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Can Taking Probiotics Improve Thyroid Health?

Many people with thyroid and autoimmune thyroid conditions are familiar with the health benefits of probiotics. And I’m sure many people reading this are currently taking probiotics. But just as is the case with many other supplements, many people don’t have a good understanding when it comes to different probiotic supplements. Many just choose a brand with multiple strains, but otherwise don’t know if it is the right probiotic for them. So in this post I will discuss some of the different “features” of probiotic supplements, including some of the strains, the potency, and other factors.

Just so you have a better understanding of the classification of different probiotics, the genus is the first name of the bacterium. Two of the most well known genus are lactobacillus and bifidobacterium. The species is a bacterium’s second name, such as “acidophilus” or “bifidum”. So lactobacillus acidophilus is one example of a species, while bifidobacterium bifidum is another example. However, what many people don’t realize is that members of different species will typically have different strains. So for example, some probiotic supplements I have used included L. acidophilus LA-5, whereas others have included L. acidophilus LA-14.

This is where it can get confusing, as two different strains can have two completely different functions. So for example, one strain in a given species might be able to survive passage through the upper part of the gastrointestinal tract, whereas another strain won’t be able to survive. Similarly, some strains will be able to kill pathogenic bacteria, while other strains won’t do this.

Many healthcare professionals aren’t aware of this, and I also personally wasn’t aware of this in the past. And so what frequently happens is that someone will be told to purchase a specific probiotic supplement based on the species, but if it isn’t the correct strain then it might not have the therapeutic effect you’re looking for. And of course most people who buy probiotics on their own aren’t aware of this either, and so they also aren’t receiving optimal benefits from the probiotic they’re taking.

What Are Some Of The Benefits Of Taking Probiotics?

I’d like to discuss some of the benefits of taking a good quality probiotic. Probiotics can have many beneficial effects. Here are some of the different benefits that probiotics can provide:

  • Helps to improve digestion and nutrient absorption
  • Modulates the immune system
  • Plays a role in the synthesis of vitamins
  • Can inhibit certain pathogens
  • Enhances motility of the gut
  • Involved in the production of short-chain fatty acids
  • Certain strains (i.e. Saccharomyces boulardii) can help improve intestinal permeability

Several animal and human studies have provided strong evidence that specific strains of probiotics are able to stimulate as well as regulate several aspects of natural and acquired immune response (1). There is also evidence that taking probiotics is effective in the prevention and/or management of acute gastroenteritis and rotavirus diarrhea, antibiotic-associated diarrhea and intestinal inflammatory disorders such as Crohn’s disease and pouchitis, and pediatric atopic disorders (1). Probiotics might also be beneficial in people with allergies, cancer, AIDS, and respiratory and urinary tract infections, and they might be able to reduce the risk of developing osteoporosis, obesity, and type 2 diabetes (2). Probiotics also can enhance the nutritional content and bioavailability of certain nutrients (3).

How Do Probiotics Work?

When going through my Masters in nutrition program, I took a course on “Gastrointestinal Imbalances”, which was taught by Dr. Jason Hawrelak. Dr. Hawrelak is a naturopathic doctor and western herbalist who focuses on both acute and chronic gastrointestinal conditions. Everything he taught was research-based, and the following were the mechanisms of action he discussed with regards to probiotics:

1) Competition from adhesion sites. For example, certain invading pathogens bind to receptors, but probiotics such as lactobacilli can bind to the same receptors. This will prevent the adhesion and subsequent invasion of the pathogen.

2) Modification of the microbial flora through the synthesis of antimicrobial compounds. Some strains of probiotics can synthesize substances which inactivate certain pathogens. One important thing to keep in mind is that not all strains of probiotics produce antimicrobial compounds.

3) Probiotics can stimulate the immune response and cause increased secretion of immunoglobulin A, elevated natural killer cells, or enhanced phagocytic activity of macrophages. While most people associate probiotics with gut health, many people don’t realize that approximately 70% of the immune system is in the gut. And taking probiotics can help to improve the health of the immune system.

4) Probiotics may compete for nutrients that would otherwise be utilized by pathogens. This is self explanatory, as if a specific pathogen needs certain nutrients to survive, and if certain strains of probiotics compete for the same nutrients, then having a healthy gut flora can lead to less nutrients available for the pathogens.

Which Strains of Probiotics Should You Take?

As I mentioned before, the strain you purchase makes a difference. For example, if someone is experiencing constipation then taking a probiotic supplement which has B. lactis Bb12 might be beneficial (4). If someone has gastrointestinal Candida then taking a probiotic with the strain L. rhamnosus GG would be beneficial (5). L. rhamnosus GG is also beneficial for intestinal dysbiosis. If someone has H. Pylori then taking a probiotic supplement with the strains L. acidophilus LA5 and B. lactis Bb12 can be beneficial (6). If someone has a urinary tract infection then the strains L. rhamnosus GR-1 and L. reuteri B-54 would be beneficial (7).

This is not how most people choose a probiotic. What usually happens is that they visit their local health food store and ask the person working there if they can recommend a good quality probiotic. Since most healthcare professionals don’t have a good understanding of probiotic strains, it’s no surprise that many people working in health food stores don’t have a great deal of knowledge in this area either. In most cases they recommend what they feel is a good quality brand, and they might recommend a specific potency depending on one’s condition. For example, if someone is taking antibiotics and is looking for a probiotic then they might recommend a high potency probiotic that has many different strains. However, if someone has a specific condition they usually won’t have a good deal of knowledge as to which strains are the most beneficial for this condition.

You want to make sure to take well-researched probiotic strains. This will greatly improve the chances of taking a supplement which will have therapeutic actions. I can’t say that I’m an expert when it comes to all of the different probiotic strains. However, I can say that when I recommend a probiotic supplement to my patients I do try to recommend probiotics which include well-researched strains.

How Do You Choose A Good Quality Probiotic?

Choosing a good quality probiotic supplement can be a challenge. Some people simply choose a product with many different strains and a high potency. If you’re sure that this probiotic supplement is from a good quality company then it might have therapeutic value. But once again, you need to realize that specific strains will have specific functions. As a result, the same probiotic supplement that works for “patient A” might not be effective for “patient B”.

When choosing a probiotic supplement, there are two main factors you need to consider. As I just mentioned, you want to be aware of the characteristics of the strain. The second factor you need to be aware of is the viability of the microorganisms. This is where the quality of the company comes into play, as the manufacturing procedures of the company is important, as is the packaging and storage. And of course most people don’t purchase probiotics directly from the company, but they either purchase them at a health food store, retail store, online, or from a healthcare professional. And so the companies which manufacture the probiotics ship the supplements to these companies, and so the transport mechanism also has to be considered.

Some strains need to be transported with an ice pack, while others are stable (unless if the temperature is extremely hot). Some probiotic supplements don’t need to be refrigerated, although even when this is the case it’s still a good idea to refrigerate them after being purchased. Although some sources will say that probiotics should be taken on an empty stomach, you ideally want to take a probiotic supplement with meals.

What Potency Is Ideal?

As for how potent your probiotic should be, it does depend on the situation. Not everyone needs to take a probiotic with 75 billion CFU. And some people don’t do well when taking high doses, as they experience gas and bloating. On the other hand, some probiotic supplements only have a few hundred million CFU, which frequently isn’t potent enough to produce a therapeutic effect.

Once again, the quality of the probiotic supplement is important. You can purchase a probiotic supplement that has 100 billion CFU, but if the strains aren’t viable then you might only be taking something equivalent to 5 billion CFU.

Can You Get Probiotics From Eating Fermented Foods?

Fermented foods can be a good source of probiotics. Some examples of fermented foods include yogurt, kefir, sauerkraut, and kimchi. Of course if someone is trying to avoid dairy (which I commonly recommend) then they won’t want to consume fermented dairy products, such as yogurt and kefir.

As for whether fermented foods have therapeutic effects, it of course depends on which food you’re eating. For example, many brands of yogurt don’t have a sufficient number of viable microorganisms, although many yogurt manufacturers routinely add certain species of probiotics. As I mentioned earlier, the strains will make a big difference. For example, both sauerkraut and kimchi have strains of L. plantarum, which have been proven to survive exposure to gastric acid and bile salts. Certain protocols such as the GAPS diet rely heavily on the use of fermented foods to help heal the gut.

Do You Need To Take A Separate Prebiotic Supplement?

Examples of prebiotics include fructooligosacharides (FOSs), galactooligosaccharides (GOSs), lactulose, and inulin, and their main purpose is to help to increase the number of beneficial bacteria, while at the same time reducing the number of pathogens. They can also enhance the immune system, improve the absorption of certain nutrients such as calcium and magnesium, help with constipation, and might help with other health issues. Some argue that taking prebiotics can serve as a substrate for candida and certain pathogens, although this is controversial.

As for whether it is necessary to take a separate prebiotic supplement, it really depends on the situation. You can get prebiotics by eating certain foods, such as asparagus, onions, garlic, artichokes, and chicory root. But if someone has an imbalanced gut flora then in some cases it might be a good idea to take a separate prebiotic supplement.

Understanding The Different Species and Strains

I’m not going to discuss all of the different species, but I did want to briefly mention the benefits of some of the strains I commonly recommend to my patients:

Lactobacillus acidophilus. This is probably the most well known species, and it is resistant to gastric acid and bile salts, along with pepsin and pancreatin. The strains Lactobacillus acidophilus LA-5 and LA-14 have been shown to inhibit certain pathogens (8) (9).

Bifidobacterium lactis. This species produces large amounts of antimicrobial substances. It also modulates the immune system response to help against pathogens. The species Bifidobacterium lactis BB-12 and HN019 are known for their antipathogenic and immune enhancement effects (10) (11) (12).

Lactobacillus casei. This probiotic also improves the health of the immune system, and can be effective against certain pathogens such as H. Pylori (13) and Candida albicans (14). There is evidence that the strains Lactobacillus casei CRL 431 and Lactobacillus rhamnosus CRL 1224 can be effective against Aspergillus flavus (15), which is a fungi.

Lactobacillus plantarum. A few strains of lactobacillus have proven to be beneficial. Lactobacillus plantarum 299v has been shown to provide effective symptom relief, particularly of abdominal pain and bloating, in patients with irritable bowel syndrome (16) (17). Lactobacillus plantarum Lp-115 also can benefit people with gastrointestinal disorders (18).

Saccharomyces boulardii. Saccharomyces bouldarii is another well-researched strain with many different benefits. It is well known for helping people with a candida infection (19) (20). It also can be useful in the maintenance treatment of Crohn’s disease (21). It can help to improve intestinal permeability (22), and also can help to reduce inflammation and dysfunction of the gastrointestinal tract in intestinal mucositis (23).

VSL#3. VSL#3 is a potent probiotic supplement consisting of multiple strains, and has numerous benefits. It can help people with ulcerative colitis (24), and also improves symptoms in children with irritable bowel syndrome (25).

Keep in mind that there are other beneficial strains besides the ones I listed. Two others worth mentioning are Bifidobacterium longum Bl-05 and lactobacillus reuteri mm53. And there are other beneficial strains as well.

Can Taking Probiotics Help People With Thyroid and Autoimmune Thyroid Conditions?

As far as I know there is no direct effect of probiotics on thyroid health. However, most people with “thyroid” conditions either have Graves’ Disease or Hashimoto’s Thyroiditis, which are autoimmune conditions that affect the thyroid gland. And since probiotics can help to improve the health of the immune system, then one can argue that many people with these conditions can benefit from taking a good quality probiotic supplement and/or making sure they eat plenty of fermented foods. But of course there are many other benefits besides modulation of the immune system, as I mentioned in this post how certain probiotic strains can inhibit pathogens, can help with intestinal dysbiosis, and even help to repair a leaky gut. All of these can be factors in people with thyroid and autoimmune thyroid conditions.

So hopefully you have a better understanding about the benefits of probiotics, including how they work, how to choose a good quality probiotic, and some of the benefits of the different species and strains. While I commonly recommend probiotic supplements to my patients, remember that fermented foods can be an excellent source of probiotics as well. Also remember that specific strains will have specific functions, and so you can’t assume that all strains within a certain species will have the same exact function, as this usually isn’t the case.



  1. susan says:

    very good very complete info – does not look like you sell supplements? do you have a brand you recommend?

  2. Guest says:

    Very interesting text.
    I am one of “Hashimoto” people and can add something maybe usefull for others, from my own experience: not all probiotics are good for me and sometimes work against me. Best example is well known branded yoghurt with L.casei, what according to information should work as a defender for body, made me several times ill from well health (strange body response). The illness – a cold with higher temperature – stopped together with using them. “Several times”, because i didn’t believe a yoghurt can do so, but it happened everytime. But the yoghurt was ok for my son (non-Hashi).
    I use sometimes other probiotics in capsules from Pharmacy and they work well for me as well as normal natural yoghurt. I only read the ingredients and try to avoid products with L.casei.

  3. Diane says:

    So where can someone find a mix of some of the above. Or all of the above?

    • Dr. Eric says:

      Hi Diane,

      I’m not aware of a probiotic supplement which has all of the different strains I mentioned. But keep in mind that most people don’t need all of the strains I discussed. In fact, one of the main points of the blog post was that different people might benefit from taking different strains based on their condition.

  4. Bruce says:

    Because of this complexity you so clearly review Dr. E., I gave up almost entirely on commercially processed bacteria after a great deal of effort and expense in unsatisfactory trials. Not only are there many strains of probiotics, but many different manufacturers and many different strain-combinations. Saccharomyces boulardii (which you mentioned) was one example I researched and tried; in my case with worse than null results, but I didn’t know if this was due to the particular manufacturer, the way it was stored before my order was shipped, or other reasons. One exception to my generally dismal results in trials was the well-known probiotic Culturelle I used on a trip in Mexico, which I believe served to crowd-out unfriendly bacteria of the dreaded Montezuma’s revenge, and kept me safe. I would be willing to use this again under similar circumstances, or as a defense during a particularly bad flu season.

    But what I have ended up doing that has helped me significantly is to use non-dairy ferments such as fresh sourdough bread, fermented hummus and any of the vegetable ferments such as pickles & Sauerkraut. I began with the Bubbies brand and have ended up learning how to home ferment. This is not a casual undertaking I can assure you! There are all kinds of issues to address foremost the farm source from which the soil bacteria naturally seed the ferment, or the mother used to start the ferment. But, it seems to work well enough for me and apparently many others. From personal experience I’ve come to view commercial probiotics as a kind of inferior processed food.

    My next project is to try beet ferment, known as Kvass. A small trial of fermented garlic also awaits in the refrigerator for a 2-month planned cold finishing ferment/cure. One of the tastiest ferments and effortless ones for me is the late fall local cider run of non-pasteurized pure apple juice. It just goes there naturally all on its own, but it is a very short season. You’ve got to keep your eye on these or you miss them. Most recently we’ve had a great run of asparagus, and it never occurred to me to ferment them and put some up for a few month’s use. But I met a local lady giving out her samples of just this at my Coop a week ago. Missed it!

    • Dr. Eric says:

      Hi Bruce,

      Thank you for your comments, and for sharing your experience with the non-dairy fermented foods.

    • Bruce says:

      PS I might add that moderation has been important for me with home ferments. If these ferments are potent and fresh, a little goes a long way
      . Better in my experience to take more portions of smaller amounts and to be watchful of the results.

  5. Linda dc says:

    I used a probiotic my naturopath prescribed to me for about a year which really helped my ibs but it didn’t stop it so I started the Fodmaps diet with great success,gave up on probiotics(only take it if I get really upset stomach) and now use Water kefir (many recipes on web)daily for maintenance.things are looking good so far,and feeling great.

  6. Kristine says:

    My stomach is no longer bloated or “gasey” since I started drinking, 8 oz of Kefir, after supper. I have Hashimotos Thyroiditis, and for me, this made me feel better. That small amount of “dairy” is fine for me. I have trouble keeping my vitamin-D up, even though I get some sun, (the winter was tough) and I take D3-2000.

    I took notes from the web seminar offered here, and I am taking those notes, to my endo, next week. I had my hormones and cortisol levels checked. I also had a candida check, and it was negative.

    Synthroid is just not cutting it for me. One woman wrote that her endo added T-3, and she lost 8.5 pds in 3.5 weeks. I exercise every day, for the last 25 years. My arms seem to not tone at all. I am sick of it.
    All that effort and eating whole foods, that I cook. We never eat fast foods. Why can’t I even lose a single pound? Maybe you could do an article on this issue. It is the most frustrating of all symptoms, IMO.

    I love this website, and all the great information. Thank you Dr. Eric~

    • Dr. Eric says:

      Hi Kristine,

      Thank you for reading my articles and blog posts, as I’m glad you have found the information to be valuable. I’m glad drinking the kefir has helped. To answer your question about the weight gain, I’ve discussed this in the past, as while eating well and exercising regularly is important, other factors commonly cause or contribute to weight gain, such as hormone imbalances, insulin resistance, and even toxins. With regards to toxins and weight gain, Dr. Walter Crinnion wrote a book about this entitled “Clean, Green, and Lean”.

    • VSSO says:


      One thing that helped in losing weight was having earlier dinner (between 5.30 and 6.00) if possible and then later in the evening drink water or milk. Initially it is a little tough because body is accustomed to getting food a little later during the evening. But after those initial few days body gets accustomed to the new routine and that helped me drop 10lbs.

      I hope that works for you too.

  7. Bruce says:

    Guest’s comment on body temperature: “The illness – a cold with higher temperature” sounds like the body’s immune response to attacking bacteria.

  8. Rene says:

    I also have Hashimoto’s and have tried probiotics once but it didn’t work for me either.
    I recently ran into an article which confirmed my experience:

    It states that:
    “Some probiotic strains have anti-inflammatory effects and provide benefit in autoimmune disease, whereas other strains may aggravate autoimmunity. For instance, a study conducted in Denmark found that specific strains of Lactobacillus acidophilus and Bifidobacterium bifidum reduced regulatory T-cell activity, which could increase inflammation and aggravate Hashimoto’s,[12] whereas another study found that Lactobacillus rhamnosus HN001 and Bifidobacterium lactis HN019 reduced inflammation without affecting Hashimoto’s antibodies.[13] ”

    The brand I was taking contained Lactobacillus acidophilus which according to the above article is pro-inflammatory.

    • Rene says:

      Maybe taking a specific type that only contains Lactobacillus rhamnosus HN001 and Bifidobacterium lactis HN019 might be beneficial?

    • Dr. Eric says:

      Hi Rene,

      If you read the article carefully again you’ll notice that it says that “specific strains” of lactobacillus acidophilus can lead to an increase in inflammation by reducing regulatory T cells. This doesn’t mean that all strains of lactobacillus acidophilus result in an increase in inflammation. And this is why in the post I stated that you want to take well-researched probiotic strains.

  9. laura says:

    I have been diagnosed with hashimotos for about 1 year. Since then I have went Gluten Free and eating Organic foods along with drinking coconut water daily and eating 1 yogurt daily because of frequent yeast infections. I have been taking the least dosage of synthroid for about 5 months now but I am still very tired and get run down every day. I have thought about taking turmeric daily and also a probiotic but there are so many. Are you familiar with Dr. Formulated Protiotics once daily womens 50 billion, with 16 probiotic strains? Thank You

  10. Janel Simien says:

    I have thyroid disease. I was diagnosed with hypothyroidism ten years ago. I stopped taking my thyroid medicine approx. five years ago. I chose to treat my thyroid with over the counter supplements, such as shatarvari. I no longer take shatavari, but, I try to eat better. Even though I still eat rice and bread every once in a while, I don’t eat it half as much as I used to. Even when I took thyroid medicine, my thyroid would hurt and I would lose my voice often. I have not loss my voice since I stopped thyroid medicine. ( I used to take Armour and Synthroid).
    However, at one time, I was taking so many supplements that my body was becoming toxic. So…..I cut down to nothing and just trying to manage with the foods I eat.
    Last year, I bought a case of probiotics and began taking them. My thyroid started hurting, so, I stopped taking them and gave the rest of the probiotic pills away. My thyroid stopped hurting.
    I recently bought the little stick powdered probiotics plus prebiotic….after a couple of days, my thyroid was hurting. I stopped taking the probiotic and magically my thyroid stopped hurting!
    All of my life, I have suffered with constipation. I desperately want to benefit from a probiotic, but, I truly don’t know what to take.
    Please, if you have experienced what I went through and have the solution, please let me know.

    Respectfully, Janel Simien

  11. Rachel says:

    Dear Dr. Eric,

    Read this article very carefully, as I recently started the AIP diet and believe it would be helpful to add probiotics. I looked for a probiotic containing b lactis Bb12. The only thing I found is Optibac Fiber, from the UK. It is said to be very harsh and contains fructose, not something one would want to add when on the AIP diet. I would also like to add L. rhamnosus GG. Another product by Optibac (for women) is the only one that I can find.

    Please, are you able to recommend products that would provide these probiotics?
    Thank you

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Get Your Free Guide Entitled
“The 6 Steps On How To Reverse Graves' Disease & Hashimoto's Through Natural Methods”
You will also receive email
updates on any future webinars
on natural thyroid health.

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Natural Treatment Methods:
Graves Disease Treatment
Hypothyroidism Treatment
Hyperthyroidism Treatment
Natural Thyroid treatment

Conventional Treatment
Radioactive Iodine
Thyroid Hormone