The human vaginal microbiota plays a key role in urogenital health. Enhancing our understanding of the dynamics of the vaginal microbiota can provide valuable insights for maintaining health and design strategies to prevent urogenital diseases. Health status evolves over time. The work by Kamiya et al. (2024) addressed the dynamic interplay between vaginal microbiota and health using a robust, high-resolution longitudinal cohort of 125 reproductive-aged women, followed for a median duration of 8.6 months in Montpellier, France. The participants were recruited within the PAPCLEAR study, which aimed to better understand the course and natural history of human papillomaviruses infections in healthy, young women (Murall et al. 2019). Each participant contributed at least three vaginal samples, from which microbiota barcoding was performed.

The vaginal microbiota was clustered using the approach developed by Ravel et al. (2011) which categorizes microbial communities in 5 community state types with varying health implications. Transitions between community states were estimated using a hierarchical Bayesian Markov model. These transitions were associated with 16 covariates covering lifestyle, sexual practices and medication. This hierarchical approach allowed for the quantification of individual differences among women. The study characterized the stability of vaginal microbial communities and identified alcohol consumption as the strongest covariate driving community transitions. The results indicated that alcohol consumption promotes non-optimal communities. 

The modelling approach, however, indicated that individual variability among the women was not fully accounted for by the selected 16 covariates, suggesting the need to explore additional key factors, including dynamic covariates. The authors clearly identified several  potential limitations of the study, including the variability associated to home sampling,  the resolution of the microbial categories, and the impact of the clustering method on the analysis.    

My decision to recommend this manuscript is supported by the solid and rigorous analysis of the study, strengthened by the clear presentation of methods, data and analysis. While applying advanced computational techniques, the authors provide a solid biological interpretation of their results. This work makes a substantial contribution by expanding the understanding of vaginal microbiota dynamics and its interplay with health. It sets a framework for further evaluation of strategies aimed at promoting vaginal health. Moreover, it presents a generic methodology that could be applied to other microbial ecosystems.   

References

Kamiya T, Tessandier N, Elie B, Bernat C, Boué V, Grasset S, Groc S, Rahmoun M, Selinger C, Humphrys MS, Bonneau M, Graf C, Foulongne V, Reynes J, Tribout V, Segondy M, Boulle N, Ravel J, Murall CL, Alizon S (2024) Factors shaping vaginal microbiota long-term community dynamics in young adult women. medRxiv, 2024.04.08.24305448, ver.3 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2024.04.08.24305448

Murall CL, Rahmoun M, Selinger C, Baldellou M, Bernat C, Bonneau M, Boué V, Buisson M, Christophe G, D’Auria G, Taroni F De, Foulongne V, Froissart R, Graf C, Grasset S, Groc S, Hirtz C, Jaussent A, Lajoie J, Lorcy F, Picot E, Picot MC, Ravel J, Reynes J, Rousset T, Seddiki A, Teirlinck M, Tribout V, Tuaillon É, Waterboer T, Jacobs N, Bravo IG, Segondy M, Boulle N, Alizon S (2019) Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open, 9, e025129. https://doi.org/10.1136/BMJOPEN-2018-025129

Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ (2011) Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences of the United States of America, 108. https://doi.org/10.1073/pnas.1002611107