The Autoimmune – Gut Connection

This post is part of a series on autoimmunity. When you get an autoimmune diagnosis, you don’t have to feel powerless about what to do. It is possible for you to achieve remission, and there are important reasons why you should do so! Read more about that here.

We talked here about the three most important triggers to get a handle on, which include food antigens, stress, and blood sugar problems. Then we talked about how low oxygen levels can be a trigger here.

Now let’s dig into autoimmunity and your digestive tract. In functional medicine, whenever there’s autoimmunity, we start with the gut.

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Your gut immune system

The bulk of your immune activity is in your digestive tract. This is because your digestive tract is considered a hollow space that is open to the outside world. It’s exposed to foods, chemicals, and microbes on a daily basis.

Your very intelligent immune system surveys everything that comes through. This happens primarily in your small intestine, which is so large that if it were spread out it would cover a football field! This vast lining provides a lot of opportunities to absorb food and nutrients. It also allows your immune system ample time for surveillance.

Your small intestine lining is only one cell thick. This means your surveillance cells, called dendritic cells, can easily reach through the thin lining to collect samples of undigested food proteins and microbes. These samples are presented to other immune cells to sort and identify. Anything that is identified as a problem is tagged as an antigen. In Chinese medicine, the small intestine is where your body “separates the pure from the impure.”

When the surveillance and sorting go well, your immune system will appropriately tag antigens and mount an attack with antibodies. And, you want this to happen when you have an overgrowth of an undesirable microbe, such as giardia or salmonella.

When gut immune surveillance goes awry

We discussed here what happens when food proteins are tagged as antigens. Generally, you don’t want foods tagged as antigens. Microbes, however, are more complicated. As you probably know, you have billions of microbes in your G.I. tract as residents. And, you want your immune system to knock down unfriendly microbes, but not react against the friendly ones.

Microbes include viruses, bacteria, archaea, protozoa, and yeast. Ideally, we live in harmony with these critters, cultivating ones that benefit us, and knocking down others that don’t. When the microbes in your gut get out of balance it’s called dysbiosis. To put it simply, dysbiosis can look like:

  • An overgrowth of unfriendly or inflammatory microbes
  • Low populations of beneficial microbes
  • A combination of the above

Dysbiosis causes inflammation, especially when there are overgrowths. Inflammation ramps up the immune activity in your small intestine, and dendritic cells become hypervigilant. The problem with this is that dendritic cells also sample fragments of your own self-tissue, and when hypervigilant because of dysbiosis, it’s much more likely that your own self-tissue will be tagged as an antigen. You never want self-tissue tagged as antigenic because this means you will mount antibodies against your own tissue – the start of autoimmunity.

In fact, many microbes are correlated with specific autoimmune diseases. Examples include:

How does digestive function fit into this?

If your digestive tract is working well, then the immune activity in your small intestine should be robust yet not overburdened or hyper-stimulated. Let’s go through what this takes from your mouth on down:


It’s important to chew your food well so that it gets broken down sufficiently by the enzymes in your saliva. You also don’t want bacterial overgrowth in your teeth or gums that you continuously swallow.


You absolutely need the right acidic pH here. This destroys microbes and signals the release of pepsin to break down proteins. You don’t want large protein molecules moving down the tract.

If you have acid reflux, it’s rarely the case that you are making too much acid. Rather, it’s a sign of poor digestion that leads to food fermenting in your stomach and bubbling up.

Secretions of the gallbladder and pancreas

Your food enters your small intestine after your stomach and needs to be at exactly the right pH to signal bile from your gallbladder to emulsify dietary fats, and enzymes from your pancreas to break down food. Proteins break down into small amino acids, and these do not trigger an autoimmune response.

Small intestine

If all the above goes well, your small intestine has the right setup for digestion and immune surveillance. Also, your small intestine should have relatively low microbial populations. If too many microbes colonize your small intestine, your immune system will be overburdened.

Large intestine/colon

This is where you should have a great abundance of beneficial microbes! They feed off fiber and make wonderful anti-inflammatory byproducts and nutrients that help you. Good digestive function and a healthy microbiome will help you poop at least once per day, with a healthy Bristol stool score of four. No constipation, loose stools, sticky stools, or diarrhea.

poop, bristol, microbe, microbiome

If you have an overgrowth of unfriendly and inflammatory microbes in your large intestine, then the valve between your small and large intestine, called the ileocecal valve, can malfunction. If this happens then bacteria and yeast can translocate up to your small intestine. This is known as small intestine bacterial or microbial overgrowth (SIBO or SIMO).

How to assess your gut

I recommend everyone with an autoimmune disease do an annual functional stool test that provides a comprehensive digestive analysis and microbial evaluation. Then if things are not perfect, get help to treat and fix the problems that are identified until your stool test is great.

Many labs offer these tests, and the gold standard is DNA PCR analysis to identify microbes. Our favorite lab is the GI Map. A few key digestive analysis markers include:

Steatocrit: Fat in your stool. If you have fat in your stool it means that you are not breaking it down which is a pancreas or liver/gallbladder issue (bile and enzymes). Sometimes the reason for this is stomach pH is off. Did you know that chronic stress lowers stomach pH?

Calprotectin: Intestine inflammation. This is a really important marker because if elevated, it can mean that an autoimmune process is brewing, particularly a gut autoimmune process like colitis or Crohn’s.

Pancreatic enzymes: These are frequently low in cases of autoimmunity. Again this could be a sign of stomach pH being off, especially with chronic stress or chronic intake of acid-blocking medication.

Secretory IgA: This measures the activity of your gut immune system, and whether it’s subpar, on target, or hyper-stimulated.

Getting help

Interpreting your functional stool analysis is not a DIY project. It’s a medical science to properly diagnose the intricacies of dysbiosis and digestive dysfunction, and then treatment is a delicate art. Each person is different and needs a thorough analysis and treatment plan.

When treating gut issues, things change fast, and it often takes close and frequent modulation of your treatment plan as your gut function and microbial populations shift and change. Plan to work closely and frequently with your practitioner to see this through. Retest, reevaluate, and update your protocol until you can rock that stool test!

Treatment interventions can include antimicrobials, probiotics, prebiotics, digestive supports like enzymes, stress reduction, and anti-inflammatories, among other things. Sometimes work resetting your vagus nerve which strongly influences digestion is necessary. Adrenal function and stress hormone chemistry also play into digestive function.

Lastly, one of the most important interventions is immune modulation. For example, if your immune system is not able to fight off intestinal pathogens, it’s likely that it’s stuck in what’s known as “Th2 dominance.” You need your immune system to shift into Th1 dominance and produce natural killer cells in order to fight off gut pathogens. If the Th2 dominance is complicated by active inflammation and autoimmunity, then these should be addressed simultaneously.

Things to do on your own right now

The first three triggers to unwind are definitely DIY projects – food antigens, stress, and blood sugar balance.

For digestion, here are DIY tips:

  • Chew your food well.
  • Use black currant seed oil or oregano oil on your toothbrush for mouth bacteria.
  • Talk to your doctor about getting off acid-blocking medication.
  • Identify and reduce stress. Learn more here.
  • Drink dandelion tea for your gallbladder, or use digestive bitters.
  • Eat fermented and cultured foods rich in beneficial microbes (if not tolerated it’s a sign of SIBO/SIMO).
  • Eat foods high in fiber (if not tolerated it’s a sign of SIBO/SIMO).
  • Lose medications that slow your digestion, such as opioids.
  • Avoid antibiotics if at all possible – since they obliterate beneficial bacteria and contribute to intestinal permeability.
  • Avoid chronic use of anti-inflammatories like ibuprofen, which damage the gut lining.
  • Reduce sugar and alcohol which feed unfriendly microbes.
  • If you see undigested food in your stool, try a digestive enzyme.
  • If you try a probiotic, go for a low number of strains with a high count.
  • Look at your poop, and make adjustments until you get a perfect Bristol score. Here are tips for constipation.
  • For inflammation, use turmeric, resveratrol, vitamin D, and zinc.
  • For gut lining support, use glutamine.

I know this is a LOT of information. If you want help, feel free to schedule a consult with me.

I welcome your input below,

paris healing arts, doctor laura paris, dr. laura paris, dr laura paris

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  1. An excellent informative newsletter Laura. As a sufferer of IBS and SIBO I try to stay well informed on what I can do to improve the day to day management of my gut health.
    Thanks for sharing your wealth of knowledge as always!

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