The vaginal microbiota is structured into five main community state types (CST) that are known to affect women's health. CST shifts can occur in less than a day, but there is a lack of follow-ups lasting more than a few months; a gap in the knowledge that hampers our understanding of long-term dynamics. Analysing a longitudinal cohort of 125 women followed for a median duration of 10 months, we show that `optimal' (CST I, II, and V) or `sub-optimal' CST III are more stable in time than the `non-optimal' CST IV. We also find that some probabilities of shifting from one CST to another are associated with covariates such reported number of sexual partners or alcohol consumption. Finally, we simulate population-level consequences of variations in behaviours. In addition to providing one of the first insights on vaginal microbiota dynamics over a year, along with a robust methodological analysis, these results open new perspectives to improve our mechanistic understanding of microbial interactions in the vaginal environment and develop new therapeutic strategies.

JReynes reports personal fees from Gilead (consulting and payment or honoraria for lectures, presentations, speaker's bureaus, manuscript writing, or educational events), Janssen (payment or honoraria for lectures, presentations, speaker's bureaus, manuscript writing, or educational events), Merck (payment or honoraria for lectures, presentations, speaker's bureaus, manuscript writing, or educational events), Theratechnologies (payment or honoraria for lectures, presentations, speaker's bureaus, manuscript writing, or educational events), and ViiV Healthcare (consulting and payment or honoraria for lectures, presentations, speaker's bureaus, manuscript writing, or educational events) and support for attending meetings and/or travel from Gilead and Pfizer, outside of the submitted work. JRavel is co-founder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutics drugs for women's health. He is Editor-in-Chief at Microbiome. All the other authors do not report any conflict of interest.

http://dx.doi.org/10.1136/bmjopen-2018-025129

This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 648963, to SA). The authors acknowledge further support from the Fondation pour la Recherche Medicale (to TK), the Agence Nationale de la Recherche contre le SIDA (ANRS-MIE, to NT and OS), and the MemoLife Labex (to BE).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The PAPCLEAR study was promoted by the CHU of Montpellier (France). This study has been approved by the Comité de Protection des Personnes (CPP) Sud Mediterranée I (reference number 2016-A00712-49); by the Comité Consultatif sur le Traitement de l'Information en mati`re de Recherche dans le domaine de la Santé (reference number 16.504); by the Commission Nationale Informatique et Libertés (reference number MMS/ ABD/ AR1612278, decision number DR-2016-488), by the Agence Nationale de Securité du Medicament et des Produits de Sante (reference 20160072000007), and is registered at ClinicalTrials.gov under the ID NCT02946346.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

All the data analysed in the present work will be made available online after peer-review.