Vaginal microbiome multi-level dynamics

The vaginal microbiota represents an ideal system from a scientific point of view, as well as a timely topic with important public health implications.

Indeed, samples fall into five main categories, classically referred to as community state types (CSTs). Furthermore, four of these comminities are dominated by a single Lactobacillus species. This strong structure and limited diversity makes it possible to perform epidemiological studies. These studies unravelled associations between the CST and important health variables revolving around fertility or susceptibility to sexually-transmitted infections.

Using samples from the PAPCLEAR clinical study [Murall et al. 2019], we analyse what drives the transitions from one community state type (CST) to another. This is based on performing metabarcoding analyses on >2,000 from >100 women with a median follow-up time of >20 months. This relies on statistical modeling with Markov chain models. In collaboration with France Génomique, we also analyse metagenomics data for >500 samples from the same cohort. These analyses will shed a new light on the effect of "perturbations" such as antibiotic treatment on the genomics of the vaginal microbiota.

Considering hosts as ecosystems, we use community ecology modeling to understand the interaction between Lactobacillus-dominated CSTs and Lactobacillus-poor communities (typically CST-4). The goal is to use these insights to guide treatments and probiotics use.

Publications

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):e025129