The Endometrial Microbiome


The endometrial microbiome is a recent area of study in reproductive medicine with significant effects on an individual’s fertility and pregnancy outcomes. This microbiome includes the bacteria living in the endometrial cavity and lining, which can influence how well the endometrium can support pregnancy.

Composition of the Endometrial Microbiome

The endometrial microbiome has fewer bacteria compared to areas like the gut. It includes different types of bacteria, with Lactobacillus being the most common and beneficial in a healthy endometrium. However, the balance of other bacteria is also important.

  • Healthy Bacteria: Lactobacillus species are the most common and beneficial bacteria in the endometrium. They help protect against harmful bacteria and support reproductive health.
  • Harmful Bacteria: Bacteria like Gardnerella, Atopobium, and Streptococcus can disrupt the healthy balance and lead to poor reproductive outcomes.

Impact on Reproductive Health

The makeup of the endometrial microbiome is closely tied to reproductive success. Studies show that a microbiome dominated by Lactobacillus may be linked to higher implantation rates, successful pregnancies, and live births. In contrast, a microbiome dominated by harmful bacteria could be linked to lower implantation rates, miscarriage, and generally poor reproductive outcomes.

  • Positive Effects: High levels of Lactobacillus in the endometrium are associated with better chances of implantation and pregnancy. These bacteria produce lactic acid, which keeps the environment acidic and prevents harmful bacteria from growing.
  • Negative Effects: Harmful bacteria like Gardnerella and Atopobium can cause inflammation and create an environment that is not conducive to embryo implantation. These bacteria are often linked to infections that can affect the endometrium and reproductive health.


  1. 16S rRNA Gene Sequencing: This technique identifies bacteria based on their genetic material. It is widely used to analyse the endometrial microbiome and detect imbalances.
  2. Culturomics: This method uses high-throughput culture techniques to identify viable bacteria that might not be detected by genetic sequencing alone. It provides a comprehensive view of the microbiome.
  3. Next-Generation Sequencing (NGS): NGS allows detailed analysis of the microbiome by sequencing many DNA molecules at once, providing insights into the diversity and abundance of bacteria in the endometrium.
  4. EMMA and ALICE Tests: EMMA (Endometrial Microbiome Metagenomic Analysis) gives a complete picture of the microbiome and recommends treatments. ALICE (Analysis of Infectious Chronic Endometritis) detects bacteria that cause chronic endometritis and suggests appropriate antibiotics.


  1. Probiotics: Administering probiotics, especially Lactobacillus species, aims to restore a healthy microbiome balance in the endometrium. This approach has shown promise in improving implantation rates and pregnancy outcomes for women undergoing assisted reproductive treatments (ART).
  2. Antibiotic Therapy: Targeted antibiotics can treat infections caused by harmful bacteria identified through tests like ALICE. This treatment is essential for resolving chronic endometritis and other microbial imbalances that hinder reproductive success.
  3. Personalized Medicine: Based on diagnostic results, personalized treatment plans can be developed to address specific microbial imbalances. This approach may include a combination of antibiotics and probiotics to optimize the endometrial environment for implantation and pregnancy.