Glossary · Microbiota
Vaginal microbiota
In one sentence
The vaginal microbiota is the community of microorganisms living in the vagina. In many women of reproductive age it is dominated by Lactobacillus species, which produce lactic acid and help keep vaginal pH low.
Also known as: vaginal flora · vaginal microbiome · vaginal ecosystem
What is the vaginal microbiota?
It is the community of bacteria, fungi and viruses that lives on the vaginal mucosa. The rules differ from the gut. In the intestinal microbiota, higher diversity is often read as a good sign; in the vagina, a low-diversity community dominated by a single Lactobacillus species is the most common pattern in women of reproductive age. These bacteria ferment glycogen from the vaginal epithelium into lactic acid, which keeps pH low and makes the environment less hospitable to other organisms.
The community is dynamic. It shifts with age, the menstrual cycle, pregnancy, menopause, antibiotic use and hygiene practices.
How it is studied
A landmark study by Ravel and colleagues (PNAS, 2011) sampled 396 asymptomatic North American women and grouped their vaginal communities into five community state types (CSTs):
- CST I: dominated by L. crispatus.
- CST II: dominated by L. gasseri.
- CST III: dominated by L. iners.
- CST V: dominated by L. jensenii.
- CST IV: fewer lactobacilli and more strict anaerobes, such as Gardnerella, Prevotella and Atopobium.
CST IV is associated with bacterial vaginosis, yet every woman in that cohort was symptom-free. A CST IV profile is therefore not a diagnosis on its own.
Two families of methods coexist. Classic bedside and microscopy tools (pH, Amsel criteria, Nugent score) assess a specific clinical picture. Molecular methods, such as 16S rRNA gene sequencing or broader NGS, report which organisms are present and their relative abundance.
Example
A gynaecologist sees a patient with recurrent discharge and discomfort that keeps returning after standard treatment. Alongside the examination and routine tests, she requests a vaginal microbiota analysis. The report shows a low proportion of lactobacilli and a predominance of Gardnerella and Prevotella, consistent with CST IV. She weighs this against the clinical findings and other results before deciding on management. The profile adds context; it does not settle the diagnosis by itself.
Limitations
- CSTs describe population-level patterns; links with symptoms and outcomes are largely associative.
- Timing matters: menstruation, recent antibiotics or intercourse can change the result.
- Sequencing reports proportions, not absolute loads, and panels and reference databases differ between laboratories.
Vaginal microbiota at Xenogene
Xenogene offers AMC Vaginal, an NGS-based analysis of the vaginal ecosystem. According to the product sheet, the report covers the dominant lactobacilli (L. crispatus, L. gasseri, L. iners), species associated with dysbiosis such as Gardnerella, Atopobium and Prevotella, diversity indices (Shannon and Simpson) and a microbiota-based estimate of vaginal pH. It also includes detection of selected sexually transmitted infections and Candida.
The test is ordered through a healthcare professional, and interpreting the result is the responsibility of the clinician who requested it, in the context of each patient.
Frequently asked questions
What does a healthy vaginal microbiome look like?
There is no single healthy profile. Many women of reproductive age have a community dominated by one Lactobacillus species, but some women without symptoms have more diverse communities. A result always needs to be read alongside symptoms and examination.
What can disrupt the vaginal microbiota?
Changes have been associated with menstruation, hormonal shifts, antibiotics, douching, smoking and sexual activity, among other factors. These are associations: people respond differently, and a short-lived change does not mean disease.
Does a vaginal microbiome test replace a smear or swab test?
No. They answer different questions. A microbiota test describes which organisms are present; cervical screening looks for cell changes, and targeted swabs or assays look for specific infections. Which test is appropriate is a decision for the clinician.
Related terms
- Lactobacillus
Lactobacillus is a genus of Gram-positive, lactic acid-producing bacteria. Species such as L. crispatus, L. gasseri, L. iners and L. jensenii commonly dominate the vaginal microbiota of women of reproductive age.
- Bacterial vaginosis
Bacterial vaginosis is a shift in the vaginal microbiota in which lactobacilli decline and anaerobic bacteria such as Gardnerella overgrow. It can cause discharge and odour, but is often symptom-free.
- Gardnerella vaginalis
Gardnerella vaginalis is a facultatively anaerobic vaginal bacterium associated with bacterial vaginosis. It is also found in women without symptoms, so its presence alone is not enough for a diagnosis.
- Candidiasis
Candidiasis is an infection caused by Candida yeasts, most often Candida albicans. It commonly affects the vulva and vagina or the mouth, and occurs when the yeast overgrows beyond normal colonisation.
- Dysbiosis
Dysbiosis is a change in the composition or function of the microbiota away from what is considered compatible with health: loss of diversity, loss of beneficial microbes or overgrowth of others.
Educational content for healthcare professionals and the general public. It does not replace assessment by a healthcare professional: ordering and interpreting any test is the responsibility of the requesting clinician.
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