What is the Vaginal Microbiome?

What is the Vaginal Microbiome?

by Melanie Kelly on May 26 2026
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    Luminary Vitamins has partnered with Evvy, a vaginal microbiome testing company. You can get 10% discount on Evvy test using a code LUMINARY10.

    Scientifically edited by Dr. Krystal Thomas-White, PhD, Dana Alloy
    Medically reviewed by Dr. Sabrina Sahni, MD NCMP, Dr. Kate McLean MD, MPH, FACOG, Dr. Christine Vo, MD 
    Source: Evvy Blog

    The vaginal microbiome is the complex ecosystem of microorganisms, including bacteria and fungi, that live inside the vagina (aka the vaginal microbiota or vaginal flora). Although you may have never heard of the vaginal microbiome, it plays a major role in your reproductive — and overall — health.

    Vaginal discomfort is one of the leading reasons women seek healthcare advice, and over 90% of these cases can be attributed to imbalances in the vaginal microbiome. Imbalances can manifest as yeast infections, bacterial vaginosis (BV), cytolytic vaginosis (CV), aerobic vaginitis (AV), and more.

    But your vaginal microbiome affects far more than just your vaginal health. An imbalanced vaginal microbiome is also associated with infertility, pregnancy complications, sexually transmitted infections (STIs), and possibly even cancer. So why is it still such a mystery?

    Microbiome research is a fascinating field that's evolving quickly. While scientists have been working on deciphering the microbiomes of different parts of our bodies (like our gut and skin) for decades, the vaginal microbiome hasn't been given as much attention as it deserves — you can blame the gender health gap for that. But that’s why we’re here!

    Keep reading to learn more about the vaginal microbiome, how it works, and how it could affect your reproductive health.

    How Does the Vaginal Microbiome Work?

    Your vaginal flora is made up of many different species of bacteria, fungi, viruses, and more. but there is one species of bacteria that plays a critical role in its health: Lactobacillus bacteria or lactobacilli, often referred to as the “good” or “protective” bacteria.

    Lactobacilli are the MVPs of the vaginal microbiome and play a crucial role in keeping your vagina safe and healthy. They do this in a few different ways:

    1. Lactobacilli produce lactic acid to maintain a low pH level (between 3.8 and 4.5), which helps protect your vagina microbiome against harmful pathogens.
    2. Lactobacilli take up space on the vaginal wall to prevent other harmful bacteria from sticking around.
    3. Lactobacilli produce bacteriocins (your body's natural antibiotic) to stop disruptive bacteria from growing.
    4. Lactobacilli can help reduce inflammation in your genital area.

    When there aren’t enough protective bacteria like lactobacili in your vaginal microbiome, disruptive bacteria like Gardnerella, E. coli, and Mycoplasma can take over, causing vaginal dysbiosis. Vaginal dysbiosis is an umbrella term used to describe a state of imbalance in the vaginal microbiome.

    Vaginal dysbiosis can cause infections like bacterial vaginosis, yeast infections, urinary tract infections (UTIs), and more, leading to unwanted symptoms like itching, burning, irritation, and unusual vaginal discharge.

    Vaginal Infections and the Microbiome

    The most common type of vaginal dysbiosis is an infection called bacterial vaginosis (BV), which is clinically defined as an overgrowth of disruptive bacteria in the vaginal microbiome. This often happens when lactobacilli are depleted and pathogenic bacteria start to overtake the microbiome.

    One in three women will get bacterial vaginosis each year, and up to 84% of these cases are asymptomatic. BV disproportionately affects Black and Hispanic women, with disappointingly lacking research as to why.

    But BV isn’t the only infection of the vaginal microbiome — there are many other forms of vaginal dysbiosis, such as yeast infections, aerobic vaginitis (AV), and cytolytic vaginosis (CV), which can have frustrating — and confusingly similar — symptoms, such as itchiness, abnormal discharge, and burning.

    If you're dealing with recurring vaginal infections, just know that you're not alone. Bacterial vaginosis is the most common cause of vaginal symptoms among women, and at any given time, 1 in 3 women are dealing with bacterial vaginosis, 1 in 3 women will have a UTI by the time they're 24, and half will experience one at some point. And that's not all — a whopping 75% of women will experience a yeast infection at least once in their lifetime.

    Despite vaginal discomfort being one of the leading causes why women and people with vaginas seek healthcare in the US, misdiagnosis and recurrence rates are high (over 50% for both!)

    The Impact of the Vaginal Microbiome on Hormonal Health & Fertility

    It turns out that composition of the vaginal microbiome doesn’t just affect vaginal infections and symptoms — it plays a crucial role in female health, and emerging research has uncovered some groundbreaking insights into how it affects our overall well-being (beyond the vagina).

    Hormones and the Vaginal MIcrobiome

    Shifts in hormone levels can alter the vaginal environment—and in some cases, make it more susceptible to infection.

    The role of estrogen in vaginal infections

    Estrogen promotes the production of a sugar called glycogen. Glycogen causes the lining of the vagina to thicken and acts as the main form of sustenance for protective bacteria called lactobacilli. When there is less estrogen present, there is less glycogen, and therefore fewer lactobacilli to maintain a healthy vaginal pH and keep “bad” bacteria at bay. This presents an opportunity for BV-causing bacteria to overgrow.

    But while too little estrogen can catalyze BV, too much estrogen can actually encourage a yeast infection.

    A vaginal yeast infection happens when a type of fungus called Candida—which naturally lives on the skin and in the vagina—overgrows, producing an itching and burning sensation around the vagina, not to mention the infamous “cottage cheese” discharge.

    Recent studies have found that the presence of estrogen causes Candida to grow differently and causes changes in yeast gene expression. These changes all help Candida grow and can even help it escape detection by the host immune response, which means, if Candida is present in your Vaginal Microbiome, it will likely turn into yeast infections when estrogen is present in high amounts.

    Cyclical hormones and fertility

    As our hormones change throughout the month, as well as when we get pregnant, give birth, and go through menopause, the risk of bacterial or yeast infections change. This also happens when switching birth controls or dealing with a hormonal condition or imbalance. If you are managing consistent or recurring hormonal changes, vaginal issues may follow suit.

    Menstruation and the vaginal microbiome

    Lastly, menstruation itself affects the vaginal environment. Vaginal pH is naturally acidic and considered ‘normal’ between 3.8 and 4.5 on the pH scale. Since blood has a pH of 7.4, during your period, vaginal pH is usually higher and more alkaline. If you have an especially long or heavy period, this can create an environment that allows certain pathogens to multiply.

    TL;DR: There are lots of ways these hormones and the microbiome can overlap. If you want to go one step further than education, try testing your vaginal microbiome. Understanding how your microbiome looks at different points in your menstrual cycle or fertility journey can show you any changes in the composition of your vaginal bacteria and fungi!

    PCOS and the vaginal microbiome

    You may have also heard about the growing body of evidence showing the connection between the gut and vaginal microbiome (aka the gut-vagina axis)? It’s also likely that PCOS-related disruptions of the gut microbiome could also impact the vaginal microbiome. Unfortunately, research on PCOS and the vaginal microbiome is still quite sparse.

    Additionally, the majority of published work in this area originates in China, a predominantly homogenous population, which limits our ability to generalize the research findings to racially diverse groups of people. Here’s what we know right now:

          Women with PCOS have a higher vaginal microbiome diversity and lower levels of protective vaginal bacteria (like Lactobacilli species) than those of women without PCOS.

          Given that Lactobacilli levels decline in response to decreased estrogen levels, and that women with PCOS have imbalances in their estrogen levels, these findings seem logical.

          The research is in conflict regarding the other vaginal bacteria potentially affected by PCOS.

          Some evidence suggests that Mycoplasma species are elevated in the vaginal microbiome of women with PCOS. These data even suggest that Mycoplasma could potentially serve as a biomarker when designing new tests to screen for PCOS, however more research is needed to confirm this finding.

    Fertility and the Vaginal Microbiome

    The vaginal microbiome can also have an impact on fertility, from getting pregnant to staying pregnant.

    A healthy vaginal microbiome also acts as a protective shield against infections that could get in the way of your fertility. When the number of Lactobacillus bacteria goes down, harmful bacteria can increase, causing infections that can harm your reproductive organs and affect your fertility.

    The vaginal environment also plays a big role in sperm survival and movement. A healthy vaginal microbiome, with the right pH and protective bacteria, can improve the chances of sperm surviving as they travel through your reproductive system. New research suggests that the makeup of your vaginal microbiome might also affect how well an embryo attaches and how healthy your pregnancy is.

    If your microbiome is unbalanced, like having less Lactobacillus dominance, it could lead to issues like preterm birth and miscarriage. For women using assisted reproductive technologies (ART), the health of your vaginal microbiome can affect how successful these treatments are. Studies have found that women with a strong presence of Lactobacillus bacteria tend to have better success rates with ART compared to those with an unbalanced microbiome. Keeping your microbiome balanced could be really important in getting the most out of fertility treatments.

    Does the Vaginal Microbiome Change?

    Your vaginal microbiome shifts with your behaviors, hormones, and more. There are many reasons that the vaginal microbiome can change, but some common ones include:

          Sex (especially new partners or multiple partners)

          Change in hormones e.g.

          Being pregnant or post-partum

          Going through menopause

          Changing birth control method

          Menstrual blood in the vagina

          Cyclical hormonal fluctuations

          Taking certain medications/supplements (especially antibiotics)

          Smoking

          Stress

          Using feminine hygiene products (especially douches)

    Not All Vaginal Microbiomes Are the Same

    Just as there are different blood types, research has shown that most vaginal microbiomes fall into one of five general categories known as "Community State Types” (CSTs).

    There are 5 general categories of CST, and the Community State Type is determined by which microbes are most dominant in your microbiome, and research has shown differences in symptoms, infections, and health outcomes across the CSTs. But the good news is that unlike blood types, you can switch from one CST to another as your microbiome shifts.

    Of the five CSTs, four of them are dominated by a specific species of lactobacilli:

          Type 1: Lactobacillus crispatus

          Type 2: Lactobacillus gasseri

          Type 3: Lactobacillus iners

          Type 5: Lactobacillus jensenii

    You're classified as Type 4 if you don't have a dominant species of lactobacilli. This group includes people experiencing vaginal infections but can also include some healthy vaginal microbiome compositions. That's why Type 4 is divided into five more subgroups.  

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