Endometritis & The Endometrial Microbiome: What You Need to Know If You’re Trying to Conceive

The uterine microbiome is an important, yet often overlooked, factor in many people’s fertility journey. We used to believe the uterus was sterile, we know now that the endometrium has its own microbiome. This tiny ecosystem impacts implantation, immune regulation and live birth outcomes. It may be the reason many are navigating unexplained infertility or early loss and may be the explanation for some cases of recurrent implantation failure.

What is the endometrial microbiome

The endometrial microbiome refers to the unique mix of microbes (mainly bacteria) that live in the lining of the uterus. In fact, the uterine microbiome plays a crucial role in regulating how the uterus functions:

·       It affects the responsiveness and sensitivity of the uterine lining

·       It controls what can and can’t grow in the womb

·       It helps shape the immune environment - creating a calm, embryo-friendly space rather than one that’s defensive or inflamed

This last point is particularly important. For implantation to occur, the immune system of the womb needs to soften, to allow something genetically “other” (a baby) to be welcomed and retained. The balance of bacteria in the endometrium helps determine whether that immune response is tolerant or reactive.

What Does a Healthy Uterine Microbiome Look Like?

Unlike in the gut, where we want diversity, a healthy uterine microbiome is made up of at least 90–95% Lactobacillus species. These beneficial bacteria help maintain a slightly acidic environment, preventing harmful bacteria from taking hold, and support a balanced immune response.

But this balance can be lost quite easily, and when it is, the gap left by Lactobacillus is often filled by other bacteria. Some of these other bacteria are clearly pathogenic (and drive inflammation), but others are less obviously harmful. Even so, this can disrupt the delicate conditions needed for implantation and pregnancy to occur.

This state of imbalance is called dysbiosis, and it can present in two main ways:

• An overgrowth of inflammatory, pathogenic bacteria

• A shift towards bacteria that aren't necessarily dangerous, but which still displace Lactobacillus and create a microbiome that isn’t optimal for pregnancy. Less than 90-95% lactobacillus results in lower rates of pregnancies and live births.

It doesn’t always take an outright infection to cause problems, just a shift in the environment that makes it harder for an embryo to implant and thrive.

What Is Endometritis?

Often confused with endometriosis, when the endometrial lining becomes chronically inflamed, we call this endometritis. It’s often driven by bacteria that shouldn’t be present, or by an exaggerated immune response, even to otherwise harmless microbes.

Unlike acute infections, chronic endometritis is usually silent (meaning there are no obvious symptoms of it). Many people have no idea they have it, but studies increasingly link it with implantation failure, miscarriage, and reduced live birth rates.

The Vaginal and Uterine Microbiome Are Closely Connected

It’s also worth noting that many cases of endometrial dysbiosis originate in the vaginal microbiome, which shares a close connection with the uterine environment. For this reason, vaginal microbiome testing is often a good first step, it’s cheaper, non-invasive, and can offer valuable insight, particularly if you’re trying to conceive naturally. For vaginal microbiome testing see here.

That said, a healthy vaginal microbiome doesn't always mean the uterus is in good shape. I’ve seen clients with excellent vaginal microbiome results who still tested positive for uterine dysbiosis or inflammation. So, if conception still isn’t happening, it may be worth digging deeper.

Menstrual Blood Microbiome Testing

A newer and less invasive option is to test the uterine microbiome using menstrual blood. This can be helpful if you're not undergoing IVF or want a more affordable entry point. See here and here for menstrual blood testing options. I would always advise consulting with a fertility specialist who can help you interpret and understand your results; otherwise, it can often feel overwhelming.

The key difference is timing. Unlike EMMA/ALICE (details below), which are done during the implantation window, menstrual blood tests are done during your period. This means they might not give as direct a view of how the lining behaves at implantation time, but they’re still a useful tool, especially if invasive testing isn’t an option right now.

What Is EMMA / ALICE Testing?

If you're undergoing IVF or have had multiple unsuccessful embryo transfers (especially if with euploid embryos), testing the uterine lining directly is often the most accurate option.

This is where EMMA and ALICE come in:

• EMMA (Endometrial Microbiome Metagenomic Analysis) looks at the makeup of bacteria in the uterus and, crucially, whether there is enough Lactobacillus.

• ALICE (Analysis of Infectious Chronic Endometritis) looks for specific harmful bacteria that can cause inflammation and chronic endometritis.

These tests involve a small endometrial biopsy (similar in sensation to a smear test). If you're already doing IVF, the biopsy can sometimes be done at the same time as your egg collection — but ideally it needs to be done during the implantation window (days 19–21 of a 28-day cycle) to give an accurate picture of what’s happening when an embryo would be trying to implant.

Who Should Consider Uterine Microbiome Testing?

While this type of testing isn't necessary for everyone, there are specific groups who may benefit significantly.

You might want to consider uterine microbiome testing if you:

• Have experienced repeated implantation failure, especially if with euploid (chromosomally normal) embryos

• Have a long history of miscarriage or biochemical pregnancies

• Had ruptured appendicitis or pelvic infections in the past

• Have a diagnosis of endometriosis, pelvic inflammatory disease, IBD, or another inflammatory condition

• Have only one or few embryos available to transfer (so you can make sure the environment is as receptive as possible)

• Have had multiple rounds of IVF with no success

In these cases, the uterine environment may not be as receptive as it needs to be — and exploring the microbiome may provide missing answers.

What Does Treatment Involve?

If your results show inflammation or dysbiosis, treatment is usually straightforward:

• A targeted course of antibiotics if pathogenic bacteria are found

• Treating sexual partners too, since bacteria can pass between you (and can also affect sperm health)

• A course of probiotics, especially strains of Lactobacillus, to encourage recolonisation and restore the protective environment

A second test is often recommended to check whether treatment has worked, and in some cases, a second course of antibiotics or further probiotic support may be needed.

It’s also important to say: your microbiome doesn’t have to be perfect for pregnancy to happen. Sometimes, simply nudging things back in the right direction, getting Lactobacillus levels up and inflammation down, is enough to create the conditions your body needs.

If you’re navigating recurrent losses, failed transfers, or just feel like something’s being missed in your fertility journey, this is an area worth exploring.

If you’re wondering whether uterine or vaginal microbiome testing is right for you, I offer tailored fertility support combining nutrition, acupuncture, and investigative analysis. Get in touch to find out how we can work together.