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Salas-Espejo E, Terrón-Camero LC, Ruiz JL, Molina NM, Andrés-León E. Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms. Semin Reprod Med 2023; 41:125-143. [PMID: 38320576 DOI: 10.1055/s-0044-1779025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.
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Affiliation(s)
- Eduardo Salas-Espejo
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Laura C Terrón-Camero
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - José L Ruiz
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN), CSIC, Granada, Spain
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Jeong S, Cho WK, Jo Y, Choi SR, Lee N, Jeon K, Park MJ, Song W, Lee KY. Immune-checkpoint proteins, cytokines, and microbiome impact on patients with cervical insufficiency and preterm birth. Front Immunol 2023; 14:1228647. [PMID: 37554329 PMCID: PMC10404982 DOI: 10.3389/fimmu.2023.1228647] [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: 05/25/2023] [Accepted: 06/30/2023] [Indexed: 08/10/2023] Open
Abstract
Background Microenvironmental factors, including microbe-induced inflammation and immune-checkpoint proteins that modulate immune cells have been associated with both cervical insufficiency and preterm delivery. These factors are incompletely understood. This study aimed to explore and compare interactions among microbiome and inflammatory factors, such as cytokines and immune-checkpoint proteins, in patients with cervical insufficiency and preterm birth. In particular, factors related to predicting preterm birth were identified and the performance of the combination of these factors was evaluated. Methods A total of 220 swab samples from 110 pregnant women, prospectively recruited at the High-Risk Maternal Neonatal Intensive Care Center, were collected between February 2020 and March 2021. This study included 63 patients with cervical insufficiency receiving cerclage and 47 control participants. Endo- and exocervical swabs and fluids were collected simultaneously. Shotgun metagenomic sequencing for the microbiome and the measurement of 34 immune-checkpoint proteins and inflammatory cytokines were performed. Results First, we demonstrated that immune-checkpoint proteins, the key immune-regulatory molecules, could be measured in endocervical and exocervical samples. Secondly, we identified significantly different microenvironments in cervical insufficiency and preterm birth, with precise cervical locations, to provide information about practically useful cervical locations in clinical settings. Finally, the presence of Moraxella osloensis (odds ratio = 14.785; P = 0.037) and chemokine CC motif ligand 2 levels higher than 73 pg/mL (odds ratio = 40.049; P = 0.005) in endocervical samples were associated with preterm birth. Combining M. osloensis and chemokine CC motif ligand 2 yielded excellent performance for predicting preterm birth (area under the receiver operating characteristic curve = 0.846, 95% confidence interval = 0.733-0.925). Conclusion Multiple relationships between microbiomes, immune-checkpoint proteins, and inflammatory cytokines in the cervical microenvironment were identified. We focus on these factors to aid in the comprehensive understanding and therapeutic modulation of local microbial and immunologic compositions for the management of cervical insufficiency and preterm birth.
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Affiliation(s)
- Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Soo-Ran Choi
- Department of Obstetrics and Gynecology, Inha University College of Medicine, Inha University Hospital, Incheon, Republic of Korea
| | - Nuri Lee
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Kibum Jeon
- Department of Laboratory Medicine, Hangang Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Keun-Young Lee
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
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Li Y, Zhu W, Jiang Y, Lessing DJ, Chu W. Synthetic bacterial consortia transplantation for the treatment of Gardnerella vaginalis-induced bacterial vaginosis in mice. MICROBIOME 2023; 11:54. [PMID: 36941732 PMCID: PMC10026434 DOI: 10.1186/s40168-023-01497-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Bacterial vaginosis (BV) is a disease caused by vaginal microbiota dysbiosis. Here, we propose the use of synthetic bacterial consortia transplantation (SBCT) for the treatment of Gardnerella vaginalis-induced BV mice. The results showed that SBCT significantly reduced vaginal tissue damage and restored the vaginal microbiota, decreased the secretion of pro-inflammatory cytokines (IL-1β and IL-8), and suppressed NF-κB activation. IL-17, iNOS, and COX-2 expression in vaginal tissue were also down-regulated. However, IL-10 and Foxp3 showed up-regulated expression in mice. Compared with vaginal microbiota transplantation (VMT), results indicated that VMT was more effective than SBCT in suppressing G. vaginalis-induced inflammation. The obtained results suggest that synthetic bacterial consortia might be used as a potential biotherapeutic agent for the treatment of G. vaginalis-induced bacterial vaginosis. Video Abstract.
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Affiliation(s)
- Yunxia Li
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Wei Zhu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Jiang
- Animal, Plant and Food Inspection Center of Nanjing Customs, Nanjing, 210019, China
| | - Duncan James Lessing
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
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van Teijlingen NH, Helgers LC, Sarrami-Forooshani R, Zijlstra-Willems EM, van Hamme JL, Segui-Perez C, van Smoorenburg MY, Borgdorff H, van de Wijgert JH, van Leeuwen E, van der Post JA, Strijbis K, Ribeiro CM, Geijtenbeek TB. Vaginal bacterium Prevotella timonensis turns protective Langerhans cells into HIV-1 reservoirs for virus dissemination. EMBO J 2022; 41:e110629. [PMID: 35968812 PMCID: PMC9531304 DOI: 10.15252/embj.2022110629] [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: 01/10/2022] [Revised: 07/08/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Dysbiosis of vaginal microbiota is associated with increased HIV-1 acquisition, but the underlying cellular mechanisms remain unclear. Vaginal Langerhans cells (LCs) protect against mucosal HIV-1 infection via autophagy-mediated degradation of HIV-1. As LCs are in continuous contact with bacterial members of the vaginal microbiome, we investigated the impact of commensal and dysbiosis-associated vaginal (an)aerobic bacterial species on the antiviral function of LCs. Most of the tested bacteria did not affect the HIV-1 restrictive function of LCs. However, Prevotella timonensis induced a vast uptake of HIV-1 by vaginal LCs. Internalized virus remained infectious for days and uptake was unaffected by antiretroviral drugs. P. timonensis-exposed LCs efficiently transmitted HIV-1 to target cells both in vitro and ex vivo. Additionally, P. timonensis exposure enhanced uptake and transmission of the HIV-1 variants that establish infection after sexual transmission, the so-called Transmitted Founder variants. Our findings, therefore, suggest that P. timonensis might set the stage for enhanced HIV-1 susceptibility during vaginal dysbiosis and advocate targeted treatment of P. timonensis during bacterial vaginosis to limit HIV-1 infection.
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Affiliation(s)
- Nienke H van Teijlingen
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Leanne C Helgers
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Ramin Sarrami-Forooshani
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Esther M Zijlstra-Willems
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
| | - John L van Hamme
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Celia Segui-Perez
- Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Marleen Y van Smoorenburg
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Hanneke Borgdorff
- Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Janneke Hhm van de Wijgert
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth van Leeuwen
- Department of Obstetrics and Gynecology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Joris Am van der Post
- Department of Obstetrics and Gynecology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Karin Strijbis
- Division Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - Carla Ms Ribeiro
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Teunis Bh Geijtenbeek
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam institute for Infection and Immunity, Amsterdam, The Netherlands
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