Vaginal microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA588856 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12640000.fastq.gz | Fastqsanger.gz | |||
| SRR12640001.fastq.gz | Fastqsanger.gz | |||
| SRR12640002.fastq.gz | Fastqsanger.gz | |||
| SRR12640003.fastq.gz | Fastqsanger.gz | |||
| SRR12640004.fastq.gz | Fastqsanger.gz |
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Project description:Clinical treatment protocols for infertility with in vitro fertilization-embryo transfer (IVF-ET) provide a unique opportunity to assess the human vaginal microbiome in defined hormonal milieu. Herein, we have investigated the association of circulating ovarian-derived estradiol (E2) and progesterone (P4) concentrations to the vaginal microbiome. Thirty IVF-ET patients were enrolled in this study, after informed consent. Blood was drawn at four time points during the IVF-ET procedure. In addition, if a pregnancy resulted, blood was drawn at 4-to-6 weeks of gestation. The serum concentrations of E2 and P4 were measured. Vaginal swabs were obtained in different hormonal milieu. Two independent genome-based technologies (and the second assayed in two different ways) were employed to identify the vaginal microbes. The vaginal microbiome underwent a transition with a decrease in E2 (and/or a decrease in P4). Novel bacteria were found in the vagina of 33% of the women undergoing IVF-ET. Our approach has enabled the discovery of novel, previously unidentified bacterial species in the human vagina in different hormonal milieu. While the relationship of hormone concentration and vaginal microbes was found to be complex, the data support a shift in the microbiome of the human vagina during IVF-ET therapy using standard protocols. The data also set the foundation for further studies examining correlations between IVF-ET outcome and the vaginal microbiome within a larger study population.
2011-10-24 | E-MEXP-2958 | biostudies-arrayexpress
Project description:characterization of cervico-vaginal microbiota associated with HPV infection
| PRJEB18720 | ENA
Project description:<p>The vagina is an interactive interface with the environment, and as such is covered by a protective epithelial surface. This surface is colonized by bacteria and other microorganisms which, through a variety of mechanisms serve to further protect the host from invasion by pathogens. Alterations in the normal vaginal microflora, particularly those associated with bacterial vaginosis, are thought to contribute to risk of spontaneous pregnancy loss in the second trimester and spontaneous preterm birth. Additionally, alterations in the vaginal microbiome may increase the likelihood of transmission of certain agents including human immunodeficiency virus type 1 (HIV-1). There are physiologic alterations in host condition (e.g., menopause and pregnancy), which are beginning to be investigated as potential selective conditions for change in the "normal" flora, and their impact on disease susceptibility and transmission remains to be more definitively elucidated. The effects of chronically abnormal physiologic states (e.g., diabetes mellitus) on normal vaginal flora have not been well described or studied. Finally, an almost unexplored area of inquiry is the genetic contribution, including race/ethnicity, to the establishment and maintenance of a "normal" vaginal flora, under normal and physiologically altered circumstances. Our research will shed light on how the vaginal microbiome contributes to adverse obstetrical outcomes and sexually transmitted infections in diverse populations. This project addresses the following questions:</p> <p><b>First: Do the genes of the host contribute to the composition of the vaginal microbiome?</b> We hypothesize that a woman's genetic composition significantly affects the ability of certain commensal, parasitic and pathogenic microbes to colonize and/or infect the genital tract. Thus, we will compare and quantify the microbial populations inhabiting the vaginas of monozygotic and dizygotic twins from the Mid Atlantic Twin Registry, and, in the process, address the question of whether there is a relationship between the microbiomes of the vagina, mouth and GI tract.</p> <p><b>Second: What changes in the vaginal microbiome are associated with common physiological perturbations or non-infectious pathological states of the host?</b>We hypothesize that "altered" physiologic (pregnancy, menopause) and pathologic (chronic disease, hysterectomy) conditions, or environmental "exposures" (exogenous hormones, antibiotics, chronic immunosuppressant, smoking; douching) can predictably alter the vaginal microenvironment. These alterations will lead to changes in microbial populations within the vagina. Changes in the microbial populations may have impacts, positive or more likely negative, on the spontaneous and future well-being of the affected individual. We are characterizing the effects of these "altered" physiologic and pathologic conditions, and environmental exposures, on the composition of the vaginal microbiome.</p> <p><b>Third: What changes in the vaginal microbiome are associated with relevant infectious diseases and conditions?</b> We are testing the hypothesis that infectious diseases predictably alter the vaginal microbiome, and that these changes have an impact on the disease susceptibility, process, and outcome. A predilection for bacterial vaginosis, vaginitis, HIV infection, or other sexually transmitted diseases, is likely associated with a women's vaginal microbial composition. Thus, we will characterize samples from women with a variety of these infectious conditions to determine the contribution of their micriobiomes to the disease process and susceptibility.</p> <p>We are addressing these questions using a combination of high throughput 'nextgen' sequencing technologies, including the Roche 454 FLX and the upgraded Illumina Genome Analyzer II instruments currently installed in the Nucleic Acids Research Facilities at VCU. Thus, segments of the 16S rRNA genes will be amplified from the complex samples taken from various target sites in and around the vagina of each study participant. These segments will be sequenced and subjected to taxonomic classification protocols to identify and quantify the bacterial taxa present in each sample. Additionally, total DNA isolated from these samples will be subjected to shotgun sequence analysis to empirically reconstruct the metabolic potential of these microbiomes. Finally, specific bacterial clones will be completely sequenced and analyzed to associate the unavoidable strain and isolate diversity with the clinical phenotypes presented.</p>
| phs000256.v2.p2 | EGA
Project description:JHU_HIV_Study Vaginal microbiome processed reads
| PRJNA430501 | ENA
Project description:<p>The focus of this study was to better understand the effects of cigarette smoking on the vaginal microbiome. There were two phases of the study, cross-sectional and longitudinal, conducted at the Center for Health Behavior Research at the University of Maryland School of Public Health. In the cross-sectional phase, 20 smokers and 20 non-smokers collected mid-vaginal swabs, measured their vaginal pH, prepared a vaginal smear on a slide for Nugent Gram stain analysis, and completed questionnaires about demographics, tobacco use, and reproductive and sexual health history. Smoking status was confirmed through self-report, carbon monoxide exhalation and saliva cotinine measures. Secretions from the mid-vaginal swabs were tested for presence/absence of HPV strains and GC-MS was used to quantify the levels of over 600 metabolites.</p> <p>In the longitudinal phase, 7 participants who were current smokers and motivated to quit smoking were recruited and followed for up to 12 weeks. On a daily basis, participants collected mid-vaginal swabs, measured their vaginal pH, and prepared a mid-vaginal smear on a slide for Nugent Gram stain analysis, and completed daily diaries on tobacco use and reproductive health. Carbon monoxide exhalation and saliva cotinine measures were collected at weekly clinical visits. In addition, participants had weekly behavioral counseling sessions about smoking cessation and used Nicoderm CQ patches to aid in quitting smoking. The self-collected vaginal swabs were used for DNA extractions,16s rRNA sequencing and measurement of metabolites in vaginal fluid.</p>
| phs001386 | dbGaP
Project description:Griffithsin (GRFT) is an anti-viral lectin with potent anti-HIV activity. GRFT’s preclinical safety, lack of systemic absorption after topical administration, and lack of cross-resistance with existing products prompted its development for topical HIV pre-exposure prophylaxis. We evaluated safety, pharmacokinetics and pharmacodynamics of PC-6500 (0.1% GRFT in a carrageenan (CG) gel) in healthy, HIV-negative, non-pregnant women following once daily vaginal gel administration for 14 days. No significant adverse events, histopathological changes in cervico-vaginal mucosa, or anti-drug (GRFT) antibodies were detected. No cervicovaginal proinflammatory responses and no changes in the ectocervical transcriptome were evident. Vaginal microbiome remained largely unchanged. Reduced abundance of vaginosis-associated bacteria and decreased levels of proinflammatory chemokines (CXCL8 and CCL20) were observed. GRFT was not detected in plasma. GRFT and GRFT/CG in CVLs dose-dependently inhibited HIV and HPV, respectively, in vitro. The data suggest GRFT/CG is a promising on-demand multipurpose prevention product that warrants further investigation.
2021-10-04 | GSE141478 | GEO