Endometriosis and the Gut - the Influence of Diet, Microbiome, and Lifestyle

In conversation with Dr. Stephanie Lilja

After five years of working at MedUni Vienna in the diagnostics of rare neuromuscular diseases, Dr. Stephanie Lilja now primarily dedicates her work to women's health. In her work, she combines the pillars of nutrition, microbiome and gut health, exercise, lifestyle, and regeneration to help women – often after a long journey of suffering – return to greater well-being and hormonal balance.

The nutrition scientist, passionate athlete and holder of a doctorate degree focuses on personalised nutrition, healthy ageing, gut health and women’s health.

We had the opportunity to speak with her about endometriosis and gut health, and in this blog post, we would like to share the most important insights and connections from our conversation.

1. What role does the gut play in endometriosis?

Is there scientific evidence for a connection between the gut microbiome and symptoms?

Yes — and a very relevant one. In the body, oestrogen is eliminated, among other routes, via urine as well as through the so-called enterohepatic circulation. In this process, the hormone is first enzymatically prepared for detoxification and excretion in the liver in two steps. Part of it is then excreted via urine, while another portion enters the gut. 

This is where the microbiome comes into play: Certain gut bacteria are capable of reactivating estrogen. They produce an enzyme called β-glucuronidase, which converts the hormone, already "destined for excretion," back into an active form. This allows it to re-enter the bloodstream and go through the enterohepatic circulation again. The totality of these bacteria is called the estrobolome (or oestrobolome).

In a healthy balance – known as homeostasis – this mechanism is a normal and useful part of metabolism. However, studies show that the gut microbiome of women with endometriosis differs in its composition from that of healthy women. In particular, differences in diversity and the occurrence of estrobolome-associated bacteria have been observed. Some of these bacterial strains are suspected of being associated with endometriosis due to their increased presence.

The enterohepatic circulation describes the recurring transport of substances between the gut, liver, and bile. Certain substances are repeatedly excreted, partially reabsorbed in the gut, and transported back to the liver.

2. What misunderstandings do you frequently encounter regarding endometriosis, and where do you see the greatest need for education?

In my view, the greatest need for education arises very early on — ideally, awareness should begin with the first menstrual period.

I myself received no education as a teenager about the hormonal aspects of the female body. For my own children, however, I very much wish this to be different, which is why we speak openly at home about female hormones and related topics.

Many girls still grow up without a solid understanding of their own hormonal balance. Yet, an open, informed approach would be crucial here to develop a healthy understanding of their bodies. 

Furthermore, I see a great need for public awareness about endometriosis itself. A central misunderstanding is that severe menstrual pain is considered "normal." 

Far too often, symptoms are tolerated and trivialized for a long time because society teaches us to do so. For affected individuals, this often unnecessarily prolongs their suffering and journey of distress. However, endometriosis is a serious illness and not an oversensitivity to menstrual pain, as one unfortunately still hears. 

In addition, many people are unaware of how complex the condition can be: in endometriosis, tissue similar to the lining of the uterus (endometrial-like cells) grows not only in the pelvic area, but potentially also on other organs such as the intestines or stomach, and in rare cases even the lungs and heart.

Precisely for these reasons, early education and targeted treatment are crucial – they can significantly contribute to alleviating symptoms and substantially improving the quality of life for affected individuals.

3. Many affected individuals report digestive problems. Which gut issues are particularly common with endometriosis and why?

Digestive problems are extremely common with endometriosis – especially when inflammation, hormonal fluctuations, or endometriosis-like tissue are present in the intestinal area.

It is also typical that many symptoms overlap with those of Irritable Bowel Syndrome. This often leads to misdiagnosis for affected individuals for years.

The most common symptoms include a pronounced bloated abdomen ("endo belly"), excessive gas, abdominal cramps, as well as constipation or diarrhea – or an alternation between the two. Furthermore, many women report pain during bowel movements, a feeling of pressure in the lower abdomen, nausea, fullness, and general bowel sluggishness. It is also characteristic that symptoms often worsen around menstruation.

The causes are multifactorial: in addition to local inflammation, hormonal influences and the close connection between the gut and immune system play a central role.

4. What kind of diet do you think can help reduce inflammation in endometriosis and simultaneously support gut health?

An anti-inflammatory diet can support endometriosis on several levels: It can modulate inflammatory processes, reduce oxidative stress, strengthen the intestinal barrier, and positively influence hormonal imbalances.

It is important to note that diet cannot "cure" endometriosis, but it has the potential to significantly improve symptoms such as pain, bloating, fatigue, digestive problems, and systemic inflammation.

Focusing on plant-based, nutrient-rich foods has proven effective in practice. This includes plenty of vegetables and polyphenol-rich foods such as berries, broccoli, green leafy vegetables, and fresh herbs. High-quality omega-3 fatty acids – for example, from fatty fish, flax or chia seeds, and walnuts – also play an important role. Furthermore, fibre-rich carbohydrates like oats, legumes, or quinoa are centrally important, as they support the microbiome and contribute to the stability of the intestinal barrier.

In summary, such a diet can not only have an anti-inflammatory effect but also positively influence estrogen metabolism via the gut and liver.

5. Are there certain foods that affected individuals should avoid – and which are particularly recommended for gut and hormone balance?

Yes – many women with endometriosis benefit from consciously reducing certain foods and specifically incorporating others into their diet.

The focus here is primarily on three things: Reducing inflammation, stabilizing the gut microbiome, and supporting estrogen metabolism. This is because the gut, immune system, and hormonal system are closely interconnected.

Foods that often cause problems are primarily highly processed foods, alcohol, and high sugar consumption. Histamine-rich foods can also exacerbate symptoms in sensitive individuals. With frequent consumption, these foods can disrupt the balance of the microbiome and promote inflammatory processes in the body, which would be counterproductive. 

On the other hand, there are foods that can have a particularly beneficial effect on gut and hormone balance. These include cruciferous vegetables such as broccoli, cabbage, or arugula, which support metabolism and the enterohepatic circulation through their secondary plant compounds (bitter substances). Furthermore – as already mentioned – polyphenol-rich foods, omega-3 fatty acids, and fibre-rich diets are central. For fibre, sufficient fluid intake is important to optimally support digestion.

Caution is advised with fermented foods: Although they are generally very gut-friendly, their histamine content can initially trigger symptoms in some affected individuals. In such cases, it is advisable to work specifically with prebiotics or probiotics, which support the diversity of the microbiome and serve as food for beneficial gut bacteria.

6. How can exercise influence well-being in endometriosis – physically and also in relation to the gut?

Exercise is a central building block for symptom control in endometriosis. Physical activity and sport generally have a positive influence on inflammatory processes. At the same time, they improve blood circulation and affect hormones and estrogen metabolism – for example, through increased insulin sensitivity and an overall more favourable regulation of hormonal balance. 

Another important aspect is the effect on pain perception: Regular exercise promotes the release of endorphins, which have a pain-modulating effect and can thus positively influence subjective pain perception.

The gut also benefits significantly from physical activity. Exercise stimulates bowel movements and thus supports healthy digestive function. Furthermore, studies show that physically active people have a different composition of the gut microbiome and a higher bacterial diversity. This in turn has a positive effect on stress regulation via the gut-brain axis. 

I recommend choosing a form of exercise that feels good and, above all, is enjoyable. What matters less is the intensity and more the consistency — that it fits easily into everyday life and remains something you genuinely enjoy in the long term.

7. In your experience, which lifestyle factors — such as stress, sleep, the menstrual cycle and daily routines — have the greatest impact on gut health and endometriosis symptoms?

In endometriosis, lifestyle factors play a much larger role than many people think. The regulation of stress and the nervous system is particularly important. Chronic stress can intensify inflammatory processes in the body, increase pain sensitivity, and at the same time negatively affect gut function.

Closely linked to this is sleep quality. It is essential for regeneration and stress processing. Even a few nights of insufficient or disturbed sleep can increase cortisol levels, weaken the intestinal barrier, increase cravings and blood sugar fluctuations, and generally promote inflammatory processes in the body.

Another important factor is the menstrual cycle itself. Many affected individuals report that symptoms change depending on the cycle. Around menstruation, there are often increased inflammatory reactions, water retention, cramps, and increased fatigue.

This leads to a central approach: instead of wanting to "function the same way" constantly in everyday life, it can be helpful to adapt nutrition, exercise, and regeneration more to the cycle and to grant the body different needs in phases.

By the way, have you heard about our Women’s Balance Bundle? It includes a microbiome test, three packs of the premium prebiotic myBioma Balance, and an exclusive e-book on cycle-based nutrition. You can find more information here: Women's Balance Bundle

8. From a nutritional science perspective, where do you see the biggest leverage points in everyday life when it comes to endometriosis?

The most important lever is still education about the disease itself. Still too few people know what endometriosis means and what far-reaching effects it has on the body. That needs to change; there is a clear societal need for improvement here.

Equally important is to provide individual advice and support to affected individuals. Every body is different, every month in a woman's world can look and be experienced differently hormonally, as so many processes play a role simultaneously. Factors such as chronic inflammation, oxidative stress, hormone metabolism, gut health, blood sugar regulation, and the nervous system intertwine and influence each other.

Therefore, I see the most important levers in everyday life primarily in the reduction of inflammatory processes. Many affected individuals benefit from an anti-inflammatory diet and lifestyle that specifically addresses this aspect.

Another central lever is gut health. The gut plays a key role in immune function and inflammation regulation, even in estrogen metabolism. Targeted support for gut health and the microbiome is therefore important for estrogen metabolism. This can positively influence hormonal balance and overall well-being.

9. What three practical tips would you give to affected individuals to improve gut health, inflammation levels, and well-being in the long term?

Basically, anything that feels good is allowed.

From a scientific perspective, the focus is quite clear:

1. Balanced, anti-inflammatory diet combined with a healthy lifestyle. This forms the basis for stable gut function, a balanced immune response, and an improved inflammatory profile.
2. Sleep and regeneration. Good sleep quality is essential for hormonal balance, stress regulation, and the recovery of the entire organism – and thus also for long-term symptom control.
3. Self-love or self-awareness and self-care. A diary can help identify individual triggers and better understand one's own body.

Equally important is the realization: You don't have to manage the disease alone.

Take symptoms seriously and seek help early if you suspect you have endometriosis. Confide in someone and contact medical or therapeutic facilities. 

Endometriosis affects many women – an estimated one in ten – although the actual number is likely higher because symptoms can be so varied. It is all the more important to talk openly about it, share experiences, and give affected individuals a voice.

10. Last but not least: What does gut health mean to you?

For me, gut health means living in symbiosis with my own microbiome and working with my body, not against it.

Our gut microbiome influences digestion, the immune system, inflammation, hormones, mood, and even our energy levels in everyday life. If this finely tuned system gets out of balance, it can affect the entire body.

Therefore, gut health means much more than just "not having symptoms"; it means creating a stable internal environment – a balance in which humans and the microbiome exist in a mutually supportive relationship.

If you'd like to learn more about the topic of "estrogen and the estrobolome," we recommend this in-depth blog article: Women's Health and Gut Health: Connections Explained.

And if you want to know about the balance of your gut microbiome, we recommend the myBioma Microbiome Tests.

Carina Gurtner BSc, BA

Nutritionist

As a nutritionist and media & communication scientist, Carina uses her expertise to communicate complex health topics in an understandable way. Her aim is to inspire others to lead a conscious, healthy and sustainable lifestyle.

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