How Your Vaginal Microbiome Could Be Affecting Your Fertility

If you're trying to conceive and facing unexpected challenges—whether that's difficulty getting pregnant, failed IVF cycles, or early miscarriages—you may have already explored hormone levels, egg quality, sperm health, and more. But there's a lesser-known factor that could be playing a critical role: your vaginal microbiome.

What Is the Vaginal Microbiome?

Your vaginal microbiome is the community of bacteria and other microbes that naturally live in the vagina. Just like your gut has a microbiome that helps with digestion and immunity, your vaginal microbiome helps protect against infection and keeps your reproductive system healthy.

In a healthy state, this microbiome is mostly made up of Lactobacillus bacteria, which help maintain an acidic environment (low pH) in the vagina. This acidity acts as a natural defence system, making it harder for harmful bacteria or viruses to thrive.

When the balance of bacteria is disrupted, it can cause changes in pH, increase inflammation, and lead to infections or other problems, some of which may impact your ability to conceive.

How Can the Vaginal Microbiome Affect Fertility?

1. Implantation Failure

The first step in a successful pregnancy is for the embryo to attach—or implant—into the uterine lining. Research shows that the types of bacteria present in the vagina (and even in the uterus) can affect whether implantation happens successfully.

• If there are too few Lactobacillus bacteria, and more harmful bacteria like Gardnerella, Atopobium, or Prevotella, it can cause low-grade inflammation that makes the uterus less welcoming for an embryo.

• Studies of women undergoing IVF have shown that those with a Lactobacillus-dominant vaginal and endometrial microbiome tend to have higher success rates compared to those with an imbalanced microbiome.

  
  

2. Sperm Survival and Movement

The vaginal environment is the first thing sperm encounter after ejaculation. A healthy, acidic environment helps protect the sperm and guides them through the cervix toward the egg.

• If the pH is too high or there are harmful bacteria present, it can reduce sperm motility (movement) and survival, making it harder for fertilisation to happen.

• Some vaginal infections can also damage sperm directly or interfere with cervical mucus, which sperm need to swim through.

  
  

3. Early Pregnancy Loss

An imbalanced microbiome might also play a role in early miscarriage. If inflammation or infection reaches the uterus, it can affect the early development of the placenta or trigger an immune response that disrupts the pregnancy.

Can You Test Your Vaginal Microbiome?

Yes—there are now ways to test your vaginal (and even endometrial) microbiome to see whether your bacteria are in balance. This can be especially helpful if you’ve had:

• Recurrent IVF failure

• Repeated early pregnancy losses

• Unexplained infertility

• A history of bacterial vaginosis (BV), STIs, or pelvic infections

  
  

Types of Microbiome Testing

There are a few different ways to test your vaginal microbiome, and it’s important to understand the differences:

1. Culture-Based Testing

• This is the traditional method used in most doctor’s offices.

• A swab is taken from the vagina and grown in a lab to see which bacteria grow.

• Limitations: Many vaginal bacteria (especially anaerobic ones) don’t grow well in culture, so this method can miss key microbes.

  
  

2. PCR (Polymerase Chain Reaction) Testing

• PCR looks for the DNA of specific bacteria, even if they can’t be grown in culture.

• It’s more accurate than culture, but still only tests for a predefined list of microbes.

• Useful, but may miss bacteria not on the test panel.

  
  

3. Next-Generation Sequencing (NGS)

• This is the most advanced and comprehensive form of testing.

• It reads the genetic material (16S rRNA gene) of all bacteria present in the sample, providing a full picture of your vaginal microbiome, including rare or hard-to-detect species.

• It can show how dominant Lactobacillus is and whether other harmful bacteria are present in high levels.

• Ideal for fertility patients who want detailed insight into their microbial environment.

The vaginal microbiome is an often-overlooked piece of the fertility puzzle. If you're struggling to conceive or facing repeated implantation failure, microbiome testing could offer important insights and potentially a path forward.

With today’s advanced testing options, it's now possible to get a clear picture of what’s going on at the microbial level and take steps to restore balance.