The Importance of the Microbiome in Hashimoto’s

Hashimoto’s and other autoimmune diseases have multiple causes. There is no single origin and, therefore, to date there is no single solution.

Instead, successful healing requires exploration into the multiple causes of the disease and healing the areas that need attention.

One such area that has recently been discovered to have a major impact on health and disease is the microbiota or the tiny living organisms that populate our bodies.

These various different species of bacteria, viruses and fungi make up the lion’s share of our DNA and are more a part of us than we realized.

In this post we explore the role of bacteria in the formation and healing of autoimmunity and Hashimoto’s.

We Are Bacteria

One of the fundamental things to understand regarding the world of microbes is that they are not separate from us. We are one. And I don’t mean this is a woo woo, philosophical sense.

I mean this is a very real, practical sense.

The Human Microbiome Project

Microbiome Global Map

The Human Microbiome Project (HMP) was a United States National Institute of Health (NIH) sponsored project whose goal was to identify and study the microorganisms (little critters) that are found in association with both healthy and diseased humans.

Launched in 2008, it was a five-year project, with a total budget of $115 million. The ultimate goal was to test how changes in the human microbiome are associated with human health or disease.

Here’s some of the things that they discovered:

•    No two people have the same microbiome, not even identical twins.

•    There are approximately 10 trillion bacteria in (and on) our bodies vs. only 1 trillion human cells.  You read that correctly.  We have 10x more bacterial cells than we do human cells.

•    Bacterial genes outnumber human genes 150:1.

•    Our cells have incorporated and use bacterial DNA.

•    There are over 1,000 species of bacteria found inside our GI tract alone.

•    There are over 1,000 different proteins made by bacteria in the gut which are essential to optimal body function.

•    Several diseases are directly associated with a disruption to the microbial ecosystem of the gut.  These include, but are not limited to: Asthma, Allergies, Crohn’s, IBS, Obesity and, in my humble opinion, Hashimoto’s.

•    Pathogenic bacteria/organisms like candida, h.pylori, etc. have evolved to be natural inhabitants of our gut, and under ideal conditions don’t always lead to illness or cause disease.  On the contrary, sometimes they provide vital functions and we’re worse off without them.

•    Destroying these pathogens completely has physiological consequences that we’re just beginning to understand. (Remember when the appendix didn’t matter? Oh yeah, we were wrong about that, too. It has been found to be a store house of good bacteria.)

The Truth About Antibiotic Therapy

One thing that looking at this research makes abundantly clear is how potentially destructive antibiotic therapy is, especially for children (for whom it is  often prescribed).

Of course, these drugs have saved countless lives, when they are used appropriately. But they have been abused and overused and we are now seeing the consequences in new bacteria resistant strains, as well as a wide variety of diseases like digestive disorders and autoimmune disease.

Giving a child or adult antibiotics every time they get an upper respiratory infection (most of which are caused by viruses not bacteria) is often doing little more than setting the table for future disease and a decline in natural immunity and actually makes them more susceptible to infections.

This also has physiological consequences in our guts and it makes us more vulnerable to pathogens because the beneficial bacteria that are killed play an important role in our immune system.

It’s time we stopped looking at medicine as, simply, a war between invading pathogens and our body. It’s more nuanced than that.

As I have written in the past, we are a collection of interacting ecosystems and researchers now know that these ecosystems are composed of a wide variety of friendly organisms.

Just like we need to learn to be good stewards of the earth and our external environment, we also need to view the insides of our bodies in this way and start caring for these internal ecosystems in the same way.

The lesson here is that we can’t just eradicate ourselves to good health. We see this time and time again with pesticides, herbicides and antibiotics.

Lots of patients and practitioners still have mind set that says, “All we need to do is kill ___________(choose your favorite pathogen), then you’ll be healthy.” And many of us have been trained to think and treat this way, whether it is with drugs or herbs and natural supplements.

Well, a lot of times this approach can result in a disruption of the ecosystem of the gut (and sometimes overgrowth of other pathogens). And this doesn’t just happen with drugs like antibiotics, it also happens with natural products like herbs that kill pathogens in our bodies.

It’s time we create a new way of doing things. Figuring tht out is beyond the scope of this post. So, first let’s try and figure out what a “healthy” microbial ecosystem is.

What Exactly Does A “Healthy” Microbiota Look Like?

Here’s the thing about your digestive tract, it’s not just one ecosystem. Really, there are several distinct ecosystems that overlap and interact with one another.

Let’s break it down:

There’s your mouth, your esophagus, your stomach, your upper and middle small intestine, your lower small intestine and your colon. The bacteria that populate each of these ecosystems is quite different.

And to complicate things, there’s the intestinal mucosa and lining which has distinctly different species than the space in side the intestine .

In addition, no two people have the same microbiota. Early research on this subject came up with the idea of “enterotypes” which are microbiota types like blood types, but they only looked at a small group of people.

After looking at a lot more people from different cultures researchers determined that it wasn’t so clear cut and there’s so much variation that it’s really hard to be definitive about this. (It’s more nuanced – I think that’s my new motto 🙂 ).

In the following diagram you can get a sense of the number and the diversity of bacteria that populate these various ecosystems.

Microbiome Species


Frankly, this makes the claims and marketing of probiotics pretty ridiculous (more on that in a moment). No one or two strains of bacteria are going to properly populate your entire digestive tract. Nor does everyone need the same strains.

Furthermore, diversity is more important than overall population of certain strains.  A diverse microbiome is the very definition of good health. With diversity comes proper function, more resistant to pathogens, infections, and overgrowth from other species of bacterial, yeast, etc.

How Do These Bacteria Get Here?

Here’s what we have learned about this:

 •    During vaginal childbirth, we are exposed to our mother’s microbiome.  This occurs via the birth canal, and exposure to feces during the birth process.

 •    We receive between 400-600 different species via breast milk.  Also, breast milk contains a powerful prebiotics (which feed good bacteria). This helps these strains to proliferate and colonize inside our GI tract.

This means that births via C-Section and feeding babies formula (rather than breast milk) can have a very real impact on the diversity and overall population of a person’s microbiome.

•    An infant’s microbiome reflects the mother’s vaginal bacteria initially, and then it begins to resemble the mother’s mouth, skin, and gut after that.

•    After the very early stages of life, the microbiome is generally populated via environmental and food exposure.

•    Skin-to-skin contact with parents provides some of the strains comprising a healthy microbiome.

This means that anti-bacterial soap, hand sanitizers and overall germ-phobia can also have a very real ( and not so beneficial) impact on the development of healthy GI flora – especially related to diversity. You want your infants and kids exposed to dirt and grime ( this news will be liberating for some parents and horrifying for others).

Environment also really matters when it comes to a healthy microbiome.

•    Those who live in rural environments generally have much greater microbiome diversity than those who live in urban environments. (Working the earth is not just good for the soul, it turns out.)

How is this Connected to Autoimmunity and Hashimoto’s

There is a good deal of evidence to support the idea that the microbiome has a profound impact on the immune system and that it is involved with the prevention as well as initiation and progression of autoimmune disease.

But the idea that probiotics are always good for people with autoimmunity is not supported in the research, at all. On the contrary, there is some evidence that opposite is true and that certain strains of bacteria cause different types of immune responses and affect different autoimmune diseases differently.

And there are many complicating factors here including genetics, environment and type of disease. And mutations and changes in the microbiome can also result in different outcomes.

Like most things, the reality is that there is enormous individual variation and determining whether or not probiotic therapy is beneficial and which probiotics are appropriate is not an easy thing to do.

The reality is that we are only beginning to understand this complex interaction between our immune systems and the microbiome. However, there are two theories about how the microbiota can help protect against autoimmune disease.

Two Theories on How Microbes Protect Against Autoimmunity

The first is known as “specific lineage hypothesis” and it says that in genetically predisposed animals or humans, the microbiota could provide signals that calm our body’s immune responses.

As a result, the microbiota stays in a homeostatic (balanced) relationship with us.

Basically, the microbes are saving themselves and we have acquired these lineages from our mother and they have been passed down.

When a specific microbial lineage is expanded, it blocks the development of autoimmunity. It does so to improve its own odds of staying in this expanded state by suppressing our inflammatory and adaptive responses.

Autoimmunity is calmed as a side effect of this microbial self-preservation.

The second theory is called the “balanced signal hypothesis” this says that the host’s interactions with microbiota are independent of the precise microbiota composition and that the host’s genetics plays a critical role in the conversation with microbes.

So that your genetic profile is more important.

Whereas a balanced host response to good bacteria and this bacteria’s effort to reduce this response do not affect disease development, the inability of the host to control the microbiota properly results in stronger negative signaling provided by the microbiota and a reduction of autoimmunity.

Again, the microbes are looking out for themselves and sending out signals that result in calming autoimmunity.

(Both theories predict that the increase of tolerance would be lost in germ-free conditions without the microbes.)

There is also evidence that the microbiota behaves in different ways depending on the circumstances. It’s not static, it adapts to changing conditions.

Here’s the thing, the microbiota always faces 2 competing problems:

  1. Making sure our immune system doesn’t destroy the microbes (they have to induce us into creating tolerance).
  2. And our immune systems must also make sure they stay under control and they don’t breach the barrier systems and get into the rest of the body and  cause infections there.

So there’s this constant balancing act that we and our microbiome must do to keep each other healthy.

Bottom line is this, you need to be cautious when using probiotics with autoimmunity and don’t just assume that any variety is going to help.

They might, in fact, not help or make things worse. So, like everything else, you need to carefully assess your need for them and then experiment and keep track to see if they are, in fact, giving you the desired result.

Choosing the Right Probiotics

One question I frequently get is “which probiotic is a good one?” As with all things Hashimoto’s related you can see that this is not a simple question and there is so much individual variability that it really depends.

Probiotics are big business. Global probiotics market was valued at $32.06 billion dollars in 2013.

There are literally hundreds of brands and many make outrageous health claims. I’ve experimented with a number of different brands both personally and professionally. For some patients the results have been good, in others, there’s been little or no noticeable effect and for some they’ve actually had adverse reactions.

Some manufacturers and proponents might say these are “die off” reactions and they may be, but it could also be that in that particular individual with that particular genetic makeup and immune profile that they were inappropriate. ( I think that sometimes practitioners use “die off” to cover incompetence).

When deciding which type of probiotic to choose  there are a few things that are really important to determine.

Will the strain actually survive digestion to be of any help?

Are the strains actually found in nature?

Are they good quality?

Let’s take a look at these issues:

Will the Strain Survive Digestion?

In order to have any benefit, a probiotic must be able to reach the desired location within your GI tract alive (and the large intestine is by far the most populated bit of real estate in the GI tract).

Many strains of bacteria included in probiotic supplements today are very fragile, some requiring refrigeration.  The human gut, on the other hand, is not a hospitable environment. It has very low pH (extremely acidic) environments, it’s body temperature, and it has evolved to keep out invading critters.

A large study done on this subject was done by the Food Standards Agency (FSA), along with Reading University, in the UK.  They tested 35 popular commercial probiotic products, mostly comprised of lactobacillus and bifidobacterium strains.

Here’s what they found:

  • At pH 1 (optimal stomach acid) – none survived. That’s right, nobody made it out of the stomach alive.
  •   At pH 2-3 (weaker stomach acid production) – 18 of 35 showed 50% survival.  So half of the bacteria, in half of the products, survived.
  • Those 18 were then put through a test to mimic the environment in the small intestine, involving bile salt tolerance.  Of those 18, only 6 showed survivability – and a chance to actually make it to the large intestine.

Those 6 were put through survival tests to determine survivability in the large intestine, and only 4 survived the large intestines.

So, at the end of the day, only 4 of the 35 strains showed any chance of survival, and even that was at, or around 50%.

These are not very good odds of survival.

It’s safe to say that many of the probiotic products on the market don’t deliver on their claims because they don’t live long enough to do anything.

Are These Strains Found In The Natural World?

This is important and often overlooked. In our arrogance, man has made the false assumption that we can improve upon and do better than billions of years of evolution. Time and time again this has been proven wrong. Remember the Biosphere 2? That experiment didn’t go well.

Mother nature is infinitely more experienced and developed than we are. If we survive as a species, it will only be because we learn to leverage that truth.

(Bacteria are among the earliest forms of life that appeared on Earth billions of years ago. Many believe that more complex cells developed as once free-living bacteria took up residence in other cells, eventually becoming the organelles in modern complex cells. The mitochondria that make energy for our body’s cells is one example.)

Those strains found in nature have a very long track record of survival and adaptation. Those manufactured in laboratories do not. It’s important that the strains you take are found in the human microbiome.

In addition, this also highlights the importance of diversity. Having variety in the gut matters. Taking high doses of a few specific strains, and eating large amounts of the same fermented foods every day can result in self-induced bacterial overgrowth where a couple of species dominate.

This is the same principle that applies to any ecosystem. When you overload a particular species, things get out of balance and it compromises the entire system.

Are These Products Good Quality?

Because probiotics are such big business and are unregulated, this is an important concern. I looked at a study from Consumerlabs, which was a thorough review of many popular probiotic products and strains.

They found that two products did not have the amount of organisms that they claimed. Essential Formulas Dr. Ohira’s Probiotics and Jameison Probitoics were 2 brands that had significantly less number of organisms than advertised. Click here to read the full report.

Spore Bacteria: The Answer?

One type of probiotic I have been experimenting with is called spore form bacteria. These are organisms that survive the stomach and small intestines quite well. They have evolved to be very stable in the environment and also to colonize the GI tract very effectively.

These check all the boxes of the questions we just looked at. They survive digestion, are found in the natural world and they are of superior quality.

What do we know about spores?
•    They are found all over the environment (in soil, vegetation, aquatic environments, and the digestive systems of many living species like insects, marine life, mammals, etc.) what this means is that as a probiotic they have evolved to be very resilient.
•    Spores remain dormant until they get to the intestinal tract and then they colonize the bowel.  They pass through the stomach and upper GI and survive.
•    They are normal organisms of our digestive tract and are part of the human biome.
•    They have been used in industries where efficacy is closely monitored, for example the pharmaceutical and agriculture industries.
•    Human studies have proven spores to be safe and effective.

Why choose spore form bacteria over others?

What’s interesting about these bacteria is that they have been shown to be effective in several ways.

In a previous post I investigated oral tolerance and since then I’ve been looking for supplements to help improve it. These spore form bacteria have been shown to do this in a number of ways:

  1. They provide pre-biotic and healthy conditions for the proliferation of beneficial flora, increasing the population and diversity of beneficial GI microbes. So, they actually create an environment that helps other good bacteria. (They also produce powerful natural antibiotics to protect against unwanted pathogenic bacteria).
  2. They help increase Short Chain Fatty Acids (SCFA) production.  SCFA’s are known to increase colonic blood flow, improve fat metabolism, lower cholesterol and triglyceride levels, and reduce gut/systemic inflammation. SCFAs like butyrate are effective in increasing oral tolerance.
  3. They help to develop GALT (Gut-Associated Lymphatic Tissue), this is important for healing leaky gut and these bacteria are helpful in healing the intestinal lining and mucosa.
  4. They produce digestive enzymes, specifically protease, which aids in the digestion and absorption of dietary proteins – this is critical in calming reactions to dietary proteins, the source of many adverse food reactions.
  5. They help in the production beneficial B-Vitamins, Vitamin K2, Quinols, Carotenoids, Asaxanthin, Lycopene, and Lutein. In fact, this is a probiotic formulation that delivers powerful, highly-bioavailable carotenoids via in-vivo production. Bacillus indicus is a patented, carotenoid rich strain.
  6. They increase T & B Lymphocytes which are critical for optimal immune function. They may help shift from a state of Th2 dominance (allergies, asthma, inflammation) to more of a Th2/Th1 (adaptive immune response) balance. They may also improve pattern recognition, which can help with autoimmune conditions – by lowering the number of instances of your immune cells attacking your own tissues by mistake.

What brand has these?

The brand that I’ve been experimenting with with promising results thus far is called Megaspore Biotic. MegaSpore

This is not available in retail stores because it is pharmaceutical grade and really requires some understanding and clinical know how in order to administer it.

It contains five bacillus spore probiotics– the value of each strain is supported by numerous studies and scientific publications. All strains are produced in a GMP facility under drug manufacturing guidelines.

It’s a very powerful spore probiotic formulation, and it delivers more than four billion live probiotic cells daily – a dose that matches and exceeds many other products on the market.

Are there any downsides?

Nothing is perfect. There are some indications that some strains in this product may be histamine producing.

But this is not only true of these strains. There are a number of different bacterial species that produce histamine. For example, these common probitoic species are all histamine producers: E. coli, Klebsiella pneumoniae, Lactobacillus bulgaricus, Lactobacillus casei, Lactobacillus helveticus, Lactobacillus reuteri. And many of these are found in yogurt and other probiotic products.

So, be aware if you have histamine intolerance that you may have to be very careful about the probiotics you choose. These species have been found to degrade histamine: Bifidobacterium infantis, Bifidobacterium longum, Lactobacillus gasseri, Lactobacillus rhamnosus, Lactobacillus plantarum, Lactobacillus salivarius

Bottom Line?

Bottom line is this. A healthy microbiome is essential to good health. I can help increase oral tolerance, help you fight infections and overgrowth of destructive species, it can help you lose weight and can also help heal autoimmunity.

However, more is not always better and different species populate different parts of the ecosystem of the gut. So varying different products and different foods that feed those species is essential.

Furthermore, using spore based probiotics can be a beneficial part of your strategy.

Finally, it’s time we stop thinking of the gut as a battlefield of the enemy. Like a farm, it must be weeded, cultivated and nurtured.

Need Help?

If you’re not sure what to do, feel lost or are not getting the results from probiotics that you hoped for, I’m available for a consultation to discuss testing and treatment options.

Click here to book a consultation: Yes! I’d like to speak with Marc.

In the meantime, take good care of your microbiome.

References: Gut microbiome in health and disease. Role of natural microbiota Role of microbiota in health and disease Microbiota and autoimmune disease Diet, gut and autoimmunity Microbiota and autoimmunity Microbiota and autoimmune disease Role of microbiota in cancer and autoimmune disease Systemic effects of gut microbiota, relationship with disease and immunomodulation Gut Microbiota and Hashimoto’s Autoimmunity and the gut Does microbiome play a role in autoimmune disease? Self-explanatory Hypothyroidism and SIBO Fecal transplants for treating autoimmunity Gut bacteria and TH-17 Assessment of Microbiome Research Self Explanatory What are the consequences of the disappearing microbiota? Has the microbiome played a critical role in the development of the adaptive immune system? Value of probiotics market Adhesion of  31 actobaccilus strains Probiotics that degrade histamine


About the Author Marc Ryan

So now, not only is it my profession, it’s my passion, and it’s personal. I’ve been joking with people lately saying it’s a blessing and a curse. A blessing because I really get it, and a curse because I really got it! ?

follow me on:

Leave a Comment: