The Role of Gut Bacteria in Metabolism and Cravings 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: The Role of Gut Bacteria in Metabolism and Cravings Part 2

• Podcast Review: The Downside of Using LDN to Lower Thyroid Antibodies

• Ask Dr. Eric: Are there natural remedies for heartburn and acid reflux?

The Role of Gut Bacteria in Metabolism and Cravings Part 2

In Part 1, we explored how gut bacteria influence cravings, appetite, and metabolism through mechanisms such as short-chain fatty acids (SCFAs) and bile acid signaling. In this second part, we’ll go deeper into how gut imbalances can disrupt hormone regulation, neurotransmitter production, and immune function—factors that can all make it more difficult to lose weight and control cravings, including in those with thyroid and autoimmune thyroid conditions.

How Gut Dysbiosis Affects Appetite-Regulating Hormones

You’ve probably heard of ghrelin (the “hunger hormone”) and leptin (the “satiety hormone”). What’s less well known is that gut dysbiosis—an imbalance in the gut microbiome—can interfere with how these hormones are regulated.

Certain gut microbes influence how the body produces and responds to leptin. In cases of gut dysbiosis, the body can become leptin resistant, meaning it no longer gets the signal to stop eating—leading to overeating, poor satiety, and weight gain.

The Connection Between SCFAs, GLP‑1, and PYY

SCFAs, especially butyrate, acetate, and propionate, are produced when beneficial gut bacteria ferment dietary fiber. These SCFAs stimulate enteroendocrine cells in the gut to release GLP‑1 (Glucagon-Like Peptide-1) and PYY (Peptide YY)—two key hormones that:

• Promote feelings of fullness

• Improve insulin sensitivity

• Help regulate blood sugar levels

When SCFA production is low—as is common in people with gut dysbiosis—it can lead to poor satiety signaling and increased hunger. This creates a vicious cycle of cravings and overeating.

For those with Graves’ disease or Hashimoto’s, this is especially relevant: studies have shown a reduction in SCFA-producing bacteria in people with autoimmune thyroid conditions, potentially contributing to impaired immune regulation and poor metabolic balance.¹

Gut Permeability, Inflammation, and Metabolic Stress

Gut dysbiosis is also associated with increased intestinal permeability, commonly known as a leaky gut. When the gut barrier is compromised, bacterial components like lipopolysaccharides (LPS) can leak into the bloodstream. This triggers low-grade systemic inflammation, which contributes to:

✅ Insulin resistance

✅ Metabolic syndrome

✅ Autoimmune flares

Fortunately, SCFAs also help to maintain the integrity of the gut lining and reduce LPS translocation, which is why supporting the gut microbiome is essential not only for metabolism, but also for immune and thyroid health.

Neurotransmitters, Cravings, and the Gut-Brain Axis

Many of our cravings—particularly for sugar and refined carbohydrates—are tied to neurotransmitters like dopamine and serotonin, which play roles in mood and reward signaling.

What’s surprising is that about 90% of the body’s serotonin is produced in the gut, and gut microbes help regulate the availability of its precursor, tryptophan. When the microbiome is imbalanced, this can shift tryptophan toward inflammatory pathways rather than serotonin synthesis—leading to:

• Mood instability

• Increased cravings

• Emotional eating tendencies

SCFAs may also influence vagus nerve activity, further supporting appetite regulation and brain-gut communication.

Putting It All Together

Let’s connect the dots:

➜ Gut dysbiosis → ↓ SCFA → ↓ GLP‑1 / PYY → poor satiety → increased cravings

➜ Leaky gut → ↑ LPS → inflammation → insulin resistance

➜ Neurotransmitter disruption → mood swings, emotional eating

➜ Reduced microbial diversity → poor metabolic flexibility, disrupted thyroid signaling

These are not minor imbalances. They can drive significant metabolic stress—especially in people already dealing with thyroid hormone fluctuations, chronic stress, or adrenal dysregulation.

Balancing the Gut Microbiome

Now that you know some of the factors that can affect metabolism and cravings, let's summarize some of the things we can do to rebalance the gut:

✅ Feed the right bacteria through prebiotic foods such as garlic, onions, leeks, asparagus, dandelion greens, and Jerusalem artichokes. You might also want to incorporate resistant starches such as green bananas.

✅ Avoid what feeds the wrong microbes, including sugar, alcohol, and ultra-processed foods.

✅ Remove factors that disrupt the intestinal barrier, including gluten, gut infections, along with reducing your exposure to environmental toxicants such as glyphosate and microplastics.

✅ Consider supplements that support the gut microbiome, including prebiotics, probiotics, and perhaps even SCFA supplements such as sodium butyrate.

✅ Support the vagus nerve through deep diaphragmatic breathing, vigorous gargling, singing out loud, humming, or cold exposure.

Conclusion

Weight gain, cravings, and sluggish metabolism are often blamed solely on calories or willpower—but your gut may be the real culprit. When the microbiome is imbalanced, key hormones and neurotransmitters that regulate hunger, fullness, and blood sugar become dysregulated. For those with Graves’ disease or Hashimoto’s, this is even more critical, as the gut and thyroid are intimately connected.

The good news is that you can shift your microbiome. By targeting gut health—through diet, lifestyle, and strategic supplementation—you can begin to tame cravings, support your metabolism, and take meaningful steps toward healing.

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 discussed “The Downside of Using Low Dose Naltrexone (LDN) To Lower Thyroid Antibodies”. This episode explores the real benefits and limitations of LDN for autoimmune conditions like Hashimoto’s and Graves’ disease. I share what the research actually says, why results are mixed, and why LDN should never replace the foundations of thyroid healing.

Listen in to get clarity before deciding if this option makes sense for you.

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: ARE THERE NATURAL REMEDIES FOR HEARTBURN AND ACID REFLUX?

Dr. Eric, are there any natural remedies that can help with heartburn and acid reflux?

Thanks for your question!

Heartburn and acid reflux are unfortunately very common symptoms. While conventional medicine often relies on proton pump inhibitors (PPIs) or other acid-suppressing medications for relief, the ultimate goal should be to identify and address the underlying cause of the problem—not just suppress the symptoms.

Let’s take a look at some of the most common root causes of heartburn and acid reflux:

Common Causes of Heartburn and Acid Reflux

Poor Diet. Certain foods can trigger acid reflux by relaxing the lower esophageal sphincter (LES) or increasing gastric pressure, allowing stomach contents to backflow into the esophagus. Common culprits include:

✅ Fried and fatty foods

✅ Spicy dishes

✅ Citrus fruits

✅ Tomatoes and tomato-based products

✅ Caffeine

✅ Chocolate

✅ Alcohol

✅ Carbonated beverages

Chronic Stress. The research shows that individuals exposed to higher levels of psychological stress are more likely to experience GERD symptoms.² Stress can impair digestion, increase stomach acid production, and weaken the function of the LES. As a result, managing your stress—through breathwork, mindfulness, yoga, or adaptogenic herbs—can play a significant role in reducing reflux symptoms.

Obesity. Obesity increases abdominal pressure, which can promote reflux of stomach contents into the esophagus. In fact, studies show that GERD may affect up to 70% of people with severe obesity.³ In such cases, losing weight—even modest amounts—may lead to a meaningful reduction in symptoms.

H. pylori Infection. Helicobacter pylori is a bacteria that can disrupt normal stomach function and contribute to acid-related symptoms. While not everyone with H. pylori will experience reflux, its presence is worth investigating—especially since it's also associated with gastritis, ulcers, and may be a potential trigger of autoimmune thyroid conditions like Hashimoto’s and Graves’ disease.

Low Stomach Acid vs. Too Much Stomach Acid

When people experience heartburn, they often assume it’s because they have too much stomach acid. However, low stomach acid (hypochlorhydria) is actually a much more common root cause—especially among those with autoimmune thyroid conditions, chronic stress, or aging digestive systems.

So how can both high and low stomach acid cause similar symptoms?

With too much stomach acid: Excess acid can irritate the lining of the esophagus if the LES is weak or compromised. This leads to the classic burning sensation associated with acid reflux. Overeating, alcohol, and certain trigger foods can worsen the problem.

With low stomach acid: The stomach still produces some acid—but not enough to fully digest food. This leads to delayed gastric emptying, food fermentation, gas buildup, and pressure that can force the LES to open. The result? Reflux of weak acid mixed with undigested food and bile—which can still irritate the esophagus and mimic high-acid symptoms.

Strategies to Support Healthy Stomach Acid Production:

✔️ Eat in a relaxed state. Avoid rushing meals or eating when stressed.

✔️ Chew thoroughly. Digestion starts in the mouth.

✔️ Don’t overhydrate with meals. Excess water can dilute gastric juices.

✔️ Consider digestive bitters or apple cider vinegar (start slowly and monitor symptoms).

✔️ Supplement with betaine HCl (with guidance from a practitioner), especially if you've tested low for stomach acid.

📌 Important: If you have active ulcers, gastritis, or are taking NSAIDs, you should not supplement with HCl without medical supervision.

Additional Thyroid-Related Resources

Click Here for Can Dental Work Keep Thyroid Antibodies High? (episode 213)

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:

(1) https://pmc.ncbi.nlm.nih.gov/articles/PMC10349397/ 

(2) https://pmc.ncbi.nlm.nih.gov/articles/PMC10635461/

(3) https://pmc.ncbi.nlm.nih.gov/articles/PMC8406336/

That’s a wrap