Thyroid-Friendly Foods That Nourish the Gut Microbiome Part 2

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 2

• Podcast Review: How Graves’ Disease Gets Ignored — And Why

• Ask Dr. Eric: Can Bad Breath Be Related to the Gut?

Thyroid-Friendly Foods That Nourish the Gut Microbiome Part 2

In the previous issue of this newsletter, I highlighted how cruciferous vegetables like broccoli and cabbage support gut health. In this second part, we'll explore a few additional foods that are both safe for those with thyroid and autoimmune thyroid conditions and beneficial for the gut microbiome.

Fermented Foods (When Tolerated). As with cruciferous vegetables, not everyone tolerates fermented foods well—especially individuals dealing with SIBO or histamine intolerance. But if your body handles them without issue, fermented foods can be a powerful ally for your gut.

Some popular fermented options include:

✅ Sauerkraut

✅ Kimchi

✅ Fermented pickles

✅ Coconut yogurt

✅ Non-dairy kefir

👉 Note: Not all of these are compliant with AIP or Paleo diets (i.e. kimchi), so choose what aligns with your personal dietary approach.

Fermented Foods vs. Probiotic Supplements

I often get asked whether someone can rely solely on fermented foods instead of taking probiotics. While I’m all for getting beneficial bacteria from food, the reality is that most people don’t eat a wide enough variety or quantity of fermented foods to see a therapeutic effect.

If you’re eating just sauerkraut a few times a week, I’d still recommend supplementing with probiotics. However, if you're consuming multiple types of fermented foods daily and rotating them regularly, you may be able to get by without a supplement—though using both together can provide broader support.

Root Vegetables and Resistant Starches. Root vegetables such as carrots, beets, sweet potatoes, parsnips, and turnips are rich in fermentable fibers and polyphenols. These help nourish beneficial gut bacteria and promote the production of short-chain fatty acids (SCFAs), which play a crucial role in gut and immune health.

Resistant starches also support the microbiome by resisting digestion in the small intestine and fermenting in the colon, increasing microbial diversity and SCFA production. Examples include:

✅ Green (unripe) bananas

✅ Cooked and cooled sweet potatoes

✅ Plantains

✅ Lentils

Avocados. Avocados are known for being a healthy fat, but they’re also high in soluble fiber. This fiber supports the microbiome by increasing SCFA levels and feeding bacteria that thrive on fermentable fibers.

A clinical study showed that people who consumed avocados daily had:¹

✔️ Reduced fecal bile acid concentrations

✔️ Higher levels of SCFAs

✔️ Increased levels of fiber-fermenting bacteria

While I'm not a huge fan of eating plain avocados, I enjoy blending them into smoothies. They give a thick, creamy texture—almost like a milkshake—while boosting both flavor and fiber content.

Wild-Caught Fatty Fish. Fish isn’t the first food that comes to mind when thinking about gut health, but omega-3 fatty acids from fish like salmon and sardines help:

➡️ Support the gut lining

➡️ Decrease inflammation

➡️ Influence the composition of the gut microbiome

Research suggests omega-3s may reduce gut permeability and promote microbial balance.^2,3

Yes, there’s always concern about mercury, PCBs, and microplastics in fish. That’s why it’s best to limit consumption to a few servings of wild-caught fatty fish per week to strike a good balance between benefits and risks.

Bone Broth. Bone broth is a go-to in many gut-healing protocols for good reason. It contains collagen, glutamine, and minerals that help repair and strengthen the gut lining. While not mandatory for healing, it can provide supportive nutrients that accelerate the process.

If you can make your own using bones from grass-fed or pasture-raised animals, that’s ideal. Otherwise, choose a high-quality store-bought brand with clean ingredients.

Some people also use bone broth protein powder. I personally add it to smoothies for extra protein, though drinking real bone broth offers a more complete nutritional profile.

Extra Virgin Olive Oil. Extra virgin olive oil (EVOO) supports the microbiome in multiple ways:

✔️ Feeds beneficial bacteria

✔️ Helps reduce gut inflammation

✔️ Protects the gut lining

EVOO is rich in polyphenols and antioxidants. Animal studies suggest it promotes the growth of “good” bacteria and reduces inflammatory strains. One study also found a potential role in reducing colorectal cancer risk.⁴

While more human studies are needed, there’s strong reason to include high-quality olive oil in your daily routine, especially as part of a Mediterranean-style diet.

Final Thoughts

You don’t need to eat every food mentioned in this article to improve your gut health. But the more variety you can include—especially whole, fiber-rich, and unprocessed foods—the better your microbiome (and thyroid) will respond.

Start small. Add a new gut-friendly food each week and monitor how you feel. Healing your gut isn’t about perfection—it’s about consistency and tuning in to your body.

Find Your Hashimoto’s Triggers

If you have Hashimoto’s thyroiditis, visiting an endocrinologist is likely to result in a prescription for thyroid hormone replacement. And while there is a time and place for thyroid hormone, the problem is that it doesn’t do anything for the autoimmune component of Hashimoto’s.

And so what happens is that many people will take thyroid hormone without doing anything to improve the health of their immune system, which means that over time further damage to their thyroid gland will take place.

The good news is that you can do things to reverse the autoimmune component of Hashimoto’s. And the best way to accomplish this is by finding and removing your triggers.

My book “Hashimoto’s Triggers” will show you how to do this. By reading this book you will discover the following:

• More than one dozen triggers of Hashimoto’s thyroiditis

• The different diet options, and how to detect your specific food triggers

• Everything you need to know to heal your gut

• How to reduce fatigue, brain fog, hair loss, lose weight, and address other common symptoms

• Strategies to lower thyroid antibodies when nothing else has worked

• Nutritional supplements and herbs for Hashimoto’s

• A comprehensive list of the blood tests you should get, along with other specific tests that can help detect your triggers

• What you need to do to achieve optimal adrenal health

• Natural treatment options for viruses, pathogenic bacteria, parasites, Candida, and SIBO

Click Here to order the book “Hashimoto’s Triggers”

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 discussed “How Graves’ Disease Gets Ignored — and Why”

Far too many people are living with misdiagnosed Graves’ or ignored hyperthyroidism and they don’t even know it yet.

I’ve heard and read countless cases of people who were told their palpitations,, anxiety, or rapid heartbeat were “just stress,” only to later learn their thyroid was the real issue. Too often, hyperthyroidism and Graves’ disease are missed because doctors rely on limited testing or dismiss subtle symptoms.

In this episode, I explain why these oversights happen, what red flags to watch for, and how to ask for the right labs. You’ll also hear how small clues like heart palpitations or low cholesterol can point to a bigger thyroid problem. My goal is to help you recognize the signs early and feel confident advocating for your health.

Tune in to uncover how Graves’ and hyperthyroidism are so often misdiagnosed and what you can do right now to avoid becoming one of those stories.

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 BAD BREATH BE RELATED TO THE GUT?

Dr Eric, I have halitosis (bad breath) and thought it might be related to my oral health, but I just got a checkup by my dentist and my gum health is pretty good. Can this be related to the gut?

Thanks for your question! While I wouldn’t call myself a halitosis expert, the research clearly shows that both the oral and gut microbiomes can contribute to bad breath.

It’s great that you’re staying on top of your dental health, but having healthy gums doesn’t always guarantee a balanced oral microbiome. There can still be microbial imbalances even if things look good on the surface.

There are a few companies that offer oral microbiome testing, although I haven’t personally recommended any of these tests to my patients. If you're curious, you can explore these on your own—but before jumping in, I suggest getting a second opinion from a biological or holistic dentist who may offer deeper insight.

That said, improving your gut health is a smart first step, especially if no obvious oral cause has been found. Cleaning up your diet alone can go a long way, but sometimes deeper investigation is needed. In these cases, I often turn to functional medicine testing, including one or more of the following:

✔️ Comprehensive stool panel (e.g., GI-MAP or GI Effects)

✔️ SIBO breath test (to check for small intestinal bacterial overgrowth)

✔️ Organic acids test (to evaluate for Candida or other microbial imbalances)

Which test to start with really depends on your history and symptoms. For instance, if you experience frequent bloating or gas—especially after eating high-FODMAP foods—a SIBO breath test might be a good choice.

In my practice, the comprehensive stool test is the one I use most often, followed by the organic acids test. And keep in mind, even if you don’t have obvious digestive symptoms, you may still have underlying gut imbalances contributing to your halitosis. I’ve seen this happen in many cases.

Final Thoughts

If your oral health checks out, don’t overlook the possibility that your gut may be the hidden culprit behind persistent bad breath. Cleaning up your diet, considering a second dental opinion, and possibly exploring functional gut testing are all excellent next steps. A healthier gut microbiome can often lead to fresher breath—and better overall health.

Additional Thyroid-Related Resources

Click Here How Graves’ Disease Gets Ignored — And Why (episode 223)

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