The Vaginal Microbiome: What Is It and Why Does It Matter?

Dr Natalie Hutchins
Jun 18
6 min read

Updated: Jun 23

what is a vaginal microbiome image of bottles in lab conditions — What is a vaginal microbiome?

When we talk about women’s health, there’s an important player that often goes unmentioned: the vaginal microbiome. It might not be something you think about every day, but it plays a major role in everything from period health to pregnancy, infections and immunity.

Understanding what your vaginal microbiome is (and how to support it) can help you take better care of your body across every life stage. So, let’s get into it.

What is a vaginal microbiome?

Your vaginal microbiome is an invisible community of microorganisms made up of bacteria, viruses and fungi that naturally live in your vagina.1 It’s a complex, dynamic ecosystem that’s constantly shifting in response to life: whether it’s hormones, sex, age, stress, hygiene, medications, or habits.

Unlike your gut (where diversity is usually a good thing) a healthy vaginal microbiome is made up of just a few different microbes:2

Lactobacilli: The good guys. A group of protective bacteria that dominate a healthy vaginal microbiome.
Gardnerella Vaginalis: The main culprit behind bacterial vaginosis (BV), it thrives when lactobacilli levels drop (triggering a strong smell and watery discharge).3
Candida Albicans: A natural yeast that can overgrow after antibiotics or hormonal shifts, causing thrush (itching, soreness and a thick white discharge).4
Prevotella and other anaerobes: Common in more diverse microbiomes, linked to BV, inflammation and a higher risk of infection.

What does a healthy vaginal microbiome look like?

There’s no one-size-fits-all when it comes to a healthy vaginal microbiome, everyone is unique.5 But generally, a healthy microbiome is dominated by lactobacilli.6 These friendly microbes are your first line of defence, keeping your microbiome in balance and infections in check.

Here’s how lactobacilli work:

Keeping pH low: They make lactic acid to keep the vagina slightly acidic (around 3.8-4.5), which stops harmful bacteria from growing.
Outcompeting invaders: They take up space and nutrients, making it difficult for harmful microbes to grow.
Making natural antibiotics: Some strains of lactobacilli produce hydrogen peroxide that acts as a natural antibiotic.
Strengthening defences: They also stick to the vaginal lining, making it more resilient to infection.

Researchers have begun to identify a few common patterns and organised microbiomes into five main Community State Types (CSTs).7

Types 1, 2, 3 and 5: Each type is dominated by specific lactobacillus species, usually with a lower pH level and better protection against infection.
Type 4: A more diverse microbiome with a mix of bacteria, linked to higher pH levels and a higher risk of disruption and infection.

While a lactobacillus dominant microbiome is generally seen as more protective, “healthy” can look different depending on your age, hormones and unique biology. What’s most important is understanding your own normal and knowing how to spot when something feels off.

Why does a healthy vaginal microbiome matter?

Think of your vaginal microbiome as your body’s built-in defence system. When it’s in balance, it quietly does a lot of heavy lifting: protecting you from infections, supporting your reproductive health and keeping things comfortable day to day.

Here’s what a healthy vaginal microbiome helps with:

Preventing infections:
It keeps common issues like bacterial vaginosis (BV), thrush, and UTIs at bay by making the vagina less welcoming to harmful microbes.6
Supporting fertility and pregnancy:
A balanced vaginal microbiome helps sperm survive the journey to the egg and is also linked to lower risk of pregnancy loss and preterm birth.8
Lowering STI risk:
Disruption can trigger inflammation, making it easier for viruses like HIV or HPV to take hold, so a healthy microbiome has the opposite effect.9
Reducing discomfort:
Imbalance can trigger symptoms like itching, dryness or unusual discharge (even without a clear infection cause).

But here’s the tricky part: you don’t always feel when your vaginal microbiome is off balance. When protective bacteria like Lactobacillus are outnumbered by harmful microbes, your vaginal microbiome enters a state called dysbiosis.10

Dysbiosis doesn’t always cause symptoms straight away, meaning issues can quietly build up. That’s why understanding your vaginal microbiome matters: by knowing what it does and how to support better balance, you can take a proactive approach to your health.

What affects my vaginal microbiome?

Your vaginal microbiome is surprisingly adaptable. It constantly shifts in response to changes in your body and environment. While it’s often good at bouncing back, some factors can tip the balance without you even realising.

Here are some of the most common influences:

Hormones

Oestrogen plays a key role in keeping your vaginal microbiome stable. It encourages the vaginal lining to produce glycogen, a natural sugar which feeds Lactobacillus. When oestrogen levels rise (like around ovulation or during pregnancy), Lactobacillus tends to thrive. When they fall (like during menopause), the balance can shift, making your microbiome more vulnerable to disruption.11

Periods

Menstrual blood isn’t as acidic as the vagina, so it temporarily raises the pH during your period. This can reduce Lactobacillus levels and allow other microbes to grow.11 Usually, things naturally rebalance within a few days, but it’s not uncommon to feel a bit “off” during your period.

Sex

Semen is also alkaline, so unprotected sex can also raise your vaginal pH and disrupt your microbiome.12 New sexual partners can also introduce unfamiliar microbes, which may destabilise your natural balance, especially if your microbiome is already under pressure. For example, a recent study discovered that bacterial vaginosis can be sexually transmitted, so it’s now recommended that both partners receive treatment.13

Contraception

Research into how contraception affects the vaginal microbiome is still evolving and the results are mixed.8 Some hormonal methods (like the pill) appear to support Lactobacillus by boosting oestrogen. On the other hand, the copper IUD has been shown to increase bacterial diversity without supporting lactobacilli to keep infections in check.14

Antibiotics and medications

Antibiotics are often necessary, but they’re broad-spectrum, meaning they wipe out both good and bad bacteria, including protective Lactobacillus.15 They can quickly throw your microbiome out of balance. If you’ve ever had irritation or recurring symptoms after treatment, this could be why.

Stress and lifestyle

It’s not just what goes into your body, it’s how you feel. High stress levels, smoking, poor diet, disrupted sleep and even intense exercise can all influence your vaginal microbiome. Chronic stress, in particular, has been shown to reduce the body’s ability to maintain microbial balance, making you more prone to infection.16

How can I support my vaginal microbiome?

There’s no perfect formula but a few simple habits can help keep your vaginal microbiome balanced and your vaginal health in check:

Skip the soaps and douching: Washing with anything other than water can strip away the protective bacteria your body relies on.
Stick to water: When it comes to cleaning your vulva, plain water is all you need to keep things fresh without disrupting the balance.
Eat to support your microbes: A diet rich in fibre and fermented foods can help support your overall microbiome health.
Choose breathable underwear: Cotton lets your skin breathe and helps prevent extra moisture, which can throw things off.
Use protection with new partners: Condoms can help reduce microbiome disruption and protect you against STIs.
Support your hormones: If you’re perimenopausal and struggling with vaginal infections, it might be worth discussing hormone support with your doctor.
Speak up: Don’t ignore symptoms. If something feels off or keeps coming back, don’t be afraid to talk to your doctor and seek support.
Consider probiotics: The research is still evolving, but some vaginal probiotics may help boost lactobacilli levels.

Making sense of the evidence

Your vaginal microbiome isn’t something you need to worry about or monitor obsessively – but understanding what it is and how it works is a strong place to start. When you learn how to support balance and avoid disruption, you can feel confident spotting changes, asking the right questions and seeking support when you need it.

Whether you're dealing with recurrent infections, navigating perimenopause, or simply curious about your body, your vaginal microbiome is an invisible but important part of your health.

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