Dr. Izabella Wentz, PharmD

Thyroid Pharmacist

The Best Probiotics for Hashimoto's

The Best Probiotics for Hashimoto’s

Medically reviewed and written by Izabella Wentz, PharmD, FASCP

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When I was searching for answers on how to get my Hashimoto’s into remission and feel like myself again after so many years of frustrating symptoms, I started by analyzing my health timeline, and then investing in functional medicine testing.

I have shared my full health timeline in my book Hashimoto’s: The Root Cause, but some notable triggers include recurrent strep throat infections, recurrent UTIs, and of course recurrent antibiotics for both!

Functional gut testing revealed that despite eating lots of yogurt, my levels of Lactobacillus bacteria were low! At the time, I was working in pharmaceutical sales, and happened to visit a pharmacy where an integrative pharmacist educated me about the difference between maintenance probiotics and therapeutic probiotics. Maintenance probiotics are meant to maintain the health of people who are already healthy, while therapeutic probiotics are used to shift the microbiome — and thus, the body — into a healthier state.

I initially thought that taking probiotics from the drugstore or eating yogurt should be enough to balance my gut microbes, but then I began to learn about how different strains of probiotics have different benefits, and how the dose of the same strain can turn a “maintenance probiotic” into a “therapeutic probiotic.”

I also learned (the hard way), that taking the wrong probiotics (or too high a dose of probiotics), can be disastrous!

Needless to say, using probiotics to heal my gut was a big part of my healing journey and became a mainstay recommendation for my clients, especially since research shows that every person with an autoimmune disorder has something called intestinal permeability, also known as a “leaky gut” — and in many cases, probiotics can help!

I am excited that new research about the Hashimoto’s and microbiome connection has come out since I published Hashimoto’s: The Root Cause. Since that time, I have also reviewed hundreds of gut tests of people with Hashimoto’s, most notably about 300 GI-MAP tests.

I will be sharing an article of my analysis of the results sometime in 2024 (I am still editing it to make it more digestible :-)), but beyond what I saw reported in the research, I also noted that people with Hashimoto’s tended to have higher levels of non-beneficial Streptococcus bacteria, which helped me to finally understand why so many people with Hashimoto’s can present with anxiety and obsessive compulsive symptoms (hint: non-beneficial Strep can cause this!).

Additionally, I’m excited to share that there is a range of probiotics in the Rootcology store to support you on your healing journey!

Discovering the right type of probiotics was an important part of healing my own gut, and in this article, I’d like to share more information about:

  • The root causes of intestinal permeability
  • Unique dysbiosis patterns in Hashimoto’s
  • Sources of probiotic-rich foods
  • Different types of probiotics
  • Tips for using probiotics

Root Causes of Intestinal Permeability

Our gut barrier has the important job of letting nutrients into the body while keeping bacteria, viruses, parasites, and toxins out. When the gut barrier is impaired, these harmful organisms can leak into the body. We call this intestinal permeability, or “leaky gut.”

A leaky gut has gaps in its lining that allow irritating molecules and substances to escape from the digestive system and enter into the bloodstream. This irritation can interrupt the immune system’s ability to regulate itself, and put the body into a perpetual “attack mode” that is counterproductive to healing.


There are various reasons why a person may have intestinal permeability.

Gluten, the protein found in wheat products, has become a well-known cause of intestinal permeability, and many individuals with autoimmune conditions have been able to find relief in symptoms by following a gluten-free diet, the Paleo diet, or another healing diet such as the Autoimmune Paleo diet (AIP). Some people have even seen a complete remission in their autoimmune condition after removing gluten from their diet. Other reasons a person may experience a leaky gut include stress, food sensitivities, nutrient deficiencies, and intestinal infections. [1]

A gut may also be more permeable due to an imbalance of probiotic (good) versus opportunistic (bad) gut bacteria, also known as dysbiosis. E. coli and Proteus bacterial species are often referred to as “opportunistic pathogens” because they only become pathogenic when the opportunity is just right. If they are outnumbered by probiotic bacteria, they behave like good citizens of the gut and may add value. When they outnumber the probiotics, they may start to bore into the gut wall, leading to intestinal permeability.

Dysbiosis Patterns Noted in Hashimoto’s

People with autoimmunity have been found to have lower amounts of the probiotic bacteria Lactobacillus and Bifidus, and higher amounts of the opportunistic E. coli and Proteus bacteria.

A 2020 review showed that those with hypothyroidism experience more gut dysbiosis and bacterial overgrowth, marked by notably lower levels of Lactobacillaceae and Bifidobacterium. This imbalance reduces the extraction and absorption of crucial nutrients, including iodine, iron, copper, selenium, and zinc. [2] (These micronutrients are often found to be deficient in those with autoimmune thyroid disease, and you can read more about that in my article on nutrient deficiencies.)

The review showed that supplementation with probiotics can support thyroid function by increasing free T4 and thyroid mass. It also found an increase in active behavior (energy levels), which may be low in hypothyroidism. Additionally, the review highlighted that probiotic supplementation had a positive effect on trace minerals like selenium, zinc, and copper. [3]

Another study from 2020 examined the effects of probiotic supplementation on thyroid function in hypothyroid patients. It followed 56 patients with hypothyroidism, where one group received a synbiotic probiotic (defined as a combination of probiotics and prebiotics, with Lactobacillus, Bifidobacterium, and Streptococcus being the components of the probiotic strain), and the other received a placebo. After eight weeks, researchers found that patients receiving the synbiotic supplementation had significantly reduced thyroid-stimulating hormone (TSH) concentration, as well as improved free T3/TSH ratio, and were able to lower their T4 medication dose. [4]

Aside from often having lower amounts of good bacteria, people with Hashimoto’s will often have higher levels of pathogenic bacteria. E. coli is a bacteria that most people have in their gut, and is protective and beneficial in the right amounts. However, it tends to be elevated in people with Hashimoto’s, and too much indicates gut dysbiosis. A recent study examined the fecal samples of 29 patients with Hashimoto’s, which showed an increased abundance of E. coli compared to the fecal samples of the control group. [5]

As mentioned, I did a yet unpublished analysis of 298 gut tests from people with Hashimoto’s that showed an unusually high level of opportunistic Strep bacteria. Fifty-eight percent of our samples had Streptococcus, although only 25 percent of these showed up in abnormal levels per lab standards.

Streptococcus spp. colonizes in the skin and mucous membranes throughout the body, and Streptococcus pyogenes is the bacteria that causes strep throat.

High levels of Strep in the intestine may be a sign of intestinal inflammatory activity, and can result from SIBO, low stomach acid, PPI use, stress, reduced digestive capacity, or constipation.

Streptococcus is of great interest to me, as it’s been implicated in anxiety and obsessive-compulsive disorder (OCD) [6] — I experienced both in my younger days. Research also suggests that high TPO antibody levels are associated with anxiety and OCD. [7] Immune system health and gut health are linked. Thus, commensal intestinal bacteria, if out of balance, may influence our neurological functioning and emotional behavior. [8]

I’ve seen this pattern of low levels of probiotic bacteria with high levels of opportunistic bacteria on my own lab tests, as well as on the tests of many clients with Hashimoto’s that have had stool testing to quantify microbial flora. You can have your functional medicine doctor order this test for you. I also have a few different channels set up where you can self-order the GI-MAP and GI Effects tests — these are Direct Labs and Rupa.

When I first took a stool test, I was shocked to see that I had zero growth of Lactobacillus bacteria, even though I was eating yogurt on a daily basis. I didn’t realize at the time that the problem with most commercial probiotics and yogurts, is that they don’t have enough beneficial bacteria to make a difference.

I started to eat fermented foods and added high doses of probiotics… and began to feel better and better. (I had already been gluten and dairy free and had hit a “healing wall.”)

I retested myself with the same test when all of my Hashimoto’s symptoms were gone, and found that my probiotic bacteria were in the optimal range, and the E. coli and Proteus species were no longer dominating my gut flora.

Thus, one of the very first recommendations I make for EVERYONE with Hashimoto’s is to be sure to get enough probiotics on board — but of course, as time went on, I learned more about using different bugs for different issues. 😉

Probiotic-Rich Foods

One of the easiest ways to introduce more beneficial bacteria to your microbiome is to eat fermented foods (like my friend and mentor Donna Gates recommends). [9]

In my book, Hashimoto’s Food Pharmacology, I’ve included some of my favorite fermented foods, which you can make in the comfort of your own home. Not only is making your fermented food simpler than you might think, it’s also delicious and will save you money at the grocery store!

Here’s a peek at one of my favorite recipes from the cookbook. I love making this coconut milk yogurt to add a dose of probiotics to my weekly diet.

Coconut Yogurt

Coconut Yogurt

Prep time: 30 minutes
Cook time: 8 to 24 hours

Serves: 4

Coconut yogurt is a delicious way to restore balance to your gut. This creamy homemade coconut yogurt provides all of the gut-healing benefits of yogurt, without the extra sugar and other additives that can complicate your health journey. I love using this in salad dressings and smoothies, or enjoying it topped with shaved coconut, pumpkin seeds, nuts, berries, or a splash of maple syrup.

Ingredients:

  • 14 ounces creamed coconut
  • ½ cup water (omit if using canned coconut cream)
  • 2 teaspoons collagen
  • 1 tablespoon maple syrup
  • Dairy-free yogurt starter, 2-4 high-quality probiotic capsules, ¼ cup yogurt starter, or ¼ cup yogurt from a previous batch

Directions:

  1. Blend the creamed coconut with water in a high-powered blender. Alternatively, if you can find an organic canned cream coconut product without additives, you may also use that (omit the water as you will not be blending the coconut cream). Heat the coconut milk to 180ºF, then cool to 110ºF.
  2. Add the yogurt starter, and then add the collagen and maple syrup. Mix to combine.
  3. Place the mixture in a yogurt maker or tightly sealed Mason jar at room temperature for 8 to 24 hours.
  4. If using a yogurt maker, remove and put into sealed containers, such as glass Mason jars.
  5. Store in the fridge for up to 2 weeks.

If you don’t want to make your own fermented foods, I’ve listed some tried and trusted brands below that I had incorporated into my own diet before I started making my own.

  • Fermented coconut yogurt: CoYo Coconut Milk Yogurt and So Delicious Dairy Free are two options sold in the United States.
  • Fermented coconut water: I love CocoBiotic by Body Ecology.
  • Fermented cabbage: Check your organic grocery store and make sure you get the kind that is refrigerated, as the probiotic bacteria only survive for a couple of weeks at room temperature. To order online, try Superkrauts, which is a great brand that ships its products, chilled to your home.

Probiotic Supplements

Probiotics have been widely researched for a variety of conditions, including irritable bowel syndrome, constipation, anxiety, depression, and even skin disorders. [10]

Probiotics can help improve digestion, enhance nutrient extraction from food, and can also help to balance the immune system.

Additionally, probiotics can help with many types of gut disorders, including small intestinal bacterial overgrowth (SIBO), which is estimated to be present in some 50 percent of people with Hashimoto’s. [11]

Types of Probiotics That I Have Used Successfully

Beneficial Yeast Probiotics

Saccharomyces boulardii (S. boulardii) is a beneficial yeast that helps to clear out dysbiosis such as pathogenic bacteria, Candida, mold, and some parasites (including Blastocystis hominis). [12] It binds to pathogenic bacteria, helping to neutralize toxins. It decreases the pathogens that adhere to the walls of the digestive system, resulting in a calming effect for an overactive immune response in the digestive system. [13]

It also helps to clear out H. pylori, an infection that has been implicated in ulcers and has been linked to Hashimoto’s. S. boulardii does not colonize the gut wall, but instead, it causes an increase of secretory IgA, which supports our own body’s natural defense against infections and opportunistic gut bacteria. [14] It can prevent the adhesion of parasites, bacteria, viruses, and other pathogens to our respiratory and gut linings. [15]

Low secretory IgA is common in autoimmune diseases like Hashimoto’s specifically. [16] I have reviewed secretory IgA test samples for 298 people with Hashimoto’s, and 53 percent had low secretory IgA levels!

Here are some other ways S. boulardii can help gut health:

  • Balances the microbiome: It restores microbial balance during and after antibiotic use (antibiotics kill off “good” bacteria alongside the targeted pathogenic bacteria). [17] While most probiotics are killed off by antibiotics, the yeast-based S. boulardii probiotic is not susceptible to antibiotics.
  • Doesn’t take up space in the gut: It does not multiply, but instead, it collects pathogens and eliminates them through the bowels.
  • May help reverse leaky gut: Alongside dietary and supplement interventions, S. boulardii can also help reverse leaky gut by removing pathogens and reducing inflammation in the digestive tract. [18]
  • May help eradicate SIBO: SIBO (small intestinal bacterial overgrowth) is a gut infection found in many people with Hashimoto’s. Bacteria and yeast from the colon migrate up into the small intestine, which normally contains small amounts of bacteria compared to the large intestine, and then becomes overpopulated with bacteria. This leads to fermentation in the gut, and causes gas, bloating, constipation, and/or diarrhea. Most probiotics can actually make this infection worse. However, S. boulardii is an exception and is generally well-tolerated and helpful for SIBO. This is because S. boulardii does not stay in the gut or populate it, but instead collects the pathogens and carries them through the digestive tract and out the colon. [19]

I really love this probiotic because it’s so broad-spectrum and actually assists our own gut with working better on its own. I’ve been recommending S. boulardii for many years, and some versions are stable at room temperature, while others need to be kept in the fridge.

As a pharmacist, I’m always looking for ways to make taking supplements easier, so I created a heat-stable version of S. Boulardii for Rootcology, so that my clients don’t forget to take it. (Remember, getting the supplement and keeping it in your home is the first step, but getting benefits from it actually requires taking it! #thingsIlearnedthehardway)

Dose: While the label of the product recommends taking two capsules per day, I used higher doses, building up to four capsules, three times per day.

Who should not use it: Those with Crohn’s disease should avoid taking S. boulardii. Crohn’s is associated with anti-Saccharomyces cerevisiae antibodies (ASCAs), and there is potential for cross-reaction with S. boulardii, as it is genetically similar. [20] There are some studies that suggest that S. boulardii supplementation can help Crohn’s, but it’s still controversial, so I prefer to err on the side of caution.

Additionally, people who are critically ill (such as those that are currently hospitalized with a central venus catheter and/or are intubated), and those who are immunocompromised (due to immune-suppressing medications or illnesses like HIV), should not take S. boulardii due to a risk of fungemia. [21] Please note that most individuals with autoimmunity are not considered immunocompromised. Generally, individuals with autoimmunity have an overactive immune system. However, those that receive immune-suppressing drugs may be at risk for becoming immunocompromised.

Lactobacillus-Based High-Dose Multi-Strain Probiotics

Most grocery stores and health food stores sell Lactobacillus-based probiotics that contain 10 billion colony forming units (CFUs) of one probiotic strain. While this seems like a really big number, in reality, we have one trillion bacteria in our gut, and that small amount is not likely to make a difference. In fact, most probiotic supplements only contain enough probiotics to maintain an already healthy gut, not to restore gut microbe balance. I personally haven’t seen major benefits from using Lactobacillus probiotics — unless taken in very high doses.

Furthermore, research is showing that probiotic diversity is associated with greater health and improved gut function. [22] I prefer probiotic blends containing Lactobacillus strains in addition to other probiotics, instead of single-strain probiotics that only contain one type of Lactobacillus. Probiotic blends generally contain various strains of Lactobacillus, Bifidobacteria, and in some cases, beneficial Streptococcus bacteria. Thus, I recommend taking higher doses of multi-strain probiotics.

If you’ve never taken probiotics, you will want to start with the 10 billion CFU probiotic, but work your way up to a higher dose over time.

High-dose multi-strain probiotics have been shown to help with the following:

  • May help with digestion and nutrient assimilation: The probiotic strains may assist with better digestion and absorption of nutrients and micronutrients, such as minerals and vitamins, including vitamin B12, folate, calcium, zinc, and iron. [23]
  • May help prevent overgrowth of harmful bacteria, like SIBO: Supplementing with high-quality probiotics may help prevent the overgrowth of harmful bacteria, as in the case of SIBO. [24]
  • May support the immune system: One of the major mechanisms of the probiotic action is through the regulation of the host’s immune response. Studies are showing that they may regulate the functions of systemic and mucosal immune cells, as well as intestinal epithelial cells, thus helping both in disease prevention and treatment. [25] Their therapeutic potential for diseases includes several immune response-related diseases, such as allergies, eczema, and viral infections. [26]
  • May help with IBS and gut health: High-dose, multi-strain therapeutic probiotics may help maintain good gut health and be effective against intestinal diseases, including infectious diarrhea, antibiotic-associated diarrhea, ulcerative colitis, and irritable bowel syndrome (IBS). [27]

Rather than taking multiple pills, numerous companies have created high-dose probiotic blends. I would love to introduce you to my new high-dose, multiple strain probiotic, Rootcology ProB 50!

  • Rootcology ProB 50 – This is a highly potent, shelf-stable, gluten- and dairy-free probiotic formulation containing 50 billion colony-forming units (CFUs) per serving. The formula consists of 18 well-researched HOWARU® probiotic strains delivered in gastro-resistant capsules. ProB 50 may be beneficial for supporting optimal digestion and nutrient assimilation, maintaining a healthy balance of bacteria in the gut, supporting a normal immune response, and maintaining bowel regularity. This formula does not require refrigeration, which I always think helps with remembering to take it, especially during busy times and while traveling. 🙂

Here are some additional options for you to consider:

  • Pure Encapsulations Probiotic 50B – This is a great high-dose probiotic to start with, and I have recommended it to many of my clients over the years. Like the Rootcology ProB 50, you may have to work your way up to a full dose, since this contains 50 billion colony forming units (CFUs). Please note that this version does have to be kept in the fridge, so keep that in mind when you are ordering.
  • Visbiome – Another high dose Lactobacillus-based probiotic that I have used with great success, and that has the most research behind it, is known as VSL #3, which contains 450 billion CFU of probiotics per dose. This particular probiotic has been clinically studied for ulcerative colitis and irritable bowel syndrome. The probiotic has been so successful in inducing remission, it has been labeled as a “medical food.” Please note, this is a very expensive probiotic, but you may be able to get it covered by your insurance if you have the right diagnosis.
    • While this used to be my go-to probiotic, in the last few years, I’ve had some negative experiences with it… Namely, a family member with new onset ulcerative colitis seemed to have a flare-up after using it. The word on the street in functional nutrition circles is that the probiotic can exacerbate inflammatory bowel conditions, which I also learned the hard way. (It was surprising, as all of the studies about this probiotic actually reported that it helped those conditions.)
    • Additionally, there was some recent controversy between the inventor and manufacturer of this probiotic. Allegedly, the inventor left the company, along with his proprietary recipe, and the product that the VSL #3 manufacturer has been making is different than the clinically tested product. According to the website of Visbiome, the inventor’s new company: “Claudio De Simone, inventor of high-potency probiotic, sued pharmaceutical companies for making false advertising claims, ownership rights to the product formula and unpaid royalties.”
  • Klaire Ther-Biotic – Another favorite high dose multi-strain probiotic of mine is made by Klaire Labs, and known as Ther-Biotic. I learned about it from my brilliant nutritionist friend, Tom Malterre, and I’ve recommended Ther-Biotic for many years now, with great outcomes.

High-dose, multi-strain probiotics can be very helpful for people with Hashimoto’s in general, and especially for those who often show low levels of them on gut lab tests. However, they may be problematic for people with SIBO, which can be caused by an overgrowth of various bacteria, including Lactobacillus and Streptococcus bacteria — often found in probiotics. It’s important to note that up to 50 percent of people with Hashimoto’s may have SIBO — and the overgrowth, in up to 75 percent, may be comprised of Lactobacillus or Streptococcus bacteria.

Spore-Based Probiotics

Spore-based probiotics came on my radar after some colleagues reported seeing excellent results while using them with their clients. Spore-based probiotics are naturally occurring and have a unique mechanism of action, which allows them to directly modulate the gut microbiome.

Unlike most traditional probiotics, they remain stable and resistant to stomach acid’s low pH, resulting in delivery of more usable probiotics to the intestines.

Spore-based probiotics have shown promise in supporting various autoimmune diseases, as well as in reducing allergies and asthma. [28] They also have an ability to boost Lactobacillus colonies, so they can be used concurrently with Lactobacillus probiotics, as well as in place of them. Unlike Lactobacillus probiotics, spore-based probiotics can reduce SIBO and increase gut diversity by boosting the growth of other beneficial flora.

Clients and colleagues with Hashimoto’s have reported the following after using them for 30 to 90 days:

  • A reduction in thyroid antibodies
  • An improved mood
  • Less pain
  • Better bowel movements
  • More energy
  • A reduction or complete elimination of food sensitivities

A recent animal study has also shown the potential of probiotics to bind to heavy metals. (There is a connection between heavy metal toxicity and Hashimoto’s, and for some it can be a root cause.) This study explored the supplemental effect of Bacillus coagulans, a spore-based probiotic, on common carp who were exposed to cadmium. After eight weeks, the groups of fish who received B. coagulans showed reduced cadmium accumulation in the gut, less oxidative stress, enhanced intestinal barrier function, and regulated intestinal microflora compared to the control group. [29]

This is very exciting new research about spore-based probiotics!

I was initially planning to add a spore-based probiotic to the Rootcology product line in 2017, as many high-quality spore-based probiotics were somewhat difficult to obtain outside of working with health care professionals. However, the licensing agreements were a little too challenging at the time. That said, I am excited to announce that Rootcology Spore Flora is finally available! 🙂

Spore Flora is a broad-spectrum, spore-based probiotic used to optimize gastrointestinal health. Spore Flora contains five targeted Bacillus strains, which have the natural ability to produce a multitude of enzymes, secretory proteins (proteins secreted by cells), antimicrobial compounds, vitamins, and carotenoids (beneficial antioxidants).

Spore Flora contains spore-based probiotics that:

  • May help protect the colon against cancer and inflammation: The strain Bacillus subtilis in Spore Flora has the ability to effectively produce propionic and butyric acid. Butyric acid (possibly the most important short-chain fatty acid for gut health) is the preferred fuel source for colonocytes (epithelial cells of the colon) and has been shown to play a protective role against colon cancer and ulcerative colitis, as it affects colonic cellular differentiation, proliferation, and apoptosis (death of damaged cells). [30]
  • May help with leaky gut: The butyric acid produced by Bacillus subtilis in Spore Flora may also improve gut barrier function through stimulating the formation of mucin (which makes up the protective mucus layer in the gut), antimicrobial peptides, and tight-junction proteins. [31]
  • May help prevent infections: The intestinal Bacilli contained in Spore Flora can be natural guards against pathogens through their ability to secrete bacteriocins, lipopeptides and other compounds that possess antimicrobial and antiviral actions.
  • May help with dysbiosis, diarrhea, and IBS: Spore Flora may have protective effects against cytotoxins and may counteract the toxic effects of two food-borne pathogens that are known to cause diarrhea and vomiting, Clostridium difficile and Bacillus cereus. This probiotic is an effective treatment for antibiotic-associated diarrhea and irritable bowel syndrome (IBS) as well. Because of its ability to improve dysbiosis and intestinal inflammation by way of rebalancing the gut microflora, Spore Flora may also improve gut mucosal damage caused by ulcerative colitis. [32]
  • May promote regularity: Spore Flora may promote regularity and normal bowel movements, helping to protect against occasional constipation or diarrhea.
  • May improve immune function: Bacillus clausii, one of the strains contained in Spore Flora, may modulate genes of the small intestines that are involved in inflammation, immune response, defense response, intestinal permeability, cellular adhesion, differentiation, growth, and signaling, as well as apoptosis (programmed cell death), signal transcription and transduction (cell communication and signaling). [33]

Dose: The starting dose for spore-based probiotics is one capsule every other day, and the therapeutic dose is two capsules per day. Once the desired effect has been seen (generally three to six months in people with Hashimoto’s), I recommend dropping down to a maintenance dose of one capsule per day.

Who Should Not Use: Consult with a physician before using if you are pregnant or breastfeeding. Avoid taking this if you are on blood thinners, and do not take them together with antibiotics.

Note: Some professionals warn against taking antibiotics with certain probiotics. This recommendation to avoid taking probiotics while taking antibiotics is based on the fact that antibiotics could reduce the effectiveness of probiotics. However, research shows that taking probiotics while taking antibiotics can help prevent diarrhea which may result from the use of antibiotics. To prevent destruction of probiotic activity, it is recommended to take probiotics and antibiotics at least two hours apart from one another.

I have also had users and clients use MegaSporeBiotic with great success, and the company has allowed me to make the supplement available to my readers through this link. 🙂

E. coli & Strep-Targeting Probiotics

Through my own work and studies, it has been found that those with Hashimoto’s have higher levels of Streptococcus bacteria and E. coli bacteria in their guts.

E. coli is the most common overgrowth associated with urinary tract infections (UTIs), but it is also implicated in SIBO, bacterial vaginosis (BV) and IBS. [34]

We usually associate Streptococcus with strep throat, but there’s a growing consensus on the link between strep and obsessive compulsive disorder (OCD). [35]

While a healthy microbiome will have the right amounts of these two bacteria, you can see how having too much can easily lead to some uncomfortable symptoms. That’s why I’m excited about Rootcology Microphage, a probiotic formula that contains four types of phages, which are benevolent viruses that selectively target bacteria, as well as seven strains of probiotics. [36]

As I was going through my client histories, I noticed a pattern of recurrent UTIs, recurrent BV, IBS, as well as recurrent strep throat. I wanted to find a probiotic strain that could help adjust the microbiome in those with this particular, and very common, health history.

Microphage is specifically formulated to displace Streptococcus and eat up pathogenic E. coli. It can also help those with EBV, recurrent strep throat, SIBO, anxiety, BV, and recurrent UTIs. Additionally, it boosts Bifidobacterium, which is commonly deficient in those with Hashimoto’s.

Here’s a deeper look at how Microphage can help gut health:

  • May help fight E. coli infections: The phages in Microphage specifically target Escherichia coli, the most prevalent infecting organism in the family of gram-negative bacteria known as Enterobacteriaceae. Considering that the antibiotic resistance of E. coli is increasing rapidly, [37] even causing physicians to hesitate when selecting antibiotics, Microphage can be very helpful!
  • May help eradicate SIBO: SIBO is usually defined by the presence of an abnormally high number of coliform bacteria in the small bowel. By targeting E. coli, Microphage may help eradicate SIBO.
  • May help improve irritable bowel syndrome (IBS): Many studies have linked IBS with SIBO, a condition that is associated with E. coli overgrowth. By targeting E. coli, Microphage may not only help eradicate SIBO but also improve IBS.
  • May help eradicate urinary tract infections (UTIs): UTIs are the most common infections caused by E. coli. UTIs are most often caused by bacteria from the GI tract being spread to the urethra and then traveling from the urinary tract to the bladder. By targeting E. coli, Microphage may help with healing UTIs. Given E. coli’s increasing resistance to antibiotics, UTIs are becoming harder to eradicate. Utilizing a supplement like Microphage may be very helpful.
  • May help eradicate vaginosis: E. coli, which is a normal inhabitant of the rectum, can cause bacterial vaginosis (BV) if spread to the vaginal area. By targeting E. coli, Microphage may help with establishing a healthy vaginal flora.

Dose: One capsule per day, with a fat-containing meal.

Who Should Not Use: Consult with a physician before using if you are pregnant or breastfeeding. Avoid taking this if you are on blood thinners, and do not take them together with antibiotics.

Note: Some professionals warn against taking antibiotics with certain probiotics. This recommendation to avoid taking probiotics while taking antibiotics is based on the fact that antibiotics could reduce the effectiveness of probiotics. However, research shows that taking probiotics while taking antibiotics can help prevent diarrhea which may result from the use of antibiotics. To prevent the destruction of probiotic activity, it is recommended to take probiotics and antibiotics at least two hours apart from one another.

I took Microphage myself during a postpartum health flare up. It helped me so much with anxiety, and normalized my digestive function!

Rootcology Probiotics

Tips for Using Probiotics

If you’ve never taken probiotics before, you will want to start low and go slow, as you may have increased symptoms if your gut flora changes too rapidly. For example, if your target dose is 50 billion CFU, then you may want to start off at a dose of 10 billion CFU, until your gut has adjusted. If you’ve found that you can tolerate that dose, but have not reached your gut health goals, you can work your way up to your target dose.

To boost the effect of probiotic supplements, I recommend making sure you are getting plenty of prebiotics in your diet. Prebiotics are the foods your microbiota feed on, and are necessary to ensure that the population of healthy bacteria in your gut grows and flourishes. [38]

Foods rich in prebiotics include: chicory root, Jerusalem artichoke, dandelion, garlic, leek, onion, bananas, apples, konjac root, cocoa, burdock root, flax seeds, yacon root, jicama, and asparagus.

Additionally, those with SIBO (small intestinal bacterial overgrowth) will need to avoid many probiotics, especially those containing prebiotics, as they will just be adding fuel to the fire.

Spore-based probiotics have been found to be effective for those with SIBO, and S. boulardii is generally safe as well.

One more thing to note when you first start taking a high-quality probiotic: the “good” bacteria will begin to colonize your gut and crowd out the “bad” bacteria that had taken up residence there. When these bad bacteria are crowded out and attacked, they may start to release toxins that build up faster than your body can get rid of them. This will cause your body to begin an immune response to clear them out, with symptoms that may include digestive discomfort, changes in bowel movements, muscle aches, headaches, and skin sensitivity.

This is often referred to as a healing crisis or a Jarisch-Herxheimer reaction. [39] While uncomfortable, this type of reaction is an indication that your probiotics are working and that you are eliminating the bad bacteria!

However, this highlights the importance of starting low and going slow when you begin taking a new probiotic, so that you can minimize the unpleasant symptoms. Staying hydrated and moving your body as much as possible will also help your body clear out the toxins more rapidly.

Sourcing Quality Probiotics

When choosing probiotics, it’s important to know that they’re not all created equally. There are various strains and doses to consider, depending on what you are trying to achieve. It’s also important to consider manufacturer quality.

Please note, I always try to provide links to the specific products I talk about to ensure that there’s no confusion on what I have liked and tried (a little pharmacist obsession, haha), and provide various options for probiotics so that you can make the best choice for your circumstances.

I only choose really high quality companies and products that I have used myself personally, including Klaire Labs, Pure Encapsulations, Designs for Health, Microbiome Labs, and of course Rootcology. Visbiome is a company that I am also now recommending, instead of VSL #3.

That said, if you order supplements through one of these companies, please be mindful of their return policy.

While I can always offer a full-refund on Rootcology products, I do not own the other companies, and don’t carry them in my office, so I link to reputable third party websites of supplement wholesale companies. The other companies I link to may have various return policies, so please be mindful of that. 🙂

The Takeaway

Gut healing is a journey; you may need various interventions like removing reactive foods and infections, taking enzymes and probiotics, and balancing nutrients. In some cases, such as after a bout of food poisoning, antibiotic treatment, or a stressful life period, you may need to start the healing process from scratch. Remember, be kind to yourself — and learn to listen to your body — so that you can support and feed it properly. You are worth it!

Wishing you all the best on your journey!

P.S. For further support on your health journey, you can download a Thyroid Diet Guide, 10 thyroid-friendly recipes, and the Nutrient Depletions and Digestion chapter of my first book for free! You will also receive occasional updates about new research, resources, giveaways and helpful information.

P.P. S. I love interacting with my readers on social media, and I encourage you to join my Facebook, Instagram, TikTok, and Pinterest community pages to stay on top of thyroid health updates and meet others who are following similar health journeys. For recipes, a FREE Thyroid Diet start guide, notifications about upcoming events, and the Nutrient Depletions and Digestion chapter from my first book for free, be sure to sign up for my email list!

References

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[2] Fröhlich E, Wahl R. Microbiota and Thyroid Interaction in Health and Disease. Trends Endocrinol Metab. 2019;30(8):479-490. doi:10.1016/j.tem.2019.05.008
[3] Knezevic J, Starchl C, Tmava Berisha A, Amrein K. Thyroid-Gut-Axis: How Does the Microbiota Influence Thyroid Function?. Nutrients. 2020;12(6):1769. Published 2020 Jun 12. doi:10.3390/nu12061769
[4] Talebi S, Karimifar M, Heidari Z, Mohammadi H, Askari G. The effects of synbiotic supplementation on thyroid function and inflammation in hypothyroid patients: A randomized, double‑blind, placebo‑controlled trial. Complement Ther Med. 2020;48:102234. doi:10.1016/j.ctim.2019.102234
[5] Ishaq HM, Mohammad IS, Guo H, et al. Molecular estimation of alteration in intestinal microbial composition in Hashimoto’s thyroiditis patients. Biomed Pharmacother. 2017;95:865-874. doi:10.1016/j.biopha.2017.08.101
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[23] Barkhidarian B, Roldos L, Iskandar MM, Saedisomeolia A, Kubow S. Probiotic Supplementation and Micronutrient Status in Healthy Subjects: A Systematic Review of Clinical Trials. Nutrients. 2021;13(9):3001. Published 2021 Aug 28. doi:10.3390/nu13093001
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[26] Yan F, Polk DB. Probiotics and immune health. Curr Opin Gastroenterol. 2011;27(6):496-501. doi:10.1097/MOG.0b013e32834baa4d
[27] Sun JR, Kong CF, Qu XK, Deng C, Lou YN, Jia LQ. Efficacy and safety of probiotics in irritable bowel syndrome: A systematic review and meta-analysis. Saudi J Gastroenterol. 2020;26(2):66-77. doi:10.4103/sjg.SJG_384_19
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[29] Chang X, Kang M, Shen Y, et al. Bacillus coagulans SCC-19 maintains intestinal health in cadmium-exposed common carp (Cyprinus carpio L.) by strengthening the gut barriers, relieving oxidative stress and modulating the intestinal microflora [published online ahead of print, 2021 Nov 13]. Ecotoxicol Environ Saf. 2021;228:112977. doi:10.1016/j.ecoenv.2021.112977
[30] Wu C, Ouyang M, Guo Q, et al. Changes in the intestinal microecology induced by bacillus subtilis inhibit the occurrence of ulcerative colitis and associated cancers: a study on the mechanisms. Am J Cancer Res. 2019;9(5):872-886. Published 2019 May 1; Xu Y, Yu Y, Shen Y, et al. Effects of Bacillus subtilis and Bacillus licheniformis on growth performance, immunity, short chain fatty acid production, antioxidant capacity, and cecal microflora in broilers. Poult Sci. 2021;100(9):101358. doi:10.1016/j.psj.2021.101358; Rhayat L, Maresca M, Nicoletti C, et al. Effect of Bacillus subtilis Strains on Intestinal Barrier Function and Inflammatory Response. Front Immunol. 2019;10:564. Published 2019 Mar 29. doi:10.3389/fimmu.2019.00564
[31] Rhayat L, Maresca M, Nicoletti C, et al. Effect of Bacillus subtilis Strains on Intestinal Barrier Function and Inflammatory Response. Front Immunol. 2019;10:564. Published 2019 Mar 29. doi:10.3389/fimmu.2019.00564
[32] Markowiak P, Śliżewska K. Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients. 2017;9(9):1021. Published 2017 Sep 15. doi:10.3390/nu9091021; Catinean A, Neag AM, Nita A, Buzea M, Buzoianu AD. Bacillus spp. Spores-A Promising Treatment Option for Patients with Irritable Bowel Syndrome. Nutrients. 2019;11(9):1968. Published 2019 Aug 21. doi:10.3390/nu11091968
[33] Acosta-Rodríguez-Bueno CP, Abreu Y Abreu AT, Guarner F, Guno MJV, Pehlivanoğlu E, Perez M 3rd. Bacillus clausii for Gastrointestinal Disorders: A Narrative Literature Review. Adv Ther. 2022;39(11):4854-4874. doi:10.1007/s12325-022-02285-0; Ghelardi E, Abreu Y Abreu AT, Marzet CB, Álvarez Calatayud G, Perez M 3rd, Moschione Castro AP. Current Progress and Future Perspectives on the Use of Bacillus clausii. Microorganisms. 2022;10(6):1246. Published 2022 Jun 17. doi:10.3390/microorganisms10061246; Di Caro S, Tao H, Grillo A, et al. Bacillus clausii effect on gene expression pattern in small bowel mucosa using DNA microarray analysis. Eur J Gastroenterol Hepatol. 2005;17(9):951-960. doi:10.1097/00042737-200509000-00011
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[35] Vogel L. Growing consensus on link between strep and obsessive-compulsive disorder. CMAJ. 2018;190(3):E86-E87. doi:10.1503/cmaj.109-5545
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[38] Davani-Davari D, Negahdaripour M, Karimzadeh I, et al. Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications. Foods. 2019;8(3):92. Published 2019 Mar 9. doi:10.3390/foods8030092
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Note: Originally published in May 2015, this article has been revised and updated for accuracy and thoroughness.

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Disclaimer: The information contained herein is for informational purposes only and should not be construed as medical advice. Please consult your physician for any health problems and before making any medical or lifestyle changes.

Lifestyle changes can result in improved thyroid function and/or an increased absorption of thyroid hormone medications, leading to a lower required dose and possible symptoms of hyperthyroidism at a dose that was previously stable. Please discuss lifestyle changes with your physician and ensure that your thyroid function is monitored every 6-8 weeks while making lifestyle changes. Symptoms of overmedication include, but are not limited to: rapid or irregular heartbeat, nervousness, irritability or mood swings, muscle weakness or tremors, diarrhea, menstrual irregularities, hair loss, weight loss, insomnia, chest pain, and excessive sweating. Do not start, change, increase, decrease or discontinue your medications without consulting with your physician.

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Comments

  1. Thanks so much for the info about probiotics. I’ve been making my own ferments but I think I’ll add probiotics now. I tried replying to the email you sent but your mailbox wouldn’t accept…just wanted to say thank-you for all you do in your work to help and support us a Hashi’s patients, it makes a difference and you are appreciated. Hope you had a beautiful weekend with your “love”, the pic was great!
    Reply

  3. What about avoiding strains of Bifidus? I have read that it should be avoided with Leaky gut ( especially with crohns and colitis) and it is in the VSL #3. I have been sticking with Acidophilus and Lactobacillus GG with good results. Interested in your thoughts. Thanks!
    Reply

  4. I have successfully been using Enzymatic acidophilus PEARLS. They are coated to bypass the stomach to best work in the intestines. Right now I only need one 1 billion CFU . Contains Lactobacillus acidophilus and Bifidobacterium longum.
    Reply

  5. I sense that I am reacting to my probiotics (VSL) and bone broth and kambucha, which leads me to believe I am Histamine inttolerant. My reactions are incredible itching. Do you have a recommendation for how to replace healthy bacteria when you have HI?
    Reply

    • Hi Kelly,
      I have the same problem with VSL#3. I take Custom Probiotics d-lactate free, Megaspore Biotic, Sacro B by Thorne, and Just Thrive by Body Ecology.
      Be well,
      Ali

      Reply

        • Dr. Wentz,

          Thank you for teaching us so much. I saw my naturopath and a medical intuitive on Sunday and they both said my biggest problem is a heavy viral load (EBV) so now I’m taking an antiviral. According to self-muscle testing I have 40/60 EBV strains probably most came from a blood transfusion when I had an apendectomy while I was four months pregnant. Yay me! It will get better.

          Ali ?

          Reply

          • Ali – thank you for following this page. Without going into too much detail, the first of the crucial defining moments in my disease development may have started during my undergraduate studies at the University of Illinois. Due to the communal living setting of dormitories (and less than stellar hygiene habits of most college students) I had recurrent strep throat infections and even contracted mononucleosis, a viral infection caused by the Epstein-Barr Virus (EBV), which is implicated in triggering many autoimmune conditions. I received multiple courses of antibiotics as well as flu shots (which may be associated with EBV infections), and started birth control for menstrual cramps.

            It is my belief that this combination had a profound impact on my gut flora, and thus my immune system.

            Epstein-Barr is a virus that causes mononucleosis (commonly called “Mono”) , a debilitating viral infection that is common among college students, and is also known as the “kissing disease,” because individuals are exposed to the virus through saliva of those who are infected.

            Specific immune cells known as CD8+ T cells are needed to fight off the Epstein-Barr virus, however, some individuals may have a low baseline level of these types of immune cells. (CD8+ T cells decrease with age, are lower in women, and in the presence of low vitamin D intake). When these fighter cells are low, the Epstein-Barr virus may take up residence in our organs (such as the thyroid) and essentially hijack the organ to help the virus hide and multiply.

            The timing of infection may also matter as well, for example, children in developing countries usually contract the Epstein-Barr Virus when they are under the age of 10. This usually results in an asymptomatic infection—one that does not cause them symptoms. In contrast, in developed countries, where individuals are not usually exposed to the virus until they are in high school or college, the infection is symptomatic in 50% of the older kids affected. This is because by the time we reach college age, CD8+ T cells, the ones that fight EBV, have declined by threefold compared with the number of cells we had in childhood.

            Additionally, animal fat and broths, soups and stews support the body’s ability to suppress the viruses. Monolaurin/lauric acid, one of the components of coconut oil, has been found to be active against the Epstein-Barr virus. Replication of many viruses including Epstein-Barr is inhibited by glycyrrhizic acid, an active component of licorice root. Quercetin, Co-Enzyme Q10, N-Acetylcysteine, and glutathione were also reported to be helpful in chronic fatigue syndrome because of their anti-viral properties.

            EPSTEIN-BARR VIRUS AND HASHIMOTO’S
            https://thyroidpharmacist.com/articles/epstein-barr-virus-and-hashimotos

          • Hi again,

            Thanks again. I have read that before and I have your book. For some reason, I muscle test poorly for quercetin. I take liposomal glutathione 3 times a day and unbiquinol once a day plus a whole bunch of other things. I’ll check out glycyrrhizic acid though.

            I just started Viru-tox for the EBV by Physica Energenics – it’s so powerful, I can only handle three drops a day.

            I have mild psoriasis, celiac, hashimoto’s, and microscopic colitis. I plan to get rid of the EBV and reverse all of the autoimmune diseases. ?

            Ali

          • Ali – I am happy you are taking charge of your health! We know that intestinal permeability (aka leaky gut) is present in every case of autoimmunity and often precedes the development of Hashimoto’s. Symptoms of leaky gut may include bloating, diarrhea, constipation, stomach aches, acid reflux and irritable bowel syndrome. According to the Institute of Functional Medicine, many people develop IBS 5-10 years before an autoimmune diagnosis. I was one of them and didn’t take my gut health as seriously as I should have. Gut problems are often caused by infections like H. pylori, parasites like Blasto, SIBO, an imbalance of bacteria, and enzyme deficiencies or food sensitivities (especially to gluten, dairy, and/or soy). Even stress can be a factor in gut permeability. The gut determines your immune system. With the exception of discussing proper thyroid medication dosing, the majority of my website and my book focuses on balancing the immune system. The info I present is based on my own research and journey for overcoming my autoimmune thyroid condition.

            Hashimoto’s Protocol
            thyroidpharmacist.com/protocol

            Hashimoto’s Root Cause
            http://www.amazon.com/gp/product/0615825796?ie=UTF8&camp=1789&creativeASIN=0615825796&linkCode=xm2&tag=thyroipharma-20

        • Hi, I bought your book Hashimoto’s protocol and had lost 25 pounds so far. Hashimoto’s had taken my life and this new eating habits have given me my life back. One I struggle with is horrible constipations mostly when I don’t drink plenty of water and eat what I am not used to eat anymore (rice, red meat, etc.) I wanted to ask is if probiotics can be taking with thyroid medication? Or is it better to take it with the other to meals so it doesn’t interfere with the medication?

          Thanks Doctor!
          Vilma

          Reply

          • Vilma – thank you so much for sharing your journey! I’m so happy to hear you are enjoying my book and are seeing results! <3 Thyroid medication absorption can be impacted by many things, including food, other medications, and supplements. Thyroid medication should be taken on an empty stomach, one to two hours before eating, taking other medications, supplements or coffee to ensure appropriate absorption. Antacids such as Tums, iron, magnesium, and calcium supplements can impair the absorption of thyroid medications. Thus, you need to have at least 4 hours of time in between your thyroid medications and these agents. Please be sure to read the directions provided with the medication. I hope you find this free ebook helpful. https://thyroidpharmacist.com/meds-ebook/

  7. I use the brand Ultimate Flora. It has 30 billion of 10 diff strains and it works great! Normally I only take one, but sometimes I will take two if I forget to take one the day before. It has helped tremendously!
    Reply

  8. I have been on probiotics for a few years w good success with suspected leaky gut, but could probably do better. Can I take one of these more expensive ones for a month or two to give my gut an extra boost and then go back to my probiotics that are half the price? (All 5 of us in the family are on probiotics that are in the billions and with a varied array of probiotics so it gets very expensive when you add in the cost of other supplements we take as well.) Hope my question makes sense. Also, our docs and pharmacists cant seem to tell me if we are supposed to stay on probiotics indefinitely or give ourselves a break. Thanks So much for the great info you put out into the world!
    Reply

  9. My dr had recommended Garden of Life Raw Probiotics for women. Can you tell me if you have heard of them or if they are any good?
    Reply

  12. Please stand me the name of the probiotic you are talking about I missed the brand an where to buy it!
    Blessings!
    Reply

  16. Did you take all the suggested probiotics at once or did you take them at separate times and the VSL was the one that worked the most?
    Reply

  17. i have Ankylosing Spondylitis, an original “leaky gut” disease that causes fusion in the spine and SI joints. Do you know the roll of KLEIBSELLA bacteria in the lower gut ? I take Align probiotic, avoid wheat/gluten and eat anti inflammatory foods.
    Reply

  18. I take Ultimate Friendly Flora by Andrew Lessman Pro Caps Laboratory. 25 billion Cfu per capsule. I have taken them for 2 years with great results! Please check them out and let me know what you think. I Have a very sensitive stomach and vitamins would make me really sick until I tried his products! The probiotics have done wonders for me!
    Reply

  19. Klaire Ther-Biotic is ONLY sold to or through healthcare professionals. Do not buy it on Amazon… read the reviews; they do not ship cold, etc. If you go to the Klaire site, you’ll see that an individual patient can NOT buy the product directly.
    Reply

  20. I was able to purchase Ther Biotic Complete online through The Natural. It was shipped with cold packs.
    Reply

  25. First of all, I would like to thank you for all information. I recently started reading about fermented foods and its benefits. I was wondering if Kombucha is safe in hypothyroid or not. And, if yes, then how much kombucha per day or week. Please reply or you can email me at health.auto15@gmail.com.
    Thanks,
    JC
    Reply

      • Anna – thank you for reaching out. <3 Kombucha can be helpful sometimes, but I recommend proceeding with caution, as some people may have adverse reactions to wild yeast. I do prefer probiotics and fermented foods like sauerkraut and fermented miso.

        Reply

  26. I was wondering if there are any less expensive probiotics that will work. I am on a limited income and these are $83.00 a bottle. Yes my health is important but I was hoping there might be a cheaper alternative.
    Reply

  27. How about making youd own kimchi ? Or sauerkraut? Any thoughts on that? Are these not good enough? I also have Hashimoto and trying to figure out best diet for me and my budget!
    Reply

  30. I has to stop dairy all together it made me so nausea and severe stomach pain and now I can’t tolerate it at . I literally will vomit and have either area diarrhea or get constipated at the same time. And I can only tolerate fruit sugar. Gluten makes me constipated. But on a good note,I found this aloe drink ,I love to drink and it dose wonders for my stomach and intestines . And I have cut back on any fungus (yeast -related ) foods . so far those are my major triggers . grains bine my stomach up .
    Reply

  33. Your posts are great and very informational. I always read them. But, you might want to mention that some folks with SIBO can’t take most probiotics. I fell into that category. Sometimes the bacteria in the small intestine is good bacteria, and mostly in the Lactate-D family. Taking most probiotics in this case makes the SIBO worse! In which case they need to find a probiotic that has no lactase D in it. This was my problem. I stay off probiotics and instead opted to buy the yogurt culture recommended by the SCD folks. I make my own almond milk yogurt. I’m too afraid to try probiotics again until i know my SIBO is gone!
    Reply

  36. I have tried Prescript Assist and Trenev Trio at my alternative Doctor’s suggestion. THEY DID NOT SEEM TO HELP MUCH. I switched to John Barron’s Probiotic and it made a big difference – they measure in the BILLIONS and are room temp stable!!!
    Reply

  37. So I am seeing a new DR. BUT feel like I have all the symptoms of hasimotos and have for years with nobody validating me. I take a pro biotic from Advocare but feel it doesn’t work. My Dr has me on multiple supplements and is adding another. Along with a hormone. I simply just want to feel better. Where do I go from here?
    Reply

  38. I just went yesterday to a chiropractor who does applied kinesiology. I have IBS, interstitial cystitis and fibromyalgia. Its all rooted in a non/low functioning thyroid from what I’ve read. Anyway he is on the way to help me heal. Igained over 20 in two tears also. I would try to find someone in your area to assess you. I’m pretty much done with the general medical doctors. Give it a try you have nothing to lose. He told me that I have most likely Hoshimoto’s. But he is not an MD so he can’t make a that medical diagnosis.
    Reply

  39. I have Hashimotos and Graves eye disease and have had great sucess with Perscript Assist probiotic….
    Reply

  40. Sherri, try going off all wheat and gluten products. If that doesn’t help try also dumping all corn products. People are shocked at the difference they feel after d o ing this.
    Reply

      • Michele – thank you for following this page. Not everyone will need every single supplement! In fact, I believe that most nutrients should come from the diet. This is why I always list food sources in the book and on the blog, for most of the nutrients, vitamins, minerals and probiotics that are depleted in Hashimoto’s. However, some may require/prefer supplements and the supplements on the website are a resource for those that do. I recommend getting tested for deficiencies to determine your need for a supplement as instructed in the book and blog. I also don’t recommend starting multiple supplements all at once. I recommend starting one at a time, and then adding another a week or so later once it has been confirmed that the first supplement is not causing any harm.

        I do have a full supplements chapter in my book. Have you checked it out? Not everyone should be taking every supplement and the book will help uncover your root cause. This will help you figure out your supplementation.

        Hashimoto’s Root Cause
        http://www.amazon.com/gp/product/0615825796?ie=UTF8&camp=1789&creativeASIN=0615825796&linkCode=xm2&tag=thyroipharma-20

        Hashimoto’s Protocol
        thyroidpharmacist.com/protocol

        Reply

        • I’m suffering so bad with hives and itching only on my neck and scalp. I have Hashimoto’s and severe gut problems. Anxiety and Uncontrollable rage. Please help. Cant eat or afford most products. I take culturelle 30 bil. The itching on scalp hurts. Lost, lost.

          Reply

          • Frances – thank you so much for reaching out and sharing. I’m so sorry you are struggling with all of this. <3 My heart goes out to you. I’ve found that many Hashimoto's patients also have the gut infection Blastocystis hominis, which has recently been connected to irritable bowel syndrome, hives AND Hashimoto’s. In the last few years, I’ve noticed that getting rid of the Blastocystis hominis infection can help people to get their Hashimoto’s into remission. You can read more about it in this article:

            A COMMON ROOT CAUSE OF HASHIMOTO'S, HIVES AND IBS
            https://thyroidpharmacist.com/articles/the-common-root-cause-of-hashimotos-hives-and-ibs

  44. Have you tried Plexus Probio5? It has Bacillus coagulans, Lactobacillus Acidophilus, Bifidobacterium Longum, Lactobacillus Plantarum, and Saccharomyces Boulardii. It also has chitosanase which helps break down the hard outer shell of Candida yeast. It’s a great product. I love it!
    Reply

  46. Hmm. I have histamine issues and the best strains for us are bifida starting strains. There are 5. I also have hashi and surely leaky gut. I’d love to know more if you have research on strains for healing
    Reply

  47. I found i developed itching and skin conditions after using kombucha. Many other people have reported the ssme. Maybe kombucha is best avoided.
    Reply

  53. I use plexus probio5. All my kids use it too. We all suffer from IBS and leaky gut. It helps tremendously. It is formulated to reach the intestines before breaking down and it also contains an anti fungal. It’s $30 for a month supply
    Reply

  54. I so agree! I was introduced to plexus from a friend and it has helped with so much. Anxiety and depression to ibs-d. I only wish I would have found it sooner!
    Reply

  55. I was taking Slipper Elm and it was doing wonders, but stopped.. It helps with IBS, GUT, and maybe more. So I should go back and take them as Thyriod, and very bad gut problems..
    Reply

  56. I was taking Plexus pink drink and their pro biotics, made me sick as a dog, that was prior to my diagnosis of hashimoto thyroiditis, my representative keep telling me to up my dose. My endocrinologist does NOT recommend plexus. Plexus products have no verifiable science behind them that is available for review. All you ever see are “miracle” stories.
    Reply

  57. For me personally, Plexus has worked. I can’t say it will work for everyone. But I had acid reflux for 18 years. 18 years of doctors, scopes, prescriptions, probiotics, OTC meds, diet changes and the only thing that helped was propping up on 4 pillows because I couldn’t lay flat or I would throw up. 18 years of never laying flat. Until I tried Plexus ProBio5. After just 8 weeks I was sleeping flat!!! And have continued to for over a year. I also have Hypothyroidism and my doctor says my numbers are great. So while it may not work for some, it was MY miracle and I think it’s worth a try.
    Reply

  58. I’m sorry to hear you were so sick. I too am taking plexus. I had my thyroid radiated 11 years ago. My endo approved my plexus. I take their slim, cleanse and probio5. I know when you start it could be part of a Candida yeast die off. You should google that. Candida causes an array of issues. I also know that it’s like everything else, not every thing works for everyone. ☺
    Reply

  59. You cannot buy Plexus products from a shelf. Through Rep only. Please message me if it interests you.
    Reply

  61. I would buy them online or check your health food store. Do a Google search of the probiotics listed by Dr Wentz in her article above . Wal-Mart and your local drug stores will most likely NOT have “good” probiotics. I don’t take those listed above but I am going to check them out for sure. Quality is important.
    Reply

  63. Refrigeration of fermented organic food is just NOT necessary. Yes, it slows the process but the science does not support your statement that probiotic bacteria die after a few weeks. Well fermented food will last years at room temp and the full strength of the good bacteria is not reached for 12 weeks, where it holds for a very long time. Love what you bring to the table-I sure would love some clear confirmation on this.
    Reply

  64. to the person that thinks they have thyroid issues….Gynecologist with do Bio identical Hormones will look into your thyroid and help you….and some DO drs but I find BIO identicals drs look at your overall health with hormones and thyroid which can be interconnected…..you can google in your area…..women can have adrenal issues, gut issues, and hormones issues from stress etc..
    Reply

  65. I am histamine intolerant, and my practitioner switched me to a different Klaire Labs product, Lactoprime Plus. Said that there are certain strains I should stay away from right now… It has 7 different Lactobacillus and 5 Bifidos strains.
    Reply

  67. I have developed Vitiligo over the past 3 years which has gotten so bad along with stomach issues recently. I am waiting for authorization to see a gastro doc but am leery of what’s next. I also believe I may have thyroid issues. I am in excellent shape and eat well so, can you possibly recommend a good probiotic as I am at my witts end? Thank You.
    Reply

  68. I have taken 2 different probiotics in the last year – Plexus probio5 and Solaray multidophilus 12 – and both have caused teeny tiny red dots (almost like blood blisters but they are not raised) all over my body and weird, almost like broken veins and discolored marks on my lower legs and large, red veins around my nose. Do you know why this happened or what causes it? It never happened when I took probiotics from Nature’s Sunshine. Can anyone answer this? I’ve also just recently been diagnosed with Hashimoto’s thyroiditis but don’t know if this has anything to do with it. Thank you for any help in this matter.
    Reply

  69. It is your body detoxing or dying off…it means these probiotics actually work and perhaps the natures sunshine wasn’t. Lower your dose and incease it slowly
    Reply

  70. So weird that you say about the red dots, because JUST THIS MORNING, I noticed the exact same thing. I also take ProBio5…I love it…but I want to know what’s up w/ these dots.
    Reply

  71. Everyone here has their own preferences for whatever probiotics works for them since each of us have different medical issues & were each unique…what works for some doesn’t work for others. For instance, my doctor’s dietitian prescribed VSL3 with the recommended dosage for my stomach problems. I had severe stomach pain with this very expensive med., so I reduced the dosage & still had pain! So there it is sitting in my refrigerator unused! I am now taking Culturell twice daily with no issues…one simple strain in this probiotic which may or may not be doing 100 % of it’s job, but I can tolerate it. So what’s the best probiotic is still an unanswered question for me!!
    Reply

  72. What do you think about ProBio5 with Plexus. I’ve had better results with my IBS with this than anything I’ve taken!
    Reply

  73. It’s been the only thing to help my ibs. I suffered panic attacks whenever i had to go somewhere. Was having panic attacks. I’ve gotten off anxiety and depression medications…even lowered thyroid medications.
    Reply

  75. I have been taking Prescript Assist and I just compared the strains with VSL #3. They are completely different so I’m wondering if I would benefit from taking each one on an every other day schedule. I don’t have IBS symptoms anymore (since 2013) so I’m just trying to get to zero antibodies, lots of energy, and optimal health. I’m almost done reading Hashimoto’s Thyrdoiditis Root Cause and I’m trying to see what else I can try. I am doing very well compared to 3 years ago, but I don’t every want to go back to that point.
    Reply

  76. Great article been fighting with Candida and blastocystis omini but am allergic to both Brewers and Baker’s east , IGG and IGM allergies class 1 and 2 . The product sheet of the S.boullardii says dont take if you are allergic to these. What would you recommend as an alternative for one who has been fighting yeast and parasites? Your reply would be very highly appreciated.Am on a standstill .
    Reply

  77. Your book was first inspiration that there was hope of getting rid of or at least controlling Hashimotos. Thank you again for the leads on probiotics. 🙂
    Reply

  79. I have Hashimoto’s and with that I have an Underactive thyroid and take synthroid for that. My blood work says I’m in “normal” ranges but still have really bad Symptoms and continues to get new symptoms. The only symptoms I have with my gut so far is bloating, should I be taking a Probiotic?
    Reply

  80. Help hypo thyroid tsh in June 29.7 an feeling very tired headaches daily tsh in Sept. .016 weight in June 143 now 118 lbs , hair falling out light headed etc
    Reply

  81. Have you looked into Plexus Probio5? It is designed to kill Candida and promote good bacteria growth! Way less cheaper than the other probiotic!
    Reply

  82. I had hashimotos. I have chronic urticaria and vitiligo. My thyroid was removed in Jan 2012 due to large nodules. Does all of this still apply to me since I no longer have a thyroid? I now take Synthroid .75mcg. I don’t feel like Ihave leaky gut symptoms. The biggest thing is that I used to be able to drop 5 lbs whenever I needed to, now I can’t. I’m 61, post-menapausal and now need to drop 20 lbs. Ughhhhh…….
    Reply

  83. I have looked in to Pure encapsulations and found one of their ingredient is Soy which is not good for us Hypothyroid people so what do you suggest in that matter ,please let me know ,thanks.
    Reply

  84. Help hypo thyroid tsh in June 29.7 an feeling very tired headaches daily tsh in Sept. .016 weight in June 143 now 118 lbs , hair falling out light headed etc
    Reply

  85. Help hypo thyroid tsh in June 29.7 an feeling very tired headaches daily tsh in Sept. .016 weight in June 143 now 118 lbs , hair falling out light headed etc
    Reply

  86. My son has Down Syndrome and diagnosed with multiple autoimmune disorders including, alopecia universalis, Hoshimoto/Compensated Hypothyroidism. and chronic constipation. He also has very dry skin. I am certain that all of these are related. His TSH was very low and Free T4 within normal range. He is only 8yrs old and is on synthroid. His diet is extremely limited as he is super picky and only eats 8 or so things…same every single day. He will only drink milk and water and will not eat any meat. His protein solely comes from milk and cheese sticks. Both I am sure are contributor to his issues. He is also nonverbal and globally delayed. I am not sure what dietary changes I can do that he will adapt to but I can hide some things in the foods he will eat. I have not found a doctor yet who is willing to help functionally for him without the standard synthroid. Not sure dosage of bro biotic you suggested are best for his age. Can you make suggestions?

    Reply

  87. OMGosh, how do you do it all! Thanks in advance for all the knowledge you continuously share. Always have recommended that pt’s change up or rotate probiotics.
    You mention & provide a link to MegasporeBiotic in your Hacking Hashimoto’s program, but didn’t mention it here. Is it still one you’d recommend?

    Reply

    • Nancy- Thank you so much for your support!! Not everyone will need every single supplement! In fact, I believe that most nutrients should come from the diet, this is why I always list food sources for most of the nutrients, vitamins, minerals and probiotics that are depleted in Hashimoto’s in the book and on the blog. However, some may require/prefer supplements and the supplements on the website are a resource for those that do. I recommend getting tested for deficiencies to determine your need for a supplement as instructed in the book and blog. I also don’t recommend starting multiple supplements all at once. I recommend starting one at a time and then adding another a week or so later once it has been confirmed that the first supplement is not causing any harm.

      I do have a full supplements chapter in my book. Have you checked it out? Not everyone should be taking every supplement and the book will help uncover your root cause. This will help you figure out your supplementation.

      Hashimoto’s Root Cause
      http://www.amazon.com/gp/product/0615825796?ie=UTF8&camp=1789&creativeASIN=0615825796&linkCode=xm2&tag=thyroipharma-20

      Hashimoto’s Protocol
      thyroidpharmacist.com/protocol

      Reply

  88. Dear Isabella
    I’ve tried many different probiotics and fermented foods and I have had a bad histamine reaction to them all. It’s the same with bone broth. Do you have any suggestions for how to heal the gut when you have a histamine intolerance? I’m currently taking L-glutamine and the prebiotic Prescript Assist but I really want to add some other foods or products if possible.
    Thank you so much for all your work. I absolutely loved your documentary. It really hit it home for me and I have started to inplement all of your advice xx

    Reply

  89. Dr. Izabella,

    What are your thoughts on the Custom Probiotics brand? Have you heard of it? It was recommended by my natural path. They have really high CFU’s. I was taking their 11 strain, but after no lactobacillus growth after several months, they recommended their D-lactate. I send in another stool sample in 6 weeks to see what my bacteria growth is at and will be anxious to see if this did the trick with facilitating the lactobacillus. Thanks so much! Tara

    Reply

  90. Should probiotics be taken with or without food? You mention you may need to reset your immune function–how do you do that? Thank you so much for sharing all the information that you do. I loved the webinar.

    Reply

  91. Have you heard of Bravo Yogurt? I just received your Hashimoto’s Protocol book. I’m thinking of doing the Root Cause Autoimmune Diet & Bravo Yogurt. What are your thoughts?

    Reply

  92. Thank you so much blazing this trail! I watched the Thyroid Secrect and learned so much! I am pretty sure I have Candida even though my GI effects test said it was negitive. I have just started your Candida Protocol and hope to get some relief soon. I recently purchased VSL#3 but did not realize it did not have S. Boulardii in it. Can I take both or should I just do S. Boulardii? Thanks so much!

    Reply

  93. What is the amount of time you should wait between taking your thyroid medication and your probiotics? Thank you for everything, you have really helped me personally!

    Reply

    • Constinteen – thank you for following this page. You should start with the directions on the bottle and adjust your dosage from there. I cannot tell you specifically what you can and cannot do over the internet as I could be held liable for what would happen to you.

      Reply

  94. Have you ever heard of PB Assist Doterra Essential oil brand of probiotics .? Have you ever heard of people having success using essential oils in treating Hashimotos? Thanks.? for all the good info.

    Reply

  95. In general do you think people with Hashmito thyroiditis need to take S. Boulardii indefinitely or are you saying in this article just until pathogenic bacteria, Candida, parasites like Blastocystis hominis, H Pylori, or some kind of an infection are cleared up and then generally S. Boulardii isn’t needed? I am not understanding if this is a short term or long term recommendation or assuming you don’t have any of the above, what do you do personally?

    Reply

  96. I wish I had known about the slow & low start recommendation for probiotics. I have certainly had more problems after taking them. Started with 50B. Is it too late or will it just take a long time to adjust? Been over 6 months.

    Reply

  97. Hi, I’m in a hashimotos group on FB and asked about experiences with VSL #3. A number of commenters said that it now contains corn starch which makes it non AIP compliant. Everyone reveres you in the group 🙂 but it was also stated that this article was written before the corn starch became an ingredient. However, after looking at the website, they say VSL has returned to Italy for production and cornstarch was always an ingredient. A bit confusing but my question is would you still recommend this for Hashi’s if corn starch, is indeed, a new ingredient in the formula. Pure encapsulations is not sold in Italy.

    Reply

  98. I have just started taking Prescript Assist. Can someone let me know if these have been successful for them. Any feedback would be greatly appreciated. They were also fairly expensive and are soil based as well.

    Reply

    • Melissa – thank you for following this page. I regret that I do not have the time to evaluate every supplement on the market. Not everyone will need every single supplement! In fact, I believe that most nutrients should come from the diet. This is why I always list food sources in the book and on the blog, for most of the nutrients, vitamins, minerals and probiotics that are depleted in Hashimoto’s. However, some may require/prefer supplements and the supplements on the website are a resource for those that do. I recommend getting tested for deficiencies to determine your need for a supplement as instructed in the book and blog. I also don’t recommend starting multiple supplements all at once. I recommend starting one at a time, and then adding another a week or so later once it has been confirmed that the first supplement is not causing any harm.

      I do have a full supplements chapter in my book. Have you checked it out? Not everyone should be taking every supplement and the book will help uncover your root cause. This will help you figure out your supplementation.

      Hashimoto’s Root Cause
      http://www.amazon.com/gp/product/0615825796?ie=UTF8&camp=1789&creativeASIN=0615825796&linkCode=xm2&tag=thyroipharma-20

      Hashimoto’s Protocol
      thyroidpharmacist.com/protocol

      Reply

  99. Dr. Wentz,

    Quick question about the GI Effects Gastrointestinal Function Comprehensive Profile (METAMETRIX KIT). When I click on the link and go to the Direct Labs Services page in the link the GI Effects Gastrointestinal Function Comprehensive Profile (Genova kit) is the one that shows up for this test. Do you know if the lab changed their name to Genova or is that test now done by a different lab (Genova vs Metametrix)? Hope you can clear up my confusion about this.

    Thanks for all your help and the great resources!
    Sam

    Reply

  100. Hi Dr. Wentz,

    I’m currently on the AIP and taking the Betaine HCL Pepsin, and currently am up to 9 pills without a real burning sensation. Could this be right, that I need up to 10 pills per meal? I was at about 6 or 7 with a slight warmth, but don’t feel a strong burn. Am I reading too much into the burn I should be feeling in my throat?

    Also, thank you for all you do. Your guidance on diet and your book have been the best thing to happen to me in years!

    Reply

    • Sherry – thank you for following this page. You should start with the directions on the bottle and adjust your dosage from there. If you’ve never taken probiotics, you will want to start low and go slow, as you may have increased symptoms if your gut flora changes too rapidly. If you’ve found that you can tolerate that dose, but have not reached your gut health goals, you can work your way up to higher doses. I do have a full supplements chapter in my book. Have you checked it out? Not everyone should be taking every supplement and the book will help uncover your root cause. This will help you figure out your supplementation.

      Hashimoto’s Root Cause
      http://www.amazon.com/gp/product/0615825796?ie=UTF8&camp=1789&creativeASIN=0615825796&linkCode=xm2&tag=thyroipharma-20

      Hashimoto’s Protocol
      thyroidpharmacist.com/protocol

      Reply

      • Hi Dr Izabella. I am trying very hard to get my hashimotos and hypothyroid under control and lose weight. There are so many probiotics out there, it is difficult to know which one to take to be most effective(hopefully reasonably priced). Could you recommend one to me? Thank you in advance for your help.

        Reply

        • Theresa – thank you for following this page. As a pharmacist, I have access to numerous high-quality brands. After much research and deliberation, I have personally decided on Pure Encapsulations brand for my own health needs. This is also the brand I recommend for family members and friends.

          Pure Encapsulations is a pharmaceutical grade brand that has extremely tight quality control and manufacturing guidelines. Each product undergoes rigorous testing by a third-party laboratory to verify label claims, potency and purity. All the products sold by Pure Encapsulations are free of gluten, dairy, and additives that may impair absorption.

          PROBIOTIC 50B
          http://www.purecapspro.com/thyroidrootcause/pe/products/product_details.asp?ProductsID=1328

          Reply

  102. Hello Dr Wentz!

    I started reading your Hashimoto’s Protocol this week and am really enjoying the information you provide, plus your website is a wealth of information too! Thank you for your calling! 🙂 I have a great functional medicine doctor, but my Hashimoto’s has been getting worse and worse the past few years. I was diagnosed with Hashimoto’s in 2003 and only recently have I been dealing with the litany of effects.. They are compounded by chronic Candida (from 2 years going undiagnosed 10 years ago), heavy metal exposure, HLA-DR mold gene, stress, etc.

    My doctor is starting therapeutic probiotic treatment for me and put me on MegaSpore 6 weeks ago. Since day 1 my energy has plummeted and I’ve been plagued by periodic debilitating die offs of some kind, even though I started out slowly at 1 pill/every other day. My doctor says to keep on it. I’m now up to 2/every day.

    I haven’t found a lot of information on MegaSpore and was keen on your experience. I’ve read that Hashimoto’s patients do really well with it, but in your experience have you seen this kind of continuous dramatic fatigue or die off when taking it? I’ve read of die offs if you start too quickly, but then people seem to have miraculous experiences. I know you can’t give personal medical advice, just trying to figure out if this is a common reaction or if it’s yet another issue to figure out.

    Thank you!
    Jill

    Reply

  103. I contacted the So Delicious company about what kind of B-12 is in there products, and was told it’s the cyanide based. So I would not recommend there brand to anyone.

    Reply

  104. Dear Wentz, My name is Jennifer and I am so grateful I found your web site and information on Hashimoto’s. My gut issues have always been an issue and this past May 2017 they got worse (feeling sick after eating, food allergies to things I have always eat (I am gluten and dairy free and have been for years), I have bad acne roseaca/itchy skin after eating, psoriasis and I have hypothyroidism (Hashimoto’s), which has gotten worse recently — my thyroid which was fine for 20 years on synthroid and is now suppressed plus my menstrual cycle is off. I am seeing this a regular/alternative doctor who diagnosed me with SIBO (currently taking Candibactrin AR and BR), but doesn’t understand the thyroid and hormone component which is frustrating. I have lost weight loss despite being low thyroid, have stomach pain, malabsorption and my hormones are out of whack. I also took a special Parasites test that was sent to a lab in Colorado, as well as a Comprehensive Stool Analysis test (Genova Diagnostics, and Intestinal Permeability test as well to rule out other digestion issues including Leaky Gut. I would love to speak with you, or perhaps you can direct me to the right doctor in my area who can help me(I am in New York City) to help me. Thank you so much!

    Reply

  105. Hello! I have had Hashimoto’s for two decades now and I have had a horrible time kicking a bad soda habit. I notice several people have inquired about the safety of Kombucha teas but their posts were either removed or not answered. I actually like the taste, and it helped me to sleep better than I have in years, but I’ve read articles contraindicating it’s use with a compromised immune system. I’d love to learn more about the safety of Kombucha and Hashimoto’s. I am not home-brewing but am drinking a natural grocery store brand.

    Reply

  106. Hello Dr. Izabella and thank you for all you do. I am a 56 year old female with adrenal fatigue and hashiamotos. I have worked with several functional medicine practitioners and it appears that we are zeroing in on a claustridial bacterial infection as the possible root cause. I have been on several rounds of biociden but it seems to keep coming back. I recently started on megaspore probiotic with hopes of successfully erradicating this infection. My question is what if any other probiotics can be used in conjunction with the megaspore. Thank you in advance for your help.

    Reply

  107. My Rx carrier recently suggested I consider a switch from my usual Armour Thyroid to NP Thyroid Tablet. I can’t find enough information about that prescription and wonder if you may enlighten me. I was also told my a PA that anyone over 65 should no longer take Armour Thyroid…..I’m 72. What is your opinion about that also?

    Reply

  108. I am writing this because im going through one of the biggest crisis of my life. And I cant find a practioner that can help me, these I tried they caused me more pain. Do you have someone good to suggest please?
    Iam suffering all my life and out of desperation I ve tried some things that a person that wasnt exacltly expert suggested me and now im ten times worse. I have chronic fatigue syndrome and hashimoto,fibromyalgia and depression and anxiety. What I ve done is that I took the product restore gut, that solved my mental issues,but then I started taking bravo probiotic,that made me feel very sick and I was taking it for one month,in the middlewhile I was taking everyday chlorella, and few times I took charchoal and I was doing everyday coffee enemas and water enemas, I was also taking many different vitamins sometimes,one liposomal multivitamin made me also very sick. I know I have malnutrition and I was doing all this detox while I had hyperthyroidism,the dose of thyroxin was too much in that period and didnt know it. I ve stopped two months ago all these things and I still suffer a lot. I ve stopped working and going out, I feel extremely weak and exhausted,I feel sick everyday, I have gastroissues,that I think enema caused me, and feel lightheaded and dizzy and a pressure on my head and neuropains on my head, I have a series of symptoms also liver pain nd yellow dark skin,but these are the main. Can somebody help me please? I dont know how to recover and the practitioners I met only made me worse with their suggestions. Its really scary feels like it will never end. 🙁
    Now im only take the restore gut in low dose,magnesium, vitamin d, dandelion and st.johns wort tea. The practitioners suggested me some supplements but was too strong for me and I quitted them. It will past? Or I made a permanent damage?
    Please help
    Thank you in advance

    Reply

  109. Dr.WENTZ ,thank you for the marveless work you do.
    I should like to ask you about prebiotics, are they good to take them with probiotics? Thank you .

    Reply

  111. I am currently following your 90 day protocol and just started the gut series a week ago. I’ve never taken probiotics but I ordered your gut bundle from Pure Encapsulations. I’m taking 1 Probiotic 50B/day and 3 Saccharomyces Boulardii/twice a day. I was going to start taking 2 Probiotic 50B today. However, I noticed yesterday afternoon that my face was feeling a little hot and my complexion was very red and breaking out a little. I’m concerned that I may be reacting to pineapple listed in the ingredients of Probiotic 50B, or is this just a side effect of taking probiotics in larger doses. I don’t want to do anything to increase antibodies in my system because I have been feeling much better, generally. I have been having no other side effects this last week.
    EDIT: I am also taking Wobenzym as recommended which has pineapple enzymes, not the probiotics. So, my question is: Am I having a reaction to something like the pineapple in Wobenzym or is this just a normal side effect of Probiotics?

    Reply

    • Elaine – thank you for reaching out. I wish I could give you more direct advice but, each person will react differently. I would advise you to ask your personal pharmacist or a trusted clinician who’s care you are under. I am not able to respond directly to these types of questions here. I also don’t recommend starting multiple supplements all at once. I recommend starting one at a time, and then adding another a week or so later once it has been confirmed that the first supplement is not causing any harm. You may also contact my team at info@thyroidpharmacist.com and they will be happy to help you. <3

      Reply

  113. Hi there,
    I’ve bought your books and also hoped to find a detailed guideline for intestinal cleansing. In this article and in your book you introduce some probiotics. Should I get all of them? I have read somewhere that when taking probiotica both useful and harmful bacteria are being destroyed therefore the prebiotic Inulin is recommended in addition. Would I need to take that extra? I honestly don’t know how to proceed here. I already eat gluten-,dairy-, sugar free incl. eggs, stopped drinking coffee and substitute them with what you and Dr. Kharrazian recommend incl. the results of my IgG test (which products I should avoid). You give a recommendation for use for Saccharomyces boulardii as well as for soil based probiotica for Lactobacillus you mention Pure E. Probiotic50B. How many do you recommend to take here? If you say you do not recommend to use all at once, would it be okay to start with one, a week later with the second and when everything is fine with the third probiotica in the third week, meaning I’d take three probiotics for the rest of the 90 day? Thanks a lot in advance, Tina.

    Best, Tina

    Reply

  114. I’ve been to several doctors (endocrinologists, rheumatologists, nutrologists, gastroenterologists) and I’m still lost… I’m diabetic, celiac and have hashimoto… I’m studying all by myself to buy my supplements… I still do not know which probiotic I should use…
    I live in Brazil, everything here is so more expensive…
    What do you think of the probiotic

    Healthy Origins, Probiotic, 30 Billion CFU’s, 150 Vcaps (https://www.iherb.com/pr/Healthy-Origins-Probiotic-30-Billion-CFU-s-150-Vcaps/19519)

    and

    Garden of Life, Primal Defense, HSO Probiotic Formula, 90 Vegetarian Caplets (https://www.iherb.com/pr/Garden-of-Life-Primal-Defense-HSO-Probiotic-Formula-90-Veggie-Caplets/3161)
    ?

    Thank you!

    Reply

  115. I’ve been taking Schiff Digestive Advantage for a few weeks now. Decided to try because someone I know was able to get off her Rx for acid reflux. Asked my endo, he was ok with it, just wait 4 hrs after the Synthroid. Started with the gummies, but couldn’t stand the thought of chewing on live thingis. 🙂 Switched to the capsules. Still have the heartburn. Figured it couldn’t hurt since I’ve been on Rx Prevacid and others for 10+ yrs. For a years been taking Prevacid OTC, and now trying to go between that and Zantac. This week started doing baby steps reducing my intake of glutten foods. Reading your Protocol book now.

    Reply

  116. Ok..2 quick things..Is a soil based veggie probiotic the same as a spore based? And though Iam kinda on Paleo Autoimmune but with Hashi’s we have our quirks, so seeds my stomach does not handle as the other normal stuff..Celiac Test was normal, but I think I have a gluten intolerance because even a bulk of non gluten has gluten..so now my bowels go then stop, yet with brain injuries, I have a delay..so eating healthy but having a stop and go, yet I am not uncomfortable..I think I need more water..I do a drink of aloe Vera gel, apple cider vinegar and organic apple juice daily and started spiralina as a supplement..found my body was odd with psyllium husk..so my weight stays at this Mark..goes up 2, then down 2 and inches just stopped yet clothes still fall off and I am finally cutting so the weight can be muscle conversion..My primary food is veggies, fruit and meat, with salads..and I occasionally started adding eggs and just picked up A2 milk to experiment..yes bone broth and I found heating Dr Axe’s powder..wow great for skin compared to liquid boxed..I have not ventured in home made..when I react I get a rash in my opening of my but..it gets red and bumpy, I take Zyrtec and it goes down, so I analyze what is different..so I feel my body progressing, but the bowels could be the message..before I found out about the Hashimoto’s..My Health was declining..the endometriosis effected my ovaries..pain that led to a hysterectomy..my kids were born in vitro because of infertility and I was an anovulator and I had a colon resection before the hysterectomy and the doc found endometriosis as the block..so many answers..thank you for your time..I know, I talk too much and yes, I have been proactive with my twins…

    Reply

  117. Dear Dr. Izabella,

    I was wondering if it was safe to take S. Boulardi during pregnancy? Also is it safe to take systemic enzymes while pregnant? Bought your books and have been following protocols and just found out that I am pregnant and just want to make sure these are safe to continue taking. Thanks so much for your reply. I know your very busy, especially with your family, and truly appreciate your help.

    Reply

    • Megan – thank you so much for reaching out and congratulations on your pregnancy! I am not able to advise on whether these supplements would be appropriate for you and your specific health needs without a comprehensive health assessment. I recommend you discuss the use of these supplements during your pregnancy with your personal doctor.

      Reply

  118. Dear Izabella
    Thank you so much for doing what you have done. I´m writing you from Spain. I didn´t know if I had Hashimoto before my pregnancy, I was always very healthy, but during pregnancy something went wrong and I was diagnosed with Hashimoto. Me baby girl was born two months before due date since I got three preecalmpsias and almost died. I started to investigate about Hashimoto only then and found your web page, I was impressed by the quantity and quality of the information you share, so I bought two of your books and followed the first three protocols and I had some improvement, but I couldn´t get into remission. Finally, I did the gut disbiosis test a month ago (it took me a while to figure out what test to do since here in Spain, we don´t have exactly the tests you suggest) and I found out that I have Blastocystis Hominis, Pseudomona spp, Clostridium coccoides and perfringens,Bacteroides and Enterobacteriaceae overgrowth additionally with low Akkermancia muciniphila. When I talk to my family doctor, endocrinologist or digestive doctor, it seems that they were born centuries ago. They have no idea even about leaky gut! I think I also had SIBO before that analysis, but I used your protocol en the book, and the syntoms are gone. Now, since I can´t find any medical help, I decided to try eradication of Blastocystis first before dealing with the bacterias, but in Spain Alinia o nitazoxanide doesn´t exist at all. I asked my friends to get it for me from Peru!It´s so terrible not being able to have an advise from any doctor. I would like to start taking nitazoxanide but I coud be pregnant. If I was, could I take it? FDA says it´s type B drug. I don´t know who else to ask… Do you do any e-mail or Skype consulting?I would be so grateful to you for any insight.. Thank you very much in advance and congradulation with you baby.
    Best wishes from Spain, Miro.

    Reply

    • Miro – thank you so much for reaching out and sharing your journey with me. <3 I am so proud of you for taking charge of your health! I highly recommend that you work with a functional medicine clinician. It’s an entire medical specialty dedicated to finding and treating underlying causes and prevention of serious chronic diseases, rather than disease symptoms.

      If you cannot find a Functional Medicine practitioner in your area, it is possible to work with an overseas practitioner remotely via Skype or some other online video platform. Here's a link which might help:

      http://www.thyroidpharmacistconsulting.com/europe1.html

      Reply

  119. Dear Dr. Izabella,
    I have been trying to take S.Boularii. I took 1x capsule twice a day. Unfortunately even with this low dose I got dizzyness and strong brain fog. I took it for about 10 days until it effected me being able to work. The reason for me taking it is that I have a strong suspecion that I have Blastocytis Hominis, I am a veterinary nurse.
    Do think I was experiencig die off symptons or could S. Boulardii just not agree with me? Do you think I could start taking it again just with a lower dose i.e. 1 capsule every other day, then 1x capsule every day, …
    It would be amazing to hear back from you. Your books have helped me so much.
    Thank you

    Reply

  121. I have been gluten free for 7 years, I was recently diagnosed with Hashimotos. Many of the dietary suggestions lean toward coconut. I am allergic to coconut, what other source is there for beneficial nutrients and MCT oils?

    Reply

    • Michele – thank you for reaching out and sharing your journey. MCT oil most often comes from coconut. You could use non dairy milks such as almond milk instead, or tigernut milk. You can also add some good fats like avocados, avocado oil and olive oil.

      Reply

  122. Thank you Dr. Wentz. I really enjoy all your articles! My daughter 8 years old was recently diagnosed with hashimoto. I feel her pediatric endocrinologist and pediatrician are less helpful trying to prescribe me alternative supplements in addition that would be helpful for my daughter other then her synthroid to help with her severe constipation. Is there a particular brand of probiotics I can look for her that maybe can help. She has had no luck with childrens probiotics and with so many to choose from it is very confusing. I appreciate all your time in knowledge on helping people on their journey with hashimotos.

    Reply

  123. Hi Isabella! I am struggling with the sequencing of my supplements (including probiotics) in the mornings. At the moment, it looks something like this:
    – 7am thyroxin (50mg)
    – 7.30am celery juice (it’s supposed to be consumed on its own on an empty stomach, 15-30 mins before of after anything else) to help with skin issues
    – 7.45am lemon water
    – 8.15am healthy breakfast + probiotics (I swap between VSL3 and Lactibiane)
    As you can see, I don’t have time to spread out my probiotics from my breakfast. Can I take my probiotics at the same time as my thyroxin? Or should I take my probiotics in the evening, just before going on bed (after digesting dinner)?
    Also, is it ok to take two different types of probiotics (e.g. VSL3 and Lactibiane) at the same time instead of alternating? I haven’t had any side effects so far…

    Reply

    • Bec – thank you for reaching out. Thyroid medication absorption can be impacted by many things, including food, other medications, and supplements. Thyroid medication should be taken on an empty stomach, one to two hours before eating, taking other medications, supplements or coffee to ensure appropriate absorption. Antacids such as Tums, iron, magnesium, and calcium supplements can impair the absorption of thyroid medications. Thus, you need to have at least 4 hours of time in between your thyroid medications and these agents. Please be sure to read the directions provided with the medication. I hope you find this free ebook helpful. https://thyroidpharmacist.com/meds-ebook/ If you have more specific questions on how and when to take particular supplements under normal circumstances, please do reach out to my team by email, at info@thyroidpharmacist.com and they will be more than happy to help ?

      Reply

  124. Oh Dr, Wentz! I have been so helped by going through your self-management protocol, but it has been slow going for me. I am now at the point where I am doing the gut cleanse. I did the 401H test and it came back high in E. Coli and medium in B. Fragilis. I suspect SIBO, but can’t get Advil-free long enough to test – I have neck and back issues. I just started the cleanse and started MegaSporeBiotic. It is wonderful and I am seeing results from it. My question is this – can I take different probiotics at the same time I am taking the MegaSpore and gut cleanse herbs? Just not sure if you can mix all that at the same time and you have said certain probiotics aren’t good for SIBO. Thank you so much for your heart to help those of us that were helpless! You are the best!! Peggy

    Reply

  125. Hello, thank you for all the amazing information once again. I am wondering how you feel about the use of kombucha for probiotic support as well?

    Reply

  127. Dear Dr. Wentz, first of all I would like to thank you for all your efforts.
    I am here becouse my daughter 17 is diagnoised with Hashi since October last year. We have been following your books advices on protocols and root couses.
    Please could you suggest proibiotics available in Europe, since the US brands you suggested does not ship in Europe. Thank you in advance.
    Greta

    Reply

  128. Dear Dr. Wentz,
    Thank you so much for compiling all this information! Since reading your articles, I switched my probiotic for MegaSporeBiotic about 3 months ago. I was taking a pretty high dose multi strain probiotic before, but didn’t really feel that it was helping my hashimotos symptoms. The difference was immediate, and stark. However, I’m wondering if there’s another probiotic I should be taking with it? I am gluten free and on Synthroid but recently developed mirrored joint pain and feel like a good probiotic should be helping with inflammation enough to limit these symptoms. Any thoughts are totally welcome.

    Thanks for your time,
    Sarah

    Reply

    • Sarah – thank you for reaching out. <3 Please understand, I am not able to advise on whether you should add another probiotic without a comprehensive health assessment. I always recommend that you discuss the addition of any supplement with your practitioner.

      Reply

  129. Hi,
    I have suspected MCAS (Mast Cell Activation Syndrome), and apparently you aren’t supposed to eat fermented foods because they can raise histamine too much in the body. However, I do find I am able to tolerate kefir (which apparently kefir’s content of kefiran has anti histamine effects) and lacto fermented pickles (Bubbies brand, if eaten in moderation). I have a bit of hard time with lacto fermented sauerkraut. I have also focused on taking saccromyces boulardii and soil based probiotics like Klaire Labs Biospora or Thrive probiotics (I have taken Megasporebiotics in the past as well but harder for me to get a hold of at a reasonable price) because apparently some Lactobacillus strains like L casei and others particularly cause histamine release with no anti histamine or anti inflammatory effects corresponding, so I’m staying away from commerical “women’s blends” or ones that have an assortment of Lactobacillus. Also, I’m not eating yogurt.

    However, due to the more restricted diet to help symptoms, I’m really needing snack ideas and I really miss having some yogurt. Can you make yogurt with probiotics that aren’t lactobacillus based, such as only with spore based probiotic capsules? There are some recipes online that say add Thrive probiotic capsules to milk to make yogurt. I’m wondering if you know if this is actually works out to do and if it would actually make a probiotic rich yogurt. The question I can’t get answered is “to make yogurt, do you HAVE TO HAVE lactobacillus to culture the milk. If yes, what on earth is happening if you mix a SBO probiotic into it??” It would be good to be able to have a probiotic friendly snack!!

    Reply

    • Angie – thank you so much for reaching out! <3 That is a great question! I don’t currently have information to share on this but, I will add it to my list for future research. I would love to hear what you find.

      Reply

  130. Since dairy should be restricted, could you recommend how to get enough calcium naturally (and by avoiding other products that are not friendly to hashimoto)? Thank you

    Reply

  131. Hello!

    I have hashimotos and was diagnosed after an extreme exposure of mold. I have been diagnosed with SIBO in the past. Now would I need to avoid Bacillus coagulans? (different from lactobacillus.)

    Reply

    • Erica – thank you for reaching out and sharing! <3 I'm so sorry you are struggling with all of this. I am not able to advise on whether this supplement would be appropriate for you and your specific health needs without a comprehensive health assessment. I recommend that you discuss this with your personal doctor.

      Reply

  132. Ugh, this article is TMI for me. If it’s titled the best probiotics for Hashimotos then just list them. It’s all too wordy and confusing to me (as Hashimotos is too!). I wish I had one to do list and one list to avoid. I feel like this is something new (Hashimotos) that physicians are all still not fully informed about or on the same page about. How can that be with such a serious condition as Hashimotos (or maybe it really isn’t?!)?

    Reply

    • Sally – thank you for sharing you feedback! ❤️ I understand how overwhelming and hard this can all be. Hashimoto’s is often a combination of food sensitivities, nutrient deficiencies, adrenal issues, gut issues as well as an impaired ability to get rid of toxins. Any of those things would prevent a person from getting better.
      Hashimoto’s is very much an individual condition. While there are root cause commonalities, each person will have their own or in some cases, more than one root cause. You will have to start with the simplest modifications, by removing triggers, followed by repairing the other broken systems to restore equilibrium, allowing the body to rebuild itself. You will need to dig down to why the immune system is imbalanced in the first place and this will tell you how you begin to finally feel better, reduce your thyroid antibodies and even take your condition into remission.
      You will have to create your own health timeline. Look back at your overall history as far back as you can remember. Look for infections, periods of severe stress, the use of medications (especially antibiotics, antacids, and oral contraceptives), accidents, and exposure to toxins. These are events that may have contributed to Hashimoto’s. Once you do, you will know what types of changes you need to implement to make yourself feel better. Here are some resources I hope you find helpful as well.

      WHERE DO I START WITH HASHIMOTO’S
      https://thyroidpharmacist.com/articles/where-do-i-start-with-hashimotos/

      OVERCOMING HASHIMOTO’S
      https://thyroidpharmacist.com/articles/overcoming-hashimotos-in-the-new-year

      BUILDING YOUR OWN HEALTH TIMELINE
      https://thyroidpharmacist.com/sample-health-timeline/

      Reply

  133. I’ve been trying to use Mega Spore Biotic off and on for about a year. I gradually built up the dose. Over the last month I’ve had more gut issues, and gradually getting worse. A few days ago, I took just a small part of a capsule and some of the stool became quite loose. I typically have slow motility. I’m going off it now and trying a different kind. My thyroid levels are good and the last time I had antibodies checked it was quite low. It’s always been a lot of trial and error for me with most of my supplements and typically can’t stay on most supplements for extended periods.

    Reply

    • Debby – thank you so much for sharing your journey. ❤️ I’m so sorry! Stopping the supplement and seeing if things improve is a good idea as well as checking in with your practitioner. I hope you will keep me posted on your progress.

      Reply

  134. added comment
    A year ago when I had GI Effects test, the microbiome was good, but had other digestive issues going on. I’ll be following up with my functional practitioner.

    Reply

  135. I am so glad you mentioned vsl#3 I purchased it for my son who’s newly diagnosed with UC and its given him the most horrendous flare ! It’s been two weeks and hes still not right.
    It was raved about by everyone including his doctor, I feel awful for giving it to him, I dont know what’s so great about it, ugh.
    Were on a soil based orobiotic now which seeks to be healing with all his sensitivities, bless him, thanks

    Reply

    • Louisa – thank you so much for sharing your son’s experience! I’m so sorry he went through all of that. I’m so glad you have found another that works better. Please keep me posted on his progress.❤️

      Reply

  136. Thank you so much for your posts and articles! They are always my go-to in addition to your books. The one thing I can’t seem to find is for how long to take S. Boulardii. We have Hashi in our family so both my 14 year old and I have been taking it for 1.5 months 2 capsules daily, but I keep hearing we need a break?

    Reply

  137. Hi Dr Wentz, I notice your products don’t ship to the UK. Do you have any recommendations for the above probiotics which are UK-based or ship to UK that you know off? Apologies if you’ve answered this in the comments previously. Thank you.

    Michael

    Reply

  138. Hi Dr. Izabella,

    I have a hard question, i have antibodies and would like to know which is the best probiotics to heal the gut, but at same time, i don’t want to use the wrong ones and increase the thyroid antibodies.
    Please let me know which is the best ones for this problem and if possible the best ones to destroy these antibodies attacking the thyroid gland.
    I already removed gluten and dairy, does kefire with Bacillus coagulans good or harmful for the gut in this hashimoto problem?
    Thank you!

    Reply

  139. Dear Dr Izabella,
    I was reading your article very carefully as it seems that you try to present the truth without just telling people “do this, or do that”.
    However after reading, most of the probiotics you recommend, may cause problems in people with hashimoto, so in the end i don’t know which ones would be beneficial at all.
    I also see you recommend Lactobacillus, i have taken both water kefir and kombucha that contain Bacillus coagulans, are they any good?
    I already take NAC, Magnesium, Vitamin D3, L-Glutamine, Zinc, Selenium, Protein supplements etc.
    If someone is feeling well, do you really recommend these probiotics?
    In the end, we end up with dozens of boxes… Imagine remembering all these and taking these everyday… and seeing no improvement at all…
    Hope you can answer this.

    Kind Regards,

    Mike

    Reply

  140. Hi, you mentioned Hashimoto 50% have Sibo but with Sibo probiotics worsen it. But you said probiotics are very helpful to Hashimoto. How does one know or check if they have Sibo? I already started probiotics without knowing if I have Sibo or not. Could I have worsened my hashimoto or illnesses? How would I reverse the damage & overgrowth? Does the Sibo stem from the probiotics use? Why do some not have Sibo with their hashimoto? How does Sibo happen/what causes it?

    Reply

  141. Hi Dr. Wentz, I’m so glad I found you and your book. You mentioned synbiotic studies related to Hashimotos and recommended other pre or probiotics. Do, you have a recommendation for a good line of synbiotic probiotics specifically to purchase? Thank you

    Reply

  142. Dr. Izabella,
    I have difficulty taking probiotic pills like for example the S. Boulardii and Spore base probiotics you make.
    Is it possible to open these capsules and put them in coconut yogurt or something else?
    Thank you!

    Reply

  143. Dr. Izabella,
    You speak about stress being one factor of hashimoto.
    What about professional football or tennis players or even rally drivers?
    If stress is major factor of everything, how come these people are always in
    good shape?
    Best Regards

    Reply

  144. Hi Dr. Wentz,

    I have read articles that say that both dairy and gluten are a no go for people with hashimoto.
    My question is, if you stay gluten free for an entire year, but take for example a slice of cake from your friend’s birthday, does it has the same impact?
    I mean, if we consume very little only in a special occasion (like once or twice a year). Does that has exact same impact as a full year or has very little to no impact at all (if you feel comfortable with it).
    Same question for dairy.

    Thank you for your time!

    Reply

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