- Patient guide · reviewed by Dr Sarafis
Endometrial microbiome
testing
The uterus is not sterile. Endometrial microbiome testing maps the bacterial balance of the endometrium and asks a simple question: is the lining dominated by the bacteria that help implantation, or not?
By Dr Vasileios Sarafis MD. UK-trained fertility specialist, Thessaloniki and Athens. Last reviewed 12 June 2026.
- NGS
- Microbiome
- Lactobacilli
For decades the uterine cavity was assumed to be sterile. It is not. It carries its own microbiome, and in a healthy state that microbiome is dominated by lactobacilli. Next-generation sequencing of a small endometrial sample is what measures it.
What the test measures
The analysis characterises the bacterial composition of the endometrium from a small biopsy and quantifies the proportion of lactobacilli present. The clinically useful threshold is whether the microbiome is lactobacilli-dominant, conventionally taken as above 90 percent, or non-dominant.
A non-dominant result, where other bacterial species make up a larger share of the community, has been associated with reduced implantation rates in several published studies. The logic is that a disturbed bacterial environment is a less hospitable place for an embryo to implant.
Microbiome and endometritis testing are usually run together.
Both are performed on the same single endometrial biopsy. Microbiome analysis describes the overall bacterial balance; testing for chronic endometritis looks specifically for associated pathogens. Together they give a fuller picture from one sample.
What happens if the result is non-dominant
The endometrial microbiome is one of the strongest areas of emerging evidence in this field, but it is still emerging. The association between a lactobacilli-dominant lining and better implantation is supported by observational data more than by large randomised trials. That is worth stating plainly. It is a reason to use microbiome testing thoughtfully, in the right patients, rather than as a routine add-on for everyone. It should be considered alongside other possible causes of recurrent implantation failure, not as a stand-alone explanation.
The honest position on the evidence
This matters because the definition of RIF assumes the embryos themselves were not the problem. A blastocyst that has been graded as good quality, and ideally one that has been genetically tested and found to be chromosomally normal (euploid), removes the most common single explanation for failure, which is the embryo itself. When euploid embryos fail repeatedly, attention turns to the endometrium, the uterine environment, and the implantation process.
Key takeaways
- The endometrium has a microbiome; in a healthy state it is lactobacilli-dominant.
- The analysis measures the bacterial balance and the proportion of lactobacilli.
- A non-dominant result is associated with reduced implantation in several studies.
- Both tests run on the same single biopsy and are usually done together.
When I recommend it
Microbiome testing earns its place in patients with recurrent implantation failure, particularly those with recurrent biochemical pregnancies or unexplained early loss. As with every investigation at Sarafis Fertility Clinic, the test is offered because the result would change the plan, not because it is available.
What about EMMA, ALICE and EndomeTRIO?
You will see these names on clinic websites and in patient forums, so it is worth being clear about what they are. EMMA (Endometrial Microbiome Metagenomic Analysis), ALICE (Analysis of Infectious Chronic Endometritis) and ERA (Endometrial Receptivity Analysis) are commercial products from a single company, Igenomix, often sold together as the EndomeTRIO panel. They are brand names, not the names of the underlying tests.
The underlying methods — next-generation sequencing of the endometrial microbiome, and molecular or histological detection of chronic endometritis — are performed by a number of laboratories, and the results answer the same clinical questions. I do not use the Igenomix panels. The endometrial testing in my practice is run by ATG (Access to Genome), and it differs in one respect that matters clinically: alongside the molecular sequencing it includes conventional culture with antibiotic sensitivity testing. A molecular panel tells you which organisms are present and suggests an antibiotic based on what usually works against them. Culture with sensitivities measures how your own isolate actually responds. When the aim is to clear an infection before a transfer, that is the difference between choosing the antibiotic from a table and choosing it from your result. Endometrial microbiome analysis is €400 and endometrial immunological testing €600, each quoted before anything is done.
I set this out plainly because you deserve to know what you are buying and from whom. If another clinic quotes you a branded panel, ask what it measures, which laboratory runs it, and what would change in your treatment depending on the result. Those three questions matter more than the name on the box.
- Where to go next
Microbiome analysis is part of a coordinated endometrial workup that also includes testing for chronic endometritis and, where indicated, advanced ultrasound and hysteroscopy, with one physician interpreting all the results.
What is the EMMA test?
Endometrial microbiome testing characterises the bacterial composition of the endometrium from a small biopsy and measures the proportion of lactobacilli. A lactobacilli-dominant lining, conventionally above 90 percent, is associated with better implantation.
Is the EMMA test done at the same time as ALICE?
Yes. Both are usually performed together on a single endometrial biopsy. The microbiome analysis describes the overall bacterial balance, while the endometritis test looks specifically for the pathogens associated with chronic endometritis.
What treatment follows an abnormal microbiome result?
Where the microbiome is non-dominant or specific species are identified, treatment is often a short, targeted course of antibiotics followed by probiotic restoration to re-establish lactobacilli dominance before the next transfer. The exact approach depends on what is found.
Common questions.
- Frequently Asked Questions
- Book your endometrial workup
Map the lining before the next transfer.
Microbiome and endometritis testing are performed on a single biopsy and interpreted alongside your full history. For most international patients the first step is to book an online fertility consultation to plan which investigations are actually indicated.
Sarafis Fertility Clinic · Thessaloniki & Athens · info@sarafisfertility.com · +30 210 444 9027
This page is for educational purposes and does not constitute medical advice. Indications for recurrent implantation failure investigation depend on individual clinical history and prior treatment. For guidance specific to your situation, book a consultation.