Charting New Territories: Mapping the Vaginal Microbiome on a Grand Scale

Charting New Territories: Mapping the Vaginal Microbiome on a Grand Scale

Chief Science Officer, Kim Capone, PhD


Dr. Kim Capone, Lead SHWI Educator, and Chief Science Officer for Vaginal Biome Science.




February 2024

When I learned of the Isala Citizen Study that recently concluded in Belgium, I knew I wanted to share it in this newsletter. Named after Isala Van Diest, the first female doctor in Belgium, this citizen science-enabled catalog of the vaginal microbiome and associated factors has created one of the most robust data sets of its kind for women's health. While it has confirmed some of what we already know, it has also lead to an entirely new set of questions. One of the surprising aspects of the study was that through voluntary enrollment, this citizen-science approach allowed researchers to recruit a majority (69%) of women in a state of health. The study ( was able to capture data on the vaginal microbiomes of 3,345 women aged 18-98, utilizing self-sampling, 16S amplicon sequencing, and detailed questionnaires to gather an extremely robust data set that would not be possible in a traditional clinical setting.

What is unique and invaluable about citizen science studies is the way they facilitate large-scale data collection by actively involving the public to enable the collection of vast amounts of data across diverse geographic locations and populations, which would be challenging, and perhaps impossible through traditional methods. One of the most limiting factors in doing medical research is the prohibitive cost, and that is what makes the results of citizen science research so powerful. Because they are so cost effective, these types of studies enable large data sets that were not previously available.  Diversity is a key advantage of citizen-science, and this inclusivity can result in more comprehensive and nuanced results, particularly when addressing complex healthcare challenges. By demonstrating the power of citizen science in robustly collecting both healthy and disease-state patient data, the Isala study contributes not only to the field of microbiome research, but also sets a precedent for leveraging community engagement to unravel complex health-related dynamics.

For the study of Women’s health, the Isala study confirmed what we have known about vaginal microbiomes in a state of health - 78% of samples exhibited dominance of Lactobacillus taxa. Notably, L. crispatus (43.2%) and L. iners (27.7%) emerged as the most prevalent species in this group. These percentages align to the community state types that have been recorded previously in other populations like the US. However, questions remain, as the prevalence of L. iners in women without complaints implies a potentially symbiotic relationship with these individuals.

Conversely, the pathobiont Gardnerella dominated the vaginal microbiome in 9.8% of the women. Previous research suggested that Gardnerella's association with symptoms and diseases depended on specific species, strains, other community members, along with host factors. In this cohort, the Gardnerella module exhibited stronger associations with host health data, including HPV vaccination status, compared to analyzing Gardnerella as an individual. Therefore, the modular approach suggests that increased Gardnerella abundance may not inherently indicate pathogenicity but rather reflects diverse bacterial relationships and/or host states.

The size of this study helped to illustrate how the intricate composition of the vaginal microbiome exhibited robust associations with diverse factors, including age, childbirth history, menstrual cycle phases, contraceptive practices, and various lifestyle choices. Through network correlation analysis, the study revealed modules of co-abundant bacteria, shedding light on the complex interplay within the microbiome. Notably, a specific module containing L. crispatus, L. jensenii, and Limosilactobacillus displayed positive associations with elevated estrogen levels and contraceptive usage, while exhibiting negative correlations with childbirth and breastfeeding.

Other modules associated with Gardnerella, Prevotella, and Bacteroides demonstrated correlations with factors such as multiple sexual partners, menopause, menstrual hygiene practices, and contraceptive use. The study also explored the association of modules with intimate lifestyle choices, including sexual behavior, pregnancy-related changes, and dietary habits. Women who had been pregnant, including those who experienced miscarriage, exhibited a distinct microbial signature that included a reduction in the L. crispatus module and an increase in anaerobic taxa. The microbial shifts observed during pregnancy may be associated with hormonal changes, immune system modulation, or other physiological alterations. Understanding these shifts is crucial as they likely have implications for maternal health, pregnancy outcomes, and the acquisition of the infant’s microbiome during childbirth.

The citizen-science approach played a pivotal role in this study, involving participants in sample collection, survey design, and result interpretation, underscoring the collaborative potential in large-scale microbiome research. Overall, the Isala study provides extensive insights into the nuanced dynamics of the vaginal microbiome, emphasizing its intricate links to reproductive health, lifestyle factors, and the significance of engaging citizens in scientific exploration.

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