EMMA (Endometrial Microbiome Metagenomic Analysis)
There are many factors that must be met for an embryo to successfully implant into the endometrium. One of these is the condition of the surrounding microbiome. In some cases, this factor can contribute to failed embryo transfer cycles during IVF, even when good-quality embryos are used. When this occurs, one of the recommended approaches is the EMMA test (Endometrial Microbiome Metagenomic Analysis).
Endometrial Microbiome and the EMMA Test
The importance of the endometrial microbiome lies in its role in maintaining reproductive health and supporting successful pregnancy. Evidence shows that the balance of bacteria within the endometrium is one of the key factors influencing embryo implantation success.
A healthy microbiome dominated by Lactobacillus bacteria is strongly associated with better embryo implantation. Conversely, bacterial imbalance (dysbiosis) may lead to implantation failure, recurrent miscarriage, infertility, and chronic inflammation. The microbial composition of the endometrium can serve as a marker of fertility disorders and is influenced by factors such as age, hormones, and immune status.
This was confirmed by a 2016 study conducted in Spain and published in the American Journal of Obstetrics and Gynecology. The study investigated whether the endometrium has its own microbial community and how this might affect female fertility.
The study sample consisted of infertile women undergoing IVF cycles with a receptive endometrium. It was found that women whose endometrium was not dominated by Lactobacillus defined as having less than 90% Lactobacillus and more than 10% other bacteria had poorer reproductive outcomes. These outcomes included lower implantation rates, pregnancy rates, ongoing pregnancy rates, and live birth rates compared to women whose endometrial microbiota was dominated by Lactobacillus.
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A meta-analysis of six cohort studies involving a total of 1,095 women also reported an association between microbiota dysbiosis and poor reproductive outcomes.
Based on these findings, the EMMA test (Endometrial Microbiome Metagenomic Analysis) was developed. This test evaluates the overall bacterial balance within the endometrium. It measures the proportion of healthy bacteria (Lactobacillus), which is linked to better pregnancy outcomes. The EMMA test also includes the ALICE test (Analysis of Infectious Chronic Endometritis), designed to detect pathogenic bacteria that cause chronic endometritis a persistent inflammation of the uterine lining that often presents without symptoms.
Statistics show that 30% of infertile women have pathogenic bacteria in their endometrium, which can reduce embryo implantation success. Pathogenic bacteria include species from the Enterobacteriaceae family (such as Klebsiella and Escherichia), Staphylococcus spp., and other Gram-negative bacteria.
EMMA Procedure
The EMMA test begins with an endometrial biopsy performed between days 15–25 of the menstrual cycle. The physician collects a small tissue sample from the endometrium, which is then tested using Next Generation Sequencing (NGS). This technology allows for comprehensive analysis of all bacterial and microbial genetic components within the endometrium.
EMMA test results are typically available within 10–15 working days after sampling. The report usually includes:
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The proportion of Lactobacillus and the ten most abundant bacterial species found in the sample
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Detection of potentially harmful bacteria that may negatively impact implantation
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Personalized treatment recommendations based on the microbiome profile, which may include antibiotics and/or Lactobacillus-containing probiotics to restore microbial balance before proceeding with embryo transfer
In some cases, a repeat biopsy may be necessary if the results are inconclusive or if the sample quality is inadequate.
Benefits of the EMMA Test
As noted above, the EMMA test can evaluate the endometrial microbiome and provide individualized treatment recommendations. By offering a detailed analysis of the endometrial microbiome, EMMA may improve pregnancy outcomes particularly for couples who have experienced repeated embryo transfer failures or recurrent miscarriages.
Side Effects of the EMMA Test
The most common side effects are related to the endometrial biopsy itself, including abdominal cramping and light vaginal bleeding. There is a small risk of infection and, in very rare cases, uterine perforation.
Effectiveness of EMMA in Improving Pregnancy Rates
The evaluation of the microbiome in infertility cases has drawn significant interest from experts, and results so far have been promising as a potential factor for improving embryo implantation rates—along with pregnancy and live birth rates—in IVF cycles.
A 2020 study conducted in Japan found that women who underwent EMMA and ALICE testing, followed by appropriate probiotic or antibiotic treatment, achieved clinical pregnancy rates of up to 64.5%, compared to 33.3% in those who did not undergo testing.
In 2025, a follow-up multicenter study by the same researchers was conducted across 14 IVF clinics in Japan. This study investigated whether correcting the endometrial microbiome could improve ongoing pregnancy rates.
A total of 527 women under the age of 42 were grouped based on their EMMA results: normal (Lactobacillus >90%), abnormal (dysbiosis with pathogenic bacteria), and mild + very low (low biomass). Treatment was individualized: antibiotics and probiotics for abnormal results, and probiotics only for mild/low biomass results. After treatment, IVF cycles continued for up to two embryo transfers.
The study found that post-treatment pregnancy rates were relatively similar among the three groups, with the abnormal group achieving pregnancy more quickly than the control group. These findings suggest that microbiome correction may contribute to favorable outcomes.
Despite these promising findings, the effectiveness of EMMA remains debated due to methodological limitations, lack of high-quality clinical trials, and inconsistent results.
A 2022 study from 22 CARE Fertility clinics in the United Kingdom provided a valid counterpoint. Between January 2017 and August 2021, 202 patients underwent one or more of the ERA, EMMA, or ALICE tests. A total of 101 women with recurrent implantation failure underwent the EMMA test. Their subsequent cycles were compared with 404 age-matched control cycles. The study found that use of the EMMA test did not improve implantation or clinical pregnancy rates compared with the control group.
Indications for EMMA in IVF Treatment
In 2023, the European Society of Human Reproduction and Embryology (ESHRE) stated that the EMMA test is not recommended for routine use in recurrent implantation failure cases or as an additional assessment in fertility workup. The test falls under the “red” (not recommended) category in their practice guidelines. This is due to limited scientific evidence, mixed and inconsistent outcomes, and numerous unanswered questions before the test can be fully adopted in clinical practice.
As of now, no official updates or consensus have been issued. However, based on available studies, EMMA is generally recommended for couples undergoing IVF who have experienced recurrent implantation failure (three or more times) or recurrent miscarriages (two or more), even when high-quality embryos were transferred.
Conclusion
The EMMA test may be most beneficial for couples undergoing IVF who have experienced recurrent implantation failure or recurrent miscarriage despite transferring good-quality embryos. However, it is not performed routinely because of the ongoing debate surrounding its effectiveness. If you are interested in the test, discuss it further with a trusted fertility specialist.
Source:
- Bamford T, Polson D, Lowe P, Easter C, Coomarasamy A. Endometrial receptivity analysis (ERA) and microbiome testing for recurrent implantation failure (RIF): a matched case control study. InHUMAN REPRODUCTION 2022 Jul 1 (Vol. 37, pp. I94-I95). GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND: OXFORD UNIV PRESS.
- Cakmak H, Taylor HS. Implantation failure: molecular mechanisms and clinical treatment. Hum Reprod Update. 2011;17(2):242-253. doi:10.1093/humupd/dmq037.
- Iwami N, Komiya S, Asada Y, Tatsumi K, Habara T, Kuramoto T, Seki M, Yoshida H, Takeuchi K, Shiotani M, Mukaida T. Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma & Alice: A multicenter prospective study. Reproductive Medicine and Biology. 2025 Jan;24(1):e12634.
- Kawamata M, Iwami N, Ozawa N, Yamamoto T, Watanabe E, Mizuuchi M, Moriwaka O, Kamiya H. Efficacy of Endometrial Microbiome Metagenomic Analysis (EMMA) and Analysis of Infectious Chronic Endometritis (ALICE) in Patients with Repeated Implantation Failure. 日本受精着床学会雑誌. 2020;37(1):34-42.
- Moreno I, Codoñer FM, Vilella F, Valbuena D, Martinez-Blanch JF, Jimenez-Almazán J, Alonso R, Alamá P, Remohí J, Pellicer A, Ramon D. Evidence that the endometrial microbiota has an effect on implantation success or failure. American journal of obstetrics and gynecology. 2016 Dec 1;215(6):684-703.
- Moreno I, Franasiak JM. Endometrial microbiota—new player in town. Fertility and sterility. 2017 Jul 1;108(1):32-9.
