How Healing Your Gut Can Help Treat Autoimmune Disease

how healing your gut can help treat autoimmune disease

Chances are good that you have heard about the importance of gut health and nearly every disease state including autoimmune disease. Chances are also good that you have been overwhelmed by information as to what “healing the gut” even means and have gotten lost more than once trying to figure out where to begin. In this article, I want to help you better understand how our guts can become compromised and how we can practically and systemically support gut healing in order to improve overall health and decrease the burden of autoimmune disease.

Summary: How Gut Healing Helps with Autoimmune Disease

  1. Gut dysfunction typically involves the disruption of either human gut tissue or the host gut microbiome (think microorganism like bacteria).
  2. The primary goal of our specialized segments of gut tissue is to propagate ingested food and facilitate the digestion and absorption of key nutrients from the ingested food stuff.
  3. The mucus barrier acts as a critical protective element for our gut tissue as well as the communication interface between our gut microbes and our immune system.
  4. The most common reasons for compromised gut health and overt gut symptoms include:
    1. Damage to specific gut cells
    2. Damage to the mucus barrier
    3. Maldigestion
    4. Disturbed gut motility
    5. Disruptions of the gut microbiome
  5. Most people with gut dysfunction WILL NOT require GI specific testing to guide treatment or see improvements in their gut symptoms.
  6. Most people can heal their guts utilizing dietary and lifestyle interventions as well as a sequential treatment approach that focuses on supportive treatments (not herbal or prescription antimicrobials).
  7. Certain forms of gut based testing CAN be helpful when individuals have failed sequential supportive treatment or when the testing results would significantly change clinical management.

What’s Wrong With My Gut?

Is my gut actually messed up?

It’s perhaps one of the most common questions I get in my clinical practice.

Do I have leaky gut? Do I have candida? Do I have H. pylori?

And so the gut spiral can go.

Before we seek to better answer these questions, it’s important we take an anatomy and physiology lesson to understand some important features and functions of our guts. Understanding how things should work will help us to understand how things can go wrong and how we can heal from these challenges.

Basic Gut Anatomy and Physiology

The gut is composed of two interconnected elements.

  1. Human gut tissue
  2. Gut microbiome

The first element that I refer to as human gut tissue includes the articulate sequence of specialized gut segments beginning at the mouth and ending with the anus. One can also include in this category of human gut tissue the accessory organs such as the gallbladder that support key functions with the gut itself. The sequence of specialized gut tissue segments from beginning to end is as follows.

Human Gut Tissue Sequence:

  1. Mouth
  2. Esophagus
  3. Stomach
  4. Small intestine (duodenum, jejunum, ileum)
  5. Large intestine or colon (cecum, ascending colon, transverse colon, descending colon, sigmoid colon, rectum)
  6. Anus

Accessory Organs:

  1. Gallbladder
  2. Pancreas
  3. Liver

The primary goal of these very specialized segments of human gut tissue is to propagate ingested food and facilitate the digestion and absorption of key nutrients from the ingested food stuff. Beginning in the mouth, we start the initial digestion of certain carbohydrates as part of their passage into the stomach through the transport tube known as the esophagus. Once ingested food has made its way through the esophagus and into the stomach, we begin the formal digestion process with a substance known as hydrochloric acid or HCl. HCl functions primarily to denature certain proteins as well as to acidify the overall stomach contents as part of a non-specific antimicrobial response to various microorganisms. From the stomach, we move into the first segment of the small intestine, which is our primary tissue for the continued digestion and absorption of all the key macronutrients: carbohydrates, proteins and fats as well as our micronutrients: vitamins and minerals.

Digestion and absorption in the small intestine is facilitated by various secretions produced by some of the accessory organs and introduced into the small intestine itself. One of the accessory organs, the liver, helps by producing bile, an essential substance for effectively digesting fats. Bile also plays a critical role in detoxification and controlling balance within the gut microbial community that we will discuss in more detail later. After its production in the liver, bile is actually stored in the gallbladder for enhanced and controlled utilization. (The reason you can remove someone’s gallbladder and have them survive is because the liver is actually the organ that produces bile). In addition to the gallbladder and liver, the pancreas introduces specialized digestive enzymes into the small intestine to further support digestion and absorption. When you take into account all internal secretions (not food) that are released into the human GI tract (saliva, stomach, small intestine, pancreas, and gallbladder/liver) we produce and introduce over 8 LITERS of secretions over a 24 hour period. Yes, you read that right. 8 liters every 24 hours.

Once we arrive at the first segment of the large intestine, also known as the cecum, all essential digestion and absorption of key nutrients: vitamins and minerals has taken place. Out of the nearly 8 liters of intestinal secretions that were introduced at some point from the mouth (saliva) to the small intestines, only about 1.5 liters remains and makes its way into the colon. Once in the colon, nearly all of these secretions will be absorbed and our colon will further secrete or absorb any water and associated ions (think sodium and chloride) to maintain an optimal total body water balance. The colon also functions as the final motility section and the ultimate creator of what we refer to as stool.

Let’s Talk About Poop

Our stool is primarily composed of three elements; water, undigested foodstuffs and bacterial biomass. As such, the most important factors that contribute to the frequency and consistency of one’s stool are the amount and types of foods consumed (think fibers), the amount and types of liquid consumed, the effectiveness of your secretory or digestive function, the average transit time for food moving through the intestines and the composition of your gut microbiome. With this in mind, let’s talk briefly about the gut microbiome!

Gut Microbiome

This topic itself could be explored as part of an entire series of blog posts so for the sake of this discussion, I simply want you to recognize that alongside our specialized gut tissues, we have a dynamic and complex ecosystem of microorganisms including bacteria, fungi and viruses that live in relationship with us throughout the entirety of the gastrointestinal tract. For practical purposes, the term “gut microbiome” most commonly refers to the highest density of these microorganisms housed within the large intestine. While researchers and clinicians commonly refer to this colonic ecosystem as “the gut microbiome”, we often see dysfunction and disease stemming from disturbances to the microorganism ecosystems within the mouth as well as the small intestine.

Human Tissue and Gut Microbiome Interface

The final point to make in this initial anatomy and physiology lesson is to point out the importance of a critical interface between the gut microbiome and our human tissue known as the mucus barrier. This mucus barrier functions to both protect the human gut tissue from various external pathogenic substances and acts as the critical communication interface between the gut microorganisms and our gut based immune system.

So How Can Things Go Wrong?

While this discussion could also be exhaustive on its own, I will use the foundation from our initial anatomy and physiology lesson to describe the main ways our guts can be compromised and manifest with symptoms and disease.

1. Damage to Specific Gut Cells

While this may seem obvious, one of the common reasons for dysfunction within the gut involves damage to the integrity and function of specific gut cells. For example, if you damage cells within the stomach that are responsible for producing stomach acid or HCl, you can develop low stomach acid and compromised digestion. Non steroidal medications like ibuprofen and alcohol are common irritants of the gastric lining and some individuals can also develop gastric autoimmunity that results in damage to gastric cells. Many of you have also likely heard of the term “leaky gut”. This term seeks to describe pathological permeability of the cells within the small intestine. The cells of the small intestine and its three segments are normally selectively permeable to allow for the targeted absorption of key nutrients as well as other intestinal secretions, water, etc. As you progress further down the small intestine, you actually become less selectively permeable and by the time you reach the final segments of the colon, these cells are nearly impermeable to elements within the GI tract. If there is damage to the cells of the small intestinal lining, one can develop heightened permeability or what we call pathological intestinal permeability whereby one experiences unregulated trafficking of contents within the GI tract to the immune system and systemic circulation. While the mechanism and concept of pathologic intestinal permeability is critical to understand within the context of gut dysfunction and its likely connection to the development of autoimmunity, it is a process that develops secondary to another insult or issue and should be evaluated and treated as a byproduct and secondary issue, not a primary pathology. Put more simply, we should likely avoid putting resources towards testing and diagnosing pathologic intestinal permeability as a singular problem and focus on the bigger reasons for why pathologic intestinal permeability may be present in the first place.

2. Damage to the Mucus Barrier

As a continuation of our previous discussion of pathologic intestinal permeability, we see that one of the primary reasons for its development usually involves damage and dysfunction of the mucus barrier. Damage to the mucus barrier can also lead to increased immune reactivity both within the gut and the body as a whole. Common reasons for damage to the mucus barrier include the ingestion of what I call “anti-food or man-made ingredients”, environmental toxins, disturbances to the gut microbiome or other GI infectious events and some medications.

3. Maldigestion

Incomplete digestion of foodstuffs can lead to a number of issues that include malabsorption or the inability to fully absorb the nutrients consumed in the original food, disturbances to the gut microbiome, and altered GI motility. Individuals experiencing maldigestion will commonly have symptoms of bloating, belching and disturbed motility such as constipation or diarrhea. Stool consistency can also be altered depending on which foodstuff is being maldigested. In thinking about the most common reasons for maldigestion in most individuals, we see that maldigestion is usually a secondary phenomenon related to either disturbances in the small intestinal gut microbiome, ingestion of “anti-food”, damage to stomach or small intestinal cells responsible for key digestive elements or a hyperreactive nervous system. While it’s easy to forgot about the function of the nervous system and our endocrine or hormonal system and their connections with gut health, one of the most common reasons for maldigestion and disturbed GI motility is a heightened ”fight or flight” or sympathetic nervous system response which decreases intestinal secretions necessary for optimal digestion. One of the challenges with addressing maldigestion is that it is usually both caused by and creates/perpetuates intestinal dysbiosis.

4. Disturbed GI Motility

Like many of our previously discussed issues, problems such as constipation or fast transit resulting in diarrhea are usually secondary to imbalances upstream in the digestive tract or even outside of the GI tract itself. Many individuals who experience disturbed GI motility have a combination of maldigestion and dysfunction with the nervous system that controls secretions and the rate of movement through the GI tract. Additionally imbalances in key hormones can also lead to altered GI motility. In rare cases, there can be more primary deficits compromising normal motility of foodstuffs through the GI tract. These types of challenges with dysmotility can exist anywhere from the esophagus and stomach to the small intestine and rectum. For example, some individuals experience issues with constipation and defecation as a result of dysfunction or damage to the pelvic floor musculature.

5. Disturbed Gut Microbiome

If I had to pick one domain as the most likely primary reason for dysfunction within the GI tract, it would be a disturbed gut microbiome. As I alluded to earlier, disturbances to the gut microbiome can occur both within the small intestine or in the colon. One of the more common myths about disturbances to the gut microbiome is that one single pathogen or organism such as the yeast candida albicans or the bacteria H. pylori is the singular cause and reason for dysfunction within the GI tract. While it is certainly the case that these organisms and many others can be primary drivers for GI dysfunction, the gut microbial ecosystem is much too complex for single organisms in most cases to be the primary drivers of disease. What we are coming to discover and what is much more likely than single organism pathologies are global imbalances within the overall gut microbiome that lead to most of the commonly observed gut issues or even allow for certain pathogenic organisms to become opportunistic drivers of disease at all. Because of this, we must be much more cautious in our testing and assessments of the gut microbiome that can hyperfocus disproportionately on single organism pathology.

How Do I Know What is Wrong With My Gut?

To put it simply, most people with gut dysfunction will not require testing of any kind to see clinical improvements in their symptoms. A thorough clinical assessment of one’s symptoms is the best method in most cases for identifying the nature of dysfunction within the GI tract. While this may sound heretical to some, most gut based treatments that are utilized in a sequential pattern will not require any specific testing to determine their potential utility. For example, it is a myth that you require stool testing to best identify which probiotics to utilize for treatment. There is no clinical data supporting this practice. It is also a myth that stool testing is 100% perfect or always necessary to identify potential pathogenic organisms. It is also a myth that if a parasite is identified with stool testing, that one needs to immediately use antimicrobial herbs or medications to treat it. Another common myth is that one requires breath testing in order to identify clinically relevant small intestinal dysbiosis or overgrowth (SIBO).

While I see a lot of misinformation about the clinical utility of gut based testing, we CAN appropriately utilize some forms of testing to better guide treatment for what I call “stuck in the mud patients” who have tried appropriate therapies for appropriate lengths of time and not seen expected benefits.

To simplify your exploration of the potential assessments and tools that may help you as part of your efforts to heal your gut, I have provided a short list of GI testing for most TO AVOID at this time, as they do not offer much if any clinical utility, as well as testing you could consider exploring in the right clinical context with your individual healthcare provider.

*Note: These lists are not exhaustive and are not personal medical advice.

Testing to Avoid

  • Viome
  • Intestinal Permeability Testing
  • Consumer based food allergen testing

Testing to Consider in Appropriate Clinical Contexts

  • PCR Stool Testing (Ex. GI MAP, Doctor’s Data)
  • SIBO Breath Testing (Ex. Triosmart breath testing)
  • Fecal Elastase, Fecal Fat
  • Fecal Calprotectin
  • Celiac Disease Serum Antibodies
  • Serum Gastrin
  • Comprehensive Metabolic Profile
  • Anti-parietal cell antibodies (APCA’s), Intrinsic Factor blocking antibodies

How Do I Approach Gut Healing?

The key to healing your gut is to first identify the primary drivers of your symptoms and then implement a methodical and systematic treatment approach. In treating patients clinically, the most common reasons for “treatment failure” involve either choosing the wrong therapy, choosing the wrong sequence or not giving a well chosen treatment enough time.

In most cases of gut dysfunction, we will first start with diet and lifestyle. We begin by removing “anti-food” and introduce nutrient-dense foods to support a more optimal gut microbiome. We seek to address the numerous stressors and environmental influences that can negatively impact our nervous system and hence our digestive function and gut motility. Optimizing sleep, spending time in nature and getting exercise can all positively improve aspects of gut function and the gut microbiome. In many cases, individuals can heal the gut simply from implementing rigorous dietary and lifestyle habits and will not require expensive supplement regimens.

If gut dysfunction persists despite making supportive dietary and lifestyle changes or an individual desires to accelerate healing, we can use a number of supportive therapies in sequence to improve gut health.

Typical supportive treatments in an example of a sequential order include:

  1. Probiotics – Including multiple types synergistically – S. Boulardii, Lactobacillus/Bifidobacterium, Soil-Based Organism (SBO’s)
  2. Mucilaginous Herbs and Mucus Barrier Support Nutrients – Slippery Elm, Pectin, Mucin, L-Glutamine, Zinc Carnosine, etc.
  3. Semi-Elemental Formula
  4. Immunoglobulins
  5. Pancreatic Enzymes and Hydrochloric Acid

Probiotics function primarily to support positive modulation of the gut microbiome and our immune system. Individuals can experience improved digestion and even improved motility through the use of probiotic therapy.

Outside of probiotics, many individuals experience some relief of symptoms using various herbs and nutrients that support a healthy mucus barrier. In addition to these mucilaginous herbs, I will commonly explore the use of immunoglobulins or antibodies in the gut that can exert positive effects on the immune system and gut microbiome. Most immunoglobulin supplements are bovine based and there is even a medical food available by prescription known as EnteraGam. Lastly, I will commonly utilize various methods for supporting and improving digestion. This can involve the use of replacement pancreatic enzymes or extra stomach acid or the use of a predigested powder known as a semi-elemental formula which provides essential nutrients in their “ready to be absorbed” state.

In my clinic, most patients with gut dysfunction can see improvement using a combination of these supportive treatments. With implementation phases lasting anywhere from 4-12 weeks, the timeline to see improvements can also be quicker than most expect. If someone does not make progress as quickly or as robustly as we desire using these therapies, we will consider some of the previously mentioned, clinically indicated testing options to look a little deeper at markers of GI inflammation, digestive function, and elements of the gut microbiome. From the results of such testing, one can begin to make targeted changes to a treatment approach that may now include the use of herbal or prescription antimicrobials.

Why So Cautious About Antimicrobials?

Herbal antimicrobials like oregano and berberine, the antibiotic Rifaximin and marketed “parasite cleanses” that contain various combinations of herbs are all widely available and commonly used to treat gut dysfunction. While they can certainly play a critical role in supporting some individuals from healing underlying gut dysfunction, I see significantly more people harmed or experience reactionary symptoms from their use as compared to the supportive gut based treatments. Because of the heightened risk for anti-therapeutic effects and negative reactions with antimicrobial based therapies as compared to supportive approaches, we should be more measured and cautious, reserving their use for those who have failed supportive treatments or have clear clinical indications from testing to support their use.

Final Thoughts on Gut Healing

Exploring gut healing can be intimidating! Using a framework that prioritizes diet and lifestyle and low risk supportive treatments will oftentimes lead to improved gut health for most patients. For those with autoimmune disease, focusing on the gut can lead to improved systemic symptoms and quality of life, and is far too often overlooked in favor of risky and more expensive treatments. If you feel stuck on how to get started or make progress, consider working with an integrative medicine provider who uses a simplified and iterative approach to addressing gut dysfunction. Additionally, my colleague and practice partner Dr. Michael Ruscio has some of the most evidenced based and accessible resources for gut health through his podcast, website and book.

About Rob Abbott, M.D.

Rob Abbott, M.D. is medical director and the functional physician for Resilient Roots: Functional and Evolutionary Medicine in Charlottesville, Virginia. He completed his family medicine internship with VCU-Shenandoah Valley in Winchester Virginia and is a graduate of the University of Virginia (U.Va.) School of Medicine where he served as a student ambassador for the U.Va. School of Nursing’s Compassionate Care Initiative, promoting resilience, compassion and self-care. He has completed additional training with the Institute for Functional Medicine, is a Kresser Institute ADAPT Level 1 trained clinician, and is an AIP Certified Coach. Rob approaches medicine from an evolutionary and functional perspective and practices what he calls “spiritually focused and evolutionarily informed functional medicine.” In his free time, Rob enjoys creative expression through writing, sharing blogs, poetry and podcasts through his website


  • Christina Tidwell says

    EXCELLENT article thank you for sharing!

  • Jolanta G says

    Any recommendations for a doctor with your specialty and knowledge in Toronto .
    I’m struggling with RA .
    Love your article.

  • Betty Hall says

    I have 5 autoimmune diseases where do I go for help?

    • Mickey Trescott says

      Betty, we’ve trained over 500 practitioners who can partner with you on various levels to guide you. You can find the listing here:

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