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What Are The Early Warning Signs of Autoimmune Disease?

Written by Dr. Ruscio on August 1, 2023

Written by Dr. Ruscio on August 1, 2023 — Reviewed by Hannah Hamlin

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.

Autoimmune Symptoms to Watch Out for and Natural Strategies for Healing

• Autoimmunity 101|
• Early Warning Signs|
• The Gut-Autoimmune Connection|
• Natural Therapies for Autoimmunity|
• Lifestyle Considerations|
• Healing Autoimmune Symptoms|

Despite more than 24 million people in the U.S. having an autoimmune disease like psoriasis, inflammatory bowel disease, celiac disease, Hashimoto’s, or type 1 diabetes, they still don’t seem to get as much airplay as other chronic diseases. Part of this may be related to our poor understanding of autoimmune diseases on the whole, including what triggers them and how best to treat them. 

But with 8 million Americans experiencing the early warning signs of autoimmune disease [1, 2, 3], which can include fatigue, digestive distress, brain fog, joint pain, and/or skin rashes, it’s important to know what can be done to help prevent someone from developing an autoimmune disease. We know there’s a genetic component, but not everyone with a gene that is predisposed to autoimmunity will develop it. 

Everyone with autoimmunity is each impacted in a unique way and can have a highly variable onset. Symptoms can pop up rapidly or develop over a period of years, can be persistent or come and go across the course of the disease, and can exist on a spectrum from mild to debilitating.

Research suggests poor gut health is an important trigger for those with autoimmunity. This is great news because it means that even if you have a genetic predisposition, developing an autoimmune disease doesn’t have to be inevitable. We can have more control over our health when we correct gut imbalances like microbial dysbiosis and intestinal inflammation.  

If you’re noticing the early warning signs of autoimmune disease, foundational strategies such as elemental diets, probiotics, nutritional supplements, and personalized lifestyle changes to heal your gut may actually interrupt and reverse the underlying autoimmune process. And if you’ve already been diagnosed with an autoimmune condition, these same strategies can be used to heal your symptoms. All this to say, there’s a lot of hope for anyone who’s at risk or has already developed an autoimmune condition.

In this article, I’ll share the role the gut plays in autoimmunity and the effective natural therapies I use in the clinic to help restore healthy immune system function. So, let’s get started by reviewing what you need to know about autoimmune diseases. 

Autoimmunity 101

Normally, the immune system protects your body from infections and illnesses by identifying and neutralizing potentially harmful foreign invaders. When someone has an autoimmune disease though, their immune system isn’t working the way it should. So, in addition to attacking truly harmful microbes, the body’s immune system also attacks its own healthy cells and tissues, which can increase the risk of other diseases, like cancer, cardiovascular disease, type 2 diabetes, and even death [1, 2, 3].

It’s thought that the body begins attacking its own cells as a result of various root causes like [1, 2, 3]:

• Genetics
• Viral or bacterial infections
• Nutrient deficiencies
• Environmental pollutants
• Excessive and/or chronic stress
• Poor gut health
• Obesity

It’s not likely that any one of the above root causes on its own is responsible for the development of an autoimmune disorder, rather research suggests autoimmune diseases are probably caused by a combination of genetic and environmental factors that are unique to an individual [3]. 

Epigenetics (the study of how environment affects genetic expression) suggests that in people with certain genetic factors, specific environmental exposures like too much sunlight, childhood poverty, agricultural chemicals, mercury, vitamin D deficiency, and cigarette smoke might increase the risk that they’ll develop an autoimmune condition [1, 2]. 

In other words, the environmental factors are probably influencing the genes, and the genes are enhancing or diminishing the effects of the environmental factors to set off the autoimmune cascade [1, 2, 3].

More than 24 million people in the United States have at least one of the 80 types of autoimmune diseases that have been identified, and at least 8 million more may be at risk of developing one [1, 2, 3]. Some of the most common types include:

• Type 1 diabetes
• Multiple sclerosis (MS)
• Rheumatoid arthritis (RA) 
• Celiac disease
• Inflammatory bowel disease (IBD)
• Psoriasis
• Psoriatic arthritis
• Sjogren’s syndrome
• Systemic lupus erythematosus (SLE)
• Grave’s disease
• Hashimoto’s thyroiditis
• Vasculitis (inflammation of the blood vessels)

While all autoimmune diseases tend to have a similar immunological mechanism of action, each one differs depending on which body parts the immune system is attacking. Autoimmune disease may impact the skin, kidneys, mouth, nervous system, lungs, eyes, heart, digestive system, and joints [3]. As such, people with autoimmune diseases can also experience an impact on their hormones, metabolic health, digestion, and many other body systems [3].

Autoimmunity can take years to develop, which means in a lot of cases we have a significant amount of time to act beforehand. So, let’s take a look at the early warning signs of autoimmune disease you need to know about.

Early Warning Signs of Autoimmune Disease

Most people with an autoimmune disease experience the signs and symptoms for several years before the development of the disease, but for some people, they may come on suddenly. Common symptoms may include:

• Fatigue [2, 4, 5, 6, 7, 8]
• Brain fog [9, 10, 11]
• Shortness of breath [2, 12]
• Hair loss
• Skin problems like rashes, sores, and dry or scaly skin [2, 4, 13]
• Fevers, frequent and often low-grade [2, 4, 5, 14]
• Digestive problems (like diarrhea, abdominal pain, and bloody stool) [4, 5, 8, 15, 16]
• Loss of appetite [2, 17, 18, 19]
• Joint pain [2, 4, 5, 20, 21, 22, 23]
• Muscle aches or muscle weakness [2, 24]
• Heat, redness, pain, and swelling of at least one part of the body [2, 25]
• Anemia 
• Vision loss
• Loss of balance

However, not everyone with autoimmunity will present with these specific symptoms, and not everyone with the above symptoms will have autoimmunity. Seeing a healthcare provider for a comprehensive work-up is important, as autoimmunity can’t be diagnosed from symptoms alone.

Where the warning signs occur can be largely dependent on what type of autoimmunity is present, though many people will experience similar symptoms of appetite loss, weight changes, low-grade fever, and/or fatigue at some point in time. 

People with thyroid autoimmunity, like Hashimoto’s thyroiditis, might first see symptoms of difficulty swallowing and cold intolerance, while someone with Crohn’s or ulcerative colitis could notice abdominal pain, and loose or frequent stool. Lupus often presents with widespread joint pain and skin rashes, as does psoriatic arthritis. 

However, even though an autoimmune condition is known to attack a specific area of the body, it can cause body-wide symptoms, due to the widespread inflammation discussed above. This is clearly evident in the case of IBD, where swollen, painful knees are fairly common, and RA where the rates of gastritis, stomach pain, and reflux occur more frequently than in the general population [15].

It’s important to understand that these symptoms often come and go – they worsen during flare-ups and then ease up for a while before the next flare [26]. There can be long periods of time with minimal to no symptoms, and may be one reason people with the early warning signs of autoimmune disease have a difficult time getting effective treatment early on.

It’s important to document your symptoms and how frequently they occur in order to help your provider recognize what’s going on. If we catch this early enough, it may be possible to reverse this process and prevent an autoimmune disease from developing [27].

I’m a gut geek, so in the clinic, I generally always consider gut health and function first. And since gut dysbiosis and dysfunction can lead to autoimmunity, it’s especially important for people with the early warning signs of autoimmune disease to take a deeper look at their gut. 

The Gut-Autoimmune Connection

Research suggests that in addition to environment and genetics, poor gut health may be a trigger for the development of autoimmune diseases [27]. One large analysis of genetic data found altered levels of normal gut flora could possibly lead to the development of type 1 diabetes and celiac disease, both of which are autoimmune diseases [28]. And several meta-analyses have found gut dysbiosis (altered gut microbiota) to be a common feature in autoimmune conditions [29]. 

While we can’t yet say gut dysbiosis causes autoimmunity, it likely contributes and gives us a great target for treating autoimmunity naturally. I’ve had many patients with autoimmune disease improve by healing their gut, so, let’s take a look at how leaky gut impacts autoimmunity.

How Leaky Gut Can Cause a Haywire Immune System

The gut environment includes a variety of microbes that live together harmoniously (symbiosis) until something (stress, toxins, drugs, food particles, and/or pathogens) disrupts the ecosystem [27]. When the contents of the gut are imbalanced, the delicate small intestinal barrier is weakened [30]. 

Once this barrier is compromised — known as leaky gut— contents that should remain in the GI tract and/or exit the body through stool (like undigested food particles, bacteria, and toxins) can cross the gut wall and enter the systemic circulation. After these foreign antigens enter the bloodstream, inflammatory signaling molecules are released that tell the immune system to be on high alert. 

The bacterial metabolites and other antigens that cross into the systemic circulation can have a molecular makeup similar to the body’s own cells (molecular mimicry), so in addition to attacking the invader, the immune system begins to attack its own tissues by mistake. Furthermore, healthy tissues of the body can be damaged just by being in the vicinity of the inflammatory/immune system response, similar to an innocent bystander. 

Over time, this process may lead to common autoimmune diseases like celiac disease, type 1 diabetes, multiple sclerosis (MS), and RA [30]. 

Here’s a nice graphic detailing this leaky gut progression [27]:

While we can’t yet say definitively that gut problems cause autoimmunity [31, 32, 33], we do know that gut dysbiosis has a significant impact on how the immune system functions and that there is a considerable link between the two [27, 29, 30]. The symptoms of poor gut health can be a sign that your immune system is overactive, making it one of the top early warning signs of autoimmune disease. Healing your gut is a great first place to start to get a hold on this process to prevent it from progressing [27]. 

As a reminder, just because poor gut health can be a common factor in people with autoimmunity, doesn’t mean that gas, bloating, or constipation are always indicative of an autoimmune process. It’s important to remember that autoimmunity is only diagnosed by a doctor through a comprehensive work-up. 

If you’re high risk for or are suspicious of an autoimmune condition, you should continue to follow up with your doctor. But if you also have symptoms of an unhealthy gut, it can be a sign that you’re experiencing inflammation and altered immune system function, and there’s a lot we can do to heal these symptoms.

Let’s discuss some of the natural therapies I use in the clinic.

Natural Therapies for Autoimmune Symptoms

There are a lot of simple, natural therapies that can be used early on (or any time for that matter) to address autoimmunity and its root causes such as gut dysbiosis, nutrient deficiencies, pollutants, stress, and obesity. 

One approach I’ve found especially effective in the clinic is to start by targeting gut dysbiosis and leaky gut with an elemental diet reset followed by an elimination diet protocol, probiotics, and other lifestyle measures. Let’s discuss why this 2-step approach seems to work and how you can implement it.

Step One: Elemental Diet Reset

As I discuss in Healthy Gut, Healthy You, elemental diets for autoimmunity haven’t been well-researched yet. But some studies have shown the elemental diet to be as effective as corticosteroids (anti-inflammatory medications) for IBD and RA, and it can improve symptoms in people with celiac disease. 

Additional research has found:

• Patients with Crohn’s disease relapse less often when they incorporate elemental dieting when compared to those who don’t [34]
• An elemental diet improves inflammatory cells and symptoms in people with eosinophilic esophagitis (a condition with a strong link to existing autoimmunity) [35]

While there’s not much long-term research available on elemental diets and autoimmunity, your gut health has a very strong influence on your immune system, so it makes sense that anything you do to improve your gut health may also help with the early warning signs of autoimmune disease. 

While the mechanisms by which an elemental diet helps will differ to some degree for every condition and person, we think this therapy works by [36, 37, 38]:

• Giving your digestive tract a break and a chance to rest, heal, and repair
• Reducing inflammation
• Starving small intestinal bacterial overgrowth (SIBO) and other overgrowths that may contribute to leaky gut [39]

The elemental diet is a meal replacement formula that’s hypoallergenic, anti-bacterial, and anti-inflammatory. It’s sold as a powder that you simply mix, blend, or shake up with water.  

Elemental diets may be used as the sole source of nutrition for several weeks and then intermittently as needed. But for a reset to quell inflammation or a flare of autoimmune symptoms, you can use it for 2–4 days. If you’re responding well, go for the full four days, if you’re having a reaction that doesn’t abate after the second day, stop at day two. 

At this point, you may be wondering, why not just start with the autoimmune protocol diet (AIP)? The AIP diet is definitely an option for anyone who has gone through this 2-step process and not found significant relief. It’s not a first option for most people though because it’s very restrictive, and in my experience, many patients with autoimmunity can find symptom relief without this level of restriction. 

Once you’ve completed your elemental diet reset, it’s time to move on to step 2 with an elimination diet plus probiotics.

Step Two: Elimination Diet Plus Probiotics

You’ll want to transition slowly back to whole foods once you’re finished with the elemental diet. But you want to be selective with this process and consider eliminating common food allergens and inflammatory foods like gluten, lactose, corn, and soy. 

These types of elimination diets have been found to help patients with Hashimoto’s thyroiditis (an autoimmune condition that impacts the thyroid gland, which can lead to hypothyroidism) reduce their thyroid autoantibodies and improve thyroid hormone levels [40]. Similarly, anti-inflammatory diets like the Mediterranean diet and other elimination-type diets have been found to improve RA outcomes [41].

You have a few different options, but I would recommend starting with the Paleo diet, since it’s pretty easy to implement and it removes allergens and inflammatory foods. Here’s an overview of the Paleo meal plan:

If you feel great on the Paleo diet after 2–3 weeks, then stick with it. If you’re not happy with your results, then you can try other elimination diets one by one for 2–3 weeks each until you find one that works best for you. 

If Paleo improved your symptoms but didn’t take care of your early warning signs of autoimmune disease completely, then move on to Paleo plus low FODMAP. If Paleo didn’t work at all, then you may want to just try the low FODMAP diet. 

Once you find the right meal plan, stick with it for several weeks until your symptoms are gone or at least significantly improved. At this point, you can begin to reintroduce the eliminated foods one by one while monitoring your symptoms. 

The ultimate goal is to have the least restrictive, most whole foods diet you possibly can while still maintaining relief from your symptoms.

Probiotics for Autoimmunity

While you’re on the elimination diet, you may want to consider adding probiotics, which have been shown in several meta-analyses to effectively help fight autoimmune diseases like RA, psoriasis, MS, and other types of autoimmune arthritis [42, 43, 44]. 

Trials assessing probiotics in autoimmunity have found they:

• Reduce C-reactive protein and inflammatory markers in RA [43]
• Improve disease severity in psoriasis [43]
• Improve symptoms in people with spondyloarthritis, juvenile idiopathic arthritis, and IBD arthritis [43]
• Positively impact certain markers of inflammation and oxidative stress that contribute to autoimmunity [42]
• Significantly improve disease progression, depression, and general health in MS patients [44].

There are three major categories of probiotics that benefit human health, and I’ve seen the best results with my patients when we use a combination of the three, which I call the Triple Therapy Probiotic approach:

• Lactobacillus/Bifidobacterium blend
• Saccharomyces boulardii (a healthy fungus)
• Soil-based (Bacillus species)

If you’d like to try probiotics, here’s a simple step-by-step guide:

1. Try a quality formula probiotic from category 1, category 2, and category 3, and take all three together.
2. Monitor your symptoms for 3–4 weeks. If you’re improving, stay on this triple therapy protocol until your improvements have plateaued.
3. Once you’ve seen your maximum improvement, stick with the triple therapy probiotics for about a month to allow your system to calibrate to these new improvements. Then reduce your dose to find the minimal effective dose, and stick with that for the long run.

If you haven’t noticed any change in your symptoms after 3–4 weeks, you can stop taking probiotics and feel confident that you’ve fully explored probiotic therapy. If you notice improvements, continue to take as long as needed, as probiotics are safe for long-term use.

Nutritional Supplements for Autoimmunity

In addition to dietary changes, some nutritional and herbal supplements may significantly impact autoimmune symptoms. 

Several studies have shown an association with vitamin D deficiency and autoimmunity [45, 46, 47, 48, 49, 50, 51], so it’s worth it to talk to your healthcare provider about getting a vitamin D blood test and supplement if needed. Patients with RA who took vitamin D supplements had reduced disease activity and inflammation [52], and those with Hashimoto’s had improved thyroid antibody levels [45].

One 2021 meta-analysis found people with RA and ulcerative colitis who took 250–1,500 milligrams of curcumin per day for 8–12 weeks had lower markers of inflammation (younger patients who took this supplement for longer than 8 weeks seemed to have the most improvement) [53].

In addition to diet and supplements, there are several lifestyle factors to consider when you’re experiencing the early signs of autoimmunity. You don’t need to wait to complete the above 2-step process to begin these additional strategies, they can be incorporated at any time.

Lifestyle Considerations for Autoimmune Symptoms

While dietary-related changes and probiotics will likely significantly improve your symptoms, additional lifestyle strategies that address stress and weight are important for autoimmune disease prevention and treatment. 

Stress and Autoimmunity

Unmanaged stress, whether physical (lack of sleep or movement) or mental, can have negative consequences on gut health via leaky gut, increased inflammation, and altered immune system function [54]. 

Indeed, negative stressful life events are associated with a higher risk of primary Sjogren’s syndrome [55], and people with RA tend to have more work-related and interpersonal stress than the general population [56]. For those who already have autoimmunity, stress is a well-known trigger of flares. 

Creating a healthy foundation for managing stress can go a long way to improving gut health and immune system function, and may help you avoid an autoimmune diagnosis and/or heal current autoimmunity. Here are a few ways to decrease stress levels and improve the early warning signs of autoimmune disease:

• Aim for 7–8 hours of restful sleep every night.
• Practice relaxation techniques and yoga [57, 58]
• Exercise routinely [59, 60]

Obesity and Autoimmunity

Unwanted weight gain/obesity is a known risk factor for developing autoimmune disease, but it also worsens outcomes for people who have already been diagnosed [61, 62, 63, 64]. If you’re overweight, losing excess weight may help to prevent the onset and progression of an autoimmune disease. 

Improving your gut health with a whole-foods diet and probiotics will also likely help with healthy weight loss. But focusing on getting restful sleep and appropriate amounts and types of exercise can also support weight loss.  

Target Gut Health to Heal the Early Warning Signs of Autoimmune Disease

Autoimmune diseases like psoriasis, IBD, and RA develop when the immune system begins to recognize its own tissues as foreign. The misguided immune system attack damages tissues and organs putting you at greater risk for other health problems and poor quality of life. 

Autoimmunity develops from the interplay of genetics and environmental factors, like poor gut health and stress. This is great news because it means that even if you have a family history, developing an autoimmune disease doesn’t have to be your fate. You absolutely have a ton of control over your autoimmune disease risk.

If you’re experiencing the early symptoms of autoimmune disease like digestive distress, skin rashes, fatigue, brain fog, and joint pain, targeting gut health with natural therapies like elemental and elimination diets, probiotics, nutritional supplements, and lifestyle-related changes can interrupt and even reverse the underlying autoimmune process. 

Check out the step-by-step gut-healing guide I outline in Healthy Gut, Healthy You, or if you’d like more personalized guidance, please reach out to us at the Ruscio Institute for Functional Health. 

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.