Good Gut Health: The Secret to Preventing Autoimmune Diseases?

A healthy gut can decrease the risk of developing autoreactive T-cells, decrease the activity of autoimmune promoting Th17 cells and boosting the function of autoimmune-protective Treg cells.

Good Gut Health

It’s pretty evident that people are concerned about having good gut health judging from the rise in probiotic products. 

What but does it mean really?  And why do some people believe it can help prevent autoimmune disease?

What do you do when your own body turns against you?  

For the 50 million Americans struggling with an autoimmune disorder, that is, unfortunately, not a rhetorical question or brain teaser.  It is a fundamental query that informs every decision they make, every minute of every day.

They have had their immune systems turn on them.  Rather than defending their bodies and keeping them safe, their immune systems have begun systematically destroying their own healthy tissues.  

Their symptoms may differ, depending on which parts of their bodies are under assault (see Table 1), but the problem they each face is inherently the same — how do they stop their own immune system from disabling, disfiguring and killing them?

Luckily, they are not without options.  Decades of dedicated research has made remarkable progress in figuring out how autoimmune diseases cause their symptoms, and how they can be stopped. 

Read Next: Top 5 Best Digestive Enzyme Supplements to Fix Leaky Gut

There are now an amazing number of medications and treatment options available that really help manage autoimmune symptoms.  

They have complicated names, and even more complicated mechanisms of action, but, in a nutshell, all of them aim to pretty much do just one thing: stop the immune system from attacking.  

Some of these treatments do this by stopping signals from moving between parts of the immune system.  Others keep certain immune cells from being able to grow and divide. 

Some others keep immune cells from moving freely through the body.   And yet others keep immune cells from releasing inflammatory chemicals responsible for actually killing off the body’s own tissues.

Table 1: Common Autoimmune Diseases and Their Symptoms

Autoimmune Disease

Destroyed Tissue


Type 1 Diabetes

Pancreatic beta-cells

Extreme hunger, thirst and frequent urination caused by high blood sugar

Multiple Sclerosis



(fatty tissue that protects nerve cells)

Fatigue; numbness; weakness trouble walking or seeing; changes in mood or cognition; muscle spasms; pain



Raised, red, itchy or painful patches of skin covered with silver-white flakes; joint pain

Crohn’s Disease


Abdominal pain, diarrhea, malnutrition, fever

Ulcerative Colitis


Diarrhea, abdominal pain

Rheumatoid Arthritis


Pain, swelling, stiffness and fever in the joints; weight loss

Hashimoto’s Disease


Fatigue, constipation, loss of hair, dry skin and nails, feeling cold, muscle aches, changes in cognition



can include:

skin, joints, kidneys, blood, brain, heart, lungs

Facial rash, joint pain, fatigue, muscle aches, changes in cognition, sensitivity to the sun, Raynaud’s, difficulty breathing, chest pain


Imperfect Treatments

Though these treatments work to keep autoimmune symptoms at bay, there is a glaring flaw in their design.  They keep the entire immune system from working.

Maybe they protect healthy body tissues from being attacked, but they also protect bacteria, parasites, viruses, and cancer cells, too.  

Trading in autoimmune symptoms for an increased risk of a life-threatening infection or tumor?  Not a fun choice at all.

But, it is the best choice medicine can offer right now.  There is, as of yet, nothing doctors can do to stop the immune attack on healthy body tissues without also hindering immune attacks on actual infections or cancer cells. 

This leaves those with autoimmune diseases in a rough spot.  They have to take medications that manage their symptoms, but these medications also put them at extreme risk for serious infections and cancer.

Now, there is no reason to believe that this will remain the case forever.

Researchers are hard at work developing better, more targeted treatments and are hot on the trail of any hint of a way to cure an autoimmune disease. Their dedication and the continual upwards progress in technology makes it likely they will, someday, find what they are looking for.

In the meantime, though, the downsides of the available treatment options make the best option for your overall health to not treat an autoimmune disease.  

No, your best bet is to never treat an autoimmune disease, because you never developed one in the first place.

Preventing Autoimmune Diseases

Researchers have identified a wide variety of dietary, lifestyle and environmental factors that can help protect you from developing an autoimmune disease, including:

  • Not smoking
  • Drinking moderate amounts of alcohol*
  • Not drinking coffee*
  • Avoiding exposure to paint thinners, nail polish remover, nail polish, dry cleaning chemicals, detergents, perfumes, glues or other environmental pollutants
  • Avoiding infections (bacterial or viral), especially chronic infections and
  • Maintaining a healthy vitamin D level

(*Note that while these behaviors — drinking less coffee and alcohol about 4x per week — have been shown to be protective for various types of autoimmune diseases, they are also associated with other health risks.  Coffee consumption is protective for liver health and longevity, while consuming even small amounts of alcohol increases the risk of cancer.  You will have to weigh the risks and benefits of drinking coffee and alcohol for yourself.  It may be helpful to speak to your doctor or nutritionist, as well.)

The most important factor in preventing autoimmunity, though, may be protecting your gut health.

Gut Health, Immune Function and Autoimmunity

Studies over the last few years have identified an unimaginably sophisticated network of communication between the immune system, the gut wall, and the millions of bacteria living in your intestines (called the gut microbiota).  

Amazingly, among these complex interactions, researchers found that gut health and the health of the gut microbiota are able to influence all three of the most important factors in developing autoimmunity:

  1. The number of autoreactive T-cells in the body
  2. The activity of helper T-cells in the body
  3. The number and activity of regulatory T-cells in the body

Let’s look at each of these, how they influence autoimmunity, and how they are influenced by gut health in detail!

Autoreactive T-cells, Autoimmunity and Gut Health

In many ways, autoreactive T-cells are the essential driving force behind an autoimmune disease.

T-cells are a type of immune cell designed to recognize and remember very specific molecules (usually bits of protein) from bacteria, viruses, parasites or cancer cells that you have already come into contact with.  

Their job is to scan your body for stubborn intruders who try to get past your defenses after you’ve already beaten them back once.  

If it finds one, it sends out an immediate alarm to the entire immune system to get back on the attack right now, and then starts multiplying like crazy to try and find other intruders.  (It is, after all, unlikely that one single bacteria slipped through all by itself — they usually live in colonies!)

In autoimmune diseases, just one single T-cell mistakenly recognizes a normal, healthy molecule in your body as the villain it’s after.  This is called an autoreactive T-cell. 

When it comes across this molecule in your body and sounds the alarm, the rest of the immune system, which has no reason to think the T-cell made a mistake, charge in with all the fury they would with a real invader.  This is what really starts an autoimmune disorder.

How does your gut health influence whether you have autoreactive T-cells in your body?  

It’s a little bit complicated, but basically, an unhealthy gut increases the total number of T-cells in your body.   This makes it more likely that one of them will accidently be autoreactive.

As I mentioned above, T-cells are made to remember foreign invaders that have made it into your body at least once.  

An unhealthy gut is really bad at keeping foreign molecules out the way it is supposed to.  It lets in bacteria, viruses, toxins, bits of food, digestive juices — all kinds of things that normally, in a healthy gut, would not be allowed into your body or anywhere near your T-cells.  Once in the body, through the wall of an unhealthy gut, each of these molecules can trigger the production of a T-cell.

If, by sheer bad luck, one of the molecules that gets through your unhealthy gut wall and makes a T-cell looks an awful lot like a molecule that exists in your body, you have a problem.  

Just like showing a police officer a blurry mug shot can result in the wrong person getting arrested — if they look similar — showing a T-cell a molecule that that is nearly identical to a molecule in your body, it can go after the wrong one, even if the details of the molecules are actually really quite different.  All at once, you have an autoreactive T-cell, simply because your gut couldn’t keep foreign molecules out of your body!

Mature Helper T-cells, Autoimmunity and Gut Health

Another key player in driving autoimmune diseases are a group of immune cells called helper T-cells.  Really, it’s mostly one specific group of helper T-cells called Th17 cells.

Th17 cells have a really important job in regulating your immune system.  They are actually responsible for telling T-cells whether they can attack anything — a bacteria, a virus, a parasite, a cancer cell, or your own body.  The T-cell can’t attack unless a Th17 cell gives it the go ahead. 

In fact, when a T-cell recognizes a villain it wants to attack, if it’s not given the green light from a Th17 cell, it has to commit suicide.  

So, though you absolutely need an autoreactive T-cell to develop an autoimmune disease, you also need unhealthy, overactive Th17 cells that just give “attack” signals all willy-nilly. 

Unfortunately, an unhealthy gut can get your Th17 cells all wound up, essentially taking the brakes off the autoreactive T-cells it helped your body make!  It’s a gourmet recipe for autoimmunity.

How does an unhealthy gut get your Th17 revved up?

Researchers think this is mostly the result of changes in the types of bacteria that live in an unhealthy gut.  The types of bacteria that live in an unhealthy gut do two things that boost your Th17 cell activity:

  • They don’t make enough short-chain fatty acids (SCFAs) SCFAs are small molecules made in massive quantities by healthy gut bacteria, but hardly at all by unhealthy gut bacteria.  They have calming effects on Th17 cells. helping keep them from running around just letting T-cells attack things.
  • They tweak the way the walls of the intestines move Signals from unhealthy bacteria living directly on the gut wall have been shown to be able to make the cells lining the wall of the intestine to change how they express their genes.  Some of the genes affected are responsible for helping keep the walls of the intestine moving normally.

Changes in the way the walls of the intestine move send up red flags for Th17 cells in the area, likely because that is serious hint you may have a stomach bug (eh-hem — everything in the gut moving… fast).  

Th17s are free to migrate through your body, though.  So, going on high alert in the gut can make them more likely to give an autoreactive T-cell in other parts of your body the go-ahead!

Regulatory T-cells, Autoimmunity and Gut Health

The third crucial factor in developing an autoimmune disease involves the dysfunction of yet one more group of T-cells, regulatory T-cells (Tregs, for short).

Tregs kind of do the opposite of what Th17 cells do.  They tell attacking T-cells, “Hey! That’s enough!  You can stop attacking and calling the rest of the immune system now!”  

Not having enough active Treg cells around not only makes it easier for an autoimmune disorder to develop (it’s hard to get an attack going if you’re shut down as soon as you send up the alarm!), but also makes sure the attack keeps going and going.  

It makes the disease chronic and keeps the attacked tissues and organs from healing.

Rounding out the autoimmune trifecta, an unhealthy gut also keeps your Treg cells from being activated, stopping them from halting T-cell attacks.

Remember those SCFAs I mentioned above that aren’t made by unhealthy bacteria?  

Well, not only do they help calm Th17 cells, they also help activate Treg cells!  They do this by physically turning on an enzyme in Treg cells, called histone deacetylase, that is responsible for letting Treg cells be Treg cells.  

See, histone deacetylase is able to turn on the genes that let a Treg cell do its job just like flipping a switch!  Without flipping that switch, the Treg cells are essentially powerless to stop a T-cell attack.

Good Gut Health: An Antidote to Autoimmunity

If bad gut health promotes autoimmunity in three essential ways, then good gut health protects against autoimmunity in all three of these ways as well!

A healthy gut, with solid walls that let no molecules in, keep your risk of developing autoreactive T-cells low.

A healthy gut, full of healthy bacteria, makes plenty of SCFAs.  These SCFAs keep your Th17 cells from letting autoreactive T-cells actually attack your body.  They also boost your Treg function so you can, hopefully, nip any autoimmune attack in the bud.

And a healthy gut should have healthier gut wall movements, keeping your Th17 cells from suspecting you have a gut infection.

Together, these effects make maintaining good gut health an amazing tool for helping prevent the development of autoimmune diseases!

Take Home Message

Though current autoimmune diseases treatments are life-savers for controlling autoimmune symptoms (sometimes literally), they are by no means perfect.  They present significant risks for serious side effects, like infections and cancer.  Preventing autoimmune disorders altogether is a safer strategy for protecting your long-term health and wellbeing. 

Evidence strongly suggests that maintaining good gut health — a solid intestinal wall and healthy gut bacteria — is a useful prevention strategy.  

A healthy gut can decrease the risk of developing autoreactive T-cells, decrease the activity of autoimmune promoting Th17 cells and boosting the function of autoimmune-protective Treg cells.

Read Next: Best Probiotic Supplements for Leaky Gut [Based on Research and Reviews]


    • Hi, Ann!

      Thank you so much for reaching out with your question!

      Unfortunately, there haven’t been a ton of human clinical trials looking at probiotics and multiple sclerosis, yet. It looks like they are on their way – the literature from the last 2-3 years is chock-full of studies analyzing the exact types of bacteria found in the gut in MS to try to identify specific species that might serve as probiotics tailored for MS patients. It shouldn’t be long before those studies start providing tangible results!

      In the meantime, we have just a couple of human studies to go on. I was able to find four!

      The first one used the commercially available VSL probiotic and reported a trend towards decreased inflammation in MS. This study only had nine subjects and didn’t report on actual symptom improvement, though. And the authors admit financial conflicts of interest, so, though it’s very plausible VSL3 is helpful in MS (this probiotic has been well tested in other conditions and proven helpful), this study has to be taken with a grain of salt.

      The next two (here and here) were conducted by the same research group and both used a probiotic strain mixture they created themselves containing Lactobacillus acidophilus, Lactobacillus casei, Bifidobacterium bifidum, and Lactobacillus fermentum (2 x 109 CFU per species). These studies had a much larger number of participants (100 between the two studies), and showed improvements in inflammatory markers and modest improvement in patients’ symptoms. This exact probiotic mixture isn’t available to purchase, though. I did find this probiotic that has all four species the researchers tested, but another 11 other species as well. It’s hard to say with 100% certainty that this combination will work the same way the one the researchers tested did.

      The final study didn’t use probiotic bacteria, but a probiotic worm, Trichuris suis (TSO), provided as eggs. The researchers had participants take 2500 microscopic TSO eggs per day for 3 months and saw a marked reduction in new MRI lesions during the trial, with the rate going back up to baseline/control after the study was over. Getting TSO eggs doesn’t appear to be easy, though. This company seems to be selling them, but they are a touch pricey and I would do some extra research into this company before ordering anything, just to make sure they really are on the up and up.

      Another potential option would be to enroll in a clinical trial looking into TSO. They seem to be a fairly regular topic of study at the moment, so if you could find one in your area, that might be a more cost-effective, supervised way of getting TSO ova.

      Sorry, that this is all the more helpful I could be with recommendations! But it’s the research we have! I suggest just checking out the studies I linked, and the probiotics, and see what you have the best feeling about. And, as always, it’s best to run adding new supplements or medications to your routine past your doctor or a pharmacist before getting started!

      Please stay in touch and let us know if you have any other questions!


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