Microbiome Core The goal of the Microbiome Core is to generate data on the abundance and concentrations of genital tract bacteria using advanced molecular methods. Vaginal swabs, male urethral swabs, and male urine samples will be analyzed. Microbiome Core laboratory staff will be responsible for performing DNA extraction on all samples and subjecting the DNA to several quality control PCR assays to assure integrity of the samples. DNA will be analyzed using broad-range 16S rRNA gene PCR with high-throughput sequencing to characterize bacterial community profiles and the relative abundance of bacterial taxa. Analysis of sequence reads will be performed using a custom-built bioinformatics pipeline with species level resolution developed at the Fred Hutchinson Cancer Research Center. Analysis of microbial community profiles over time will be completed in conjunction with our colleagues in the Biostatistics and Computational Biology Core. In addition, the Microbiome Core will generate data on concentrations of key bacterial taxa or species using a panel of quantitative PCR (qPCR) assays. The use of both broad range 16S rRNA gene PCR and taxon-directed qPCR is a major strength of this proposal since these assays provide complementary information about the nature of the microbial communities. Data generated from the Microbiome Core will be used to advance our understanding of the role of the genital tract microbiota in sexually transmitted infections (STI) and bacterial vaginosis (BV). More specifically, the Microbiome Core will provide the tools to study the interactions between BV-associated bacteria and herpes simplex virus infections, the potential for complex microbial communities to produce non-gonococcal urethritis in men, the dynamics of the vaginal bacterial biota and relationships with BV onset, and the impact of an intravaginal contraceptive ring on the vaginal microbiota and risk of STI. There is great potential for cross project interactions and collaboration since approaches developed or findings discovered in one project may be useful in other projects. The human microbiome is a common thread that ties these projects together, and the data generated by this core are critical in fulfilling the aims of each project.
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