Section: Microbiology
Topic: Ecology, Microbiology, Statistics

Factors shaping vaginal microbiota long-term community dynamics in young adult women

Kamiya, Tsukushi1  ; Tessandier, Nicolas1 ; Elie, Baptiste1, 2 ; Bernat, Claire2, 3; Boué, Vanina2; Grasset, Sophie2; Groc, Soraya2, 4; Rahmoun, Massilva2; Selinger, Christian2; Humphrys, Michael S.5; Bonneau, Marine6; Graf, Christelle6; Foulongne, Vinccent4; Reynes, Jacques7; Tribout, Vincent7; Segondy, Michel4; Boulle, Nathalie4; Ravel, Jacques5 ; Lía Murall, Carmen2, 8 ; Alizon, Samuel1  
1 Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
2 MIVEGEC, CNRS, IRD, Université de Montpellier, France
3 Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
4 PCCEI, Univ. Montpellier, Inserm, EFS, Montpellier, France
5 Institute for Genomic Sciences, University of Baltimore, USA
6 Department of Obstetrics and Gynaecology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
7 Department of Infectious and Tropical Diseases, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
8 National Microbiology Laboratory (NML), Montreal Public Health Agency of Canada (PHAC), Canada

Corresponding author(s): Kamiya, Tsukushi (tsukushi.kamiya@college-de-france.fr); Alizon, Samuel (samuel.alizon@college-de-france.fr)

10.24072/pcjournal.527 - Peer Community Journal, Volume 5 (2025), article no. e30.

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The vaginal microbiota is known to affect women's health. Yet, there is a notable paucity of high-resolution follow-up studies lasting several months, which would be required to interrogate the long-term dynamics and associations with demographic and behavioural covariates. Here, we present a high-resolution longitudinal cohort study of 125 women, followed for a median duration of 8.6 months, with a median of 11 samples collected per woman. Using a hierarchical Bayesian Markov model, we characterised the patterns of vaginal microbiota community persistence and transition, simultaneously estimated the impact of 16 covariates and quantified individual variability among women. We showed that “optimal” (Community State Type (CST) I, II, and V) and “sub-optimal” (CST III) communities are more stable over time than “non-optimal” (CST IV) ones. Furthermore, we found that some covariates — most notably alcohol consumption — impacted the probability of shifting from one CST to another. We performed counterfactual simulations to confirm that alterations of key covariates, such as alcohol consumption, could shape the prevalence of different microbiota communities in the population. Finally, our analyses indicated that there is a relatively canalised pathway leading to the deterioration of vaginal microbiota communities, whereas the paths to recovery can be highly individualised among women. In addition to providing one of the first insights into vaginal microbiota dynamics over a year, our study showcases a novel application of a hierarchical Bayesian Markov model to clinical cohort data with many covariates. Our findings pave the way for an improved mechanistic understanding of microbial dynamics in the vaginal environment and the development of novel preventative and therapeutic strategies to improve vaginal health.

Published online:
DOI: 10.24072/pcjournal.527
Type: Research article

Kamiya, Tsukushi 1; Tessandier, Nicolas 1; Elie, Baptiste 1, 2; Bernat, Claire 2, 3; Boué, Vanina 2; Grasset, Sophie 2; Groc, Soraya 2, 4; Rahmoun, Massilva 2; Selinger, Christian 2; Humphrys, Michael S. 5; Bonneau, Marine 6; Graf, Christelle 6; Foulongne, Vinccent 4; Reynes, Jacques 7; Tribout, Vincent 7; Segondy, Michel 4; Boulle, Nathalie 4; Ravel, Jacques 5; Lía Murall, Carmen 2, 8; Alizon, Samuel 1

1 Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
2 MIVEGEC, CNRS, IRD, Université de Montpellier, France
3 Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
4 PCCEI, Univ. Montpellier, Inserm, EFS, Montpellier, France
5 Institute for Genomic Sciences, University of Baltimore, USA
6 Department of Obstetrics and Gynaecology, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
7 Department of Infectious and Tropical Diseases, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
8 National Microbiology Laboratory (NML), Montreal Public Health Agency of Canada (PHAC), Canada
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_527,
     author = {Kamiya, Tsukushi and Tessandier, Nicolas and Elie, Baptiste and Bernat, Claire and Bou\'e, Vanina and Grasset, Sophie and Groc, Soraya and Rahmoun, Massilva and Selinger, Christian and Humphrys, Michael S. and Bonneau, Marine and Graf, Christelle and Foulongne, Vinccent and Reynes, Jacques and Tribout, Vincent and Segondy, Michel and Boulle, Nathalie and Ravel, Jacques and L{\'\i}a Murall, Carmen and Alizon, Samuel},
     title = {Factors shaping vaginal microbiota long-term community dynamics in young adult women},
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Kamiya, Tsukushi; Tessandier, Nicolas; Elie, Baptiste; Bernat, Claire; Boué, Vanina; Grasset, Sophie; Groc, Soraya; Rahmoun, Massilva; Selinger, Christian; Humphrys, Michael S.; Bonneau, Marine; Graf, Christelle; Foulongne, Vinccent; Reynes, Jacques; Tribout, Vincent; Segondy, Michel; Boulle, Nathalie; Ravel, Jacques; Lía Murall, Carmen; Alizon, Samuel. Factors shaping vaginal microbiota long-term community dynamics in young adult women. Peer Community Journal, Volume 5 (2025), article  no. e30. doi : 10.24072/pcjournal.527. https://peercommunityjournal.org/articles/10.24072/pcjournal.527/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.microbiol.100157

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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