Gum Disease and Gut Dysbiosis: A Hidden Connection

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: Gum Disease and Gut Dysbiosis: A Hidden Connection

• Podcast Review: Common Myths of Balancing Hormones During Menopause

• Ask Dr. Eric: Can Methylene Blue Disrupt the Gut Microbiome?

Gum Disease and Gut Dysbiosis: A Hidden Connection

When someone has tooth pain, bleeding gums, or other oral symptoms, they typically visit a dentist. If someone experiences gut issues—bloating, reflux, constipation—they may turn to a gastroenterologist, or perhaps a functional medicine practitioner with expertise in the gut microbiome.

But what most people (including many conventional providers) don’t realize is that the health of your mouth and the health of your gut are intimately connected through what’s known as the oral–gut axis. And since both the gut and immune system play essential roles in thyroid health, understanding this connection is critical for those with Graves’ disease, Hashimoto’s, or other autoimmune conditions.

For years, I’ve spoken about how mercury amalgams and root canals can potentially negatively affect thyroid health. But recent research suggests that oral microbial imbalance—oral dysbiosis—may be just as important, particularly in its effects on the gut and immune system.

Let’s explore what the latest science tells us—and what steps you can take to support this overlooked connection.

The Oral Microbiome and Systemic Health

Like the gut, the mouth is home to its own diverse ecosystem of microorganisms, including bacteria, fungi, and viruses. When the oral microbiome is healthy, it acts as a frontline defense—helping to digest food, preventing pathogen overgrowth, and even supporting immune tolerance.

But when the balance is disrupted, oral dysbiosis can contribute to inflammation and systemic dysfunction.

Just as you can develop gut dysbiosis from diet, antibiotics, or chronic stress, you can also experience dysbiosis in your mouth. And these two systems don’t operate in isolation—oral dysbiosis can negatively affect the gut microbiome, and vice versa. This makes oral health an important (and often overlooked) pillar of thyroid and gut healing.

Could Your Mouthwash Be Doing More Harm Than Good?

Many people reach for mouthwash to freshen breath or improve oral hygiene. But some commercial mouthwashes—especially those containing chlorhexidine—may actually harm the oral microbiome by indiscriminately killing both good and bad bacteria.

A 2023 study published in the journal Antibiotics found that chlorhexidine mouthwash altered microbial diversity and pH in the oral cavity, potentially contributing to long-term dysbiosis.¹ So while it might temporarily mask bad breath, it could be worsening the root cause.

Tip: If you struggle with halitosis (bad breath), it's wise to explore whether it's being driven by gut dysbiosis, SIBO, or poor oral microbial balance—rather than masking the problem with harsh chemicals.

Consider switching to a natural mouthwash made with xylitol, essential oils, or herbal extracts—and focus on correcting the underlying microbial imbalance.

What Is the Oral–Gut Axis?

The oral–gut axis describes the biological crosstalk between the oral microbiome and the intestinal microbiome. Research confirms that bacteria from the mouth can travel to the gut, especially when the oral environment becomes imbalanced or inflamed.

For example, in people with inflammatory bowel disease (IBD), oral pathobionts (opportunistic microbes that can trigger disease under certain conditions) have been shown to migrate to the gut and worsen colitis. Oral-primed Th17 immune cells—associated with autoimmune inflammation—can also migrate and promote gut inflammation.²

Additionally, patients with IBD and other chronic gastrointestinal disorders often show higher levels of gum disease, bleeding gums, and oral microbial imbalance, indicating a bidirectional relationship.

Can Gum Disease Reshape Your Gut Microbiome?

Yes. A study published in Frontiers in Cellular and Infection Microbiology showed that periodontal pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis—commonly associated with gum disease—can translocate to the gut, disrupt the intestinal barrier, and trigger systemic inflammation.³

In other words, your bleeding gums could be fueling gut inflammation—and possibly autoimmune thyroid flare-ups.

Oral-Gut Crosstalk Affects Metabolism, Immunity, and Barrier Function

Beyond inflammation, oral-gut crosstalk also impacts metabolism. One review article highlighted how dysbiosis in the mouth and gut influences immune signaling, nutrient metabolism, and gut barrier integrity, all of which play key roles in thyroid function, detoxification, and energy production.⁴

In fact, poor oral health has been linked to metabolic syndrome, insulin resistance, and type 2 diabetes⁵—all of which are risk factors for developing thyroid disorders.

If you’re struggling with blood sugar issues, cravings, weight gain, or fatigue, oral health may be a missing piece of the puzzle.

What Contributes to Oral and Gut Dysbiosis?

Here are some of the most common factors that disrupt both the oral and gut microbiome:

✅ Western diet – Diets high in sugar, refined carbs, and processed foods promote acid-producing bacteria in the mouth and pro-inflammatory microbes in the gut.

✅ Antibiotic use (especially in early life) – Antibiotics can wipe out beneficial bacteria and create long-term microbial imbalances.

✅ Poor oral hygiene – Infrequent brushing, flossing, and lack of tongue scraping can allow harmful bacteria to thrive.

✅ Mouth breathing – Chronic mouth breathing dries the oral cavity and can increase acid-loving bacteria.

✅ Certain medications – PPIs, antihistamines, and NSAIDs may harm the oral and gut microbiome.

✅ Toxins in dental materials – Mercury amalgams, fluoride, and bisphenol-based composites can influence immune function and oral flora.

A Holistic Approach: See a Biological Dentist

If you're dealing with chronic gut or thyroid issues—and especially if you’ve had persistent bad breath, bleeding gums, or dental procedures like root canals—consider seeing a biological or holistic dentist. These professionals are trained to evaluate the oral microbiome, identify dental materials that may be triggering immune reactions, and support whole-body health through advanced testing and detoxification protocols.

To search for a biological dentist in your area visit the International Academy of Oral Medicine and Toxicology

Conclusion

The mouth is the gateway to the gut—and your gut is a gateway to thyroid and immune health. If you're dealing with Graves’ disease, Hashimoto’s, metabolic issues, or chronic gut symptoms, don’t overlook your oral health.

Addressing the oral–gut–thyroid axis could be a key piece of your healing puzzle.

Graves’ Disease Survival Roadmap Training

Recently I released a new training called "The Graves' Disease Survival Roadmap", which you can find in my new Healing Graves' Naturally Skool Community. It is completely free, and includes eight modules.

 Click Here to access the free training

As for the community, if you have Graves’ disease you’ll want to check out this community, as includes the following:

🚀 A community for those with Graves' disease and other types of hyperthyroidism looking to regain their health and avoid RAI and surgery.

💥 When someone is diagnosed with Graves' disease by an endocrinologist, the three options given are 1) antithyroid medication, 2) radioactive iodine, and 3) thyroid surgery.

While there is a time and place for conventional treatment, since 2009 I've been helping people with Graves' disease regain their health naturally and avoid RAI and surgery

Join to access the following:

✅ FREE Graves' Survival Roadmap Training

✅ FREE Monthly Hyperthyroid Healing Diet Q & A call

✅ 24/7 Community Access

 Click Here to join the community access the free training

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 episode I chatted with Dr. Sharon Stills about common myths of balancing hormones during menopause. Many women are fearful of estrogen, especially with everything out there related to “estrogen dominance”. What if the real danger isn’t estrogen but it’s misinformation?

During the episode Dr. Sharon discusses why so many women are misled into avoiding estrogen, why it’s never “too late” to find balance, and how adrenal and thyroid health fit into the bigger hormonal picture. You’ll also hear her take on bioidentical hormones, proper testing, and why chasing symptoms without addressing root causes rarely works.

Tune in to learn how to make informed, confident choices about your hormones without fear, hype, or confusion.

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 METHYLENE BLUE DISRUPT THE GUT MICROBIOME?

Dr. Eric, I've heard that methylene blue can act as an antimicrobial, but I've also heard that it can negative affect the good bacteria? Have you done any research related to this?

Thanks for your question! While I haven’t conducted extensive research on methylene blue, I recently interviewed Dr. Scott Sherr, a leading expert on methylene blue and integrative therapies. During our conversation, I asked him this exact question—whether methylene blue could negatively affect the gut microbiome—and I’d like to share some of his insights here (even though the full interview won’t be published for a little while).

Can Methylene Blue Harm Beneficial Gut Bacteria?

I brought up the concern that some people have regarding methylene blue acting similarly to compounds like oregano oil—which can be effective antimicrobials but may also harm beneficial microbes. Dr. Sherr acknowledged that methylene blue can have antimicrobial effects, but emphasized that dosage and duration are key factors in determining its impact.

Dose Makes the Difference

According to Dr. Sherr, methylene blue at higher doses—approximately 1 mg per kilogram of body weight—can indeed act as a broad-spectrum antimicrobial. At this dosage, it may potentially disrupt not only harmful pathogens but also beneficial members of the gut microbiota.

For example:

• A person weighing 120 pounds (approximately 54 kg) would reach this antimicrobial threshold at around 54 mg of methylene blue.

• If someone were using this dosage, it should be part of a targeted protocol, such as for treating an infection—and only for a short period of time.

Low Doses for Mitochondrial Support

In contrast, lower doses of methylene blue are commonly used to support mitochondrial function, enhance cellular energy production, and reduce oxidative stress. When used this way, the risk of negatively impacting the gut microbiome is much lower.

So ultimately, just like with other natural antimicrobials, it comes down to the balance of risk vs. benefit, and the reason you're using it in the first place.

Final Thoughts

If you’re considering methylene blue—especially as part of a gut-healing or thyroid-healing protocol—it’s essential to:

✅ Use it under the guidance of a qualified practitioner

✅ Understand your goals (i.e., infection control vs. mitochondrial support)

✅ Be mindful of dose and duration

It’s also worth remembering that the gut microbiome is resilient, and short-term use of antimicrobials doesn’t necessarily lead to long-term damage—especially if you’re also supporting your gut with a nutrient-dense diet, prebiotics, and probiotics.

Additional Thyroid-Related Resources

Click Here for Common Myths of Balancing Hormones During Menopause (episode 220)

Click Here to access the International Academy of Oral Medicine and Toxicology website

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