Thyroid-Friendly Foods That Nourish the Gut Microbiome Part 1

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:

• Main Topic: Thyroid-Friendly Foods That Nourish the Gut Microbiome Part 1

• Podcast Review: Stop Believing this Hair Loss Myth

• Ask Dr. Eric: Why does my gut retest results look worse?

Thyroid-Friendly Foods That Nourish The Gut Microbiome Part 1

I’m not shy about recommending nutritional supplements and herbs to my patients, and when I dealt with Graves’ disease in 2008–2009 I also took numerous supplements. But you also want to do as much as you can through the food you eat.

So I decided to write an article where I discuss some of the foods you can eat that are “thyroid-friendly” and at the same time will improve the health of your gut microbiome. I realize that everyone is different, and so if for any reason you currently can’t tolerate any of these foods, then of course focus on the foods you are able to eat.

This will be a two-part article, as this article will focus on the health benefits and thyroid-related controversy surround cruciferous vegetables. And then in the next edition I’ll discuss other thyroid-friendly foods that can benefit the gut microbiome.

Cruciferous Vegetables (Broccoli, Kale, Brussels Sprouts)

I’m intentionally starting with one of the most controversial foods with regards to thyroid health. Cruciferous vegetables are often labeled as “goitrogenic,” meaning (in theory) that they can interfere with thyroid function.

Traditional concerns focus on compounds like glucosinolates, which can theoretically interfere with iodine uptake. In real-world dietary patterns, however, these foods rarely cause clinically significant decreases in thyroid hormones when consumed at typical dietary levels—especially once they’re cooked (which reduces the goitrogenic potential).

The main concern has historically been for those with hypothyroidism and Hashimoto’s—because if someone already has low or suboptimal thyroid hormones, it wouldn’t seem ideal to eat a food that might further decrease them. But for most people, crucifers are safe and beneficial.

My Experiment with Raw Broccoli

I work with many patients with hyperthyroidism, and not everyone chooses—or is able—to take antithyroid medication. This is especially true for pregnant women with hyperthyroidism, as many understandably prefer not to take medication.

Many years ago, I recommended that my pregnant hyperthyroid patients who didn’t want antithyroid medication try large amounts of raw cruciferous vegetables (mainly broccoli) to see whether this could lower their thyroid hormones. Unfortunately, it did not work.

And so this serves as further proof that eating normal amounts of cruciferous vegetables usually won't negatively affect thyroid function…even when they’re raw. While over the years a few patients have told me they experienced thyroid swelling upon consuming cruciferous vegetables, this isn’t common.

Raw vs. Cooked Cruciferous Vegetables

While I think it’s fine for most people with a thyroid or autoimmune thyroid condition to eat a few servings of raw cruciferous vegetables per day, if you’re concerned then you can always cook them. Even lightly steaming broccoli will reduce its “goitrogenic properties,” making it less likely—if any—to interfere with thyroid function.

Once again, if you have hyperthyroidism then you should have zero fear of eating raw or cooked cruciferous vegetables with regard to thyroid impact. But even if you have hypothyroidism or Hashimoto’s, you shouldn’t completely cut them out unless you have a true intolerance.

Cruciferous Vegetables Nourish Your Gut

Cruciferous vegetables are not only safe for most people with thyroid conditions—they’re nutrient-dense powerhouses with research-backed benefits for the gut microbiome and overall health.

Gut Microbiome Benefits

✔ They Alter Gut Microbial Composition. In controlled feeding studies, consuming cruciferous vegetables like broccoli (e.g., 200 g/day) significantly changed the structure of adults’ gastrointestinal microbiota, especially increasing beneficial Bacteroidetes populations, which are associated with positive metabolic and immune effects.¹

✔ They Modulate Microbial Metabolism of Bioactive Compounds. Cruciferous vegetable compounds such as glucosinolates aren’t fully digested in the upper gut. Instead, gut bacteria metabolize them into bioactive isothiocyanates (e.g., sulforaphane) and indoles—which have anti-inflammatory properties—and influence host physiology.²

✔ They May Enhance Production of Anti-Inflammatory Metabolites. Emerging research indicates that microbial processing of cruciferous compounds contributes to the production of metabolites that can support gut and systemic inflammation control.³

✔ They Support Prebiotic Activity. The fiber in cruciferous vegetables serves as prebiotic fuel for beneficial bacteria. As gut microbes ferment this fiber, they produce short-chain fatty acids (SCFAs) and other compounds that help maintain intestinal health and immune balance.⁴

✔ They May Influence Gut Barrier Functions. Animal and ex vivo research suggests that cruciferous intake can help support gut barrier integrity—an essential factor in maintaining healthy immune function and reducing systemic inflammation.⁵

How Broccoli Helps With Estrogen Metabolism

Cruciferous vegetables like broccoli don’t just support gut health — they also help the body break down and balance estrogen more effectively. This is largely due to glucosinolates, which are converted into beneficial compounds when broccoli is chopped, chewed, or digested.

Two of the most important compounds formed are indole-3-carbinol (I3C) and diindolylmethane (DIM). These compounds have been well-studied for their role in supporting healthy estrogen metabolism.⁶

Helping the Body Favor “Safer” Estrogen Pathways

Estrogen doesn’t exist in just one form. After it’s produced, the body breaks it down into different estrogen metabolites, some of which are more biologically active than others.

Research shows that compounds found in broccoli and other cruciferous vegetables can help shift estrogen metabolism toward pathways that are generally considered more favorable. Specifically, studies have shown an increase in the ratio of 2-hydroxyestrone (2-OHE1) to 16α-hydroxyestrone (16α-OHE1).

This matters because:

2-OHE1 is a weaker, less estrogenic metabolite

16α-OHE1 is more strongly estrogenic and has been associated with greater biological activity

By encouraging the body to produce more 2-OHE1 and less 16α-OHE1, broccoli may help promote a more balanced estrogen profile.⁷

What About 4-OHE1?

Another estrogen metabolite worth mentioning is 4-hydroxyestrone (4-OHE1). Unlike 2-OHE1, 4-OHE1 is considered more reactive, meaning it can be more stressful to cells when present in higher amounts.

Estrogen metabolism plays a key role here as well. Compounds found in broccoli help influence the enzymes that control how estrogen is broken down, reducing the likelihood that estrogen will follow pathways that lead to higher levels of reactive metabolites like 4-OHE1.

How I3C and DIM Support Estrogen Processing

The reason broccoli has these effects comes down to how I3C and DIM interact with the body’s detoxification systems.

These compounds influence enzymes involved in estrogen metabolism — particularly cytochrome P450 enzymes and phase II detoxification pathways. As a result, the body is encouraged to convert estrogen into its 2-hydroxylated (less estrogenic) forms, while also supporting the detoxification of more reactive metabolites.⁸

Research has shown that I3C, which comes from cruciferous vegetables, can predictably shift estrogen metabolism. It increases the production of 2-OHE1 and may reduce the formation of more proliferative metabolites such as 16α-OHE1.⁹

DIM, which is formed from I3C in the stomach, has also been studied in humans. Research suggests that DIM can help lower levels of both 16α-OHE1 and 4-OHE1, further supporting balanced estrogen metabolism.¹⁰

Why This Matters for Hormone-Related Health

Eating normal servings of broccoli isn’t a treatment, but population studies show that people who regularly eat cruciferous vegetables tend to have a lower risk of hormone-related cancers, such as breast cancer. These benefits are believed to be partly related to how cruciferous vegetables influence estrogen metabolism.¹¹

The Gut–Estrogen Connection

Estrogen metabolism isn’t influenced by diet alone — the gut microbiome also plays an important role. I actually discussed this in a previous newsletter, but will actually expand upon the information here.

Gut bacteria help regulate estrogen levels through processes such as:

Recycling estrogen via enterohepatic circulation

Modifying estrogen activity using enzymes like β-glucuronidase

Emerging research highlights this gut–estrogen axis, showing that a healthy gut microbiome helps keep estrogen levels and metabolites in balance.¹² Because broccoli supports both gut health and estrogen metabolism, its benefits may work together to support overall hormone balance.

How Sulforaphane Fits Into Estrogen Metabolism

Sulforaphane is another powerful compound found in broccoli — especially broccoli sprouts — but it works through a different mechanism than I3C and DIM.

I3C & DIM → mainly influence how estrogen is broken down (Phase I metabolism: 2-OHE1, 4-OHE1, 16α-OHE1)

Sulforaphane → mainly supports how estrogen metabolites are neutralized and eliminated (Phase II detoxification)

So instead of changing which estrogen metabolites are made, sulforaphane helps the body safely process and clear them.

Other Health Benefits of Cruciferous Vegetables

✔ Rich in Fiber & Nutrients. Crucifers are high in both soluble and insoluble fiber, vitamins C and K, and minerals—critical for digestion, regularity, and overall nutritional status.13

✔ Bioactive Phytochemicals with Protective Effects. Compounds like sulforaphane have been studied for anti-oxidative and cellular protective effects, including lowering inflammation and potentially reducing disease risk.14

Cruciferous Veggies and Intestinal Symptoms

Even though cruciferous vegetables offer profound health benefits, some people can’t tolerate them. There can be numerous reasons for this, and while some individuals can eat small amounts of broccoli and other crucifers without digestive symptoms, others may be sensitive even in small doses.

Certain cruciferous vegetables (e.g., broccoli, cauliflower) are considered higher-FODMAP foods, meaning they may cause gas or bloating for people with small intestinal bacterial overgrowth (SIBO) or some other digestive issues. If you’re unable to tolerate high-FODMAP crucifers, opt for lower-FODMAP options like kale or bok choy—or try smaller portions (e.g., ¼ cup steamed vs. ½ cup). Adjust based on your comfort and digestive response.

Next Edition

In the next edition of this newsletter I’ll discuss some of the other thyroid-friendly foods that can be beneficial to the gut microbiome—plus practical ways to include them on your plate.

Not All Gut Healing Supplements Are The Same

Since most of the immune cells are located in the gut, a healthy gut is essential for a healthy immune system. In fact, Hippocrates himself said that “all disease begins in the gut”. And so whether someone has Graves’ disease, Hashimoto’s thyroiditis, or another health condition, having a healthy gut is important to achieve optimal health.

When choosing a gut healing supplement you want one that does the following:

• Promotes optimal function of the GI lining

• Rejuvenates health of intestinal mucosa

• Supports healthy inflammatory response

• Builds immune support

• Thyroid-friendly ingredients

The Gut Healing Bundle includes the following:

SMT-GI Restore. Combines effective clinical levels of well-researched (and thyroid-friendly) nutrients and botanicals specifically formulated to support optimal gastrointestinal health and function without any added flavors, colors, sweeteners, gums or common allergens.

Enzymes Plus. Comprised of a proprietary blend of digestive enzymes along with betaine HCL and ox bile to support optimal digestion of proteins, fats, and carbohydrates. Also contains the special protease DPP IV (dipeptidyl peptidase IV), which aids in the breakdown of the peptides gluteomorphin (from gluten) and casomorphin (from casein). Although you don’t need to be experiencing digestive symptoms to use Enzymes Plus, it may be helpful for those who experience gas and bloating after eating, occasional constipation or diarrhea, or a feeling of fullness after eating.

SMT-Probio. Choosing a good quality and effective probiotic can be a challenge, as there are so many probiotic supplements on the market. Unfortunately many probiotic supplements only list the species, and not the specific strains. Others list the strains but aren’t diverse or potent enough. SMT-Probio Complete provide 18 different strains belonging to 13 different species of three different genera. For consumer convenience, this formula is available encapsulated at a maintenance dose of 45 billion CFUs per capsule. The HOWARU and FloraFIT strains that comprise these formulas are stable, proven, and trusted worldwide.

To learn more about The Gut Healing Bundle visit www.guthealingbundle.com

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 podcast episode I had a conversation with hair loss expert Julie Olson, as we chatted about one of the common myths related to hair loss…taking biotin. Many people reach for biotin the moment they notice more hair in the shower drain. But only few realize it can do more harm than good…

In the episode, Julie discusses what’s really going on behind hair loss and the confusion around biotin. We get into why true biotin deficiency is rare, how high doses can interfere with other nutrients, and why it’s so important to step back and look at the bigger picture things like gut health, inflammation, toxin exposure, and hormone balance. Julie also shares the five main root causes she sees in women struggling with hair loss and how proper testing can make all the difference.

If your hair keeps thinning no matter what you try, this episode reveals why biotin might not be the quick fix it seems.

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: WHY DOES MY GUT RETEST RESULTS LOOK WORSE?

Dr. Eric, I've been working with a functional medicine doctor and did a GI-MAP, which showed H. pylori and some other findings, and then I retested it a few months later and it looked even worse! Can you explain why this would happen even though I followed the recommendations strictly?

Thank you for your question! I've done a lot of GI-MAPs over the years, and there are times when follow-up results look worse, and there can be a few reasons for this:

Reason #1: Biofilm disruption. If you're following any type of herbal antimicrobial protocol, chances are you're breaking biofilm. After breaking biofilm, microbes (i.e. bacteria, yeast) can become more detectable when they weren't before.

This can be the reason why your H. pylori results look worse on a retest, or why parasites might show up negative on the first test but then show up on a second test. Although it might be frustrating, the good news is that this doesn't mean that the health of your gut microbiome is worsening. Of course the downside is that this means there is more work to do.

Reason #2: Retesting too early. It takes time to eradicate gut infections, and if you retest too early things might look worse. For H. pylori, parasites, and other potentially "pathogenic" microbes you usually don't want to retest sooner than two months when using herbs.

Also, keep in mind that the GI-MAP uses quantitative PCR technology, and so it actually gives a value for gut microbes, rather than just saying if something is positive or negative. For example, if you run a H. pylori stool antigen or urea breath test at a local lab and it's positive, and two months later you retest and it's still positive, you don't know if it's worse or better. All you know is that it's still positive.

This is even true if you were to take antibiotics for two weeks and retest and the H. pylori was still there. Either way, if it's still positive you might choose to modify the antimicrobial protocol.

Reason #3: Resistance to the antimicrobials. This usually isn't the case, and is more common with antibiotics. But it's still possible for some microorganisms to be resistant to certain herbs, which can cause the follow-up test results to worsen. And so if one antimicrobial protocol doesn't seem effective it once again makes sense to switch to a different one.

There of course can be other reasons for this as well. Lab error is certainly a possibility, but thankfully in most cases this isn't the reason why someone's GI-MAP retest results would look worse.

If someone's GI-MAP retest results look worse you'll want to consider the points I mentioned here, and if you have GI symptoms and they're not improving then it probably makes sense to ask the practitioner you're working with if you can switch to a different herbal antimicrobial protocol.

Additional Thyroid-Related Resources

Click Here for Stop Believing this Hair Loss Myth (episode #225)

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 for the references

That’s a wrap