Vaginal Microbiome Testing 101
Last updated 10 September 2026
This article was written by Danni Bichler BHSc (Naturopathy).
Danni Bichler is a Clinical Naturopath and Pain Reprocessing Therapy practitioner passionate about helping women better understand their bodies.
To learn more or book an online consultation with Danni visit aliviohealth.com.au. You can also follow her on Instagram at @alivio.health.
Disclaimer
This content is for general informational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. Always consult a qualified healthcare provider with any questions about your health or personal care.
If you experience recurrent thrush, bacterial vaginosis or unexplained vaginal symptoms, you may have been told that your vaginal swab is “normal.”
But your symptoms are still there.
This can be confusing and frustrating. It may also leave you wondering whether something has been missed.
A standard vaginal swab and a vaginal microbiome test can both provide useful information. However, they do not test for exactly the same things. Understanding the difference can help you decide which option may be most appropriate for you.
Firstly what is the vaginal microbiome?
The vaginal microbiome is the ecosystem of bacteria and other microbes living inside the vagina.
A healthy vaginal microbiome is often dominated by Lactobacillus bacteria. These bacteria produce lactic acid, hydrogen peroxide and other compounds that help keep the vaginal environment acidic. This makes it harder for potentially disruptive bacteria to overgrow.
The vaginal microbiome is not the same for everyone. It can also change over time. Hormones, menstruation, intimacy, pregnancy, antibiotics and vaginal products can all influence its balance.
What is a vaginal microbiome test?
A vaginal microbiome test provides a detailed picture of the microbes found within a vaginal sample.
The sample is usually collected at home using a vaginal swab, which is then sent to a laboratory for analysis.
Unlike a standard vaginal swab, which may only look for specific infections, microbiome testing can provide a broader picture of the vaginal environment. This includes the protective bacteria present and any potentially disruptive organisms.
Which vaginal microbiome tests are available?
Not all vaginal microbiome tests provide the same level of detail.
Some use targeted PCR testing, which looks for a selected list of microbes. Others use next generation sequencing, known as NGS, to provide a much broader view of the vaginal ecosystem.
If you are investing in vaginal microbiome testing, check that the test uses NGS. This type of testing looks at the whole vaginal microbiome and can detect a much wider range of bacteria and yeasts, rather than searching only for selected organisms.
Companies offering NGS vaginal microbiome testing include Juno Bio, ScreenMe in the UK and Evvy. Availability will depend on where you live.
These tests are not a replacement for STI screening. If you are concerned about chlamydia, gonorrhoea or another STI, speak with your healthcare provider about appropriate testing.
NGS results generally show which microbes were detected and their relative abundance. This means the percentage of the microbiome made up by each organism.
For example, a result may show that the microbiome is mostly made up of one Lactobacillus species. Another may show low Lactobacillus alongside bacteria associated with bacterial vaginosis or aerobic vaginitis.
This helps us understand the overall vaginal environment, rather than looking for only one infection.
When might vaginal microbiome testing be helpful?
Microbiome testing may be worth considering if you experience:
Recurrent bacterial vaginosis
Recurrent thrush
Symptoms that return soon after treatment
Ongoing odour, irritation or unusual discharge
Conflicting or repeatedly negative standard swabs
Symptoms that change after intimacy or menstruation
Persistent symptoms without a clear explanation
Fertility concerns where the vaginal environment may be relevant
Testing may identify patterns that are not obvious on routine swabs.
For example, a result may show low protective Lactobacillus alongside several BV-associated bacteria. Another may show Lactobacillus dominance, but mainly a less stable species such as Lactobacillus iners.
These findings can offer more insight into why symptoms keep returning, even when a standard swab does not identify a clear infection.
What can affect your results?
The timing of your test matters.
Antibiotics, antifungals, boric acid, vaginal probiotics and other treatments may temporarily change what is detected. Menstruation and recent sex can also influence the sample.
When investigating a recurring pattern, I generally recommend testing while symptoms are present or around the time they usually flare. For example, this may be just before your period if that is when symptoms typically return.
Always follow the collection instructions provided with your test. Let your practitioner know about any recent medications, treatments or vaginal products you have used.
A single test is still only a snapshot. The vaginal microbiome can change, so results should always be considered alongside:
Your current symptoms
Your vaginal pH
The amounts and combination of organisms detected
The level and species of protective Lactobacillus
Recent antibiotics, antifungals or vaginal treatments
Menstruation, hormonal changes and recent sex
Standard swabs, cultures or STI testing where appropriate
Your wider medical and vaginal health history
For example, a small amount of a BV-associated bacterium may not be concerning when protective Lactobacillus levels are high and no symptoms are present.
The same organism may be more relevant when Lactobacillus levels are low, several disruptive bacteria are elevated and symptoms are present.
The purpose of testing is not to treat every organism detected. It is to understand the overall ecosystem.
When microbiome results are interpreted alongside your symptoms and health history, they can help guide a more personalised and considered treatment plan. This may help support a healthier vaginal environment and longer-lasting results.
If you are experiencing recurrent vaginal infections or ongoing symptoms, microbiome testing may provide a clearer picture of what is happening.
At Alivio Health, I can help you choose the most appropriate test, interpret your results and create a personalised treatment plan based on your symptoms and health history.
To learn more or book an online consultation, visit aliviohealth.com.au. You can also follow me on Instagram at @alivio.health.
Danni BichlerBHSc (Naturopathy)
