Why Biofilms May Be Preventing You From Healing Your Gut—and Your Thyroid

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: Why Biofilms May Be Preventing You From Healing Your Gut—and Your Thyroid

• Podcast Review: Thyroid and Weight Loss: What Actually Helps

• Ask Dr. Eric: Can coffee enemas and colonics benefit gut health?

Why Biofilms May Be Preventing You From Healing Your Gut and Thyroid

When it comes to gut health—and thyroid health by extension—biofilms are something that often fly under the radar.

A biofilm is a structured community of microorganisms (such as bacteria or yeast) that form a protective matrix around themselves. This protective layer allows microbes to survive in harsh environments and makes them far more resistant to antibiotics, disinfectants, immune system defenses, and even antifungal medications. In other words, biofilms can help infections stick around much longer than they otherwise would.

This is especially relevant because many people with thyroid and autoimmune thyroid conditions also deal with bacterial gut infections or yeast overgrowth. If biofilms are present, they can significantly reduce the effectiveness of treatment—whether that treatment is pharmaceutical or natural.

Why Biofilms Are a Problem

One of the biggest challenges with biofilms is that most conventional lab tests don’t assess whether an infection is protected by one. So when treating a bacterial or yeast infection, you’re usually faced with two options:

✔️ Treat the infection and hope a biofilm isn’t present

✔️ Assume biofilms may be involved and include a biofilm-disrupting strategy

Research strongly supports the second approach. Authors of a study on antibiofilm peptides estimated that biofilm-related infections may account for up to 65% of all human infections.¹ If that’s even close to accurate, then ignoring biofilms could be one of the biggest reasons infections fail to fully resolve.

Microorganisms Known to Form Biofilms

Many microorganisms can form biofilms. Below are some of the more common ones—especially those frequently seen in people with thyroid and autoimmune thyroid conditions.

✅ Helicobacter pylori. H. pylori is a well-known trigger of both thyroid dysfunction and autoimmune thyroid conditions. While antibiotics are commonly used for eradication, treatment failure rates have increased, even with triple or quadruple therapy. One major reason is that H. pylori forms biofilms along the gastric mucosa,^2,3 shielding it from treatment. This is why addressing biofilm is so important when dealing with H. pylori infections.

✅ Borrelia burgdorferi. This is the bacterium responsible for Lyme disease. When Lyme is not caught early, it can become chronic and extremely difficult to treat. Evidence suggests that Borrelia can form biofilms, which likely contributes to treatment resistance.

✅ Yersinia enterocolitica. Yersinia has been strongly associated with both Graves’ disease and Hashimoto’s thyroiditis. In one study, all 60 strains examined were capable of producing biofilms, and most were resistant to multiple antimicrobial agents.⁴

✅ Escherichia coli. While E. coli is not a classic thyroid trigger, it’s one of the most studied bacteria. Many strains are harmless, but others can cause urinary tract infections and gastrointestinal illness. Both commensal and pathogenic strains of E. coli are capable of forming biofilms.

✅ Klebsiella pneumoniae. This gram-negative bacterium can cause pneumonia, urinary tract infections, and other systemic infections. Like many gram-negative organisms, it readily forms biofilms,⁵ contributing to persistence and resistance.

✅ Mycoplasma species. There are many species of mycoplasma, several of which are pathogenic. Research shows that many mycoplasma species are capable of forming biofilms,⁶ which may explain why they are so difficult to eliminate.

✅ Candida albicans. Candida is a fungus rather than a bacterium, but it is one of the best-documented biofilm-forming organisms.⁷ Candida biofilms can significantly reduce the effectiveness of antifungal medications such as fluconazole, making treatment more challenging.

Natural Agents That Can Help Disrupt Biofilm

The good news is that there are several natural agents with research-backed antibiofilm activity. Below are some of the most commonly used.

N-Acetylcysteine (NAC). Many people know NAC for its role in supporting glutathione production, but it also has impressive antibiofilm effects. Research shows that NAC can degrade the extracellular polysaccharide matrix that holds biofilms together.

In one study, using NAC before antibiotic therapy led to complete disappearance of gastric biofilm in patients with H. pylori.⁸ NAC has also been shown to inhibit Candida albicans biofilm formation,⁹ making it useful for both bacterial and fungal overgrowth.

Proteolytic Enzymes. Biofilms are largely composed of proteins, polysaccharides, and DNA. Proteolytic enzymes—enzymes that break down proteins—have been shown in multiple studies to help degrade biofilms.¹⁰

One commonly used practitioner product is Interfase, which contains a blend of proteolytic enzymes specifically designed for biofilm disruption.

Colloidal Silver. Although not something I routinely recommend, research does show that colloidal silver has antibiofilm activity, particularly against Candida albicans.¹¹ Additional studies also demonstrate effects against Staphylococcus aureus biofilms.¹² When used appropriately, it may be helpful in certain cases.

Lactoferrin. Lactoferrin is an iron-binding protein found in milk and colostrum. By sequestering iron, it limits bacterial growth and has well-documented antimicrobial and antibiofilm properties.¹³ This is one reason colostrum supplements can support immune and gut health.

Final Thoughts

Both bacteria and yeast are capable of forming biofilms, and these biofilms can make infections far more resistant to treatment. Organisms such as H. pylori, Borrelia, Yersinia, E. coli, Mycoplasma, and Candida are all known biofilm producers.

When someone is dealing with a chronic bacterial or yeast infection—it often makes sense to address biofilms as part of the overall strategy. Natural agents such as NAC, proteolytic enzymes, lactoferrin, and (in select cases) colloidal silver may help make treatment more effective and improve long-term outcomes.

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 Philip Pape and I dug into the deeper reasons why so many people struggle with fat loss, muscle loss, and long-term consistency, especially when thyroid health or chronic stress is part of the picture. We talked about protein needs, the role of strength training as we age, why fasting isn’t a magic solution, and how undereating can work against your goals. Philip also shares a very down-to-earth way of thinking about metabolism, recovery, and flexible nutrition that I find a lot of people benefit from hearing again in a simple, practical way.

For anyone who’s been frustrated by slow progress, tuning in may help you understand what your body has been trying to tell 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: CAN COFFEE ENEMAS AND COLONICS BENEFIT GUT HEALTH?

Dr. Eric, I’ve heard some great things about coffee enemas and colon hydrotherapy, and I was wondering if you recommend either of these to your patients?

Thanks for your question! Over the years, I’ve had some patients do coffee enemas and colon hydrotherapy on their own, but I can’t say that I routinely recommend either one to my patients.

That said, when I went through my Master’s in Nutrition program from 2012 to 2014, one of my instructors was the late Dr. Walter Crinnion, a well-known naturopathic physician who focused on environmental medicine. Not surprisingly, he taught a detoxification and biotransformation class, and I learned a lot about different ways to support detoxification.

I remember Dr. Crinnion saying that if he could only choose one method of detoxification, it would be colon hydrotherapy. On the other hand, he didn’t speak as highly of coffee enemas. However, I know they can be effective in certain situations, as they’re part of Gerson Therapy, which is a natural approach used in cancer care.

In my own practice, I definitely encourage patients to support detoxification, but I usually focus on more foundational strategies. This includes eating plenty of whole, healthy foods, using certain supplements (such as NAC or liposomal glutathione), and incorporating infrared sauna therapy. Supporting lymphatics is also important.

This is also the approach I personally follow. I try to eat a good amount of plant-based foods, while also making sure I get adequate protein, since amino acids are essential for detoxification. In addition, I use infrared sauna therapy two to three times per week.

Of course, this is just my approach, and it doesn’t mean that coffee enemas or colon hydrotherapy can’t be helpful in specific cases. It really comes down to the individual and what makes the most sense for their unique situation.

Additional Thyroid-Related Resources

Click Here for Thyroid and Weight Loss: What Actually Helps (episode 228)

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:

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That’s a wrap