Vaginal microbiome analysis

A healthy vaginal microbiome is crucial for a woman’s health. An imbalance in the vaginal microbiome has been associated with an increased risk of several diseases, varying from fungal infections to sexually transmitted infections and preterm births. The analysis of the vaginal microbiome is complicated since its composition not only varies with general factors like age, genomic background and life style, but also varies temporally related to the menstrual cycle and sexual activity. Moreover, menopause, pregnancy and birth probably have a large impact on the composition of a woman’s vaginal microbiome.

A vaginal microbiome analysis might be necessary for the development of probiotics and other treatments for vaginal infections and dysbiosis in the vaginal microbiome, to show their efficacy. Such an analysis might also help to prove that your intimate care products are microbiome friendly.

The vaginal microbiome

The vaginal microbiome mainly consists of Lactobacillus species, more specifically L. crispatus, L. iners, L. jensenii and L. gasseri. These contribute to the maintenance of the vaginal homeostatis and prevent colonization and growth of other, unwanted microorganisms, by producing lactic acid. In case of infections or dysbiosis however, other microbes are involved like Gardnerella vaginalis, Mycoplasma hominis and Prevotella species. The vaginal microbiome has recently been described in a publicly available gene catalog, VIRGO.

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Vaginal Microbiome Analysis

Our approach for vaginal microbiome analysis

Study design & expert advice

For the initial phase of research projects and clinical studies, we offer consultancy and support for project and study design. Our team includes a number of experienced PhD-level experts, who can advise you regarding the design of your research project and/or clinical trial, the optimal sampling methods, practical aspects regarding storage and logistics and the most appropriate technical approach.

Sampling, shipping and storage

Vaginal sampling is generally done using swabs that are not prewetted. Of course, we can advise you about the instructions on the sampling for the involved nurses to standardize the sampling as much as possible. We can also supply all materials for storage and shipping with stabilizing buffers that allow for shipment at room temperature. Upon understanding the aim of the project, we can present our advice on study design & size and sample collection procedure.

Fully automated 16S rRNA and ITS gene-based profiling

We offer a complete microbial community analysis service, including fully automated DNA/RNA extraction from the skin samples. By using PCR and NGS technology we can determine the composition of bacteria, Archaea and fungi in your sample. Standard solutions for microbial profiling include 16S and/or ITS amplicon analysis for taxonomic classification and relative frequencies.

Quantification & tracking of specific strains within the microbiome using qPCR

Using a qPCR approach, we can measure changes in the abundance of specific strains within the skin microbiome. We offer this service including project design and performing the assays. Due to the quantitative method that is used, we can deliver the absolute abundance of the strains that are analyzed.

Shotgun metagenomics for species level identification and functional analysis

With our state-of-the-art shotgun metagenomics pipeline, we offer a full analysis service, including quality control of the data, metagenome assembly and generation of tables that describe the abundance of different functional units and pathways across different samples. To this end, we use an in-house, improved analysis suite that includes metagenome assembly, gene prediction, gene catalogue creation and annotation, as well as abundance estimation of annotated genes and other functional units. For this analysis, we use specific curated databases for the vaginal microbiome.

Data visualization & Interpretation

Interactive data visualization tool on BaseClear’s proprietary Genome Explorer browser including basic biostatical analysis options (e.g. PCA, RDA). Data interpretation to support your ‘microbiome friendly’-claim

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