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The Vaginal and Uterine Microbiome: A Window into Fertility and Vaginal Health

drtanyawilliams - November 29, 2023 - 19 comments

Lately, we’re seeing more research on the human microbiome. The more we look, the more we see that our resident microbiota are crucial to normal reproductive functions

So if you’re hoping or struggling to conceive, your vaginal microbiome might be an important place to look. So is the health of your endometrium (uterine lining), which is an essential for successful pregnancy. 

You might be surprised to learn just how much this tiny ecosystem can impact your journey to motherhood. If the levels of healthy bacteria in the endometrium are low, or there are harmful bacteria, your chance of pregnancy might be lower. 

Your vaginal and uterine microbiome is truly a powerhouse. From tackling recurrent vulvovaginal infections, to playing a key role in fertility and pregnancy outcomes.

In this article, we’ll dive deeper into the vaginal and uterine microbiome. What they affect, and what solutions might be available to support your fertility. 

What is the vaginal microbiome?

The vaginal microbiota is the diverse microbial populations that inhabit the female genital tract, and it influences the vaginal environment’s homeostasis, or its “steady state”.

Everyone’s vaginal microbiome has a different composition. It is expected to change throughout your life based on age, diet, sexual activity, and hormonal changes. Just as your body and the environment around it are always changing, your vagina is constantly changing, too.

When the vaginal microbiome is in equilibrium, its healthy state, we call it eubiosis. Basically, the microorganisms in the vagina are working in synergy and not causing disease.

So what’s in a “normal” vaginal microbiome? 

While every individual’s is different, 73% of female microbiomes have a dominance of lactobacillus, which produces lactic acid. This may help lower the vagina’s pH to below 4.5, what we consider a “protective environment” with regard to vulvovaginal infections, pregnancy, and fertility outcomes.

Why is the vaginal microbiome important?

Why should we pay attention to the vaginal microbiome? Well, its composition can affect your health over a lifetime. 

Just as eubiosis in the vagina means no disease, dysbiosis in the vagina can lead to disease, which has been seen as early as the mid-20th century.

The vaginal microbiota’s composition is clearly linked to your risk of vaginal infections, reproductive health issues, and other medical conditions. 

Let’s look at each of these links more closely.

The microbiome and vulvovaginal infections

Have you had infections in your vagina or vulva that keep coming back? Many people suffer from recurrent vulvovaginal infection (RVVI), which is defined as four or more infections per year. 

Your vaginal microbiome could be linked to bacterial vaginosis (BV), candidiasis (fungal infection), and recurrent vaginal infection.

A common infection is BV, which happens when the vaginal pH increases, the vagina’s normal bacterial balance shifts, and certain bacteria are able to overgrow. Another common one is recurrent vulvovaginal candidiasis (RVVC), an infectious disease linked most often to the fungus Candida albicans.

So what role does the vaginal microbiome play in this? 

When your vaginal microbiome is imbalanced, for example containing fewer Lactobacillus species and more pathogenic bacteria, you may be more at risk for recurrent BV. Studies have also found that having fewer Lactobacillus species is linked to hr-HPV infection, and its progression.

The microbiome and fertility

Beyond infection, the microbiome plays an important role in fertility. The genital tract microbiome can influence your potential fertility before and during assisted reproductive treatments, including IVF.

How does this work? 

Having certain microbiota in your genital tract, or a shift in this microbiota, can cause problems with fertilization, implantation, pregnancy, and the development of embryos. This could cause fertility treatments to fail and end in fewer live births.

Remember that lactobacillus is dominant in 73% of female vaginal microbiomes. This environment is more receptive than one with high diversity of bacteria and less Lactobacilli

It is also true that the uterine cavity is dominated by lactobacillus species. Although the specific strains may be different from those found in the vagina.  

A 2016 study by Moreno et al. found that women with a Lactobacillus-dominant microbiota in the uterus have a higher success rate in implantation. The study showed 60% compared to 23% in non-Lactobacillus-dominant microbiota. 

When it comes to IVF-embryo transfer, the single most important event determining success. After ensuring a genetically normal embryo, is the embryo implanting in the endometrium. 

A key factor in embryo implantation is the presence of microbial colonization of the upper genital tract. In fact, a study of 265 women saw significantly lower clinical pregnancy rates. Ongoing pregnancy rates, and implantation rates in the women with cervical micro-organisms.

The uterine microbiome and pregnancy outcomes

The uterine microbiota’s composition also seriously affects pregnancy and neonatal outcomes.  

Moreno and colleagues’ 2016 study found that Lactobacillus-dominance significantly increases the chance of successful pregnancy and live birth. Also, reduces the miscarriage rate, compared to non-Lactobacillus-dominance.

Newborn baby is held over a scale in the hands of a man with a tattooed arm and blue hospital scrubs.

Bacterial vaginosis (BV), a common disturbance in the vaginal microbiome which we mentioned earlier, is linked to a higher risk of early pregnancy loss. As seen in studies by DiGiulio et al. and van Oostrum et al.. Premature birth is also often linked to infections inside the uterus. 

However, BV doesn’t seem to affect the chances of getting pregnant. Nonetheless, we should handle these results with caution. 

Let’s not forget that the vaginal and uterine microbiome of a mother influences the offspring’s microbiome. That means as a mother, your microbiome will seed your baby’s microbiome at birth. Which could influence your child’s microbiome composition and health over their lifetime. 

What affects the vaginal and uterine microbiome

The vaginal and uterine microbiome are constantly changing. As a woman’s body deals with different challenges from the environment and within. 

Various factors like tobacco, alcohol, cannabis, stress, physical activity, infections, lack of sleep, body mass index, antibiotic or drug exposure, sexual activity, diabetes, and hygiene habits can affect the balance of the microbiome. 

Let’s look at how each of these factors impacts the microbiota.


Your choice of contraceptive method can impact the composition of your vaginal microbiome. However, due to limited research, it is hard to draw definitive conclusions on this relationship at the moment.


Using preventive oral antibiotics before embryo transfer in IVF/ICSI might lower the level of microbial colonization in the upper genital tract. Thus, potentially affecting pregnancy rates. However, current research findings are conflicting, and the direct impact of antibiotics on the microbiome during IVF is still not thoroughly understood. 

It’s important to remember that antibiotics should not be used routinely to alter the vaginal microbiome. While some patients with repeated implantation failure (RIF) might benefit from antibiotic therapy. Particularly if they have certain pathogenic bacteria, the American Society for Reproductive Medicine strongly advises against the routine use of antibiotics before embryo transfer.


Hormones circulating in the body significantly influence the vaginal microbiome and a woman’s susceptibility to infections. 

Researchers, like Jakobsson and Forsum in 2008, have examined how changes in Lactobacillus Bacteria during fertility treatments impact the vaginal and uterine flora. Understanding these hormonal influences is vital in fertility treatments like IVF.

Understanding these various influences on the vaginal microbiome is crucial for women’s reproductive health. We need more research to fully understand how these factors interact and affect the delicate balance of the vaginal microbiome.

Solutions for a healthy vaginal and uterine microbiome

Now that we’ve seen how an imbalanced vaginal and uterine microbiome can cause problems for infection and fertility. Let’s look at what you can do to maintain a healthy microbiome.

Lifestyle changes

If you’re looking to conceive, talking to your doctor first can be an important first step to making sure your body is prepared for a successful pregnancy.

Research suggests that your diet can impact the good bacteria in your gut. Which could make a difference if you’re struggling to get pregnant. Making lifestyle changes, like losing weight, staying active, and adjusting your daily routine, can also help your chances of getting pregnant. 


If you’re looking to boost your chances of successful pregnancy. Especially if you’re going through in vitro fertilization (IVF), here is some interesting news. 

Researchers suggest that screening and treating women undergoing IVF with probiotics might make a real difference in their fertility journey. 

Probiotics are tiny living organisms, mainly bacteria, that can do some incredible things for your body. They help improve your overall health, strengthen your immune system, and even reduce inflammation. They can also play a key role in balancing your vaginal microbiome. 

Research shows that oral probiotics can help bring down the pH levels in your vagina and restore the healthy bacteria that should be there. This is great news for women who’ve been dealing with vaginal infections, especially BV. 

Oral supplements of Lactobacillus rhamnosus and Lactobacillus fermentum can restore a healthy bacterial balance. In the vagina for as many as 82% of women who previously had issues with imbalanced vaginal bacteria.

We still need more research to determine if taking probiotics directly improves reproductive health. Also, while we’ve seen some promising results, it’s important to remember that not everyone responds the same way to probiotics. 

But this is an exciting avenue of research which may lead to new ways to improve women’s health, so keep an eye out for more studies in the future.

Looking to the future

Researchers are working hard to understand how to improve the balance of bacteria in our bodies before and during pregnancy. This could help reduce the risk of early pregnancy loss and delivering prematurely. 

The future holds promise for personalized probiotic treatment.

Research suggests that some women might respond differently to probiotics because of the type of bacteria already present in their bodies. That means that knowing what kind of bacteria a woman has could help doctors prescribe the right probiotics to help even more. This could be a game-changer for women dealing with infections and struggling to conceive. We expect to see more research to confirm this hypothesis in the coming years.

While we’ve studied vaginal bacteria extensively, the ones in the uterus have received less attention.

New techniques now allow us to evaluate endometrial flora with genetic sequencing tests on biopsy specimens. This provides more information for personalized antibiotic and probiotic treatment, aiming for better reproductive outcomes.  

When it comes to men, we’re just starting to understand how infections and inflammation might affect their fertility. Some bacteria can even hurt sperm function directly, which can affect fertility.

Taking care of your body and making healthy choices can significantly impact fertility and pregnancy, even though we’re still learning about the role of body bacteria.

Discover more related blogs from Dr. Tanya Williams Fertility Centre:

Are your fitness goals helping or hurting your fertility: An Evidence-Based Look at 5 Common Practices

6 Steps to Mentally Prepare for your IVF Journey

Vitamin D Deficiency and its Link to Fertility: What You Need to Know

Fertility Supplements: Which ones actually work? 

7 Health Tips to Support Fertility

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