Vaginal Microbiota : Sampling, Clinical Equivalence, and Combined Sequencing

Vaginal microbiota is an important determinant of vaginal health, and it has been studied for over 100 years. The novel technologies, especially sequencing, have revealed the unforeseen complexity of vaginal microbiota communities, and revealed associations to various adverse outcomes including pre-term birth, cancer, and acquisition of sexually transmitted diseases. New data about the vaginal microbiota is cumulating rapidly, but more comprehensive and robust study methods are needed to unravel mechanisms and causalities. The vaginal microbiota is traditionally divided into categories based on microscopic findings on lactobacilli, other bacteria, and host cells. These categories have usually been “normal”, “bacterial vaginosis”, “candidiasis”, and for the last 20 years also “aerobic vaginitis”. However, even the most common of these categories, bacterial vaginosis, is still not fully understood and lacks efficient treatment with lasting effect. At the time when the research for this dissertation began, there were no previous studies on the vaginal microbiota being carried out in Finland and only a handful of studies across Europe. First, we performed a pilot study that set out to identify the feasibility, reproducibility, and comparability of seven different sampling strategies in a study cohort of ten women. We observed that several strategies, including self-sampling, were suitable for vaginal microbiota sampling. Next, we collected samples from 50 healthy Finnish women and through questionnaires, gathered extensive background variables from all participants to study the effect of technical, biological, and socioeconomic factors on the vaginal microbiota and identify potential confounding variables in the study. Furthermore, we used light microscopy to visually categorise samples based on the microbial communities observed and compare them to the sequencing results. To our surprise socioeconomic factors of the subject had larger impact on vaginal microbiota in variance partitioning analysis than technical or hormonal factors. Educational level of the subject was the main factor among socioeconomic factors. Light microscopy and sequencing produced coherent results. Thus, this study underlines the importance on background factors as covariates in microbiota research and reassures clinicians to continue using microscopy in clinical work. The rapidly advancing research on vaginal bacterial communities have shadowed the research on vaginal fungal communities as only a handful of publications have assessed them with sequencing. We developed a parallel sequencing method to study vaginal microbiota and mycobiota in a single sequencing run, and since taxonomic profiling with the ever-growing reference databases was getting noisy, we also developed a text-mining based annotation algorithm. We were able to profile bacterial and fungal communities accurately with over 30% cost reduction compared to separate bacterial and fungal amplicon sequencing. We validated the parallel sequencing and our novel annotation algorithm with shotgun metagenomic sequencing. We failed to validate the fungal results with metagenome, as even a very deep metagenomic sequencing is not able to fully cover the fungal communities of vagina.

Grantor dc:publisher

Helsingin yliopisto

Year dc:date.issued

2025

Author dc:creator

• Virtanen, Seppo

• naistentaudit ja synnytykset

Statement dc:rights

• This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
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• Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden.

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/10138/593521

OAI record oai:identifier

https://helda.helsinki.fi/server/oai/request?verb=GetRecord&metadataPrefix=dim&identifier=oai%3Ahelda.helsinki.fi%3A10138%2F593521