Dr. Paul Deglmann
Meghan Feir Walker
While everyone knows that the gut is responsible for digesting food, the gut does so much more in the body and plays a vital role in regulating hormones. In this article, we’ll be explaining how gut health and hormones are connected and how you can better regulate your hormones by taking care of your digestive health.
The liver-gut-hormone connection
To understand how gut health and hormones are connected, you first need to understand the connection between your liver and your gut.
After the liver metabolizes excess hormones into a water-soluble form, the gut helps eliminate them. The hormones are excreted into the gut via the bile (made in the liver) and then eliminated through the stool. This is a crucial process because if these excess hormones and metabolites get recirculated in the body, this can lead to hormonal imbalances, toxicity, and other problems.
Hormonal imbalances and toxicity can lead to significant symptoms during menstruation, pregnancy, postpartum, and menopause. Some of these symptoms may include bloating, mood changes, fatigue, pain, and many other intense symptoms.
How the gut and hormones are connected
Certain nutrients are vital for the endocrine system to produce and regulate hormones.
To create hormones, your body needs macronutrients, such as fats and proteins, and vitamins and minerals are absolutely necessary for the processes that hormones need to go through.
In order for your hormones to get these nutrients, your gut must help break down food so you have access to the food’s micronutrients. These micronutrients are then absorbed through the small intestine.
The gut microbiome’s role in hormone metabolism
The state of your gut’s microbiome is also incredibly important in hormone health.
The healthy beneficial bacteria in the microbiome help regulate estrogen levels, assist the body in converting T4 (the inactive form of thyroid hormone) into T3 (our active form of thyroid hormone), and can also impact other hormones such as cortisol and insulin.
Hormones also influence the gut
Estrogen is more immune-stimulating, and progesterone is more immune-suppressive.
Estrogen levels are the highest in the first half of the menstrual cycle (the follicular phase). During this time, the right amount of estrogen promotes integrity within the intestinal barrier/gut wall.
Progesterone is most prevalent during the second half of the menstrual cycle (the luteal phase). Progesterone naturally slows down motility, which can make some women more prone to constipation and bloating in this phase of the cycle. Progesterone can also cause changes within the microbiome.
With the sudden drop in hormones at the onset of menses, it’s normal to have a brief increase in intestinal permeability or leaky gut, so paying special attention to what you eat during this time can help or harm your gut.
The gut-hormone feedback loop
The body is interconnected. Different areas are not siloed from the other parts of the body, and what’s occurring in one area can affect so many others.
Changes in the microbiome can impact hormones, and changes in hormones can impact gut health. If your gut health is poor, then it will likely contribute to hormonal balance. If hormones are not balanced, it will likely impact your microbiome and gut health negatively.
Signs of hormonal imbalance that may be linked to gut health
Physical and emotional signs to watch for
- Persistent bloating or constipation
- Acne or skin flare-ups
- Irregular menstrual cycles
- PMS symptoms or mood swings
- Poor sleep
- Blood sugar swings
- Unexplained fatigue or brain fog
- Weight gain, especially around the midsection
- And more

What these signs may indicate
These symptoms may be warning signs that your gut health and hormones aren’t functioning properly, especially when multiple symptoms are affecting you.
How gut imbalances can disrupt hormonal health
Inflammation and increased intestinal permeability ("leaky gut")
Inflammation in the gut can exacerbate leaky gut, allowing microbes and toxins, like endotoxins from bacteria, to enter the bloodstream and disrupt hormonal signaling. This can promote estrogen dominance and/or high cortisol levels.
Nutrient absorption and hormonal production
When gut inflammation is present, it also compromises the gut lining, which then negatively impacts your body’s ability to absorb key nutrients into the bloodstream, such as zinc, magnesium, B vitamins, and many others that are essential for building and regulating hormones.
Without these nutrients at optimal levels, this can promote hormonal imbalance or hormonal deficiencies.
Microbial overgrowth and estrogen recycling
If certain bacteria become overgrown in the gut, an overproduction of an enzyme called β-glucuronidase can occur. This enzyme can then negatively impact the body’s ability to detoxify and eliminate estrogen.
When this enzyme is elevated, the estrogens get recirculated instead of being eliminated, which can contribute to estrogen dominance and hormonal imbalance.
How to test your gut and hormone health
Common gut-related functional tests
At RHS, we may use various tests to get a better picture of what’s happening in your gut.
Common gut-related functional tests we use include:
- Stool testing, which looks at the levels of beneficial bacteria, H. Pylori, opportunistic/overgrowth bacteria, yeast/Candida, and parasites, along with intestinal health markers like fat in the stool, digestive enzyme production (elastase-1), and immune/inflammatory markers.
- The Organic Acids Test (OAT), which looks at metabolites in the urine that can be more sensitive for catching yeast/candida overgrowth. It also takes a thorough look at bacterial metabolites, including metabolites that come from clostridia species. The OAT also has a few markers that look at detoxification and mitochondrial function.
For more information on gut testing, click here.
Hormonal testing options
Hormone testing is a matter of preference for many practitioners. Some practitioners love testing hormones in the blood, while others prefer testing hormones through saliva. Others yet prefer using tests like the DUTCH hormone tests, which measure hormones in the urine.
At RHS, we predominantly like to test hormones through the urine using DUTCH tests, but we also test the blood for certain hormone levels. Some hormones can only be tested in the blood, and some hormone levels seem to be more accurately represented in the blood.
The hormone tests we use measure DHEA, pregnenolone, estrogens (estrone, estradiol, estriol), progesterone, testosterone, cortisol, melatonin, and other hormone levels, along with conducting a full thyroid panel.
Why combined testing is often useful
I can’t stress enough how important it is to look at both gut/microbiome testing and hormone testing. You need to test them all to get a more complete picture of your gut and hormone health. This can help us understand how your gut health and hormone health are playing off each other.
We want to restore balance to your body, and to do so, we need thorough testing.
How to reset your gut and hormones naturally
Focus on gut-nourishing nutrition
To support your gut health and skin, it’s important to get the right nutrients every day through your diet.
- Eat prebiotic-rich foods (onions, garlic, bananas, asparagus)
- Add fermented foods (sauerkraut, kimchi, kefir)
- Avoid processed sugars and inflammatory oils
- Try to choose organic vegetables and fruit when possible
- Opt for organic, grass-fed, pasture-raised meat and wild-caught fish when possible
- Stay hydrated with clean, filtered water to support detoxification
Lifestyle support for hormone balance
Having a healthy body requires practicing good habits regularly.
Helpful lifestyle tips:
- Sleep hygiene: Optimize your sleep by avoiding blue light 2-3 hours before bed, going to bed by 10 p.m., and getting between 7-9 hours of good, restful sleep.
- Morning sunlight: Try to step outside after you get up to get exposure to the sun’s red light. This can help balance and support gut and hormonal rhythms.
- Hydration: Drink plenty of water and consider adding electrolytes to your morning glass of water to optimize cell hydration throughout the day.
- Diet: Try to eat anti-inflammatory foods and beverages, avoid foods that promote inflammation, and practice mindful eating. Take time when you’re eating. Don’t eat on the run, and remember to chew your food thoroughly (20-30 bites of food before swallowing).
- Relaxation: Practice deep breathing exercises, meditate and/or pray, and relax with activities and hobbies you enjoy.

Supporting hormone elimination via the gut
In order to remove excess hormones and toxins from your body, you must be able to have regular bowel movements.
*To support microbiome health, your daily diet should include:
- Fiber
- Prebiotics
- Probiotics
- Fermented foods
*While high-fiber, probiotic-rich, prebiotic-rich, and fermented foods support microbiome health for many people, other patients, especially those with SIBO and MCAS/histamine issues, typically can’t tolerate high-fiber, fermented, and probiotic-rich foods well. This is why it’s important to test and consult with a functional medicine practitioner who can determine if these foods will help or negatively impact your condition further.
For more tips on resetting your gut, click here.

When gut-hormone balance matters most
Balancing your gut and hormones is necessary for good health at any stage of life. Whether you are just starting your menstrual cycle, are perimenopausal, have just reached menopause, or are 20 years post-menopausal, the gut-hormone balance is always important at each and every stage.
Postpartum and early motherhood
After giving birth, hormone levels rapidly shift, which can greatly change your gut microbiome. This can influence mood, immunity, and recovery. It’s important to keep this in mind and support yourself with a healthy diet, as much rest as is possible with a newborn, and getting the help you need from your functional medicine practitioner. You may need help readjusting hormone levels as you recover.
Perimenopause and menopause
During perimenopause and menopause, the drastic hormone changes can also affect gut diversity and estrogen metabolism. This can also contribute to new digestive or mood symptoms. Once again, we recommend getting tested and finding the support and strategies you need from your functional medicine practitioner.
Stressful or high-demand seasons
Chronic stress affects both the gut lining and cortisol regulation. This is especially important for women who are balancing careers, caregiving, and more to keep in mind. While life doesn’t always go as planned, try to incorporate some stress-management practices alongside your busy life. Consider breathwork, prayer/meditation, exercise, eating healthy, and our other recommended lifestyle tips.
Key points on restoring gut and hormone health
Gut health is a powerful foundation for hormonal balance, and both can influence each other. Improving digestion and microbiome diversity can positively impact energy, mood, skin, and menstrual cycles.
Support your gut and hormone health with these key takeaways:
- For hormones to get the nutrients they need to function, you need your gut to help break down food so you have access to the food’s micronutrients. These micronutrients are then absorbed through the small intestine.
- The healthy beneficial bacteria in the microbiome can actually help regulate estrogen levels, help the body convert T4 (the inactive form of thyroid hormone) into T3 (the active form of thyroid hormone), and can also impact other hormones such as cortisol and insulin.
- Estrogen is more immune-stimulating, and progesterone is more immune-suppressive.
- When estrogen is most prevalent in the first half of the menstrual cycle (the follicular phase), the right amount of estrogen promotes integrity within the intestinal barrier/gut wall.
- When progesterone is most prevalent during the second half of the menstrual cycle (the luteal phase), progesterone naturally slows down motility, making some women more prone to constipation and bloating.
- Changes in the microbiome can impact hormones, and changes in hormones can affect gut health.
- Signs that may indicate gut health and hormones aren’t functioning properly include:
- Persistent bloating or constipation
- Acne or skin flare-ups
- Irregular menstrual cycles
- PMS symptoms or mood swings
- Poor sleep
- Blood sugar swings
- Unexplained fatigue or brain fog
- Weight gain, especially around the midsection
- And more
- At RHS, we often use OAT and stool tests to see what’s happening in the gut.
- Different lifestyle choices can support your gut and hormone health, including eating an anti-inflammatory diet, getting good sleep, exposing yourself to morning red light from the sun, moving and exercising every day, and being intentional about stress management and relaxation.
- At different points in females’ lives, special care needs to be paid to balancing hormones.
How Restorative Health Solutions can help with gut and hormone balance
At RHS, we take into account your history and symptoms, along with following the “Test, don’t guess” approach.
When it comes to gut and hormones, we test both areas thoroughly by doing a comprehensive stool test and OAT for gut testing and hormone testing through urine and blood. Outside of these tests, we also consider food allergy/food sensitivity testing, toxin overload testing, nutritional deficiencies testing, and more.
After the results are in, we combine your history with your test results and put together a personalized protocol for you that includes dietary modifications, lifestyle adjustments, and an individualized supplement protocol based on the test results and your history. This is a very one-size-fits-one protocol, and this is where working with an experienced functional medicine practitioner can make all the difference.
Ready to support your gut and hormones? We can help
By learning more about your digestive and hormone health and the reasons they became imbalanced, you can take proactive steps toward enhancing your whole-body health and overall quality of life.
Are you ready to improve your gut and hormone health? Read more on our blog about gut health, or schedule your free 15-minute consultation with Dr. Paul to explore a personalized, functional approach for a helpful and effective path to recovery.
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