How does the endometrial microbiome impact embryo implantation?

Maria Navas
Nutritionist, Maria Navas Nutrition, Health and Women
From this video you will find out:
  • What does microbiota mean, and why is it so important?
  • Is there a relationship between microbiota and repeated implantation failure (RIF)?
  • What do studies say on endometrial microbiota and how it can affect recurrent reproductive failure?
  • What factors influence microbiota and how can it be improved?

How does the endometrial microbiome impact embryo implantation?

During this event, Maria Navas, Nutritionist and an expert in the microbiome and women’s health, explained how the endometrial microbiome can have an impact on embryo implantation and what can be done to achieve the best possible outcome.

Microbiota – what does it mean?

The term “microbiota” refers to all the microorganisms that live on and inside our bodies. We have them in our skin, cavities (such as the mouth and nose), and almost everywhere else. These microorganisms play important roles in our health and well-being. A good microbiota can make us healthier, help with nutrient absorption in the gut, and even influence our mood, energy levels, and physical appearance. Some consider it to be like an additional organ in our body.

It’s important to note that we still have limited knowledge about microbiota, but we recognize its significant impact on our bodies and health. The infographic provided here illustrates various functions of the microbiota. One crucial aspect is its role in regulating our immune system. A healthy microbiota can make it more challenging for us to get sick, while a weak or imbalanced microbiota may increase our susceptibility to illnesses. When we discuss microbiota, it’s not limited to bacteria alone; we also consider fungi and viruses. However, most studies focus on bacterial microbiota, which is what we’ll discuss further.

The bacterial microbiota has a key role in immune system development and modulation. It synthesizes essential molecules for our well-being, especially in our gut. In the female reproductive system, the most notable microbiota resides in the vagina. When there’s an infection in the vagina, it disrupts the normal balance of bacteria, allowing other microorganisms to grow and potentially cause harmful symptoms. One of the vital functions of the microbiota is to protect us.

Contrary to previous beliefs, the female reproductive system is not sterile. We now know that there are microorganisms in different parts of the reproductive system. In this context, we’ll focus on the endometrium, which is the part adjacent to the uterus. Lactobacillus is a type of bacteria that we want in our reproductive system, primarily in the vagina, as it helps fight against pathogens in the vagina and uterus.

Studies have shown that having more than 90% of lactobacillus in the reproductive system increases the chances of getting pregnant. If the percentage is lower, it might be more challenging, but not impossible, to conceive. When a patient is having difficulty getting pregnant despite seemingly normal conditions, it may be necessary to investigate the microbial composition of the uterus. However, such tests are expensive and carry some risks, so they are not typically performed at the beginning of treatment. Nevertheless, we should be aware of the important role of microbiota and take care of our health and microbiota.

In a recent webinar, how to maintain a healthy microbiota was discussed. If you experience gastrointestinal problems, digestion issues, or frequent bloating, it might be worth examining your gut microbiota before focusing on the uterus. Often, addressing digestive problems can help resolve the situation.

Microbiota & implantation failure

There are some databases where you can find studies and reports on the relationship between microbiota and implantation failure.
If you search for “implantation and IVF,” you can see that there have been articles since the 80s, with 317 articles last year. If you add the term “microbiota” and search for “implantation IVF microbiota,” we can see that the studies started around 2010, and last year, in 2022, there were 77 articles. That is why it is crucial to understand that there’s still much we don’t know about microbiota, and we are constantly learning. In the world of microbiota, it’s difficult to give definite answers like “take a specific probiotic for a headache.” We can’t make such claims because we don’t have a consensus on what constitutes a healthy microbiota. While it’s better to have more than 90% lactobacillus, we can’t provide specific percentages for other bacteria. There are many unanswered questions.

Additionally, we don’t know if dysbiosis (when the microbiota is not as it should be) causes problems or if problems lead to dysbiosis. This is something we’re still trying to understand. Many questions remain unanswered, but fortunately, we have made progress, and more people are learning about microbiota every day. Now, let’s discuss the key factors for achieving pregnancy. To get a woman pregnant, we need a good quality, viable embryo and a suitable endometrium. We need to ensure that the endometrium is functioning correctly, undergoing hormonal changes and has no physical barriers to implantation. But sometimes, even when everything seems ideal, implantation fails. In such cases, we may need to consider the role of microbiota.

Case study

She had her first cycle, but unfortunately, she experienced a miscarriage. They performed a microbiota test and collected a sample. Then, she went on vacation. During her vacation, she had another cycle, and it was positive, but she had a spontaneous abortion. After her vacation, in September, she returned to the clinic to start a new cycle, not knowing that she was already four weeks pregnant. They took another sample. Surprisingly, this time she got pregnant naturally, without any assistance. So, we compared the microbiota before and after. What do we see? During the miscarriage, we had many different microorganisms, different colours, not lactobacillus. But during the subsequent pregnancy, the main colour was lactobacillus. It was more than 90% of the microbiota. So maybe in this case, not having enough lactobacillus or having other microorganisms that were not helpful was the problem.

We have to be careful because identifying the microorganisms that are there is one thing, but understanding which one is doing the trick, and which one is making the difference, is a little bit difficult. Maybe having 10% of lactobacillus that are very active and very influential is more beneficial than having 20% of another bacteria that is very passive. This is something very complex, and this is why we have to continue with research and continue to learn.


The microbiota is something very complex. It’s difficult to give a definitive answer. But, by studying the cases and trying to understand the impact of the microbiota, we can try to find a solution for some of the problems.

- Questions and Answers

I did a test, and it shows that I have an abnormal endometrial microbiome. The doctor recommended taking vaginal probiotics. Which strain of probiotics can I take? Is 10 billion okay?

The appropriate CFU (colony-forming units) count for probiotics can vary depending on the specific strain and formulation. While 10 billion CFU can be beneficial in some cases, it’s important to consult with your doctor to determine the optimal dosage for your condition. They can consider factors such as your medical history, the severity of the condition, and other individual factors to guide you in selecting the right probiotic dosage.

I live a healthy lifestyle and don’t take antibiotics. What could be causing my abnormal endometrial microbiome?

Several factors can influence the microbiota, even if you maintain a healthy lifestyle. Living in a city, previous vaginal infections, digestive problems, and the use of medications like antacids or hormone therapies can all impact the microbiota. It’s important to consider these factors and discuss them with your doctor to better understand the possible causes in your case.

How come there is still no lactobacillus in the microbiome despite taking probiotics?

The presence of lactobacillus in the microbiome can depend on various factors, including the duration of probiotic use and overall lifestyle and nutrition. It’s essential to maintain a consistent probiotic regimen for an extended period, rather than just one month, to allow for the potential repopulation of lactobacillus. Additionally, focusing on a healthy diet that supports the growth of beneficial bacteria can be beneficial.

What can be done if vaginal probiotics are no longer available due to EU regulations?

Regulatory changes can indeed affect the availability of certain vaginal probiotics. In such cases, oral probiotics can be considered as an alternative. Studies have shown that oral probiotics can still have positive effects, and they are generally more accessible. Discussing this option with your doctor can help determine the most suitable course of action based on your specific needs and circumstances. In conclusion, it’s crucial to consult with your doctor regarding strain-specific recommendations for probiotics, considering factors such as the absence of lactobacillus in the microbiome and the availability of vaginal probiotics. Your doctor can provide personalized advice and guide you in selecting the most appropriate approach to address your specific concerns.

Our doctor doesn’t know which vaginal probiotics to recommend. Are there no more probiotics available on the market?

In some places, like Spain, it can be challenging to find vaginal probiotics in pharmacies. However, they can still be purchased online. The availability may vary depending on the country and its regulations. Exploring online options might provide more choices.

What are the benefits of oral probiotics compared to vaginal probiotics?

Oral probiotics offer benefits primarily due to their ease of adherence. It is more convenient to take oral probiotics consistently over three months compared to vaginal probiotics. Additionally, studies have shown that oral probiotics can improve the adherence of lactobacillus to the epithelium better than vaginal probiotics. It’s also important to ensure a healthy mucosal environment by addressing vaginal dryness, as it can impact the effectiveness of probiotics.

How long will it take for probiotics to improve lactobacillus levels? I am starting an IVF cycle in a month.

It is advisable to start taking probiotics as soon as possible. It is better to take them and potentially lose some money rather than not take them at all. Probiotics may take varying amounts of time to show results for different individuals, but it is generally recommended to take them for an extended period to allow for potential improvement.

What kind of food should I consume to improve lactobacillus in my body?

It is important to focus on foods that are beneficial for your microbiota. Avoid processed foods with unfamiliar ingredients. Include plenty of vegetables, fruits, whole grains, legumes, and high-quality meats and fish in your diet. Being mindful of the ingredients in your food and making healthy choices can support the growth of lactobacillus and a balanced microbiota.

What tests and microbiome analysis do you recommend?

The Igenomix test is one option for microbiome testing that I have come across. However, it’s important to consult with a healthcare professional or a specialist who can guide you in selecting the most appropriate test for your specific needs.

Are there any supplements or over-the-counter oral/vaginal options available?

While there are supplements available, it is advised not to purchase and take supplements without proper guidance. It is essential to consult with a knowledgeable professional who can assess your lifestyle, sleeping patterns, dietary habits, current medications, and supplements. They can provide personalized advice and recommend suitable supplements, ensuring safety and effectiveness.

Is there any link between the microbiota and RPL?

In the second study, the woman had implantation but then had a miscarriage. So, yes, there can be a link between the microbiota and RPL. At the end of the day, our endometrium needs to be receptive and strong to accept and support the embryo.

I did ERA (Endometrial Receptivity Analysis) previously, and there were no bad bacteria detected, although the level of lactobacillus was undetectable. Would you suggest increasing the level of lactobacillus before transfer?

In such cases, it is surprising to find undetectable levels of lactobacillus. It’s recommended to consult a professional who can analyze the situation comprehensively and provide guidance on taking a good probiotic, as well as considering lifestyle factors, such as food, exercise, and stress management.

Regarding hormone therapy, specifically estrogen and progesterone, what is its effect on the microbiome?

Hormonal changes, including those caused by hormone therapy, can affect the microbiota. Stress, medication, and hormonal changes can all impact the microbiome.

Do you have dietary recommendations for vegan women?

While probiotic-rich foods like homemade soy-based yoghurt can provide some benefits, not all bacteria in probiotic foods may survive digestion. It’s suggested to continue with probiotic-rich foods but also considers taking probiotic supplements for more reliable results. Regarding anticoagulants, there doesn’t seem to be a direct relation to vaginal microbiota.

What is the impact of coffee on the microbiome? I had double antibiotics to treat H. pylori. Can I take women’s probiotic GI Nutra with 60 billion live CFU 2x daily for my FET in 2 weeks?

Yes, it’s good. It’s also important to take probiotics when treating H. pylori because antibiotics kill all bacteria, not just H. pylori. So it’s important to replenish with probiotics. About coffee, if you take heavily toasted coffee that is burnt, it’s not good because it can act as a stressor. It’s better to consume high-quality coffee that is less toasted for the benefits of antioxidants.

For how long are endometrial testing valid, and are there any risks associated with going ahead with the testing?

Every intervention has risks, and there can be some risks associated with endometrial testing, such as bleeding or prolonged pain. However, it’s not frequent. So my advice is to try other approaches before opting for testing unless there are clear indications. The tests are valid for a moment, but changes can occur depending on various factors and how your body responds. If lactobacillus levels are low and treatment is given. It depends on the case. If there’s only one last chance, retesting may not be necessary due to cost considerations. However, if there are more chances, it’s recommended to focus on implementing changes, taking probiotics, and improving diet without repeating the test.

What tests can I do to test the guts?

There are a lot of tests, the important thing is to know what you are looking for, and once you know what you’re looking for, go and take the test that will find what you look for. There are different tests in different countries. Sometimes you just need to go to a specialist who will be able to maybe narrow it down a little bit and give you some possible suggestions, and that’s how it could help.

What lubricant can you use for vagina dryness when trying to conceive? I learned most water-based ones are not good when trying to conceive.

Yes, there are lubricants made specifically for vaginal dryness when trying to conceive. Look for one that has less water content and is mostly made of other ingredients.

What oral probiotics brand and dose do you recommend to your patients?

The choice of oral probiotics brand depends on the patient and the problem. Garden of Life is a brand that has been recommended, although it’s not personally used much. Fertiliotic is a brand in Spain that has shown good results.

Can inflammation happen after an ERA test or other testing uterus?

Yes, inflammation can happen after an ERA test or other testing of the uterus. It is one of the risks associated with such procedures.

If lactobacillus is zero, how long could it take to repopulate?

The time it takes to repopulate lactobacillus depends on the person’s baseline microbiota and other factors. It’s not a straightforward answer and varies from person to person.

Is it important for my partner to take probiotics too?

Your partner needs to have a healthy lifestyle as it impacts semen quality. While there is not much evidence on the impact of probiotics on semen quality, maintaining a healthy lifestyle is crucial.

Could it be bad to take too many probiotics?

Taking too many probiotics is generally not harmful unless you have immune deficiencies or specific immune diseases. In most cases, the worst thing that can happen is that they don’t work as expected.
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Maria Navas

Maria Navas is a nutritionist located in Spain, she graduated in Human Nutrition and Dietetics. She began her journey in private practice in 2020, where she focused on improving women's habits. She soon identified a series of common problems in women. They were related to their hormonal status, which affects their mood, fatigue, weight problems, menstrual alterations, etc. She decided to train in this field to see how to improve this through nutrition and lifestyle. As a result of the Postgraduate Diploma in Clinical Nutrition, she realized that many diseases of this century go hand in hand with an alteration in the microbiota. She specialized in it through a Master's in Microbiota, Probiotics, and Prebiotics. Maria continues her work on constant training through courses, books, congresses, and experiences with her patients on a daily basis.
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Caroline Kulczycka is managing MyIVFAnswers.com and has been hosting IVFWEBINARS dedicated to patients struggling with infertility since 2020. She's highly motivated and believes that educating patients so that they can make informed decisions is essential in their IVF journey. In the past, she has been working as an International Patient Coordinator, where she was helping and directing patients on their right path. She also worked in the tourism industry, and dealt with international customers on a daily basis, including working abroad. In her free time, you’ll find her travelling, biking, learning new things, or spending time outdoors.
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