Are Probiotics Right for You?

In the past, I’ve spoken about gut health and its importance in managing inflammation in our bodies. For us living with Hashimoto’s, the importance of achieving this balance is even more imperative. One of the simplest ways of contributing to our microbiome is in the form of probiotics. Do you wonder if you’re taking the right amount, or if the probiotic of your choice is working properly? I’ll help you demystify what’s inside those capsules and fermented foods by taking a closer look at how probiotics work in our bodies, and when they are necessary.

What Are Probiotics?

You’re probably familiar with the term probiotics. You may even incorporate them into your daily health routine. But do you know what they are? Probiotics are naturally occurring live microorganisms that are beneficial to our digestive tracts. These bacteria are native to our bodies, and can be overrun or depleted in various ways, including antibiotic usage, an overgrowth of “bad” bacteria, stress, aging, hormone replacement therapy, and a host of other issues. When you consume fermented foods or take a probiotic supplement, you’re ingesting strains of bacteria identified by genus, species or subspecies, and strain. Each one of these strains serves a different function in our digestive systems. In most successful cases, these bacteria enter your GI tract, pass through your stomach and make their way into the small intestine and colon, where they will reside and colonize.

Why Do I Need Probiotics?

It is no secret that we’re living more complicated lives these days which can take a toll on our intestinal flora. High-stress workdays, rushing through meals, and inadequate rest all contribute to the depletion of beneficial bacteria in our systems. Restoring healthy bacteria balance can help us get the most nutrition from the foods we eat, and can improve many digestive complaints. But for us with Hashimoto’s, there’s an even greater reason to replenish these bacteria. Intestinal sulfatase is a type of bacteria that converts inactive T4 into T3, the active thyroid hormone. Overgrowth of non-beneficial bacteria called lipopolysaccharides (LPS) can reduce thyroid hormone levels, dull thyroid hormone receptor sites, increase amounts of inactive T3, decrease TSH (Kresser) and potentially exacerbate Hashimoto’s symptoms.  By replenishing beneficial bacteria, you are supporting your thyroid and the proper functioning of your gut.

What Goes Wrong?

Despite being a $30 million industry, probiotics are not always as effective as we want (or need) them to be. There are several reasons why.

Hashimoto’s:  Probiotics or Fermented Foods – Which is Best?

For some, beneficial intestinal flora can be replenished by consuming fermented foods in moderation.  I always recommend introducing fermented foods very slowly and limiting them to a fork-size serving.   Sometimes fermented foods trigger histamine issues, bloating or contribute to yeast overgrowth in people who have an autoimmune condition including Hashimoto’s.  

Have you ever experienced an “intoxicated feeling” after consuming Kombucha or other fermented beverages or food?  I have, and this is a signal that you are overdoing it on fermented products.  More is not better.

As for probiotics, I am always for targeted strains found in probiotic supplements.  The higher quality supplements will have scientific research behind them to support their quality, manufacturing standards, and efficacy.  Just like with fermented foods, I always recommend starting low and increase the dose very slowly.

Probiotics “crowd out” the bad bacteria and this die off can result in you experiencing a host of distressing gastrointestinal symptoms.  Taking a conservative approach to starting any probiotic is best.

Researchers are also starting to take a second look regarding how long we should use probiotics.  Should we be taking them long-term on a daily basis or forever?

It depends on a few factors

Inundating your body with bacteria, good or bad, can lead to an overgrowth of bacteria.  It does happen.  If you’ve ever experienced or know anyone who has experienced Small Intestinal Bacteria Overgrowth (SIBO) you know, it’s a challenging situation.

However, if your diet is poor, e.g. based on the Standard American Diet (SAD) and you are not eating organic foods then your body is being overloaded with antibiotics from conventional foods (especially meat and dairy) and the bacteria in your GI tract is being killed off every day.

In this case, the use of probiotics is probably wise – but not the same probiotic over and over.  It is crucial to rotate strains to prevent dominance or overgrowth of one species.

On the other hand, if your diet is rich in living organic fruits and vegetables and grass-fed organic beef and pastured organic chicken at some point your microbiome should be able to take over.  The chronic use of probiotics daily and forever, for someone who is eating healthy and managing stress is currently a focus for researchers.  Dr. Zack Bush recommends in his article Why Probiotics Don’t Always Work  patients who have been on chronic probiotics should stop them cold turkey.”

There is Not Enough Variety in Our Strains

Many probiotic supplements and foods have a limited number of strains. Lactobacillus and Bifidobacterium are two of the most common types of probiotics, with many foods containing only one of these or a few additional, all the while our bodies are meant to host over 25,000 species.  And while we may experience relief of gastrointestinal and other symptoms when starting a regimen of these positive bacteria, our results are guaranteed to taper off after a short while. Wondering why this happens? The microorganisms we are introducing have already taken up residence!


Supplement with the right probiotic! Choose a probiotic that contains at least 35 billion colony-forming units (CFU) with as many strains as possible. While some supplements offer as many as 24 strains, they likely do not provide the diversity our bodies require. Remember that each type of bacteria is responsible for a different process!

The Probiotic Strains May Already Be Dead

Since probiotics are living organisms, they must be maintained properly.  Preparation, packaging, shipping, and shelf-life often contribute to the elimination of the bacteria.


Ensure that any supplement you purchase is superior quality and requires refrigeration if necessary (most high-quality probiotic supplements do). The recommendations listed below under Resources are all packaged and shipped with the delicate nature of the bacteria in mind.

Probiotics Can’t Survive Stomach Acid or Bile

For these beneficial bacteria to thrive and populate they must make it all the way into your small intestine and colon. That’s a long way to go for these microscopic organisms! Hydrochloric acid, the digestive juice in your stomach as well as bile produced by the liver can break down many of these cultures.


Choose supplements in capsule or sachet form that ensures controlled delivery. These are more stable and more likely to reach their destination and colonize.

Remember to Consider: Are Probiotic Supplements Needed Long-term?

As previously mentioned, taking the same probiotic for some time replenishes the same strains over and over again. If you begin to feel worse while taking a supplement, it may be a signal to stop. By repeatedly supporting the growth of distinct strains, we create a type of monoculture. An overgrowth of good bacteria can still be problematic. Appropriate supplementation is typically one to two weeks in people eating a healthy anti-inflammatory diet devoid of antibiotics. Communication between the bacteria and the gut can only find a healthy balance once supplementation has ceased.

You may have experienced great results when first introducing probiotics into your diet, but even the best supplement cannot heal intestinal permeability, also known as Leaky Gut Syndrome, which is the pathway to autoimmune disease. Probiotics also will not eliminate a food sensitivity. Hashimoto’s introduced many uncomfortable symptoms into my life, and though probiotics can help prevent digestive distress, they are in no way a cure-all. If you have been supplementing long-term or using fermented foods to replace beneficial bacteria, you may find that your digestive system improves by stopping the probiotic altogether.

In Summary

If you’ve been required to take an antibiotic, or have gastrointestinal complaints such as diarrhea or constipation, high-quality probiotic supplements can help to ensure that your intestinal flora is in balance. For most of us, the stress of our daily lives and managing the ups and downs of Hashimoto’s is enough to deplete many of the beneficial bacteria our bodies require to thrive. Probiotics can help, but remember to encourage your microbiome to take over again. If you worry that you’ll miss out on beneficial bacteria, know that fresh air, organic produce picked from your garden, and your favorite pet all expose you to these microorganisms. You deserve to live the fullest life possible, and encouraging your system to find balance is a wonderful way to boost the health of your entire body.


If you do opt for probiotic supplements, it is vital to choose the highest quality and those with scientific research to support their use.  It is also important to know the quality control and standardization practices of the manufacturer.  Always be mindful of what you choose to put into your body carefully.   I recommend the following as the best probiotics for Hashimoto’s:

Probiotic 50B

Saccharomyces boulardii

ProbioMax Daily DF*

Saccharomycin DF*

VSL #3

Theralac, Truflora, and Trufiber (Rotation Protocol)

*For Xymogen Products, please use our new patient referral code Well1


  1. Bush, Z. (2016, June). Why Probiotics Don’t Always Work. Holistic Primary Care, 17(2), 9-9. Print  
  2. The Thyroid-Gut Connection. Chris Kresser. (n.d.). Retrieved from