Collection Methods for Vaginal Samples

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The vaginal microbiome harbors diverse communities of microorganisms, known as vaginal flora. Alterations in the vaginal microbiota and host-microbe interactions have been implicated in many gynecological and obstetric conditions, such as bacterial vaginosis, cervical cancer, infertility, preterm birth, and sexually transmitted infections. Bacteria dominate largely vaginal microbiome. Studies of the vaginal microbiome as part of the human microbiome project have shown a relationship between bacteria present in the vagina and disease. Therefore, an understanding of vaginal microbiota composition is needed to better understand this vaginal condition, as well as host-microbiota interactions.

Changes in the composition of vaginal microbiome throughout women's life.Fig.1 Changes in the composition of vaginal microbiome throughout women's life. (Auriemma, 2021)

Vaginal Microbiota Sampling Techniques

Several techniques have been described for obtaining samples to sequence bacterial DNA to study the human vaginal microbiota in a variety of patient cohorts, the most common being swabs, but the use of cytobrushes, as well as cervicovaginal lavage, epithelial scrapes, and biopsies, have also been reported. A comparison of the two sets of different sampling techniques also revealed that the relative abundances of bacterial taxa were highly comparable between all swabs and cell brushes.

  • Cytobrush

Cytobrushes are made of polyethylene, which lacks any absorptive capacity. The most commonly used sampling device, cytobrushes may disrupt biofilms leading to variation in vaginal microbiota composition. Cytobrushes collected a higher total bacterial load. They may be superior to swabs because they can have greater surface area contact with cervical epithelium, ensuring that bacteria in closest contact with that mucosal surface are collected. They provide a reliable and robust sampling tool for the analysis of the vaginal microbiota.

  • Swab

Rayon swabs are a common muscle-sampling device widely used for the next-generation sequencing-based analysis of cervical-vaginal microbial composition. In addition, in the vagina, especially in the case of bacterial vaginosis, biofilms can exist that are densely packed with bacteria. A relatively soft-tipped swab may be unable to disturb these biofilm resulting in a sampling of primarily planktonic bacteria, not in direct contact with the cervical epithelium.

Profiling the Vaginal Microbiota at Creative Biolabs

Modern molecular methods have opened a range of new possibilities for the characterization of the vaginal microbiota, allowing us to not only establish which microorganisms are present but also to begin to understand their functional properties.

In contrast to targeted 16s rRNA profiling, unbiased metagenomic sequencing of microbial flora enables strain-level analysis of the existing microorganisms.

  • Functional Genomics

We can characterize the vaginal microbiota according to function rather than taxonomy. Metatranscriptomic, metaproteomic, and metabolomic analyses may provide more relevant data to inform causal relationships.

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  1. Auriemma, R.S.; et al. The vaginal microbiome: long urogenital colonization throughout a woman life. Frontiers in Cellular and Infection Microbiology. 2021, 11: 613.

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