1
|
Tamarelle J, Thiébaut ACM, de Barbeyrac B, Bébéar C, Bourret A, Fauconnier A, Ravel J, Delarocque-Astagneau E. Vaginal microbiota stability over 18 months in young student women in France. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04943-3. [PMID: 39302529 DOI: 10.1007/s10096-024-04943-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024]
Abstract
PURPOSE Non-optimal vaginal microbiota lacking lactobacilli and comprising a wide array of anaerobic bacteria, typified by community state type (CST) IV, have been associated with adverse gynecological and pregnancy outcomes. Here, we investigate the stability of the vaginal microbiota sampled every 6 months over 18 months and how samples distantly collected combined with exposures could provide insight on future microbiota compositional changes. METHODS Vaginal microbiota dynamics were analyzed in 241 female students aged 18-24 years and negative for Chlamydia trachomatis and Neisseria gonorrhoeae. The vaginal microbiota was characterized using 16S rRNA gene amplicon sequencing and assigned to CSTs. Vaginal microbiota longitudinal profiles were determined through hierarchical clustering. RESULTS At baseline, 11.2% of participants had a CST IV, 40.5% a CST I (Lactobacillus crispatus-dominated), and 38.1% a CST III (Lactobacillus iners-dominated). A total of 345 CST transitions were observed over the study period. Pain during sexual intercourse was associated with a higher probability of transition from CST III to CST IV, while self-reported yeast infection was associated with a higher probability of transition from CST IV to CST I. Over the study period, 32.0% participants displayed a stable CST trajectory. Composition of the vaginal microbiota of a single sample predicted with good accuracy the CST trajectory over the following 18 months. CONCLUSION Vaginal longitudinal CST patterns over 18 months could be clustered into three main groups of trajectories. Performing molecular characterization at a single time point could contribute to improved preventive care and optimization of young women's reproductive and sexual health. CLINICALTRIALS gov Identifier: NCT02904811. Registration date: September 19, 2016.
Collapse
Affiliation(s)
- Jeanne Tamarelle
- Epidemiology and Modelling of Antibiotic Evasion Unit, Institut Pasteur, 75475, Paris, France
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Anne C M Thiébaut
- High Dimensional Biostatistics for Drug Safety and Genomics Team, Université Paris-Saclay, UVSQ, Inserm, CESP, 94807, Villejuif, France.
| | - Bertille de Barbeyrac
- Bacteriology department, Bordeaux University Hospital, French National Reference Center for Bacterial STIs, 33000, Bordeaux, France
| | - Cécile Bébéar
- Bacteriology department, Bordeaux University Hospital, French National Reference Center for Bacterial STIs, 33000, Bordeaux, France
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, 33000, Bordeaux, France
| | - Antoine Bourret
- Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Assistance Publique des Hôpitaux de Paris (AP-HP), Service de Gynécologie, Hôpital Universitaire Paris Centre (HUPC), Obstétrique II, Paris, France
| | - Arnaud Fauconnier
- Unité de Recherche 7285 « Risques Cliniques Et Sécurité en Santé Des Femmes Et en Santé Périnatale » (RISCQ), Université Paris-Saclay, UVSQ, 78180, Montigny-Le-Bretonneux, France
- Centre Hospitalier Intercommunal de Poissy-Saint-Germain-en-Laye, Service de Gynécologie & Obstétrique, 78300, Poissy, France
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elisabeth Delarocque-Astagneau
- Anti-Infective Evasion and Pharmacoepidemiology Team, Université Paris-Saclay, UVSQ, Inserm, CESP, 78180, Montigny-le-Bretonneux, France
- Raymond Poincaré Hospital, Epidemiology and Public Health Department, AP-HP, GHU Paris-Saclay University, 92380, Garches, France
| |
Collapse
|
2
|
Sousa LGV, Novak J, França A, Muzny CA, Cerca N. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia Strongly Influence Each Other's Transcriptome in Triple-Species Biofilms. MICROBIAL ECOLOGY 2024; 87:117. [PMID: 39294302 PMCID: PMC11410844 DOI: 10.1007/s00248-024-02433-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024]
Abstract
Bacterial vaginosis (BV), the most common vaginal infection worldwide, is characterized by the development of a polymicrobial biofilm on the vaginal epithelium. While Gardnerella spp. have been shown to have a prominent role in BV, little is known regarding how other species can influence BV development. Thus, we aimed to study the transcriptome of Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia, when growing in triple-species biofilms. Single and triple-species biofilms were formed in vitro, and RNA was extracted and sent for sequencing. cDNA libraries were prepared and sequenced. Quantitative PCR analysis (qPCR) was performed on the triple-species biofilms to evaluate the biofilm composition. The qPCR results revealed that the triple-species biofilms were mainly composed by G. vaginalis and P. bivia was the species with the lowest percentage. The RNA-sequencing analysis revealed a total of 432, 126, and 39 differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively, when growing together. Gene ontology enrichment of G. vaginalis downregulated genes revealed several functions associated with metabolism, indicating a low metabolic activity of G. vaginalis when growing in polymicrobial biofilms. This work highlighted that the presence of 3 different BV-associated bacteria in the biofilm influenced each other's transcriptome and provided insight into the molecular mechanisms that enhanced the virulence potential of polymicrobial consortia. These findings will contribute to understand the development of incident BV and the interactions occurring within the biofilm.
Collapse
Affiliation(s)
- Lúcia G V Sousa
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Braga, Portugal
| | - Juliano Novak
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Braga, Portugal
- Botucatu Medical School, Department of Pathology, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Angela França
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga, Portugal.
| |
Collapse
|
3
|
Carter KA, France MT, Rutt L, Bilski L, Martinez-Greiwe S, Regan M, Brotman RM, Ravel J. Sexual transmission of urogenital bacteria: whole metagenome sequencing evidence from a sexual network study. mSphere 2024; 9:e0003024. [PMID: 38358269 PMCID: PMC10964427 DOI: 10.1128/msphere.00030-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
Sexual transmission of the urogenital microbiota may contribute to adverse sexual and reproductive health outcomes. The extent of sexual transmission of the urogenital microbiota is unclear as prior studies largely investigated specific pathogens. We used epidemiologic data and whole metagenome sequencing to characterize urogenital microbiota strain concordance between participants of a sexual network study. Individuals who screened positive for genital Chlamydia trachomatis were enrolled and referred their sexual contacts from the prior 60-180 days. Snowball recruitment of sexual contacts continued for up to four waves. Vaginal swabs and penile urethral swabs were collected for whole metagenome sequencing. We evaluated bacterial strain concordance using inStrain and network analysis. We defined concordance as ≥99.99% average nucleotide identity over ≥50% shared coverage; we defined putative sexual transmission as concordance between sexual contacts with <5 single-nucleotide polymorphisms per megabase. Of 138 participants, 74 (54%) were female; 120 (87%) had genital chlamydia; and 43 (31%) were recruited contacts. We identified 115 strain-concordance events among 54 participants representing 25 bacterial species. Seven events (6%) were between sexual contacts including putative heterosexual transmission of Fannyhessea vaginae, Gardnerella leopoldii, Prevotella amnii, Sneathia sanguinegens, and Sneathia vaginalis (one strain each), and putative sexual transmission of Lactobacillus iners between female contacts. Most concordance events (108, 94%) were between non-contacts, including eight female participants connected through 18 Lactobacillus crispatus and 3 Lactobacillus jensenii concordant strains, and 14 female and 2 male participants densely interconnected through 52 Gardnerella swidsinskii concordance events.IMPORTANCEEpidemiologic evidence consistently indicates bacterial vaginosis (BV) is sexually associated and may be sexually transmitted, though sexual transmission remains subject to debate. This study is not capable of demonstrating BV sexual transmission; however, we do provide strain-level metagenomic evidence that strongly supports heterosexual transmission of BV-associated species. These findings strengthen the evidence base that supports ongoing investigations of concurrent male partner treatment for reducing BV recurrence. Our data suggest that measuring the impact of male partner treatment on F. vaginae, G. leopoldii, P. amnii, S. sanguinegens, and S. vaginalis may provide insight into why a regimen does or does not perform well. We also observed a high degree of strain concordance between non-sexual-contact female participants. We posit that this may reflect limited dispersal capacity of vaginal bacteria coupled with individuals' comembership in regional transmission networks where transmission may occur between parent and child at birth, cohabiting individuals, or sexual contacts.
Collapse
Affiliation(s)
- Kayla A. Carter
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Michael T. France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lindsay Rutt
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lisa Bilski
- School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | | | - Mary Regan
- School of Nursing, University of Maryland, Baltimore, Maryland, USA
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
4
|
Ardizzone CM, Taylor CM, Toh E, Lillis RA, Elnaggar JH, Lammons JW, Mott PD, Duffy EL, Shen L, Quayle AJ. Association of Chlamydia trachomatis burden with the vaginal microbiota, bacterial vaginosis, and metronidazole treatment. Front Cell Infect Microbiol 2023; 13:1289449. [PMID: 38149008 PMCID: PMC10750252 DOI: 10.3389/fcimb.2023.1289449] [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: 09/05/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is a common coinfection with Chlamydia trachomatis (Ct), and BV-associated bacteria (BVAB) and their products have been implicated in aiding Ct evade natural immunity. Here, we determined if a non-optimal vaginal microbiota was associated with a higher genital Ct burden and if metronidazole, a standard treatment for BV, would reduce Ct burden or aid in natural clearance of Ct infection. Cervicovaginal samples were collected from women at enrollment and, if testing positive for Ct infection, at a follow-up visit approximately one week later. Cervical Ct burden was assessed by inclusion forming units (IFU) and Ct genome copy number (GCN), and 16S rRNA gene sequencing was used to determine the composition of the vaginal microbiota. We observed a six-log spectrum of IFU and an eight-log spectrum of GCN in our study participants at their enrollment visit, but BV, as indicated by Amsel's criteria, Nugent scoring, or VALENCIA community state typing, did not predict infectious and total Ct burden, although IFU : GCN increased with Amsel and Nugent scores and in BV-like community state types. Ct burden was, however, associated with the abundance of bacterial species in the vaginal microbiota, negatively with Lactobacillus crispatus and positively with Prevotella bivia. Women diagnosed with BV were treated with metronidazole, and Ct burden was significantly reduced in those who resolved BV with treatment. A subset of women naturally cleared Ct infection in the interim, typified by low Ct burden at enrollment and resolution of BV. Abundance of many BVAB decreased, and Lactobacillus increased, in response to metronidazole treatment, but no changes in abundances of specific vaginal bacteria were unique to women who spontaneously cleared Ct infection.
Collapse
Affiliation(s)
- Caleb M. Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Evelyn Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rebecca A. Lillis
- Department of Medicine, Section of Infectious Diseases, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - John W. Lammons
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Patricia Dehon Mott
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Emily L. Duffy
- Department of Medicine, Section of Infectious Diseases, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Li Shen
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Alison J. Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| |
Collapse
|
5
|
Symul L, Jeganathan P, Costello EK, France M, Bloom SM, Kwon DS, Ravel J, Relman DA, Holmes S. Sub-communities of the vaginal microbiota in pregnant and non-pregnant women. Proc Biol Sci 2023; 290:20231461. [PMID: 38018105 PMCID: PMC10685114 DOI: 10.1098/rspb.2023.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Diverse and non-Lactobacillus-dominated vaginal microbial communities are associated with adverse health outcomes such as preterm birth and the acquisition of sexually transmitted infections. Despite the importance of recognizing and understanding the key risk-associated features of these communities, their heterogeneous structure and properties remain ill-defined. Clustering approaches are commonly used to characterize vaginal communities, but they lack sensitivity and robustness in resolving substructures and revealing transitions between potential sub-communities. Here, we address this need with an approach based on mixed membership topic models. Using longitudinal data from cohorts of pregnant and non-pregnant study participants, we show that topic models more accurately describe sample composition, longitudinal changes, and better predict the loss of Lactobacillus dominance. We identify several non-Lactobacillus-dominated sub-communities common to both cohorts and independent of reproductive status. In non-pregnant individuals, we find that the menstrual cycle modulates transitions between and within sub-communities, as well as the concentrations of half of the cytokines and 18% of metabolites. Overall, our analyses based on mixed membership models reveal substructures of vaginal ecosystems which may have important clinical and biological associations.
Collapse
Affiliation(s)
- Laura Symul
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, CA 94305, USA
| | - Pratheepa Jeganathan
- Department of Mathematics and Statistics, McMaster University, 1280 Main Street, West Hamilton, Ontario, Canada L8S 4K1
| | - Elizabeth K. Costello
- Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Michael France
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W. Baltimore Street, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, HSF-I Suite 380, Baltimore, MD 21201, USA
| | - Seth M. Bloom
- Division of Infectious Diseases, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139, USA
| | - Douglas S. Kwon
- Division of Infectious Diseases, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W. Baltimore Street, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, HSF-I Suite 380, Baltimore, MD 21201, USA
| | - David A. Relman
- Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
- Department of Microbiology & Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, 390 Jane Stanford Way, Stanford, CA 94305, USA
| |
Collapse
|
6
|
Muzny CA, Cerca N, Elnaggar JH, Taylor CM, Sobel JD, Van Der Pol B. State of the Art for Diagnosis of Bacterial Vaginosis. J Clin Microbiol 2023; 61:e0083722. [PMID: 37199636 PMCID: PMC10446871 DOI: 10.1128/jcm.00837-22] [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] [Indexed: 05/19/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common cause of vaginal discharge among reproductive-age women. It is associated with multiple adverse health outcomes, including increased risk of acquisition of HIV and other sexually transmitted infections (STIs), in addition to adverse birth outcomes. While it is known that BV is a vaginal dysbiosis characterized by a shift in the vaginal microbiota from protective Lactobacillus species to an increase in facultative and strict anaerobic bacteria, its exact etiology remains unknown. The purpose of this minireview is to provide an updated overview of the range of tests currently used for the diagnosis of BV in both clinical and research settings. This article is divided into two primary sections: traditional BV diagnostics and molecular diagnostics. Molecular diagnostic assays, particularly 16S rRNA gene sequencing, shotgun metagenomic sequencing, and fluorescence in situ hybridization (FISH), are specifically highlighted, in addition to multiplex nucleic acid amplification tests (NAATs), given their increasing use in clinical practice (NAATs) and research studies (16S rRNA gene sequencing, shotgun metagenomic sequencing, and FISH) regarding the vaginal microbiota and BV pathogenesis. We also provide a discussion of the strengths and weaknesses of current BV diagnostic tests and discuss future challenges in this field of research.
Collapse
Affiliation(s)
- Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Jack D. Sobel
- Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
| | - Barbara Van Der Pol
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|
7
|
Romero R, Theis KR, Gomez-Lopez N, Winters AD, Panzer JJ, Lin H, Galaz J, Greenberg JM, Shaffer Z, Kracht DJ, Chaiworapongsa T, Jung E, Gotsch F, Ravel J, Peddada SD, Tarca AL. The Vaginal Microbiota of Pregnant Women Varies with Gestational Age, Maternal Age, and Parity. Microbiol Spectr 2023; 11:e0342922. [PMID: 37486223 PMCID: PMC10434204 DOI: 10.1128/spectrum.03429-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/25/2023] [Indexed: 07/25/2023] Open
Abstract
The composition of the vaginal microbiota is heavily influenced by pregnancy and may factor into pregnancy complications, including spontaneous preterm birth. However, results among studies have been inconsistent due, in part, to variation in sample sizes and ethnicity. Thus, an association between the vaginal microbiota and preterm labor continues to be debated. Yet, before assessing associations between the composition of the vaginal microbiota and preterm labor, a robust and in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required. Here, we report a large longitudinal study (n = 474 women, 1,862 vaginal samples) of a predominantly African-American cohort-a population that experiences a relatively high rate of pregnancy complications-evaluating associations between individual identity, gestational age, and other maternal characteristics with the composition of the vaginal microbiota throughout gestation resulting in term delivery. The principal factors influencing the composition of the vaginal microbiota in pregnancy are individual identity and gestational age at sampling. Other factors are maternal age, parity, obesity, and self-reported Cannabis use. The general pattern across gestation is for the vaginal microbiota to remain or transition to a state of Lactobacillus dominance. This pattern can be modified by maternal parity and obesity. Regardless, network analyses reveal dynamic associations among specific bacterial taxa within the vaginal ecosystem, which shift throughout the course of pregnancy. This study provides a robust foundational understanding of the vaginal microbiota in pregnancy and sets the stage for further investigation of this microbiota in obstetrical disease. IMPORTANCE There is debate regarding links between the vaginal microbiota and pregnancy complications, especially spontaneous preterm birth. Inconsistencies in results among studies are likely due to differences in sample sizes and cohort ethnicity. Ethnicity is a complicating factor because, although all bacterial taxa commonly inhabiting the vagina are present among all ethnicities, the frequencies of these taxa vary among ethnicities. Therefore, an in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required prior to evaluating associations between the vaginal microbiota and obstetrical disease. This initial investigation is a large longitudinal study of the vaginal microbiota throughout gestation resulting in a term delivery in a predominantly African-American cohort, a population that experiences disproportionally negative maternal-fetal health outcomes. It establishes the magnitude of associations between maternal characteristics, such as age, parity, body mass index, and self-reported Cannabis use, on the vaginal microbiota in pregnancy.
Collapse
Affiliation(s)
- Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Kevin R. Theis
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Andrew D. Winters
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jonathan J. Panzer
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Huang Lin
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jonathan M. Greenberg
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Zachary Shaffer
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - David J. Kracht
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Tinnakorn Chaiworapongsa
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Eunjung Jung
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Francesca Gotsch
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shyamal D. Peddada
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Adi L. Tarca
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, USA
| |
Collapse
|
8
|
Osei Sekyere J, Oyenihi AB, Trama J, Adelson ME. Species-Specific Analysis of Bacterial Vaginosis-Associated Bacteria. Microbiol Spectr 2023; 11:e0467622. [PMID: 37347202 PMCID: PMC10434177 DOI: 10.1128/spectrum.04676-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/04/2023] [Indexed: 06/23/2023] Open
Abstract
Vaginal dysbiosis in women reduces the abundance of Lactobacillus species and increases that of anaerobic fastidious bacteria. This dysbiotic condition in the vagina, called bacterial vaginosis (BV), can be symptomatic with odorous vaginal discharges or asymptomatic and affects a third of women of reproductive age. Three unclassified bacterial species designated BV-associated bacteria 1, 2, and 3 (BVAB-1, -2, and -3) in 2005 were found to be highly preponderant in the vagina of females with BV. Here, we used sequence homology and phylogenetics analyses to identify the actual species of BVAB-1, -2, and -3 and found BVAB-1 to be Clostridiales genomosp. BVAB-1, BVAB-2 to be Oscillospiraceae bacterium strain CHIC02, and BVAB-3 to be Mageeibacillus indolicus, respectively. These are anaerobic and uncultured species that can be identified only through metagenomics. Long-read sequencing of BV specimens can also enable a genomic reassembly of these species' genomes from metagenomes. Species-specific identification of these pathogens and the availability of their genomes from assembled metagenomes will advance our understanding of their biology, facilitate the design of sensitive diagnostics and drugs, and enhance the treatment of BV. IMPORTANCE For many years since 2005, BVAB, an important pathogen of the female vaginal tract that is associated with BV, has been identified using PCR without knowing its actual species. Without a full genome of these pathogens, a better understanding of their pathogenicity, treatment, resistance, and diagnostics cannot be reached. In this analysis, we use the DNA of BVAB-1, -2, and -3 to determine their actual species to enhance further research into their pathogenicity, resistance, diagnosis, and treatment.
Collapse
Affiliation(s)
- John Osei Sekyere
- Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton Township, New Jersey, USA
| | - Ayodeji B. Oyenihi
- Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton Township, New Jersey, USA
| | - Jason Trama
- Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton Township, New Jersey, USA
| | - Martin E. Adelson
- Medical Diagnostic Laboratories, Genesis Biotechnology Group, Hamilton Township, New Jersey, USA
| |
Collapse
|
9
|
Costello EK, DiGiulio DB, Robaczewska A, Symul L, Wong RJ, Shaw GM, Stevenson DK, Holmes SP, Kwon DS, Relman DA. Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth. Nat Commun 2023; 14:4141. [PMID: 37438386 PMCID: PMC10338445 DOI: 10.1038/s41467-023-39849-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
The vaginal ecosystem is closely tied to human health and reproductive outcomes, yet its dynamics in the wake of childbirth remain poorly characterized. Here, we profile the vaginal microbiota and cytokine milieu of participants sampled longitudinally throughout pregnancy and for at least one year postpartum. We show that delivery, regardless of mode, is associated with a vaginal pro-inflammatory cytokine response and the loss of Lactobacillus dominance. By contrast, neither the progression of gestation nor the approach of labor strongly altered the vaginal ecosystem. At 9.5-months postpartum-the latest timepoint at which cytokines were assessed-elevated inflammation coincided with vaginal bacterial communities that had remained perturbed (highly diverse) from the time of delivery. Time-to-event analysis indicated a one-year postpartum probability of transitioning to Lactobacillus dominance of 49.4%. As diversity and inflammation declined during the postpartum period, dominance by L. crispatus, the quintessential health-associated commensal, failed to return: its prevalence before, immediately after, and one year after delivery was 41%, 4%, and 9%, respectively. Revisiting our pre-delivery data, we found that a prior live birth was associated with a lower odds of L. crispatus dominance in pregnant participants-an outcome modestly tempered by a longer ( > 18-month) interpregnancy interval. Our results suggest that reproductive history and childbirth in particular remodel the vaginal ecosystem and that the timing and degree of recovery from delivery may help determine the subsequent health of the woman and of future pregnancies.
Collapse
Affiliation(s)
- Elizabeth K Costello
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Daniel B DiGiulio
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Anna Robaczewska
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura Symul
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Section of Infectious Diseases, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
| |
Collapse
|
10
|
Correia GD, Marchesi JR, MacIntyre DA. Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods. Curr Opin Microbiol 2023; 73:102292. [PMID: 36931094 DOI: 10.1016/j.mib.2023.102292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/17/2023]
Abstract
Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.
Collapse
Affiliation(s)
- Gonçalo Ds Correia
- Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Julian R Marchesi
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK; Centre for Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, Imperial College London, London W2 1NY, UK
| | - David A MacIntyre
- Institute of Reproductive and Developmental Biology, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK.
| |
Collapse
|
11
|
Carter KA, Fodor AA, Balkus JE, Zhang A, Serrano MG, Buck GA, Engel SM, Wu MC, Sun S. Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition. mSystems 2023; 8:e0100322. [PMID: 36975801 PMCID: PMC10134888 DOI: 10.1128/msystems.01003-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.
Collapse
Affiliation(s)
- Kayla A. Carter
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jennifer E. Balkus
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Angela Zhang
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Gregory A. Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Stephanie M. Engel
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael C. Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Shan Sun
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| |
Collapse
|
12
|
Lee CY, Dillard LR, Papin JA, Arnold KB. New perspectives into the vaginal microbiome with systems biology. Trends Microbiol 2023; 31:356-368. [PMID: 36272885 DOI: 10.1016/j.tim.2022.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 10/28/2022]
Abstract
The vaginal microbiome (VMB) is critical to female reproductive health; however, the mechanisms associated with optimal and non-optimal states remain poorly understood due to the complex community structure and dynamic nature. Quantitative systems biology techniques applied to the VMB have improved understanding of community composition and function using primarily statistical methods. In contrast, fewer mechanistic models that use a priori knowledge of VMB features to develop predictive models have been implemented despite their use for microbiomes at other sites, including the gastrointestinal tract. Here, we explore systems biology approaches that have been applied in the VMB, highlighting successful techniques and discussing new directions that hold promise for improving understanding of health and disease.
Collapse
Affiliation(s)
- Christina Y Lee
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Lillian R Dillard
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Kelly B Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
13
|
Edfeldt G, Kaldhusdal V, Czarnewski P, Bradley F, Bergström S, Lajoie J, Xu J, Månberg A, Kimani J, Oyugi J, Nilsson P, Tjernlund A, Fowke KR, Kwon DS, Broliden K. Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers. MICROBIOME 2023; 11:67. [PMID: 37004130 PMCID: PMC10064689 DOI: 10.1186/s40168-023-01502-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The majority of studies characterizing female genital tract microbiota have focused on luminal organisms, while the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that these communities may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a cohort of Kenyan female sex workers. RESULTS We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners-dominated luminal samples had a corresponding Gardnerella-dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbial community was associated with epithelial remodeling and pro-inflammatory pathways. Tissue-adherent communities dominated by L. iners and Gardnerella were associated with lower host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, although with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. CONCLUSION We identified ectocervical tissue-adherent bacterial communities in all study participants of a female sex worker cohort. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. We further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community could possibly act as a reservoir that seed the lumen with less optimal, non-Lactobacillus, bacteria. Video Abstract.
Collapse
Affiliation(s)
- Gabriella Edfeldt
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Vilde Kaldhusdal
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Solna, Sweden
| | - Frideborg Bradley
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Julie Lajoie
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jiawu Xu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joshua Kimani
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Partners for Health and Development in Africa, Nairobi, Kenya
| | - Julius Oyugi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annelie Tjernlund
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Keith R Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Partners for Health and Development in Africa, Nairobi, Kenya
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kristina Broliden
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden.
| |
Collapse
|
14
|
Mabugana MC, Dias BDC, Muller EE, Kufa T, Gumede L, Mahlangu MP, Maseko DV, Kularatne RS. The evaluation of the Allplex™ BV molecular assay for the diagnosis of bacterial vaginosis in symptomatic South African females. Diagn Microbiol Infect Dis 2023; 106:115924. [PMID: 37030281 DOI: 10.1016/j.diagmicrobio.2023.115924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Bacterial vaginosis (BV) is a dysbiosis of vaginal microbiota characterized by a shift from Lactobacillus species predomination to a heterogeneous mixture of anaerobes. We compared the performance characteristics of the Allplex ™ BV molecular assay with the reference test, Nugent score microscopy, for vaginal swab specimens from symptomatic South African women. A total of 213 patients were enrolled, of whom 99 (46.5%) and 132 (62.0%) were diagnosed with BV by Nugent and Allplex™, respectively. The Allplex™ BV assay displayed a sensitivity of 94.9% (95% CI, 88.7%-97.8%) and a specificity of 66.7% (95% CI, 57.6%-74.6%), with an agreement of 79.8% (95% CI, 73.9%-84.7%) (κ = 0.60). Assay design may be enhanced for improved specificity by accounting for differences in healthy and BV-associated vaginal microbiomes among women of different ethnicities.
Collapse
|
15
|
Compositional Changes in the Vaginal Bacterial Microbiome of Healthy Pregnant Women across the Three Gestational Trimesters in Ismailia, Egypt. Microorganisms 2023; 11:microorganisms11010139. [PMID: 36677431 PMCID: PMC9862816 DOI: 10.3390/microorganisms11010139] [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: 11/28/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
The composition of the vaginal microbiome may lead to adverse pregnancy outcomes. Normal pregnancy is associated with changes in the vaginal bacterial community composition, which tend to be more enriched with one or two Lactobacillus species promoting a healthy vagina and favorable birth outcomes. The aim of the current study was to determine compositional changes in the healthy vaginal microbiome composition during the three trimesters of pregnancy in Ismailia, Egypt using Illumina MiSeq sequencing of the V3-V4 region of the 16S rRNA. The phylum Firmicutes and the genus Lactobacillus dominated across the three trimesters of pregnancy. L. iners was the most abundant species. However, L. coleohominis and L. reuteri represented the least dominant vaginal lactobacilli. Core microbiome analyses showed the Lactobacillus genus and L. iners species to have the highest prevalence in all the samples of our study groups. The phylum Firmicutes was found to be negatively correlated with almost all other vaginal phyla during pregnancy. Likewise, a negative correlation between Lactobacillus and almost all other genera was detected, including significant negative correlations with Dialister and Prevotella. Furthermore, negative correlations of L. iners were detected with almost all other species, including a significant negative correlation with L. helveticus, G. vaginalis, S. anginosus, and S. agalactiae.
Collapse
|
16
|
Roachford OSE, Alleyne AT, Nelson KE. Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries. PeerJ 2022; 10:e14449. [PMID: 36518275 PMCID: PMC9744153 DOI: 10.7717/peerj.14449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022] Open
Abstract
Background Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes. Results In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis-dominant (N = 6, 21.8%); CST VII (Prevotella-dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 "taxa with high pathogenic potential" (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = -0.68, p < 2.2e-16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = -0.13, p = 0.1). However, at the individual level, Mycoplasma hominis exhibited moderate positive correlations with Gardnerella (r = 0.46, p = 2.6e-09) and Prevotella spp. (r = 0.47, p = 1.4e-09). Conclusions These findings while supporting the idea that vaginal microbiomes vary with ethnicity, also suggest that CSTs are more wide-ranging and not exclusive to any particular ethnic group. This study offers additional insight into the structure of the vaginal microbiome and contributes to the description and subcategorization of non-Lactobacillus-dominated CSTs.
Collapse
Affiliation(s)
- Orville St. E. Roachford
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Angela T. Alleyne
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, MD, United States of America
- J. Craig Venter Institute, La Jolla, CA, United States of America
| |
Collapse
|
17
|
HIV-associated vaginal microbiome and inflammation predict spontaneous preterm birth in Zambia. Sci Rep 2022; 12:8573. [PMID: 35595739 PMCID: PMC9123167 DOI: 10.1038/s41598-022-12424-w] [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: 01/25/2022] [Accepted: 04/26/2022] [Indexed: 11/27/2022] Open
Abstract
A Lactobacillus-deficient, anaerobe-rich vaginal microbiome has been associated with local inflammation and spontaneous preterm birth (sPTB), but few studies have assessed this association in the setting of HIV. We performed metagenomic sequencing and inflammatory marker assays on vaginal swabs collected in pregnancy. We grouped samples into 7 metagenomic clusters (mgClust) using the non-redundant VIRGO catalogue, and derived inflammatory scores by factor analysis. Of 221 participants, median Shannon diversity index (SDI) was highest in HIV+ with detectable viral load (1.31, IQR: 0.85–1.66; p < 0.001) and HIV+ with undetectable virus (1.17, IQR: 0.51–1.66; p = 0.01) compared to HIV− (0.74, IQR: 0.35–1.26). Inflammatory scores positively correlated with SDI (+ 0.66, 95%CI 0.28, 1.03; p = 0.001), highest among anaerobe-rich mgClust2–mgClust6. HIV was associated with predominance of anaerobe-rich mgClust5 (17% vs. 6%; p = 0.02) and mgClust6 (27% vs. 11%; p = 0.002). Relative abundance of a novel Gardnerella metagenomic subspecies > 50% predicted sPTB (RR 2.6; 95%CI: 1.1, 6.4) and was higher in HIV+ (23% vs. 10%; p = 0.001). A novel Gardnerella metagenomic subspecies more abundant in women with HIV predicted sPTB. The risk of sPTB among women with HIV may be mediated by the vaginal microbiome and inflammation, suggesting potential targets for prevention.
Collapse
|
18
|
Thurman AR, Ravel J, Gajer P, Marzinke MA, Ouattara LA, Jacot T, Peet MM, Clark MR, Doncel GF. Vaginal Microbiota and Mucosal Pharmacokinetics of Tenofovir in Healthy Women Using a 90-Day Tenofovir/Levonorgestrel Vaginal Ring. Front Cell Infect Microbiol 2022; 12:799501. [PMID: 35350436 PMCID: PMC8957918 DOI: 10.3389/fcimb.2022.799501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/09/2022] [Indexed: 01/04/2023] Open
Abstract
Background A relationship between the vaginal microbiota and tenofovir (TFV) concentrations and activity after topical administration has been previously reported. Objective CONRAD A15-138 was a randomized, placebo-controlled Phase I study aimed at characterizing the safety, pharmacokinetics (PK), and pharmacodynamics (PD) of TFV and levonorgestrel (LNG) administered through a vaginal ring (IVR) for 90 days. Herein, we describe changes from baseline in the vaginal microbiota with IVR use and the impact of the vaginal microbiota on mucosal TFV PK. Methods The study screened 68 participants and randomized 47 (37 TFV/LNG, 10 placebo), assessing the vaginal microbiota by sequencing the V3-V4 regions of 16S rRNA genes prior to IVR insertion and monthly for 3 months. Concentrations of TFV in vaginal fluid (VF), and TFV and TFV-diphosphate (TFV-DP) in vaginal tissue, and modeled PD against HIV-1 in vitro were measured before and after treatment. Results There were no clinically significant changes in relative abundance of vaginal bacterial phylotypes from pre-insertion baseline at any month among active and placebo IVR users. There were no significant changes in community state type (CST) with IVR use. Participants with diverse, anaerobic CST IVA/B microbiota had higher in vivo release of TFV from the IVR compared to women with Lactobacillus-dominated (LbD) microbiota, who had expected in vivo TFV release rates. Median VF TFV concentrations were significantly higher among women with CST IVA/B microbiota in months 1 (3,135 ng/mg VF) and 2 (3,800 ng/mg). Women with LbD microbiota had significantly higher median VF TFV concentration (1,423 ng/mg) and median TFV (103 ng/mg) and TFV-DP (5,877 fmol/mg) tissue concentrations versus women with CST IVA/B microbiota at month 3. All women demonstrated a significant increase from pre-insertion baseline of in vitro HIV-1 inhibition by VF (p values <0.05). PD differences in tissue according to CST, however, were not statistically significant. Conclusion TFV/LNG IVR use did not change the vaginal microbiota nor increase the incidence of CST IVA/B. Vaginal microbiota, and in particular CST IVA/B, possibly through increased vaginal pH, impacted in vivo TFV release and cervicovaginal (CV) PK, but both PK and PD data suggest CV protection against HIV-1. Clinical Trial Registration ClinicalTrials.gov (#NCT03279120).
Collapse
Affiliation(s)
- Andrea R. Thurman
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Pawel Gajer
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mark A. Marzinke
- Departments of Pathology and Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Louise A. Ouattara
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Terry Jacot
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - M. Melissa Peet
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Meredith R. Clark
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Gustavo F. Doncel
- Department of Obstetrics and Gynecology, CONRAD, Eastern Virginia Medical School, Norfolk, VA, United States
| |
Collapse
|
19
|
Towards a deeper understanding of the vaginal microbiota. Nat Microbiol 2022; 7:367-378. [PMID: 35246662 DOI: 10.1038/s41564-022-01083-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/03/2022] [Indexed: 12/30/2022]
Abstract
The human vaginal microbiota is a critical determinant of vaginal health. These communities live in close association with the vaginal epithelium and rely on host tissues for resources. Although often dominated by lactobacilli, the vaginal microbiota is also frequently composed of a collection of facultative and obligate anaerobes. The prevalence of these communities with a paucity of Lactobacillus species varies among women, and epidemiological studies have associated them with an increased risk of adverse health outcomes. The mechanisms that drive these associations have yet to be described in detail, with few studies establishing causative relationships. Here, we review our current understanding of the vaginal microbiota and its connection with host health. We centre our discussion around the biology of the vaginal microbiota when Lactobacillus species are dominant versus when they are not, including host factors that are implicated in shaping these microbial communities and the resulting adverse health outcomes. We discuss current approaches to modulate the vaginal microbiota, including probiotics and vaginal microbiome transplants, and argue that new model systems of the cervicovaginal environment that incorporate the vaginal microbiota are needed to progress from association to mechanism and this will prove invaluable for future research.
Collapse
|
20
|
Lovett A, Seña AC, Macintyre AN, Sempowski GD, Duncan JA, Waltmann A. Cervicovaginal Microbiota Predicts Neisseria gonorrhoeae Clinical Presentation. Front Microbiol 2022; 12:790531. [PMID: 35222300 PMCID: PMC8867028 DOI: 10.3389/fmicb.2021.790531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/13/2021] [Indexed: 01/11/2023] Open
Abstract
Neisseria gonorrhoeae infection of the female lower genital tract can present with a spectrum of phenotypes ranging from asymptomatic carriage to symptomatic cervical inflammation, or cervicitis. The factors that contribute to the development of asymptomatic or symptomatic infections are largely uncharacterized. We conducted a pilot study to assess differences in the cervicovaginal microbial community of patients presenting with symptomatic vs. asymptomatic N. gonorrhoeae infections to a sexually transmitted infections (STI) clinic. DNA was isolated from cervicovaginal swab specimens from women who tested positive for N. gonorrhoeae infection using a clinical diagnostic nucleic acid amplification test. We performed deep sequencing of 16S ribosomal RNA gene amplicons, followed by microbiome analyses with QIIME, and species-specific real-time PCR to assess the composition of microbial communities cohabitating the lower genital tract with the infecting N. gonorrhoeae. Specimens collected from asymptomatic individuals with N. gonorrhoeae infection and no co-infection with Chlamydia trachomatis and/or Trichomonas vaginalis carried Lactobacillus-dominant microbial communities more frequently than symptomatic patients without co-infection. When compared to asymptomatic individuals, symptomatic women had microbial communities characterized by more diverse and heterogenous bacterial taxa, typically associated with bacterial vaginosis (BV) [Prevotella, Sneathia, Mycoplasma hominis, and Bacterial Vaginosis-Associated Bacterium-1 (BVAB1)/"Candidatus Lachnocurva vaginae"]. Both symptomatic and asymptomatic N. gonorrhoeae patients with additional STI co-infection displayed a BV-like microbial community. These findings suggest that Lactobacillus-dominant vaginal microbial community may protect individuals from developing symptoms during lower genital tract infection with N. gonorrhoeae.
Collapse
Affiliation(s)
- Angela Lovett
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Arlene C. Seña
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew N. Macintyre
- School of Medicine and Duke Human Vaccine Institute, Duke University, Durham, NC, United States
| | - Gregory D. Sempowski
- School of Medicine and Duke Human Vaccine Institute, Duke University, Durham, NC, United States
| | - Joseph A. Duncan
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andreea Waltmann
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Andreea Waltmann,
| |
Collapse
|
21
|
De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis. Int J Mol Sci 2022; 23:ijms23031621. [PMID: 35163545 PMCID: PMC8835865 DOI: 10.3390/ijms23031621] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/17/2022] Open
Abstract
The vaginal microbiome plays an important role in women’s health and disease. Here we reanalyzed 40 vaginal transcriptomes from a previous study of de novo assembly (metaT-Assembly) followed by functional annotation. We identified 286,293 contigs and further assigned them to 25 phyla, 209 genera, and 339 species. Lactobacillus iners and Lactobacillus crispatus dominated the microbiome of non-bacterial vaginosis (BV) samples, while a complex of microbiota was identified from BV-associated samples. The metaT-Assembly identified a higher number of bacterial species than the 16S rRNA amplicon and metaT-Kraken methods. However, metaT-Assembly and metaT-Kraken exhibited similar major bacterial composition at the species level. Binning of metatranscriptome data resulted in 176 bins from major known bacteria and several unidentified bacteria in the vagina. Functional analyses based on Clusters of Orthologous Genes (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways suggested that a higher number of transcripts were expressed by the microbiome complex in the BV-associated samples than in non-BV-associated samples. The KEGG pathway analysis with an individual bacterial genome identified specific functions of the identified bacterial genome. Taken together, we demonstrated that the metaT-Assembly approach is an efficient tool to understand the dynamic microbial communities and their functional roles associated with the human vagina.
Collapse
|
22
|
Villani A, Fontana A, Barone S, de Stefani S, Primiterra M, Copetti M, Panebianco C, Parri C, Sciannamè N, Quitadamo PA, Tiezzi A, Santana L, Maglione A, D’Amato F, Perri F, Palini S, Pazienza V. Identifying Predictive Bacterial Markers from Cervical Swab Microbiota on Pregnancy Outcome in Woman Undergoing Assisted Reproductive Technologies. J Clin Med 2022; 11:jcm11030680. [PMID: 35160131 PMCID: PMC8836651 DOI: 10.3390/jcm11030680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
Background and aims: Failure of the embryo to implant causes about three-fourths of lost pregnancies. Female genital tract microbiota has been associated to Assisted Reproductive Technologies (ART) outcomes. The objective of this study was to analyze the microbiota of human cervical swab and to correlate these findings with the ART outcomes. Materials and Methods: In this study, 88 cervical swabs were collected from women undergoing ART cycles, with various causes of infertility, at the beginning of the ART protocols. After microbial DNA extraction, V3–V4 variable regions of the 16S rRNA gene were amplified and sequenced on the Illumina MiSeq platform. PEnalized LOgistic Regression Analysis (PELORA) was performed to identify clusters of bacterial populations with differential abundances between patients with unfavorable and favorable pregnancy outcome groups, respectively. Results: We identified a core of microorganisms at lower taxonomic levels that were predictive of women’s pregnancy outcomes. Statistically significant differences were identified at species levels with Lactobacillus salivarius, Lactobacillus rhamnosus among others. Moreover the abundance of Lactobacillus crispatus and iners, respectively increased and decreased in favorable group as compared to unfavorable group, resulted within the core of microorganisms associated to positive ART outcome. Although the predominance of lactobacilli is generally considered to be advantageous for ART outcome, we found that also the presence of Bifidobacterium (together with the other lactobacilli) was more abundant in the favorable group. Discussion: Cervix is colonized by microorganisms which can play a role in ART outcomes as seen by an overall decrease in embryo attachment rates and pregnancy rates in both fertile and infertile women. If confirmed in a larger cohort, the abundance of these bacteria can be useful not only as a marker of unfavorable pregnancy outcome but also they may open the way to new interventional strategies based on genital tract microbiota manipulation in order to increase the pregnancy rates in woman undergoing assisted reproductive technologies.
Collapse
Affiliation(s)
- Annacandida Villani
- Gastoenterology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Padre Pio 4, 71013 San Giovanni Rotondo, Italy; (A.V.); (C.P.); (F.P.)
| | - Andrea Fontana
- Unit of Biostatistic, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Padre Pio 4, 71013 San Giovanni Rotondo, Italy; (A.F.); (M.C.)
| | - Stefano Barone
- Unità Sanitaria Locale USL Toscana Nordovest, Assisted Reproductive Center Ospedale Versilia, 55041 Lido di Camaiore, Italy; (S.B.); (C.P.)
| | - Silvia de Stefani
- PMA Unit, Clinica Nuova Ricerca, Via Settembrini 17/h, 47923 Rimini, Italy; (S.d.S.); (M.P.); (A.T.); (L.S.)
| | - Mariangela Primiterra
- PMA Unit, Clinica Nuova Ricerca, Via Settembrini 17/h, 47923 Rimini, Italy; (S.d.S.); (M.P.); (A.T.); (L.S.)
| | - Massimiliano Copetti
- Unit of Biostatistic, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Padre Pio 4, 71013 San Giovanni Rotondo, Italy; (A.F.); (M.C.)
| | - Concetta Panebianco
- Gastoenterology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Padre Pio 4, 71013 San Giovanni Rotondo, Italy; (A.V.); (C.P.); (F.P.)
| | - Cristiana Parri
- Unità Sanitaria Locale USL Toscana Nordovest, Assisted Reproductive Center Ospedale Versilia, 55041 Lido di Camaiore, Italy; (S.B.); (C.P.)
| | - Natale Sciannamè
- Gynecology and Obstetrics Department, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (N.S.); (A.M.)
| | - Pasqua Anna Quitadamo
- Neonatology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy;
| | - Alessandra Tiezzi
- PMA Unit, Clinica Nuova Ricerca, Via Settembrini 17/h, 47923 Rimini, Italy; (S.d.S.); (M.P.); (A.T.); (L.S.)
| | - Liliana Santana
- PMA Unit, Clinica Nuova Ricerca, Via Settembrini 17/h, 47923 Rimini, Italy; (S.d.S.); (M.P.); (A.T.); (L.S.)
| | - Annamaria Maglione
- Gynecology and Obstetrics Department, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (N.S.); (A.M.)
| | - Federica D’Amato
- PMA Unit, Villa Margherita Hospital, Viale di Villa Massimo, 48, 00161 Roma, Italy;
| | - Francesco Perri
- Gastoenterology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Padre Pio 4, 71013 San Giovanni Rotondo, Italy; (A.V.); (C.P.); (F.P.)
| | - Simone Palini
- Pathophysiology of Reproduction Unit, Ospedale “Cervesi” di Cattolica—AUSL Romagna, Via Ludwig Van Beethoven, 1, 47841 Cattolica, Italy;
| | - Valerio Pazienza
- Gastoenterology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Padre Pio 4, 71013 San Giovanni Rotondo, Italy; (A.V.); (C.P.); (F.P.)
- Correspondence:
| |
Collapse
|
23
|
Krakowsky Y, Potter E, Hallarn J, Monari B, Wilcox H, Bauer G, Ravel J, Prodger JL. The Effect of Gender-Affirming Medical Care on the Vaginal and Neovaginal Microbiomes of Transgender and Gender-Diverse People. Front Cell Infect Microbiol 2022; 11:769950. [PMID: 35127550 PMCID: PMC8814107 DOI: 10.3389/fcimb.2021.769950] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/14/2021] [Indexed: 01/07/2023] Open
Abstract
Transgender and gender diverse individuals may seek gender-affirming medical care, such as hormone therapy or surgery, to produce primary and/or secondary sex characteristics that are more congruent with their gender. Gender-affirming medical care for transmasculine individuals can include testosterone therapy, which suppresses circulating estrogen and can lead to changes in the vaginal epithelium that are reminiscent of the post-menopausal period in cisgender females. Among transfeminine individuals, gender-affirming medical care can include vaginoplasty, which is the surgical creation of a vulva and neovaginal canal, commonly using penile and scrotal skin. The effect of gender-affirming medical care on the vagina of transmasculine individuals and on the neovagina of transfeminine individuals is poorly characterized. This review summarizes what is known of the epithelium and local microbiota of the testosterone-exposed vagina and the neovagina. We focus on potential pathogens and determinants of gynecological health and identify key knowledge gaps for future research.
Collapse
Affiliation(s)
- Yonah Krakowsky
- Division of Urology, Department of Surgery, Women’s College Hospital and Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada,Transition Related Surgery, Department of Surgery, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
| | - Emery Potter
- Transition Related Surgery, Department of Surgery, Women’s College Hospital, University of Toronto, Toronto, ON, Canada
| | - Jason Hallarn
- Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Bern Monari
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Hannah Wilcox
- Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Greta Bauer
- Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jessica L. Prodger
- Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada,Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada,*Correspondence: Jessica L. Prodger,
| |
Collapse
|
24
|
Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|
25
|
Characterization of the Gastrointestinal and Reproductive Tract Microbiota in Fertile and Infertile Pakistani Couples. BIOLOGY 2021; 11:biology11010040. [PMID: 35053038 PMCID: PMC8773429 DOI: 10.3390/biology11010040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary We describe microbial taxa associated with the gastrointestinal and reproductive tracts of married Pakistani couples. We highlight differences in microbial composition and diversity that are associated with fertile and infertile couples and provide a baseline for future in-depth studies to target the association of the human microbiome with infertility. Abstract The human microbiota is recognized as a vital “virtual” organ of the human body that influences human health, metabolism, and physiology. While the microbiomes of the gut, oral cavity, and skin have been extensively studied in the literature, relatively little work has been done on characterizing the microbiota of the human reproductive tract organs, and specifically on investigating its association to fertility. Here, we implemented a 16S ribosomal RNA (rRNA) amplicon sequencing approach to sequence and characterize the gut and genital tract microbiomes from several married Pakistani couples. The recruited individuals included 31 fertile and 35 infertile individuals, with ages ranging from 19–45 years. We identified several fluctuations in the diversity and composition of the gut and genital microbiota among fertile and infertile samples. For example, measures of α-diversity varied significantly between the genital samples donated by fertile and infertile men and there was overall greater between-sample variability in genital samples regardless of gender. In terms of taxonomic composition, Actinobacteria, Bacteroidetes, and Firmicutes fluctuated significantly between the gut microbiomes of fertile and infertile samples. Finally, biomarker analyses identified features (genera and molecular functions and pathways) that differed significantly between the fertile and infertile samples and in the past have been associated with bacterial vaginosis. However, we emphasize that 16S amplicon data alone has no bearing on individual health and is merely representative of microbial taxonomic differences that could also arise due to multiple other factors. Our findings, however, represent the first effort to characterize the microbiome associated with fertile and infertile couples in Pakistan and will hopefully pave the way for more comprehensive and broad-scale investigations in the future.
Collapse
|
26
|
Wolf EA, Rettig HC, Lupatsii M, Schlüter B, Schäfer K, Friedrich D, Graspeuntner S, Rupp J. Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections. Int J Mol Sci 2021; 22:ijms221910815. [PMID: 34639153 PMCID: PMC8509341 DOI: 10.3390/ijms221910815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.
Collapse
Affiliation(s)
- Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Britta Schlüter
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany;
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Dirk Friedrich
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
- Correspondence:
| |
Collapse
|
27
|
Joseph RJ, Ser HL, Kuai YH, Tan LTH, Arasoo VJT, Letchumanan V, Wang L, Pusparajah P, Goh BH, Ab Mutalib NS, Chan KG, Lee LH. Finding a Balance in the Vaginal Microbiome: How Do We Treat and Prevent the Occurrence of Bacterial Vaginosis? Antibiotics (Basel) 2021; 10:719. [PMID: 34203908 PMCID: PMC8232816 DOI: 10.3390/antibiotics10060719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/27/2021] [Accepted: 06/10/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial vaginosis (BV) has been reported in one-third of women worldwide at different life stages, due to the complex balance in the ecology of the vaginal microbiota. It is a common cause of abnormal vaginal discharge and is associated with other health issues. Since the first description of anaerobic microbes associated with BV like Gardnerella vaginalis in the 1950s, researchers have stepped up the game by incorporating advanced molecular tools to monitor and evaluate the extent of dysbiosis within the vaginal microbiome, particularly on how specific microbial population changes compared to a healthy state. Moreover, treatment failure and BV recurrence rate remain high despite the standard antibiotic treatment. Consequently, researchers have been probing into alternative or adjunct treatments, including probiotics or even vaginal microbiota transplants, to ensure successful treatment outcomes and reduce the colonization by pathogenic microbes of the female reproductive tract. The current review summarizes the latest findings in probiotics use for BV and explores the potential of vaginal microbiota transplants in restoring vaginal health.
Collapse
Affiliation(s)
- Rebecca Jane Joseph
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
| | - Hooi-Leng Ser
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
| | - Yi-He Kuai
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
- Clinical School Johor Bahru, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Johor Bahru 80100, Malaysia;
| | | | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
| | - Lijing Wang
- Vascular Biology Research Institute, Guangdong Pharmaceutical University, Guangzhou 510006, China;
| | - Priyia Pusparajah
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
| | - Bey-Hing Goh
- Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Nurul-Syakima Ab Mutalib
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbes and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (R.J.J.); (H.-L.S.); (Y.-H.K.); (L.T.-H.T.); (V.L.); (P.P.); (N.-S.A.M.)
| |
Collapse
|
28
|
Li Y, Jin Y, Zhang J, Pan H, Wu L, Liu D, Liu J, Hu J, Shen J. Recovery of human gut microbiota genomes with third-generation sequencing. Cell Death Dis 2021; 12:569. [PMID: 34078878 PMCID: PMC8172872 DOI: 10.1038/s41419-021-03829-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022]
Abstract
Human gut microbiota modulates normal physiological functions, such as maintenance of barrier homeostasis and modulation of metabolism, as well as various chronic diseases including type 2 diabetes and gastrointestinal cancer. Despite decades of research, the composition of the gut microbiota remains poorly understood. Here, we established an effective extraction method to obtain high quality gut microbiota genomes, and analyzed them with third-generation sequencing technology. We acquired a large quantity of data from each sample and assembled large numbers of reliable contigs. With this approach, we constructed tens of completed bacterial genomes in which there were several new bacteria species. We also identified a new conditional pathogen, Enterococcus tongjius, which is a member of Enterococci. This work provided a novel and reliable approach to recover gut microbiota genomes, facilitating the discovery of new bacteria species and furthering our understanding of the microbiome that underlies human health and diseases.
Collapse
Affiliation(s)
- Yanfei Li
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China.,School of Basic Medical Sciences and Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, 201318, Shanghai, China
| | - Yueling Jin
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | | | - Haoying Pan
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | - Lan Wu
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China.,School of Basic Medical Sciences and Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, 201318, Shanghai, China
| | - Dingsheng Liu
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | - Jinlong Liu
- Shanghai University of Medicine & Health Sciences affiliated Zhoupu Hospital, 201318, Shanghai, China
| | - Jing Hu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 201204, Shanghai, China.
| | - Junwei Shen
- Shanghai East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
| |
Collapse
|
29
|
Dabee S, Passmore JAS, Heffron R, Jaspan HB. The Complex Link between the Female Genital Microbiota, Genital Infections, and Inflammation. Infect Immun 2021; 89:e00487-20. [PMID: 33558324 PMCID: PMC8091093 DOI: 10.1128/iai.00487-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The female genital tract microbiota is part of a complex ecosystem influenced by several physiological, genetic, and behavioral factors. It is uniquely linked to a woman's mucosal immunity and plays a critical role in the regulation of genital inflammation. A vaginal microbiota characterized by a high abundance of lactobacilli and low overall bacterial diversity is associated with lower inflammation. On the other hand, a more diverse microbiota is linked to high mucosal inflammation levels, a compromised genital epithelial barrier, and an increased risk of sexually transmitted infections and other conditions. Several bacterial taxa such as Gardnerella spp., Prevotella spp., Sneathia spp., and Atopobium spp. are well known to have adverse effects; however, the definitive cause of this microbial dysbiosis is yet to be fully elucidated. The aim of this review is to discuss the multiple ways in which the microbiota influences the overall genital inflammatory milieu and to explore the causes and consequences of this inflammatory response. While there is abundant evidence linking a diverse genital microbiota to elevated inflammation, understanding the risk factors and mechanisms through which it affects genital health is essential. A robust appreciation of these factors is important for identifying effective prevention and treatment strategies.
Collapse
Affiliation(s)
- Smritee Dabee
- Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- CAPRISA Centre of Excellence in HIV Prevention, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | | | - Heather B Jaspan
- Seattle Children's Research Institute, Seattle, Washington, USA
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- University of Washington, Seattle, Washington, USA
| |
Collapse
|
30
|
Mott PD, Taylor CM, Lillis RA, Ardizzone CM, Albritton HL, Luo M, Calabresi KG, Martin DH, Myers L, Quayle AJ. Differences in the Genital Microbiota in Women Who Naturally Clear Chlamydia trachomatis Infection Compared to Women Who Do Not Clear; A Pilot Study. Front Cell Infect Microbiol 2021; 11:615770. [PMID: 33912473 PMCID: PMC8072278 DOI: 10.3389/fcimb.2021.615770] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
In vitro studies indicate IFNγ is central to Chlamydia trachomatis (Ct) eradication, but its function may be compromised by anaerobes typically associated with bacterial vaginosis (BV), a frequent co-morbidity in women with Ct. Here we investigated the associations between natural clearance of cervical Ct infection, the vaginal microbiome, and the requirements for IFNγ by evaluating the vaginal microbial and cytokine composition of Ct treatment visit samples from women who cleared Ct infection in the interim between their Ct screening and Ct treatment visit. The pilot cohort was young, predominantly African American, and characterized by a high rate of BV that was treated with metronidazole at the Ct screening visit. The rate of natural Ct clearance was 23.6% by the Ct treatment visit (median 9 days). 16S rRNA gene sequencing revealed that metronidazole-treated women who had a Lactobacillus spp.-dominant vaginal microbiota (CST 2 or 3) at the Ct treatment visit, were more prevalent in the Ct clearing population than the non-clearing population (86% v. 50%). L. iners (CST2) was the major Lactobacillus spp. present in Ct clearers, and 33% still remained anaerobe-dominant (CST1). Vaginal IFNγ levels were not significantly different in Ct clearers and non-clearers and were several logs lower than that required for killing Ct in vitro. An expanded panel of IFNγ-induced and proinflammatory cytokines and chemokines also did not reveal differences between Ct clearers and non-clearers, but, rather, suggested signatures better associated with specific CSTs. Taken together, these findings suggest that BV-associated bacteria may impede Ct clearance, but a Lactobacillus spp.-dominant microbiome is not an absolute requirement to clear. Further, IFNγ may be required at lower concentrations than in vitro modeling indicates, suggesting it may act together with other factors in vivo. Data also revealed that the vaginal bacteria-driven inflammation add complexity to the genital cytokine milieu, but changes in this microbiota may contribute to, or provide cytokine biomarkers, for a shift to Ct clearance.
Collapse
Affiliation(s)
- Patricia Dehon Mott
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Christopher M. Taylor
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Rebecca A. Lillis
- Division of Infectious Diseases, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Caleb M. Ardizzone
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Hannah L. Albritton
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Meng Luo
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Kaitlyn G. Calabresi
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - David H. Martin
- Division of Infectious Diseases, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Leann Myers
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Alison J. Quayle
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| |
Collapse
|
31
|
Lamont RF, van den Munckhof EHA, Luef BM, Vinter CA, Jørgensen JS. Recent advances in cultivation-independent molecular-based techniques for the characterization of vaginal eubiosis and dysbiosis. Fac Rev 2020; 9:21. [PMID: 33659953 PMCID: PMC7886079 DOI: 10.12703/r/9-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
“The bacterial vaginosis syndrome” has significant adverse effects for women and babies, including preterm birth and increased risk of acquisition of sexually transmitted infections and HIV. Currently, the gold standard for diagnosis is Gram stain microscopy of vaginal secretions, which is not readily available, is somewhat subjective, and does not differentiate between the likely different subtypes of vaginal dysbioses that may have different etiologies, microbiology, responses to antibiotics, and phenotypic outcomes. With new information from molecular-based, cultivation-independent studies, there is increasing interest in the use of molecular techniques for the diagnosis of bacterial vaginosis. We reviewed the current evidence on and the rationale behind the use of molecular techniques for the diagnosis of bacterial vaginosis. We found a number of commercially available molecular diagnostic tests, a few of which have US Food and Drug Administration (FDA) and/or Conformité Européenne in vitro diagnostic (CE-IVD) approval, and we have compared their performance with respect to sensitivities and specificities. Molecular-based tests have the advantage of objectivity, quantification, detection of fastidious organisms, and validity for self-obtained vaginal swabs. The performance of the molecular tests against standard microscopy is impressive, but further education of users on interpretation is needed. Bacterial vaginosis is the major cause of vaginal dysbiosis and should be recognized for the threat it is to women’s genital tract health. Quantitative assessment of microbial abundance, the diversity of other organisms present, specific primers for gene sequence regions, and clades and biovars of target microbes should be recognized and incorporated into future molecular diagnostic tests to better differentiate between vaginal eubiosis and dysbiosis.
Collapse
Affiliation(s)
- Ronald F Lamont
- Department of Gynecology and Obstetrics, University of Southern Denmark, Institute of Clinical Research, Research Unit of Gynaecology and Obstetrics, Kløvervænget 10, 10th floor, 5000 Odense C, Denmark
- Division of Surgery, University College London, Northwick Park Institute of Medical Research Campus, London, HA1 3UJ, UK
| | | | - Birgitte Møller Luef
- Department of Gynecology and Obstetrics, University of Southern Denmark, Institute of Clinical Research, Research Unit of Gynaecology and Obstetrics, Kløvervænget 10, 10th floor, 5000 Odense C, Denmark
| | - Christina Anne Vinter
- Department of Gynecology and Obstetrics, University of Southern Denmark, Institute of Clinical Research, Research Unit of Gynaecology and Obstetrics, Kløvervænget 10, 10th floor, 5000 Odense C, Denmark
| | - Jan Stener Jørgensen
- Department of Gynecology and Obstetrics, University of Southern Denmark, Institute of Clinical Research, Research Unit of Gynaecology and Obstetrics, Kløvervænget 10, 10th floor, 5000 Odense C, Denmark
| |
Collapse
|
32
|
France MT, Ma B, Gajer P, Brown S, Humphrys MS, Holm JB, Waetjen LE, Brotman RM, Ravel J. VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. MICROBIOME 2020; 8:166. [PMID: 33228810 PMCID: PMC7684964 DOI: 10.1186/s40168-020-00934-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epidemiological studies, and statistical modeling. Vaginal communities are typically assigned to CSTs based on the results of hierarchical clustering of the pairwise distances between samples. However, this approach is problematic because it complicates between-study comparisons and because the results are entirely dependent on the particular set of samples that were analyzed. We sought to standardize and advance the assignment of samples to CSTs. RESULTS We developed VALENCIA (VAginaL community state typE Nearest CentroId clAssifier), a nearest centroid-based tool which classifies samples based on their similarity to a set of reference centroids. The references were defined using a comprehensive set of 13,160 taxonomic profiles from 1975 women in the USA. This large dataset allowed us to comprehensively identify, define, and characterize vaginal CSTs common to reproductive age women and expand upon the CSTs that had been defined in previous studies. We validated the broad applicability of VALENCIA for the classification of vaginal microbial communities by using it to classify three test datasets which included reproductive age eastern and southern African women, adolescent girls, and a racially/ethnically and geographically diverse sample of postmenopausal women. VALENCIA performed well on all three datasets despite the substantial variations in sequencing strategies and bioinformatics pipelines, indicating its broad application to vaginal microbiota. We further describe the relationships between community characteristics (vaginal pH, Nugent score) and participant demographics (race, age) and the CSTs defined by VALENCIA. CONCLUSION VALENCIA provides a much-needed solution for the robust and reproducible assignment of vaginal community state types. This will allow unbiased analysis of both small and large vaginal microbiota datasets, comparisons between datasets and meta-analyses that combine multiple datasets. Video abstract.
Collapse
Affiliation(s)
- Michael T France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Sarah Brown
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Johanna B Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - L Elaine Waetjen
- Department of Obstetrics and Gynecology, University of California Davis School of Medicine, Sacramento, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA.
| |
Collapse
|
33
|
Alisoltani A, Manhanzva MT, Potgieter M, Balle C, Bell L, Ross E, Iranzadeh A, du Plessis M, Radzey N, McDonald Z, Calder B, Allali I, Mulder N, Dabee S, Barnabas S, Gamieldien H, Godzik A, Blackburn JM, Tabb DL, Bekker LG, Jaspan HB, Passmore JAS, Masson L. Microbial function and genital inflammation in young South African women at high risk of HIV infection. MICROBIOME 2020; 8:165. [PMID: 33220709 PMCID: PMC7679981 DOI: 10.1186/s40168-020-00932-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium, or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations. RESULTS A total of 3186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p < 0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women 9 weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women. CONCLUSIONS Both the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-DB application that is available at http://fgtdb.org/ . Video Abstract.
Collapse
Affiliation(s)
- Arghavan Alisoltani
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Monalisa T Manhanzva
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Matthys Potgieter
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Christina Balle
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Elizabeth Ross
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | | | - Nina Radzey
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Zac McDonald
- Centre for Proteomic and Genomic Research, Cape Town, 7925, South Africa
| | - Bridget Calder
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology and Genomic Center of Human Pathologies, Mohammed V University, Rabat, Morocco
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for Infectious Diseases Research (CIDRI) in Africa Wellcome Trust Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Smritee Dabee
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Shaun Barnabas
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Hoyam Gamieldien
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, 92521, USA
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
| | - David L Tabb
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Bioinformatics Unit, South African Tuberculosis Bioinformatics Initiative, Stellenbosch University, Stellenbosch, 7602, South Africa
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, 7925, South Africa
| | - Heather B Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Seattle Children's Research Institute, University of Washington, Seattle, WA, 98101, USA
| | - Jo-Ann S Passmore
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa
- National Health Laboratory Service, Cape Town, 7925, South Africa
| | - Lindi Masson
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, 7925, South Africa.
- Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, 7925, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, 4013, South Africa.
- Disease Elimination Program, Life Sciences Discipline, Burnet Institute, 85 Commercial Road, Melbourne, Victoria, 3004, Australia.
- Central Clinical School, Monash University, Melbourne, 3004, Australia.
| |
Collapse
|