The Gut-Estrogen Connection, Restrictive Diets

Welcome to Healthy Gut Healthy Thyroid!

This is your weekly roundup of the BEST actionable steps for those people with thyroid and autoimmune thyroid conditions who want to restore their health…by healing their gut. Whether you have hyperthyroidism or Hashimoto’s you will benefit from the content in this newsletter.

In today's issue:

• Announcement: Free 5-Day Accelerated Thyroid Healing Challenge

• Main Topic: The Gut-Estrogen Connection

• Podcast Review: Can you still save your thyroid?

• Understand Your Tests: Markers Related to Estrogen Metabolism

• Ask Dr. Eric: Can restrictive diets harm the gut microbiome?

The Gut-Estrogen Connection

Estrogen is a critical hormone for overall health—not only for reproductive function, but also for immune regulation, brain function, and gut integrity. While both women and men require healthy levels of endogenous estrogens, imbalances can lead to a variety of health challenges, particularly when the gut microbiome is compromised.

Why Estrogen Balance Matters

Low estrogen levels are associated with negative outcomes in immune and cognitive function, gut health, and fertility.^1,2 On the other hand, excess or poorly metabolized estrogen—whether from internal production or external exposure—can increase the risk of hormone-related conditions such as breast cancer, endometriosis, and thyroid nodules.

Synthetic estrogens from oral contraceptives and xenoestrogens from plastics, cosmetics, and household products further compound the issue.

The Gut Microbiome and Estrogen Metabolism

The gut plays a surprisingly significant role in regulating estrogen through a group of bacterial genes called the estrobolome. The estrobolome encodes enzymes—particularly Beta-glucuronidase—that help to deconjugate estrogen, and I’ll discuss this more in the Understand Your Tests section below.

This reactivation process must be tightly regulated. If β-glucuronidase activity is too high due to dysbiosis (imbalance of the gut flora) or poor gut function, excess estrogen may recirculate, potentially leading to estrogen dominance or related health conditions.

Research shows that disruptions to the gut microbiota and estrobolome function are linked to estrogen-related disorders, including:³

• Breast and endometrial cancer

• Polycystic ovarian syndrome (PCOS)

• Fibroids and endometriosis

• Thyroid nodules

What is Estrogen Dominance?

Estrogen dominance refers to an excess or relative excess of estrogen, either due to:

• Elevated estrogen levels

• Low progesterone

• Impaired estrogen metabolism

So you don’t need high estrogen levels to be estrogen dominant—imbalances in how your body processes estrogen or a drop in progesterone are still considered to be forms of estrogen dominance.

Common Signs and Symptoms of Estrogen Dominance⁴

✔️Irregular or heavy periods

✔️Painful menstruation

✔️Breast tenderness

✔️Mood swings

✔️Bloating

✔️Fatigue

✔️Uterine fibroids

✔️Weight gain (especially around hips and thighs)

✔️Thyroid nodules

How to Test for Estrogen Dominance

When a patient presents with symptoms of estrogen dominance—or a history of fibroids, endometriosis, or thyroid nodules—I often recommend a DUTCH test to assess estrogen levels and metabolism.

Markers evaluated include:

• Estradiol (E2), Estrone (E1), and Estriol (E3)

• 2-OH, 4-OH, and 16-OH estrogen metabolites

• Methylation capacity via 2-Methoxyestrone

A comprehensive stool panel can also be useful, especially if we suspect poor gut health or elevated β-glucuronidase levels.

How to Address Estrogen Dominance

To address estrogen dominance, it’s essential to both optimize estrogen metabolism and improve gut health:

✅ Eat foods that support estrogen detoxification:

Cruciferous vegetables (e.g., broccoli, broccoli sprouts, cauliflower, kale)

Flaxseeds and chia seeds

High-fiber foods to promote regular elimination

✅ Support the gut microbiome:

Eat fermented foods like sauerkraut

Take probiotic and prebiotic supplements

Avoid processed foods and excessive sugar

✅ Take supportive supplements:

DIM (Diindolylmethane) for healthy estrogen metabolism (as long as estrogen levels aren't too low)

Calcium-D-glucarate to lower β-glucuronidase

Methylated B vitamins to support estrogen metabolism

Magnesium and liver-support herbs (e.g., milk thistle)

✅ Reduce xenoestrogen exposure:

Choose glass or stainless steel over plastic

Use clean skincare and household products

Filter your drinking and shower water

✅ Consider advanced testing:

Comprehensive stool analysis

SIBO testing if bloating and gas are present

Hormone panels beyond the DUTCH test if warranted

Conclusion

Estrogen imbalances are more than a hormonal issue—they’re often a gut issue too. The gut microbiome directly affects how estrogen is metabolized and cleared, and when the microbiome is out of balance, symptoms of estrogen dominance can emerge—even if estrogen levels appear “normal.”

By supporting gut health, reducing toxic exposures, and improving estrogen detox pathways, you can restore balance and reduce your risk of estrogen-related conditions.

Free 5-Day Accelerated Thyroid Healing Challenge

If you have a thyroid or autoimmune thyroid condition and have restored your health through dietary changes alone...then this challenge probably IS NOT for you.

While some people receive excellent results with making changes to their diet, the truth is that eating well alone usually isn't sufficient to restore your thyroid and immune system health.

Don't get me wrong, as eating well is important, and a small percentage of people are able to restore their thyroid and immune system health by eliminating gluten and other common food allergens.

But this isn't the case with most people who have a thyroid or autoimmune thyroid condition, which is why I decided to put together this challenge.

Healthy Immune System = Healthy Thyroid Gland?

Even though the challenge is entitled the "Accelerated Thyroid Healing Challenge", most people with thyroid conditions have Graves' disease or Hashimoto's (and sometimes they have the antibodies to both). While this challenge can also benefit people with non-autoimmune thyroid conditions, for those with thyroid autoimmunity, having a healthy immune system is important to achieve optimal thyroid health.

Click Here to register for the free 5-day challenge

During this 5-day challenge you will…

• Learn how to overcome both common and overlooked "roadblocks" that are preventing your thyroid/immune system from healing

• Discover how to reduce your "toxic thyroid"

• ​Find out why removing the trigger doesn't always break the chronic inflammatory cycle associated with Graves' disease and Hashimoto's, and what you can do to stop this cycle

• ​Discover some of the "hidden" thyroid triggers

• ​Create your thyroid/immune healing action plan

Click Here to register for the free 5-day challenge

Save My Thyroid Podcast Review

I have a podcast called "Save My Thyroid", where I discuss how people with hyperthyroidism and Hashimoto's can save their thyroid and regain their health. And during each edition of this newsletter I'll briefly discuss a recent podcast episode.

In a recent Q & A podcast episode I answered the question “Is it too late to save my thyroid?” Many don’t realize how much healing can happen by addressing autoimmune triggers and restoring gut health. Surgery and radioactive iodine aren’t the only options for hyperthyroidism, and those with Hashimoto’s can save their thyroid as well. Natural approaches can help protect your thyroid and even reduce the need for hormone replacement over time. This episode breaks down what really matters when it comes to saving your thyroid and gives practical steps you can take today.

Understand Your Tests

Markers Related to Estrogen Metabolism

There are several ways to evaluate estrogen metabolism, with the most direct method being the assessment of estrogen metabolites via dried urine testing. The DUTCH test is the most widely used tool for this purpose. It measures key estrogen metabolites, including:

2-Hydroxyestrone (2-OH)

4-Hydroxyestrone (4-OH)

16α-Hydroxyestrone (16-OH)

Interpreting Estrogen Metabolites

Ideally, 2-OH should be the most predominant metabolite, as it is considered the “cleanest” estrogen detoxification pathway. Elevated levels of 4-OH (Patient Test #1) or 16-OH metabolites (Patient Test #2) can be problematic, as these pathways are associated with increased oxidative stress and potential estrogen-related health risks.

If either the 4-OH or 16-OH metabolites are elevated, it is important to support estrogen metabolism through dietary and lifestyle strategies—such as increasing cruciferous vegetables, taking DIM (diindolylmethane), and reducing xenoestrogen exposure—as outlined in the main section.

Beta-Glucuronidase: An Indirect Marker

Another important, though indirect, marker of estrogen metabolism is Beta-glucuronidase (Patient Test #3), which I briefly mentioned earlier. This enzyme is measured on certain comprehensive stool panels, including the GI-MAP and GI Effects tests.

Elevated beta-glucuronidase activity may indicate intestinal dysbiosis, or an imbalance in the gut microbiota. High levels of this enzyme can impair the glucuronidation pathway, which is responsible for the detoxification and elimination of estrogens. When beta-glucuronidase is elevated, it can lead to the reabsorption of estrogen, increasing the risk of estrogen dominance and related symptoms or conditions.

Ask Dr. Eric

During every issue I'll answer a question or two that I think can benefit most people with a thyroid or autoimmune thyroid condition. If you'd like for me to consider your question for a future edition of this newsletter email your question to [email protected].

QUESTION: CAN RESTRICTIVE DIETS HARM THE GUT MICROBIOME?

Dr. Eric, is it true that a restrictive diet such as AIP can be harmful to the gut microbiome?

Thanks for your question! Restrictive diets have become increasingly popular, particularly among those seeking relief from autoimmune conditions and chronic digestive issues. Some common examples include the ketogenic diet, carnivore diet, and even the Autoimmune Paleo (AIP) diet.

Many of my patients follow a strict AIP diet. While this excludes a number of foods, it still allows for a wide variety of nutrient-dense fruits and vegetables, which can have a positive impact on the gut microbiome. In contrast, diets that lack diversity in plant-based foods—such as the carnivore diet—may pose concerns regarding long-term gut health.

Short-Term Benefits vs. Long-Term Risks

There’s no question that some individuals with autoimmune conditions such as Graves' disease or Hashimoto's report short-term improvement on restrictive diets. For example, those following a carnivore diet may experience reduced bloating, fewer food sensitivities, and improved energy. However, the long-term effects on the gut microbiome remain unclear, largely due to the limited research in this area.

One of the major concerns with highly restrictive diets is the lack of dietary fiber and polyphenols, which serve as fuel for beneficial gut bacteria. A lack of these substrates can lead to reduced microbial diversity and potentially weaken gut resilience over time.

The low FODMAP diet is another example. While it is effective for managing symptoms of small intestinal bacterial overgrowth (SIBO), it should ideally be followed for no more than a few months in order to avoid negative effects on the microbiome.

Duration and Diversity Matter

The impact of any restrictive diet on the gut microbiome often comes down to how long it's followed and the diversity of foods still included. In the case of the AIP diet, I typically recommend following it for about 90 days, especially in those with autoimmune thyroid conditions. However, if someone is consuming a wide variety of AIP-compliant fruits and vegetables, it’s possible to extend the diet safely for longer without significant negative effects on the microbiome.

Additional Thyroid-Related Resources

Click Here for Is It Too Late to Save My Thyroid?

Click Here to access hundreds of thyroid-related articles and blog posts

Click Here to join the Graves’ disease and Hashimoto’s community

Click Here to purchase one of Dr. Eric’s thyroid-related books

Click Here to work with Dr. Eric and his team

References:

Click Here to access the references

That’s a wrap