Metagenomics generates such an avalanche of data (or 'reads') that we find ourselves quickly looking for a needle in a haystack ... without even knowing if there is a needle to find. This is particularly true for virome assays. The idea is to enrich the samples by amplifying the DNA of organisms or DNA fragments of interest.
Using samples from the PAPCLEAR clinical study [Murall et al. 2019], we will first perform a descriptive analysis of the viral flora and plasmids. Then, we will study the structure of the characterized floras. Thanks to the metadata of the PAPCLEAR clinical study, we will have access to menstrual cycles, but also to "perturbations" such as antibiotic or antifungals treatments. In a third type of analyses, we will study interactions using mechanistic models derived from population dynamics to estimate interaction parameters.
More than 20 participants of the PAPCLEAR study have already gone through 7 or more visits, spaced by 2 months. Knowing that the participants bring back 8 self-samples between two visits (one per week), this is more than 50 points per longitudinal follow-up.
From a conceptual point of view, this project will provide a better understanding of the virome and “plasmidome” of the vaginal microbiota in relation to perturbations. Because of the relative simplicity of the vaginal microbiota compared to the intestinal microbiota, these results may be of general importance. Finally, from a more applied point of view, this project will lead to a better understanding of the role of the microbiota in pathologies such as vaginal dysbiosis or genital warts.
Murall CL & 42 others (2019) Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open 9(6):e025129For further details, see our publications »