Women’s Health in Microbiome Research


In medicine, women’s health refers to the category of conditions and experiences that are unique to women such as pregnancy and menstruation. The term can also be applied to conditions experienced by both men and women, but that impact women differently due to biological difference, e.g., heart disease.

The History of Women’s Health

Women respond differently to drugs and women’s health conditions are under-researched.

Historically, due to societal discrimination, women’s health was widely neglected by the medical field. In fact, prior to the 1990s, until the NIH mandated their inclusion, women were excluded from clinical testing. This lack of testing on women has led to large gaps in understanding how female biology impacts drug metabolism, and the likelihood of their adverse effects. It is now known that the pharmacokinetics of drugs differs significantly between females and males.

On top of being excluded from clinical trials, the lack of consideration for female bodies within scientific research has left female-dominant conditions under-studied.

The Vaginal Microbiome

Women’s health in the microbiome field is largely studied via the vaginal microbiome.

Microbiomes refer to the collection of microorganisms in a given environment, currently the most studied components of microbiomes are bacteria. Across the human body there are a number of distinct microbiomes including but not limited to: the gut microbiome, oral microbiome, vaginal microbiome, and skin microbiome. Human microbiomes modulate host health through complex host-microbiome interactions. Researchers are attempting to understand these interactions by leveraging next-generation sequencing and -omics technology. Understanding the function of microbiomes in regulating human health presents an opportunity to improve health outcomes for patients and consumers alike.

Human microbiomes are being researched for their role in women’s health conditions. A significant part of this research takes place via analysis of the vaginal microbiome. Although, women’s health research has been conducted on the skin and gut microbiome too. For instance, a 2021 research paper identified skin microbiome changes associated with menopause, and research has also identified alterations in gut microbiome diversity between pre-menopausal and post-menopausal women.

The vaginal microbiome refers to the community of microbes that exist within the vagina. Unlike the gut microbiome, a healthy vaginal microbiome is marked by limited bacterial diversity, and Lactobacillus dominance. Lactobacillus bacterial strains work to protect the microbiome from invasive pathogens through the production of antimicrobials such as bacteriocins and hydrogen peroxide.

When the balance of bacteria in the vagina is disrupted vaginal dysbiosis occurs. The disruption of the vaginal flora can be caused by several factors including contraceptive medication, sex practices, and menstrual hormone fluctuations. Dysbiosis is linked to conditions such as bacterial vaginosis, urinary tract infection, preterm birth, and sexually transmitted infections. Several drugs and products are in development to therapeutically target vaginal dysbiosis.

Product Development for the Vaginal Microbiome

Product development for the women’s health category is on the rise.

Whilst a historical gap exists between funding of male-dominant and female-dominant diseases, research and development for women’s health product development is on the rise. The women’s health market was valued at approximately USD 35.02 billion in 2019 and is projected to reach USD 41.05 billion by 2027, according to Fortune Business Insights. Within the microbiome category, products in development, and on the market, targeted to the women’s health category include OTC probiotics, at-home vaginal microbiome test kits, and live biotherapeutics for vaginal conditions.

Challenges to Vaginal Microbiome Research

Analyzing microbiomes is difficult, and the vaginal microbiome is no different.

To develop a deeper understanding of the vaginal microbiome, further research must be undertaken in analyzing its function and composition. This presents several challenges, including:

  • Sample Collection

The first challenge is to obtain high-quality samples for sequencing. As mentioned earlier the balance of vaginal bacteria can be impacted by a range of factors. The hormonal flux from the menstrual cycle, for instance, causes community composition to differ at different points in the cycle. The collection of samples should be standardized to minimize the impact of these factors on the microbiome.

  • DNA Extraction

The next challenge is to extract DNA from the collected samples. DNA extraction can be difficult for many sample types in general. This is no different for the vaginal microbiome, which has an added challenge of samples that often have low biomass. Therefore, optimizing the DNA extraction method is crucial to obtain high-quality DNA for sequencing.

  • Sequencing Depth and Coverage

Sequencing depth and coverage are critical factors that impact the accuracy of microbiome analysis. Specifically, within the vaginal microbiome, several important urogenital tract pathogens are low abundance, particularly STI-causing bacteria. Thus, selecting the right sequencing method is important to ensure their detection.

  • Microbial Community Analysis

The vaginal microbiome is composed of diverse microbial communities that are challenging to analyse due to their dynamic nature. The microbial communities can shift rapidly due to various factors such as administration of antibiotics, sexual activity, and menstrual cycle. Therefore, it is crucial to analyse the microbiome at multiple time points to accurately capture the dynamic changes.

  • Statistical Analysis

Statistical analysis is essential for accurately interpreting microbiome sequence data. The vaginal microbiome contains complex microbial communities that require advanced statistical tools to analyse. Moreover, the presence of low-abundance microorganisms can affect the statistical power of the analysis, making it challenging to identify significant differences between the microbial communities.

Zymo Research supports Women’s Health research in the microbiome field.

Zymo Research offers solutions for studying the vaginal microbiome, including sample collection devices, microbiome products for extraction and preparation, and various sequencing services. Their service team offers workflow design, extraction, sequencing, and analysis services. They offer Next-Generation sequencing using Illumina sequencing technology and are a Certified PacBio Provider. Sample sequencing is performed in-house at their state-of-the-art research facilities. They also have automation capabilities and an Automation team available for support, scripts, and collaborations. Zymo Research provides high-quality samples, optimized DNA extraction, and advanced statistical analysis tools to address the challenges of studying the vaginal microbiome. Zymo is dedicated to facilitating the future of women’s health research within the microbiome field.

“At Zymo Research, we recognize the pivotal role that microbiome testing plays in advancing the scientific understanding of women’s health. Our mission is to connect innovative researchers with our cutting-edge microbiome analysis tools and services, driving collaborative efforts that unravel the mysteries of women’s well-being.”

Keith Booher, PhD, Director, Research Services at Zymo Research.


Due to historical discrimination, there is a knowledge gap for how drug interactions and disease varies in women’s bodies. The study of the vaginal microbiome presents an opportunity to improve women’s health outcomes in a range of conditions including preterm birth, infertility, recurrent UTI, and bacterial vaginosis. There are research challenges related to studying the vaginal microbiome including: sample collection, DNA extraction, sequencing depth and coverage, microbial community analysis, and statistical analysis. Zymo Research offers a range of products and services designed to solve these challenges and facilitate the advancement of women’s health research.

If you are conducting or starting a microbiome study, you can talk to a microbiome scientist from Zymo Research to maximize your study’s success with the right analytic services and peer-utilized technologies.