The endometrial microbiome
The endometrial microbiome is an ecosystem of microbes that reside in the endometrium (the inner lining of the uterus).
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The uterine endometrium was long considered sterile, but studies have shown that it is composed of a “microbial community” dominated by lactobacilli. Lactobacilli create a specific environment that prevents the growth of pathogenic (disease-causing) microflora. That is why the balance of the microbiome is important for the proper functioning of the reproductive system:
- Fertility – A microbiome rich in lactobacilli increases the chances of embryo (fertilized egg) implantation
- Infection prevention – a balanced microbiome protects the endometrium from pathogenic bacteria
- Immune balance – the microbiome is involved in the regulation of immune responses, which is important for maintaining pregnancy.
- Gynecological diseases – Imbalances can be associated with chronic endometritis, endometriosis, and pregnancy failure.
Vaginal microbiome
According to studies, lactobacilli are the most common bacteria in the vaginal flora of women of reproductive age.
The main role of lactobacilli is to produce lactic acid, which maintains a low pH (3.5–4.5), i.e. an acidic environment in the vagina and reduces the risk of the growth of pathogenic bacteria. Lactobacilli are especially active during puberty, when the level of glycogen in the cells increases under the influence of estrogen. With the participation of lactobacilli, glycogen is converted into lactic acid, which ensures the maintenance of a low pH.
Microbiome in the uterus and cervix
The endometrial microbiome of the uterus is somewhat different from the vaginal microbiome. Lactobacilli dominate here as well, maintaining the low pH of the endometrium, although other bacteria are also present: Acinetobacter, Pseudomonas, and Comamonadaceae.
According to research, the endometrial microbiome consists of the following groups:
- Lactobacilli – the most important “good” bacteria
- Gardnerella – especially multiplies during imbalance
- Escherichia – an intestinal bacterium that can cause inflammation when found in the endometrium
- Prevotella – an anaerobic bacteria that grows when there is an imbalance
- Streptococcus – sometimes found in women with endometrial polyps
- Fungi – about 10% of the endometrial microbiome
- Viruses – about 5%
The cervical microbiome is a “transition zone” between the vaginal and endometrial microbiomes. Its composition is represented by:
Lactobacilli (30.6%)
Pseudomonas (9%)
Acinetobacter (9%)
Vagococcus (7.2%)
Sphingobium (5%)
What happens during an imbalance?
If the balance of the microbiome is disrupted, lactobacilli decrease and microflora multiply, which can cause diseases:
Chronic endometritis – Persistent inflammation of the endometrium, which often occurs invisibly. This is due to a decrease in lactobacilli and an increase in pathogenic microbes. Treatment with antibiotics often improves the condition and increases the chances of embryo implantation
Implantation failure – When the embryo fails to “implant” in the uterus. This is often related to the fact that the microbiome is no longer dominated by lactobacilli, which disrupts the physiological environment of the endometrium. A combination of antibiotics and probiotics can sometimes restore balance.
Endometriosis and adenomyosis – Women with these diseases often have a reduced microbiome diversity with reduced lactobacilli, which also increases the likelihood of developing inflammation
Pregnancy – A vaginal microbiome rich in lactobacilli reduces the risk of miscarriage and premature birth. While a “bacterial vaginosis-like” environment increases the likelihood of complications
Microbiome and infertility
The balance of the uterine microbiome is one of the most important factors in a woman's fertility and reproductive health. Its disruption increases the risk of infertility, implantation failure, and various gynecological diseases.
Studies have shown that the number of lactobacilli in the endometrium of patients requiring in vitro fertilization is significantly reduced – approximately halved compared to the number of lactobacilli in healthy women.
Endometriosis and its connection to microbiome imbalance
Endometriosis is often observed in women with reduced numbers of lactobacilli in the uterine microbiome. In such women, pathogenic microflora often multiply: Pseudomonas, Acinetobacter, Vagococcus, Sphingobium, and others.
Microbiome changes during the cycle
The endometrial microbiome in healthy women undergoes certain changes during the proliferative and secretory phases of the cycle. However, the composition of the microbiome is significantly disrupted in women with menstrual cycle disorders. At this time, an excess of anaerobic microflora is observed, which indicates an imbalance in the microbiome and an increased risk of infection.
Endometrial polyps and chronic endometritis
Bacterial infections in the uterine cavity increase the risk of developing chronic endometritis (CE), further highlighting the role of the microbiome. Studies have also shown that infertility is associated with chronic endometritis.
Changes in the microbiome are often observed in women with endometrial polyps. Increased numbers of Lactobacilli, Bifidobacteria, Gardnerella, Streptococcus, Alteromonas, and Euryarchaeota have been observed in such women. The proliferation of Lactobacilli is not always associated with maintaining a balance in the microbiome.
Short-chain fatty acids (SCFAs) and fertility
During the enzymatic processes of glycogen conversion by lactobacilli, short-chain fatty acids are also formed: acetate, propionate, and butyrate. These molecules perform a signaling function and participate in the regulation of immune and inflammatory responses. Fatty acids reduce the activity of inflammatory cytokines in the endometrium, promote embryo implantation, and stabilize pregnancy.
The balance of the endometrial microbiome is one of the most important factors in a woman's fertility and reproductive health. Its disruption increases the risk of infertility, endometriosis, and pregnancy complications.
Uterine microbiome research method
Ebiom+ / Comprehensive study of the endometrial microbiome and chronic endometritis – a test that simultaneously assesses the balance of the microbiome and the pathogens that cause chronic endometritis, which allows for a more accurate diagnostics and individual treatment planning.
Technology: Next Generation Sequencing (NGS).
Comprehensive analysis of the endometrial microbiome allows the identification of both beneficial and harmful bacteria. This study is especially important for identifying bacteria that cause chronic endometritis. Timely diagnostics and treatment of chronic endometritis improves fertility management.
How can the microbiome be maintained?
Probiotics – help restore lactobacilli
Antibiotics – used during infections to reduce pathogenic bacteria
Nutrition – high-fiber foods, fermented foods, and a healthy diet
Healthy lifestyle – stress management, regular physical activity, and sleep hygiene
New methods – for example, vaginal microbiome transplantation – are in the research stage.
Source:
https://academic.oup.com/humrep/article/36/4/1021/6141565?utm_source
https://www.sciencedirect.com/science/article/pii/S0015028226000397
- How does the microbiome influence female fertility? EurekAlert. February 24, 2025. Accessed March 7, 2025. https://www.eurekalert.org/news-releases/1074654
- Manish K, Luhan J, Hoi-Lan L, et al. Impact of microbiota on female fertility and gynecological problems. Reproductive and Developmental Medicine,2025;8(4):242-251. doi:10.1097/RD9.0000000000000082
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