolstered the notion that microbes might play a role in bladder cancer. Although microbial involvement in bladder neoplastic transformation and metastatic progression, except schisto somiasis, has not been established, accumulating research suggests that dysbiosis of the urinary microbiome can produce a chronically inflammatory urothelial microenvironment and lead to bladder cancer. In this review, we describe how the urinary microbiome might facilitate the development of bladder cancer by altering the host immune system and the kind of cytokines that are directly involved in these responses. We investigated the therapeutic possibilities of modulating the urinary microbiome, including immune checkpoint therapy. The responsiveness of patients to intravesical Bacillus Calmette-Guerin therapy was evaluated with respect to microbiome composition. We conclude by noting that the application of microbes to orchestrate the inflammatory response in the bladder may facilitate the development of treatments for bladder cancer.
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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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Sen T, Thummer RP. The Impact of Human Microbiotas in Hematopoietic Stem Cell and Organ Transplantation. Front Immunol 2022; 13:932228. [PMID: 35874759 PMCID: PMC9300833 DOI: 10.3389/fimmu.2022.932228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
The human microbiota heavily influences most vital aspects of human physiology including organ transplantation outcomes and transplant rejection risk. A variety of organ transplantation scenarios such as lung and heart transplantation as well as hematopoietic stem cell transplantation is heavily influenced by the human microbiotas. The human microbiota refers to a rich, diverse, and complex ecosystem of bacteria, fungi, archaea, helminths, protozoans, parasites, and viruses. Research accumulating over the past decade has established the existence of complex cross-species, cross-kingdom interactions between the residents of the various human microbiotas and the human body. Since the gut microbiota is the densest, most popular, and most studied human microbiota, the impact of other human microbiotas such as the oral, lung, urinary, and genital microbiotas is often overshadowed. However, these microbiotas also provide critical and unique insights pertaining to transplantation success, rejection risk, and overall host health, across multiple different transplantation scenarios. Organ transplantation as well as the pre-, peri-, and post-transplant pharmacological regimens patients undergo is known to adversely impact the microbiotas, thereby increasing the risk of adverse patient outcomes. Over the past decade, holistic approaches to post-transplant patient care such as the administration of clinical and dietary interventions aiming at restoring deranged microbiota community structures have been gaining momentum. Examples of these include prebiotic and probiotic administration, fecal microbial transplantation, and bacteriophage-mediated multidrug-resistant bacterial decolonization. This review will discuss these perspectives and explore the role of different human microbiotas in the context of various transplantation scenarios.
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Affiliation(s)
| | - Rajkumar P. Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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The Urobiome and Its Role in Overactive Bladder. Int Neurourol J 2022; 26:190-200. [PMID: 35468617 PMCID: PMC9537439 DOI: 10.5213/inj.2244016.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Urine is no longer considered to be sterile. After the existence of the microbiome was revealed through metagenomic analysis using next-generation sequencing, the relationship between characteristics of the microbiome and diseases have been studied and published in various journals. A microbiome exists in the urinary tract and is associated with urinary tract infection, malignancy of the genitourinary tract, and lower urinary tract symptoms. Based on the urine sampling method, sampling site, culture method, and sex, the characteristics of the microbiome vary. Most of the Lactobacillus species are identified mainly in women, and various other species are identified in men. These microorganisms can cause or prevent various diseases. Variations in the microbiome are seen in those with and without disease, and an asymptomatic status does not indicate the absence of microbes. This microbiome has been implicated in a variety of lower urinary tract symptoms and diseases, in particular, overactive bladder. The microbiome differs between patients with urgency and urge urinary incontinence and healthy individuals. There are many aspects of the microbiome yet to be studied in relation to other lower urinary tract symptoms.
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Wehedy E, Shatat IF, Al Khodor S. The Human Microbiome in Chronic Kidney Disease: A Double-Edged Sword. Front Med (Lausanne) 2022; 8:790783. [PMID: 35111779 PMCID: PMC8801809 DOI: 10.3389/fmed.2021.790783] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease (CKD) is an increasing global health burden. Current treatments for CKD include therapeutics to target factors that contribute to CKD progression, including renin–angiotensin–aldosterone system inhibitors, and drugs to control blood pressure and proteinuria control. Recently, associations between chronic disease processes and the human microbiota and its metabolites have been demonstrated. Dysbiosis—a change in the microbial diversity—has been observed in patients with CKD. The relationship between CKD and dysbiosis is bidirectional; gut-derived metabolites and toxins affect the progression of CKD, and the uremic milieu affects the microbiota. The accumulation of microbial metabolites and toxins is linked to the loss of kidney functions and increased mortality risk, yet renoprotective metabolites such as short-chain fatty acids and bile acids help restore kidney functions and increase the survival rate in CKD patients. Specific dietary interventions to alter the gut microbiome could improve clinical outcomes in patients with CKD. Low-protein and high-fiber diets increase the abundance of bacteria that produce short-chain fatty acids and anti-inflammatory bacteria. Fluctuations in the urinary microbiome are linked to increased susceptibility to infection and antibiotic resistance. In this review, we describe the potential role of the gut, urinary and blood microbiome in CKD pathophysiology and assess the feasibility of modulating the gut microbiota as a therapeutic tool for treating CKD.
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Affiliation(s)
- Eman Wehedy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Souhaila Al Khodor
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Research Department, Sidra Medicine, Doha, Qatar
- *Correspondence: Souhaila Al Khodor
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Abstract
PURPOSE OF REVIEW Research in the past decade has revealed important implications for the microbiome in human health. Studies have defined a distinct gut microbiota in kidney transplant recipients and have recently linked the microbiota to infectious complications, similar to the allogeneic stem cell transplant population. RECENT FINDINGS In this review, we focus on the metabolism of immunosuppressive medications by the gut microbiota and on the urinary microbiome in the setting of infectious and immunological complications. We highlight seminal studies showing the role of specific gut microbiota in the direct metabolism of tacrolimus into a lesser effective immunosuppressant as well as the role of the gut microbiota in the metabolism of mycophenolic acid (MPA) glucuronide. We describe distinct urinary microbiota patterns in kidney transplant recipients with interstitial fibrosis tubular atrophy, chronic allograft nephropathy, tolerance, and bacterial and viral complications. SUMMARY The microbiota has important implications for immunosuppressive medications and immunological outcomes in kidney transplant recipients. Further research is needed to better delineate the impact of the metabolism of tacrolimus and MPA by gut bacteria and the role of the urine microbiota in the development of immunological and infectious complications.
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Affiliation(s)
| | | | - Tarek Barbar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York, 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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Orr TJ, Hayssen V. The Female Snark Is Still a Boojum: Looking toward the Future of Studying Female Reproductive Biology. Integr Comp Biol 2021; 60:782-795. [PMID: 32702114 DOI: 10.1093/icb/icaa091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Philosophical truths are hidden in Lewis Carroll's nonsense poems, such as "The hunting of the snark." When the poem is used as a scientific allegory, a snark stands for the pursuit of scientific truth, while a boojum is a spurious discovery. In the study of female biology, boojums have been the result of the use of cultural stereotypes to frame hypotheses and methodologies. Although female reproduction is key for the continuation of sexually reproducing species, not only have females been understudied in many regards, but also data have commonly been interpreted in the context of now-outdated social mores. Spurious discoveries, boojums, are the result. In this article, we highlight specific gaps in our knowledge of female reproductive biology and provide a jumping-off point for future research. We discuss the promise of emerging methodologies (e.g., micro-CT scanning, high-throughput sequencing, proteomics, big-data analysis, CRISPR-Cas9, and viral vector technology) that can yield insights into previously cryptic processes and features. For example, in mice, deoxyribonucleic acid sequencing via chromatin immunoprecipitation followed by sequencing is already unveiling how epigenetics lead to sex differences in brain development. Similarly, new explorations, including microbiome research, are rapidly debunking dogmas such as the notion of the "sterile womb." Finally, we highlight how understanding female reproductive biology is well suited to the National Science Foundation's big idea, "Predicting Rules of Life." Studies of female reproductive biology will enable scholars to (1) traverse levels of biological organization from reproductive proteins at the molecular level, through anatomical details of the ovum and female reproductive tract, into physiological aspects of whole-organism performance, leading to behaviors associated with mating and maternal care, and eventually reaching population structure and ecology; (2) discover generalizable rules such as the co-evolution of maternal-offspring phenotypes in gestation and lactation; and (3) predict the impacts of changes to reproductive timing when the reliability of environmental cues becomes unpredictable. Studies in these key areas relative to female reproduction are sure to further our understanding across a range of diverse taxa.
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Affiliation(s)
- Teri J Orr
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Virginia Hayssen
- Department of Biological Sciences, Smith College, Northampton, MA, USA
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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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Salvadori M, Tsalouchos A. Microbiota, renal disease and renal transplantation. World J Transplant 2021; 11:16-36. [PMID: 33816144 PMCID: PMC8009061 DOI: 10.5500/wjt.v11.i3.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/06/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Aim of this frontier review has been to highlight the role of microbiota in healthy subjects and in patients affected by renal diseases with particular reference to renal transplantation. The microbiota has a relevant role in conditioning the healthy status and the diseases. In particular gut microbiota is essential in the metabolism of food and has a relevant role for its relationship with the immune system. The indigenous microbiota in patients with chronic renal failure is completely different than that of the healthy subjects and pathobionts appear. This abnormality in microbiota composition is called dysbiosis and may cause a rapid deterioration of the renal function both for activating the immune system and producing large quantity of uremic toxins. Similarly, after renal trans-plantation the microbiota changes with the appearance of pathobionts, principally in the first period because of the assumption of immunosuppressive drugs and antibiotics. These changes may deeply interfere with the graft outcome causing acute rejection, renal infections, diarrhea, and renal interstitial fibrosis. In addition, change in the microbiota may modify the metabolism of immuno-suppressive drugs causing in some patients the need of modifying the immunosuppressant dosing. The restoration of the indigenous microbiota after transplantation is important, either to avoiding the complications that impair the normal renal graft, and because recent studies have documented the role of an indigenous microbiota in inducing tolerance towards the graft. The use of prebiotics, probiotics, smart bacteria and diet modification may restore the indigenous microbiota, but these studies are just at their beginning and more data are needed to draw definitive conclusions.
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Affiliation(s)
- Maurizio Salvadori
- Department of Transplantation Renal Unit, Careggi University Hospital, Florence 50139, Italy
| | - Aris Tsalouchos
- Nephrology and Dialysis Unit, Saints Cosmas and Damian Hospital, Pescia 51017, Italy
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Qiu F, Lu W, Ye S, Liu H, Zeng Q, Huang H, Liang CL, Chen Y, Zheng F, Zhang Q, Lu CJ, Dai Z. Berberine Promotes Induction of Immunological Tolerance to an Allograft via Downregulating Memory CD8 + T-Cells Through Altering the Gut Microbiota. Front Immunol 2021; 12:646831. [PMID: 33643325 PMCID: PMC7907598 DOI: 10.3389/fimmu.2021.646831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Emerging evidence has linked the gut microbiota dysbiosis to transplant rejection while memory T-cells pose a threat to long-term transplant survival. However, it's unclear if the gut microbiome alters the formation and function of alloreactive memory T-cells. Here we studied the effects of berberine, a narrow-spectrum antibiotic that is barely absorbed when orally administered, on the gut microbiota, memory T-cells, and allograft survival. In this study, C57BL/6 mice transplanted with islets or a heart from BALB/c mice were treated orally with berberine. Allograft survival was observed, while spleen, and lymph node T-cells from recipient mice were analyzed using a flow cytometer. High-throughput sequencing and qPCR were performed to analyze the gut microbiota. CD8+ T-cells from recipients were cultured with the bacteria to determine potential T-cell memory cross-reactivity to a specific pathogen. We found that berberine suppressed islet allograft rejection, reduced effector CD8+CD44highCD62Llow and central memory CD8+CD44highCD62Lhigh T-cells (TCM), altered the gut microbiota composition and specifically lowered Bacillus cereus abundance. Further, berberine promoted long-term islet allograft survival induced by conventional costimulatory blockade and induced cardiac allograft tolerance as well. Re-colonization of B. cereus upregulated CD8+ TCM cells and reversed long-term islet allograft survival induced by berberine plus the conventional costimulatory blockade. Finally, alloantigen-experienced memory CD8+ T-cells from transplanted recipients rapidly responded to B. cereus in vitro. Thus, berberine prolonged allograft survival by repressing CD8+ TCM through regulating the gut microbiota. We have provided the first evidence that donor-specific memory T-cell generation is linked to a specific microbe and uncovered a novel mechanism underlying the therapeutic effects of berberine. This study may be implicated for suppressing human transplant rejection since berberine is already used in clinic to treat intestinal infections.
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Affiliation(s)
- Feifei Qiu
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weihui Lu
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shulin Ye
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huazhen Liu
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiaohuang Zeng
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haiding Huang
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chun-Ling Liang
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuchao Chen
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fang Zheng
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qunfang Zhang
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chuan-Jian Lu
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhenhua Dai
- Section of Immunology and Joint Immunology Program, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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36
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Campbell PM, Humphreys GJ, Summers AM, Konkel JE, Knight CG, Augustine T, McBain AJ. Does the Microbiome Affect the Outcome of Renal Transplantation? Front Cell Infect Microbiol 2020; 10:558644. [PMID: 33425774 PMCID: PMC7785772 DOI: 10.3389/fcimb.2020.558644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/17/2020] [Indexed: 12/31/2022] Open
Abstract
The role of the human microbiome in health and disease is becoming increasingly apparent. Emerging evidence suggests that the microbiome is affected by solid organ transplantation. Kidney transplantation is the gold standard treatment for End-Stage Renal Disease (ESRD), the advanced stage of Chronic Kidney Disease (CKD). The question of how ESRD and transplantation affect the microbiome and vice versa includes how the microbiome is affected by increased concentrations of toxins such as urea and creatinine (which are elevated in ESRD), whether restoration of renal function following transplantation alters the composition of the microbiome, and the impact of lifelong administration of immunosuppressive drugs on the microbiome. Changes in microbiome composition and activity have been reported in ESRD and in therapeutic immunosuppression, but the effect on the outcome of transplantation is not well-understood. Here, we consider the current evidence that changes in kidney function and immunosuppression following transplantation influence the oral, gut, and urinary microbiomes in kidney transplant patients. The potential for changes in these microbiomes to lead to disease, systemic inflammation, or rejection of the organ itself is discussed, along with the possibility that restoration of kidney function might re-establish orthobiosis.
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Affiliation(s)
- Paul M Campbell
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Gavin J Humphreys
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Angela M Summers
- Department of Renal and Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Joanne E Konkel
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Christopher G Knight
- School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, United Kingdom
| | - Titus Augustine
- Department of Renal and Pancreatic Transplantation, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Andrew J McBain
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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37
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Goodfellow M, Thompson ER, Tingle SJ, Wilson CH. Early versus late removal of urinary catheter after kidney transplantation. Hippokratia 2020. [DOI: 10.1002/14651858.cd013788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Goodfellow
- Institute of Transplantation; The Freeman Hospital; Newcastle upon Tyne UK
| | - Emily R Thompson
- Institute of Transplantation; The Freeman Hospital; Newcastle upon Tyne UK
| | - Samuel J Tingle
- Institute of Transplantation; The Freeman Hospital; Newcastle upon Tyne UK
| | - Colin H Wilson
- Institute of Transplantation; The Freeman Hospital; Newcastle upon Tyne UK
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38
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Lathe R, St Clair D. From conifers to cognition: Microbes, brain and behavior. GENES BRAIN AND BEHAVIOR 2020; 19:e12680. [PMID: 32515128 DOI: 10.1111/gbb.12680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022]
Abstract
A diversity of bacteria, protozoans and viruses ("endozoites") were recently uncovered within healthy tissues including the human brain. By contrast, it was already recognized a century ago that healthy plants tissues contain abundant endogenous microbes ("endophytes"). Taking endophytes as an informative precedent, we overview the nature, prevalence, and role of endozoites in mammalian tissues, centrally focusing on the brain, concluding that endozoites are ubiquitous in diverse tissues. These passengers often remain subclinical, but they are not silent. We address their routes of entry, mechanisms of persistence, tissue specificity, and potential to cause long-term behavioral changes and/or immunosuppression in mammals, where rabies virus is the exemplar. We extend the discussion to Herpesviridae, Coronaviridae, and Toxoplasma, as well as to diverse bacteria and yeasts, and debate the advantages and disadvantages that endozoite infection might afford to the host and to the ecosystem. We provide a clinical perspective in which endozoites are implicated in neurodegenerative disease, anxiety/depression, and schizophrenia. We conclude that endozoites are instrumental in the delicate balance between health and disease, including age-related brain disease, and that endozoites have played an important role in the evolution of brain function and human behavior.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh Medical School, Edinburgh, UK
| | - David St Clair
- Institute of Medical Sciences, School of Medicine, University of Aberdeen, Aberdeen, UK
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Cumpanas AA, Bratu OG, Bardan RT, Ferician OC, Cumpanas AD, Horhat FG, Licker M, Pricop C, Cretu OM. Urinary Microbiota-Are We Ready for Prime Time? A Literature Review of Study Methods' Critical Steps in Avoiding Contamination and Minimizing Biased Results. Diagnostics (Basel) 2020; 10:diagnostics10060343. [PMID: 32471022 PMCID: PMC7345871 DOI: 10.3390/diagnostics10060343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research.
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Affiliation(s)
- Alin Adrian Cumpanas
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Gabriel Bratu
- Department of Urology, Emergency Military Central Hospital, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Razvan Tiberiu Bardan
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Catalin Ferician
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Andrei Dragos Cumpanas
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Correspondence:
| | - Florin George Horhat
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Monica Licker
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Catalin Pricop
- Department of Urology, Gr.Tr.Popa University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Octavian Marius Cretu
- Department of Surgery, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
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Sepulveda M, Pirozzolo I, Alegre ML. Impact of the microbiota on solid organ transplant rejection. Curr Opin Organ Transplant 2020; 24:679-686. [PMID: 31577594 DOI: 10.1097/mot.0000000000000702] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW The microbiota in mammalian hosts can affect maturation and function of the immune system and has been associated with health and disease. We will review new findings on how this dynamic environmental factor impacts alloimmunity and therapy in transplant hosts. RECENT FINDINGS The microbiota changes after transplantation and immunosuppressive therapy. New data indicate that different microbial community structures have distinct impact on graft outcome, from promoting, to inhibiting or being neutral to transplant survival. In addition, we will address reciprocal interactions between the microbiota and immunosuppressive drugs, as well as the suitability of the microbiota as a predictive biomarker and its utility as adjunct therapy in transplantation. SUMMARY Advances in microbiome sequencing and wider availability of gnotobiotic facilities are enabling mechanistic investigations into the commensal communities and pathways that modulate allograft outcome, responsiveness to immunosuppression and side effects of drugs. A better understanding of the functions of the microbiota may help mitigate drug toxicity, predict drug dosage and dampen alloimmunity in transplant patients.
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Ackerman AL, Chai TC. The Bladder is Not Sterile: an Update on the Urinary Microbiome. CURRENT BLADDER DYSFUNCTION REPORTS 2019; 14:331-341. [PMID: 32612735 DOI: 10.1007/s11884-019-00543-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purpose of Review The article discusses (1) techniques used to study bacterial urinary microbiota; (2) existence of non-bacterial urinary microbiota; (3) associations between changes in urinary microbiota and various benign lower urinary tract disorders. Recent Findings Urine harbors a diverse microbial community that resides within it. A multitude of studies have identified differences in these communities associated with urologic conditions, suggesting that microbial communities may maintain normal bladder homeostasis. Technological advances in analytic approaches have improved our understanding of the urinary microbiome. The choice of urine sampling method (voided, catheterized, or aspirated) will significantly influence microbiome findings. Sex and age highly influence urinary microbiota; in addition to rigorous inclusion criteria, microbial studies must be sufficiently powered to overcome the substantial interindividual variability of urinary microbiota. Regardless of these complicating factors, studies have identified microbial patterns correlating with both urologic diagnoses and treatment responses. Summary Without a clear understanding of the variability of and exogenous influences on the urinary microbiota in the absence of disease, it has been challenging to reveal the microbial patterns responsible for disease pathophysiology. Host mechanisms in response to the urinary microbiome are also poorly understood. Additional research can address whether the manipulation of urinary microbiota will benefit lower urinary tract health.
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Affiliation(s)
- A Lenore Ackerman
- Cedars-Sinai Medical Center, 99 N. La Cienega Blvd. Suite M102, Beverly Hills, CA 90211, USA
| | - Toby C Chai
- Boston Medical Center, Boston University School of Medicine, 725 Albany St., Suite 3B, Shapiro Building, Boston, MA 02118, USA
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Wojciuk B, Salabura A, Grygorcewicz B, Kędzierska K, Ciechanowski K, Dołęgowska B. Urobiome: In Sickness and in Health. Microorganisms 2019; 7:microorganisms7110548. [PMID: 31717688 PMCID: PMC6921077 DOI: 10.3390/microorganisms7110548] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/16/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022] Open
Abstract
The human microbiome has been proven to contribute to the human condition, both in health and in disease. The metagenomic approach based on next-generation sequencing has challenged the dogma of urine sterility. The human urobiome consists of bacteria and eukaryotic viruses as well as bacteriophages, which potentially represent the key factor. There have been several significant findings with respect to the urobiome in the context of urological disorders. Still, the research on the urobiome in chronic kidney disease and kidney transplantation remains underrepresented, as does research on the role of the virome in the urinary microbiota. In this review, we present recent findings on the urobiome with a particular emphasis on chronic kidney disease and post-kidney transplantation status. Challenges and opportunities arising from the research on the human urobiome will also be discussed.
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Affiliation(s)
- Bartosz Wojciuk
- Department of Immunological Diagnostics, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland
- Correspondence: ; Tel.: +48-914-661-654
| | - Agata Salabura
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Bartłomiej Grygorcewicz
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (B.G.); (B.D.)
| | - Karolina Kędzierska
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Kazimierz Ciechanowski
- Clinic of Nephrology, Internal Medicine and Transplantation, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (A.S.); (K.K.); (K.C.)
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-123 Szczecin, Poland; (B.G.); (B.D.)
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Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Nat Commun 2019; 10:1906. [PMID: 31015506 PMCID: PMC6479061 DOI: 10.1038/s41467-019-09930-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 04/02/2019] [Indexed: 01/25/2023] Open
Abstract
Studying immune repertoire in the context of organ transplant provides important information on how adaptive immunity may contribute and modulate graft rejection. Here we characterize the peripheral blood immune repertoire of individuals before and after kidney transplant using B cell receptor sequencing in a longitudinal clinical study. Individuals who develop rejection after transplantation have a more diverse immune repertoire before transplant, suggesting a predisposition for post-transplant rejection risk. Additionally, over 2 years of follow-up, patients who develop rejection demonstrate a specific set of expanded clones that persist after the rejection. While there is an overall reduction of peripheral B cell diversity, likely due to increased general immunosuppression exposure in this cohort, the detection of specific IGHV gene usage across all rejecting patients supports that a common pool of immunogenic antigens may drive post-transplant rejection. Our findings may have clinical implications for the prediction and clinical management of kidney transplant rejection.
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MESH Headings
- Adolescent
- Adult
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Child
- Child, Preschool
- Clone Cells
- Female
- Gene Expression
- Graft Rejection/genetics
- Graft Rejection/immunology
- Graft Rejection/pathology
- Graft Survival/genetics
- Humans
- Immunocompromised Host
- Infant
- Kidney/immunology
- Kidney/pathology
- Kidney/surgery
- Kidney Transplantation
- Longitudinal Studies
- Male
- Middle Aged
- Polymorphism, Genetic/immunology
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Renal Insufficiency, Chronic/genetics
- Renal Insufficiency, Chronic/immunology
- Renal Insufficiency, Chronic/pathology
- Renal Insufficiency, Chronic/surgery
- Sequence Analysis, DNA
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Affiliation(s)
- Silvia Pineda
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Tara K Sigdel
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Juliane M Liberto
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Flavio Vincenti
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
- Department of Pediatrics, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
| | - Minnie M Sarwal
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA.
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Wu JF, Muthusamy A, Al-Ghalith GA, Knights D, Guo B, Wu B, Remmel RP, Schladt DP, Alegre ML, Oetting WS, Jacobson PA, Israni AK. Urinary microbiome associated with chronic allograft dysfunction in kidney transplant recipients. Clin Transplant 2018; 32:e13436. [PMID: 30372560 PMCID: PMC6984979 DOI: 10.1111/ctr.13436] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/14/2018] [Accepted: 10/21/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND We performed a study to identify differences in the urinary microbiome associated with chronic allograft dysfunction (CAD) and compared the urinary microbiome of male and female transplant recipients with CAD. METHODS This case-control study enrolled 67 patients within the Deterioration of Kidney Allograft Function (DeKAF) Genomics cohort at two transplant centers. CAD was defined as a greater than 25% rise in serum creatinine relative to a 3 month post-transplant baseline. Urine samples from patients with and without CAD were analyzed using 16S V4 bacterial ribosomal DNA sequences. RESULTS Corynebacterium was more prevalent in female and male patients with CAD compared to non-CAD female patients (P = 0.0005). A total 21 distinct Operational Taxonomic Unit (OTUs) were identified as significantly different when comparing CAD and non-CAD patients using Kruskal-Wallis (P < 0.01). A subset analysis of female patients with CAD compared to non-CAD females identified similar differentially abundant OTUs, including the genera Corynebacterium and Staphylococcus (Kruskal-Wallis; P = 0.01; P = 0.004, respectively). Male CAD vs female CAD analysis showed greater abundance of phylum Proteobacteria in males. CONCLUSION There were differences in the urinary microbiome when comparing female and male CAD patients with their female non-CAD counterparts and these differences persisted in the subset analysis limited to female patients only.
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Affiliation(s)
- Jennifer F. Wu
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
| | | | | | - Dan Knights
- Department of Computer Science and Biotechnology Institute, University of Minnesota, Minneapolis, MN
| | - Bin Guo
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Baolin Wu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN
| | - Rory P. Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN
| | | | - Maria-Luisa Alegre
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL
| | - William S. Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN
| | - Ajay K. Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare, Minneapolis, MN
- Hennepin Healthcare Research Institute, Minneapolis, MN
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Akgül T, Karakan T. The role of probiotics in women with recurrent urinary tract infections. Turk J Urol 2018; 44:377-383. [PMID: 30487041 DOI: 10.5152/tud.2018.48742] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/18/2018] [Indexed: 12/21/2022]
Abstract
Urinary tract infections (UTIs) still represent a significant bother for women and result in high costs to the health system. Increasing antimicrobial resistance has stimulated interest in non-antibiotic prophylaxis of recurrent UTIs. Evidence shows that the microorganisms inhabit many sites of the body, including the urinary tract which has long been assumed to be sterile in healthy individuals, might have a role in maintaining urinary health. Studies of the urinary microbiota (UM) have identified remarkable differences between healthy populations and those with urologic diseases. The depletion of these organisms in women susceptible to UTIs raised the question of whether artificial supplementation of these microorganisms as probiotics could lower infection rates. In the literature, probiotic interventions were shown to have some efficacy in the treatment and prevention of urogenital infections. Despite previous controversy regarding the use of probiotics, as treatment for UTIs, there are increasing signs that it may be possible to use them as a first step in regulating the UM so as to reduce the risk of or as a treatment for certain urinary diseases. However, further future clinical trials, involving large numbers of patients, will be mandatory to achieve definite evidence of the preventive and curative role of probiotics in UTIs. Details about correct formulations in terms of amount of bacteria, viability and associated growth factors, will be required in order to standardize the administration schedule and achieve homogeneous and comparable results on selected patients.
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Affiliation(s)
- Turgay Akgül
- Department of Urology, University of Health Sciences Ankara Training and Research Hospital, Ankara, Turkey
| | - Tolga Karakan
- Department of Urology, University of Health Sciences Ankara Training and Research Hospital, Ankara, Turkey
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Polyomavirus BK Nephropathy-Associated Transcriptomic Signatures: A Critical Reevaluation. Transplant Direct 2018; 4:e339. [PMID: 29464200 PMCID: PMC5811268 DOI: 10.1097/txd.0000000000000752] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/07/2017] [Indexed: 12/29/2022] Open
Abstract
Background Recent work using DNA microarrays has suggested that genes related to DNA replication, RNA polymerase assembly, and pathogen recognition receptors can serve as surrogate tissue biomarkers for polyomavirus BK nephropathy (BKPyVN). Methods We have examined this premise by looking for differential regulation of these genes using a different technology platform (RNA-seq) and an independent set 25 biopsies covering a wide spectrum of diagnoses. Results RNA-seq could discriminate T cell–mediated rejection from other common lesions seen in formalin fixed biopsy material. However, overlapping RNA-seq signatures were found among all disease processes investigated. Specifically, genes previously reported as being specific for the diagnosis of BKPyVN were found to be significantly upregulated in T cell–mediated rejection, inflamed areas of fibrosis/tubular atrophy, as well as acute tubular injury. Conclusions In conclusion, the search for virus specific molecular signatures is confounded by substantial overlap in pathogenetic mechanisms between BKPyVN and nonviral forms of allograft injury. Clinical heterogeneity, overlapping exposures, and different morphologic patterns and stage of disease are a source of substantial variability in “Omics” experiments. These variables should be better controlled in future biomarker studies on BKPyVN, T cell–mediated rejection, and other forms of allograft injury, before widespread implementation of these tests in the transplant clinic.
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47
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Li Y, Xu J, Su X. Analysis of Urine Composition in Type II Diabetic Mice after Intervention Therapy Using Holothurian Polypeptides. Front Chem 2017; 5:54. [PMID: 28798909 PMCID: PMC5526924 DOI: 10.3389/fchem.2017.00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Hydrolysates and peptide fractions (PF) obtained from sea cucumber with commercial enzyme were studied on the hyperglycemic and renal protective effects on db/db rats using urine metabolomics. Compared with the control group the polypeptides from the two species could significantly reduce the urine glucose and urea. We also tried to address the compositions of highly expressed urinary proteins using a proteomics approach. They were serum albumins, AMBP proteins, negative trypsin, elastase, and urinary protein, GAPDH, a receptor of urokinase-type plasminogen activator (uPAR), and Ig kappa chain C region. We used the electronic nose to quickly detect changes in the volatile substances in mice urine after holothurian polypeptides (HPP) fed, and the results show it can identify the difference between treatment groups with the control group without overlapping. The protein express mechanism of HPP treating diabetes was discussed, and we suggested these two peptides with the hypoglycemic and renal protective activity might be utilized as nutraceuticals.
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Affiliation(s)
- Yanyan Li
- School of Marine Science, Ningbo UniversityZhejiang, China
- Department of Food Science, Cornell UniversityIthaca, NY, United States
| | - Jiajie Xu
- School of Marine Science, Ningbo UniversityZhejiang, China
- College of Engineering, China Agricultural UniversityBeijing, China
| | - Xiurong Su
- School of Marine Science, Ningbo UniversityZhejiang, China
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