The Role of Gut Bacteria in Metabolism and Cravings 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: The Role of Gut Bacteria in Metabolism and Cravings Part 1

• Podcast Review: Can Dental Work Keep Thyroid Antibodies High? (Mercury & Root Canals Explained)

• Ask Dr. Eric: Should I take black seed oil?

The Role of Gut Bacteria in Metabolism and Cravings Part 1

Many people struggle with intense cravings for sugar and ultra-processed foods—even when they’re doing their best to eat clean and stay on track. While blood sugar imbalances are often a factor, a lesser-known contributor is gut dysbiosis, or an imbalance in the gut microbiota.

Research shows that the gut microbiome doesn’t just affect digestion—it communicates with your brain, influences your metabolism, and can even shape your food preferences and cravings through a range of chemical messengers and metabolites.

The Brain-Gut-Microbiome Axis

The brain and gut are in constant communication via the autonomic nervous system and the hypothalamic-pituitary-adrenal (HPA) axis. This connection affects key functions like:

• Intestinal motility and transit time

• Mucus secretion and gut barrier function

• Immune activation and inflammation

• Gut permeability (“leaky gut”)

• Appetite and energy regulation

In return, your gut microbiota produces hundreds of metabolites that can send messages back to the brain, reinforcing food behaviors like sugar or junk food cravings.

Why Gut Health Matters in Weight Gain and Obesity

Obesity rates have tripled since 1975, with 39% of adults overweight and 13% obese by 2016.¹ Many factors drive this epidemic—but increasing evidence suggests that disruptions in the gut microbiome are a key root cause.

Cravings, poor satiety signaling, and altered glucose metabolism are all downstream effects of an imbalanced gut. This means that addressing gut health is often more effective than simply counting calories or cutting carbs.

Short-Chain Fatty Acids (SCFAs): The Gut’s Secret Weapon

SCFAs are byproducts of microbial fermentation of dietary fiber—primarily acetate, propionate, and butyrate. These compounds help to:²

• Regulate immune function

• Enhance gut barrier integrity

• Reduce inflammation

• Signal satiety and regulate metabolism

SCFAs are also essential players in the brain-gut communication loop.

👉 Why fiber matters: Animal-based diets (e.g., carnivore) may lack the necessary plant-based fibers to produce SCFAs, potentially impairing satiety and weight regulation.

While SCFA supplements exist, more research is needed to confirm whether they are as effective as naturally produced SCFAs from whole foods.

GLP-1: Your Body’s Natural Ozempic?

One powerful mechanism by which SCFAs impact metabolism is by stimulating L-cells in the gut to release:

✔️ Glucagon-Like Peptide-1 (GLP-1)

✔️ Peptide YY (PYY)

These hormones promote satiety, improve insulin sensitivity, and regulate glucose levels.

This is the same pathway targeted by popular weight-loss drugs like Ozempic (semaglutide). The difference? You can naturally enhance GLP-1 and PYY by supporting SCFA production through a high-fiber, gut-friendly diet.

Bile Acids and Metabolic Signaling

Bile acids—produced in the liver and stored in the gallbladder—aren’t just for digesting fats. Once in the gut, they interact with gut microbes, transforming into secondary bile acids that:³

• Regulate FXR and TGR5 receptors

• Influence blood sugar balance

• Affect fat storage and energy use

If bile metabolism or signaling is disrupted, it can significantly impair your metabolic function and make it harder to lose weight—even if you’re eating well and exercising.

💡 Simplified takeaway: Bile acid signaling works like a thermostat for your metabolism—and your gut bacteria control the settings. When your microbiome is imbalanced, the system malfunctions.

Conclusion

Your gut is far more than a digestive organ—it’s a metabolic control center that regulates hunger, cravings, energy expenditure, and fat storage. In this first part of the series, we’ve explored how gut bacteria and their metabolites like SCFAs and bile acids play a direct role in weight and appetite regulation.

In the next newsletter, we’ll dive deeper into:

✔️ The influence of specific bacterial species on weight gain

✔️ Gut permeability and inflammation’s role in cravings

✔️ Natural ways to modulate your microbiome for metabolic health

Stay tuned!

Find Your Graves’ Disease Triggers

If you have been diagnosed with Graves' disease and have been told that your only three options are 1) antithyroid medication, 2) radioactive iodine, or 3) thyroid surgery, then you might be interested in a FREE 5-day "Find Your Graves' Disease Triggers" challenge I'll be hosting from September 27th through October 1st.

During this 5-day challenge you will...

• Discover the 3 biggest mistakes people with Graves' disease make

• Learn the real root causes of Graves’ disease

• Find out how to become your own health detective and start uncovering some of your triggers on your own

• Learn when to move beyond guesswork—discover which tests actually matter, what they reveal, and how to determine which ones you should specifically do

How Does The Challenge Work?

Every day I'll present a live lesson on Zoom, starting on September 27th at noon EDT. If you're unable to attend live there will be a limited time window where you can watch the recordings.

There will also be a Healing Graves' Naturally community associated with the challenge. This community IS NOT on Facebook, and while it's not necessary to join the community to attend the live Zoom calls, this community is where the engagement will take place, and you'll also have the opportunity to win some great prizes!

For more information please visit the following:

https://savemythyroid.com/findyourtriggers 

Best of health,

Dr. Eric

P.S. Although the 5-day challenge is free, after you register there will be an option to upgrade to VIP.  This is completely optional, and while it includes extra live calls and some cool bonuses, even if you only take advantage of the free challenge I'm confident you will receive a lot of value from it.  

P.P.S. Although the main focus will be on finding Graves' disease triggers, if you have a different type of hyperthyroid condition you will also benefit from a lot of the information presented.

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 the potential impact of mercury amalgams and root canals on thyroid autoimmunity. I’ll explain what mercury amalgams are, why some people feel better after removing them, and why others do not. We’ll also cover the debate around root canals and whether they can create ongoing immune stress. The focus isn’t on quick fixes but on helping you think through risks and benefits so you can decide what makes the most sense for your healing journey.

If your heightened antibodies haven’t budged despite your best efforts, this could give you a new angle to explore. Tune in now!

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: SHOULD I TAKE BLACK SEED OIL?

This question has been asked a few different times in my Hyperthyroid Healing Facebook community, which you can check out by Clicking Here.

Black cumin, also known as Nigella sativa (N. sativa), is a medicinal plant belonging to the Ranunculaceae family.⁴ The seeds of Nigella sativa are the primary source of its bioactive compounds. And so black cumin and black seed oil are essentially the same.

Its most prominent and widely studied constituent is thymoquinone, which possesses well-documented antioxidant, anti-inflammatory, and anti-cancer properties. ^5,6,7

Black Cumin and Thyroid Health

While research is still in its early stages, there is some evidence that Nigella sativa may benefit those with thyroid conditions:

Hashimoto’s Thyroiditis: One small human clinical trial involving 40 participants found that black cumin supplementation helped lower thyroid antibodies in individuals with Hashimoto’s thyroiditis. Although promising, the study's limited size means more research is necessary before drawing firm conclusions.

Animal Research: A rat study found that black seed essential oil may have protective effects on the thyroid gland in both hypothyroidism and hyperthyroidism. These effects were attributed to its antioxidant activity.⁸

Other Potential Health Benefits of Black Cumin

Beyond thyroid health, black cumin has demonstrated a wide range of other health benefits in the scientific literature. These include:

✅ Antibacterial and Antifungal Activity: May support the body’s defense against pathogens.

✅ Anti-Parasitic Properties: Shown to inhibit certain parasitic infections.

✅ Antidiabetic Effects: Helps regulate blood sugar levels and improve insulin sensitivity.

✅ Anticancer Potential: Thymoquinone has shown tumor-suppressing properties in preclinical models.

✅ Immunomodulatory Effects: Supports immune balance, particularly in autoimmune conditions.

✅ Anti-inflammatory and Antioxidant Actions: Helps reduce systemic inflammation and oxidative stress.

✅ Lipid-Lowering Effects: May assist in managing cholesterol and improving lipid profiles.

✅ Hepatoprotective Effects: Supports liver health and may protect against liver damage.

Should You Take Black Cumin?

While the potential benefits of Nigella sativa are compelling, it’s not a supplement I routinely recommend for all patients with thyroid or autoimmune thyroid conditions. That said, some individuals may experience benefits—especially those looking to support inflammation, immune function, or metabolic health through natural means.

As with any supplement, it’s essential to consider individual health status, medications, and goals before adding it to your regimen. Consulting with a knowledgeable practitioner can help determine whether black cumin is appropriate for you.

Additional Thyroid-Related Resources

Click Here for Can Dental Work Keep Thyroid Antibodies High? (Mercury & Root Canals Explained)

Click Here for Can Black Cumin Help with Hypothyroidism and Hashimoto’s? (article)

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