Today we are going to take a deep dive into the microbiome-endometriosis link. Although it is not often talked about, there have actually been quite a few studies on this connection. Let’s unpack all of that information so you can have a better understanding of how this can impact your own health and pathway towards healing.

Before we dig into that though, let’s talk for a moment about how we as a society are sicker than ever before. Chronic illness is on the rise. There is more autoimmune disease, diabetes, degenerative disease, and cancer than ever before. 

Symptoms like bloating, period pain, and fatigue have become so common that they are simply normalized. Most people don’t even realize that you don’t have to live like that because everyone around them is living like that too!

At the same time, our microbiomes are unhealthier than ever. We’ll dive deeper into what that means and why that is the case in a moment.

What is your gut microbiome?

If we are going to unpack the microbiome-endometriosis link, it is important to first understand what your microbiome is and how it impacts your overall health.

Your gut microbiome is composed of trillions of microorganisms. This includes bacteria, yeast, viruses, and archaea that reside right inside of your intestines. 

Fun fact: the human body actually contains over 10 times more microbial cells than human cells. 

So fun to think about, right??

I know, I know, it feels a little gross to picture trillions of bacteria roaming around in your gut, but they actually can be of huge benefit to your health. I say “can be” because it is all a matter of balance. 

In a healthy, balanced microbiome, these microorganisms are very beneficial to us. They break down foods that we otherwise wouldn’t be able to digest, they produce vitamins like K and B12. These organisms also are critical for immune health, hormone health, and metabolic health. 

Your microbiome and your immune system are constantly communicating with each other. They exchange signals about what is harmful and what is helpful in your body. This is a key element we are going to circle back to. 

This all sounds amazing! So how can my microbiome be a problem and what is the microbiome-endometriosis link?

What I described above is a healthy, picture-perfect, balanced microbiome. As you may have guessed, that is not always the case. 

Think of your microbiome like a garden. A healthy garden would be full of beautiful flowers with soil that is full of nutrients. But if that garden is not cared for, it can fill up with weeds. The weeds will begin to take over and the flowers will slowly wilt and die.

That is similar to what happens in your gut. 

When the gut microbiome gets out of balance and the pathogenic species start to take over (think of these as the “bad gut bugs” or the weeds from our garden), it can have massive impacts on our health. 

For starters, you are missing out on the benefits of the beneficial species (the “good gut bugs” or the flowers of the garden). 

These pathogenic species also will communicate with receptor cells in your gut. When the beneficial species communicate with these receptor cells, they help to identify dangers and to repair damage. When the bad guys are communicating instead, you end up with immune dysregulation, you become more susceptible to disease, and even autoimmune diseases. 

Some researchers say that up to 90% of all diseases can be linked back to the health of your gut and microbiome. That is no coincidence, my friend! 

woman planting garden

Wow that is pretty crazy! So how exactly does your microbiome get so out of balance like that?

This is an excellent question and one of the major reasons why diet and lifestyle changes can have such major impacts on your health.

For starters, there is a massive overuse of antibiotics in our culture. Don’t get me wrong, antibiotics can be life saving. There are occasions where they are absolutely necessary. But they are also way overused and each round of antibiotics helps to kill off the beautiful garden you have been growing.

Another reason is that in general, our digestive function is not what it should be. So many people have dysfunction in their digestive systems and this can lead to imbalances further down the line of your digestive tract. For example, many people are heavily deficient in stomach acid. I know, I know, we are often told the exact opposite. That’s why there are so many antacid commercials out there. But really symptoms like bloating, heartburn, indigestion…all signs of low stomach acid

This is important because stomach acid is our first line of defense against pathogens. When pathogenic bacteria or parasites or even viruses enter your digestive tract, they should be immediately killed off by your stomach acid before they are able to get in and do any damage. Not enough stomach acid? Free reign for the bad guys! It’s like not having any security at the bank.

Mind blown! What else contributes to the microbiome imbalance?

Here’s another big one: we live in an overly sanitized world. Everything we hear is all about hand sanitizer, disinfectants, and generally avoiding germs. Now I’m not telling you to stop washing your hands after you go to the bathroom (please do!). Good hygiene is still a thing.

But believe it or not, we actually need to be exposed to germs. It’s good for our health (and our microbiome!). So go play in the dirt a little. Interact with animals. Get up in other people’s space (with their full permission of course!). Your garden will thank you.

Okay and then there is our food. Most people only eat about 10 different foods. Think about it. What are your go-to foods that you eat and how often do you actually venture outside of that? 

Different foods contain different nutrients and different fibers. We need variety in order to have a healthy microbiome! Focus on fruits and veggies and get lots of colors on your plate. More colors=more variety in nutrients. Challenge yourself to have at least 3 different colors of produce on your plate in each meal!

Other impacting factors include the quality and quantity of your sleep, stress levels, and medications. 

Let’s get back to the microbiome-endometriosis link 

We have taken some time to explore the impacts of the microbiome on overall health and how your diet and lifestyle impact the health of your microbiome. 

Now let’s dive in and take a good look at how exactly this impacts endometriosis specifically. 

In a study of women with stage 3 or 4 endometriosis, they found a decreased diversity in the microbiome. They also found significant increases in specific types of bacteria, including Actinobacteria, Cyanobacteria, Saccharibacteria, Fusobacteria, and Acidobacteria. 

The increase in these particular bacteria is associated with inflammation and higher concentrations of urinary estrogen, both factors that add fuel to the fire for endo. 

I mentioned before the link between your microbiome and immune system. This is absolutely  a key element with endo. The presence of these types of pathogenic bacteria in your gut sends signals to your immune system that something is off, which causes your immune system to react. This is what we call inflammation.

When that response is happening all the time, it becomes chronic inflammation and it can spread to your entire body. That is why your symptoms may show up as period pain or fatigue rather than direct gut-related symptoms. 

There is one theory of endometriosis that proposes that everyone actually gets endometrial-like tissue outside of their uterus, but in a healthy body the immune system is able to clean it right back up. In an imbalanced body, the immune system may be so busy elsewhere that it is slacking on that job. 

Think of your immune system like an army. It only has so many troops at any given time. When they are all busy attacking one job, there may not be enough reserves for some of these other day to day tasks they should be doing.

So my microbiome is out of balance. What can I do about it?

As always, this is my very favorite part! The beautiful thing is that there is something we can do.

Typically in the Western medical world, endometriosis is treated with some type of hormone-suppressing medication and/or surgery to remove the disease. The problem is that these “solutions” are really only temporary if you are not addressing the root of the problem in the first place. 

Excision surgery can be extremely beneficial and may be necessary to find relief for some, but recurrence rate post surgery is quite high. So many women end up going in for repeat surgery after surgery.

Insert supporting your gut.

Here is how I address this with my clients: we begin by using functional testing, my faves being the GI-Map which is a comprehensive stool test that actually gives us a breakdown of exactly what is going on in your microbiome. I like to use that alongside an MRT food sensitivity test. This is a highly sensitive blood test which measures immune reactions in your blood directly to see what is causing your immune system to react.

Then I take that information to help you create a personalized gut healing protocol. This includes supplements, such as eradication agents to kill off any unwanted bacteria, yeast, or fungi, as well as biofilm disruptors to ensure the microorganisms can be killed off plus binders to ensure that everything is actually eliminated from your body and doesn’t just die off in there and make you super sick.

This is why if you are planning to go through a gut healing protocol, it is necessary to do it alongside a knowledgeable practitioner. Approaching something like this without the proper tools can actually leave you feeling sicker than ever before.

At the same time we are working through a gut healing protocol, we would also be working to support your digestive health, detoxification pathways, stress, lifestyle, and of course nutrition so that moving forward you can maintain a healthy microbiome for the long term.

Coming out the other side of the protocol, my clients experience much fewer digestive symptoms, more energy, reduced pain levels, more balanced hormones, and so much more.

This approach is so life changing and is so much less invasive than surgery after surgery after surgery!

fruits and veggies

The microbiome-endometriosis link recap:

If you were scrolling through this one (I get it!), here is a quick overview of what we talked about today:

  • In general in our society, humans are unhealthier than ever before and microbiomes are more out of balance than ever before.
  • This is due to factors like overuse of antibiotics, over-sanitization, lack of diversity in diet, lifestyle factors, medications, and more. 
  • A healthy microbiome lives in harmony with your body. It produces vitamins, helps to break down food, and communicates with your immune system.
  • An imbalanced microbiome contributes to inflammation, hormone imbalance, and many of the digestive symptoms we experience.
  • Correlations have been found in studies of women with endometriosis with diversity of the microbiome and overgrowth of certain strains of bacteria. 
  • These imbalances contribute to your endo symptoms and to the continued progression of the disease.
  • Rebalancing your microbiome using comprehensive stool testing, gut healing protocol, and nutrition can have massive impacts on your health.

Next steps for addressing the microbiome-endometriosis link

If you have struggled with endo symptoms and haven’t found relief in any other way, this well could be the holy grail for your journey. I know that it was for me and so many of my clients!

If it is time for you to move forward and find support for yourself. Locate a practitioner who specializes in gut health and endometriosis.

I do this work with clients virtually and would be more than happy to be a part of your healing journey. Click here to learn more and schedule a free strategy session today!

Much love!

endometriosis, whole woman wellness, alyssa chavez, holistic support for endometriosis

Other articles you might enjoy:

The Endo-Gut Connection

Does the Low FODMAP Diet Help Endometriosis?

Bloating from Endometriosis

Endometriosis and Gluten: What You Need to Know


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Qin, Rui; Tian, Gengren; Liu, Junbao; Cao, Lu. (2022). Microbiota and endometriosis: From pathogenesis to diagnosis and treatment. Retrieved from:

Shreiner, Andrew B.; Kao, John Y.; Young, Vincent B. (2015). The gut microbiome in health and disease. Retrieved from:

Ser, Hooi-Leng; Yong, Siu-Jung Au; Shafiee, Mohamed Nasir; Mokhtar, Norfilza Mohd; Ali, Raja Affendi Raja. (2023). Current Updates on the Role of Microbiome in Endometriosis: A Narrative Review. Retrieved from:

Svensson, Agnes; Brunkwall, Louise; Roth, Bodil; Ortho-Melander, Marju; Ohlsson, Bodil. (2021). Associations Between Endometriosis and Gut Microbiota. Retrieved from: 

Khan, Khaleque N.; Fujishita, Akira; Hiraki, Koichi; Kitajima, Michio; Nakashima, Masahiro; Fushiki, Shinji; Kitawaki, Jo. (2018). Bacterial contamination hypothesis: a new concept in endometriosis. Retrieved from:

Alyssa Chavez endo belly girl




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