Quick answer: Gut health and autoimmunity are connected because a large share of the body’s immune activity happens in and around the digestive tract, so problems there can affect how the immune system behaves elsewhere. That does not mean every person with an autoimmune condition has the same gut problem, so at Dr. Harrison’s Center of Functional Medicine in Westminster, CO, the gut is evaluated case by case as one part of a broader workup, alongside the care your physician provides.
Why does the gut matter for the immune system?
The digestive system is where the body meets most of the outside world: food, bacteria, and anything else you swallow. A large portion of the immune system lives in and around the gut to deal with that contact. When the digestive tract or the microbiome (the bacteria that live in the gut) is out of balance, that imbalance can show up as symptoms far from the stomach.
Autoimmune conditions happen when the immune system attacks the body’s own healthy cells. The exact cause is unknown, and genetic, environmental, and hormonal factors all appear to play a role. Because the gut is such an active part of the immune system, it is one of the areas functional medicine looks at when trying to understand what may be contributing to autoimmune symptoms. Our gut health page and autoimmune health page cover both topics in more detail.
What does the gut and autoimmunity connection mean, and what does it not mean?
This topic gets oversimplified online. Here is a plain summary:
| It does mean | It does not mean |
|---|---|
| Gut health is worth asking about if you have an autoimmune condition, even without obvious digestive symptoms. | Every person with an autoimmune condition has the same gut problem. |
| Digestive symptoms such as bloating, constipation, or diarrhea deserve their own evaluation. | Fixing the gut will cure an autoimmune disease. |
| Food triggers, the microbiome, stress, and nutrient status can all be part of the picture. | You should start a restrictive diet or supplement plan on your own. |
| Gut testing can add information when your history and symptoms point that way. | Everyone needs every gut test. |
| Gut-focused care can be added to your existing medical care. | You should stop or change prescribed medication. |
The relationship between the gut, the microbiome, the immune system, and inflammation is still an active area of research. That is why a careful, individual evaluation matters more than any one-size-fits-all protocol.
Which gut symptoms are worth mentioning if I have an autoimmune condition?
Tell both your physician and any functional medicine provider if you have:
- Bloating, gas, or abdominal discomfort that keeps coming back
- Constipation, loose stools, or alternating between the two
- Reacting to more and more foods over time
- Heartburn or indigestion that does not settle
- Skin, energy, joint, or mood symptoms that seem to flare along with digestive problems
These symptoms do not prove a gut connection to your autoimmune condition. They are signals that digestion is worth including in the evaluation.
How is the gut evaluated in an autoimmune workup?
At Dr. Harrison’s Center of Functional Medicine, testing is chosen based on your symptoms and history, not run as a fixed panel. Every new patient follows the same four steps: a free 15-minute discovery call, a virtual discovery session to review your history and previous labs, an in-person, problem-focused physical exam, and a lab review where your Clinical Master Plan is explained. Learn more on Our Unique Approach.
When the gut is part of the picture, tests that may be considered include:
- Comprehensive stool testing for digestion, inflammation, and the balance of gut bacteria. See our stool testing guide.
- A SIBO breath test when bacterial overgrowth in the small intestine is suspected. See IBS vs. SIBO.
- Food sensitivity testing when food reactions are part of the story. See allergies and food sensitivities.
Gut results are reviewed together with other findings. For thyroid autoimmunity such as Hashimoto’s, that usually includes a fuller thyroid panel with TPO and TG antibodies, plus nutrient, blood sugar, inflammation, and cortisol markers. See our thyroid health page.
How is this different from a leaky gut protocol?
Intestinal permeability, often called leaky gut, is one possible gut finding, and we cover it in depth in Leaky Gut Syndrome: What It Is and How to Heal It. This article is a step earlier: deciding whether the gut belongs in your workup at all, and what to expect if it does. For a broader overview of autoimmunity itself, read What Is Autoimmune Disease?
Does gut-focused care replace my doctor?
No. Dr. Harrison’s program works in conjunction with your primary doctor. Dr. Glenn Harrison, DC, does not prescribe medication or advise you to stop any medication. Those decisions stay with you and your prescribing doctor.
When to see your medical doctor promptly: blood in your stool or excess mucus, black or tarry stools, constant vomiting or frequent diarrhea, rapid or unexplained weight loss, persistent or severe abdominal pain, or a fever. These need medical evaluation first. If you have a medical emergency, call 911.
Frequently asked questions
Can gut problems cause autoimmune disease?
The exact cause of autoimmune disease is unknown, and genetic, environmental, and hormonal factors are all thought to play a role. Because so much immune activity happens in and around the gut, gut health is one of the factors functional medicine looks at. It is one part of the picture, not a single explanation that applies to everyone.
If I have no digestive symptoms, should my gut still be checked?
Not automatically. Gut testing is chosen based on your history, symptoms, and other findings. Some people with autoimmune conditions and few digestive complaints still have patterns worth looking into, and others do not. Dr. Harrison decides with you, during the evaluation, whether gut testing is likely to answer a useful question in your case.
Should I try an elimination diet on my own first?
It is better to talk with a provider first. There is no single autoimmune diet that fits everyone, and very restrictive diets can create nutritional gaps if they are not planned carefully. Testing and a detailed history can help decide which changes make sense for you, and your physician should know about any major dietary change.
Can I keep my gastroenterologist and still work with you?
Yes. Dr. Harrison’s Center of Functional Medicine works alongside patients’ existing medical providers, including gastroenterologists, rheumatologists, and primary care doctors. A functional stool panel is not a replacement for a colonoscopy or cancer screening. Keep the screenings and follow-up your medical team recommends, and bring recent results to your virtual discovery session.
How do I get started?
Every new patient starts with a free 15-minute discovery call, so you can describe what you are dealing with and find out whether the approach fits. Book your free discovery call or call 720-449-6217. We are at 9035 Wadsworth Pkwy #3300, Westminster, CO 80021, and video consultations are available.