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The Importance of Not Ignoring the Fundamentals of Managing Autoimmune or Chronic Health Conditions


Even those well attuned to the care of their personal health and well-being sometimes overlook these six basic fundamentals of self-care.

Functional medicine is complex because, no “one pill for one symptom” model exists to manage chronic gut health, hypothyroid, autoimmune, or other conditions. Instead, multiple systems in the body typically play a role.

Though evidence-based, a non-pharmaceutical diet and lifestyle approach is not covered by insurance and does not require shopping for a “life-changing” product that will fix everything. Rather, it requires changes, work, and self-education on behalf of the patient.

Many people are not willing to travel down the path of functional medicine until the pain of the problem outweighs the pain of the solution. The good news is that once the path is chosen, the results are often profound and lasting, and people finally feel they are in the driver’s seat of their health.

Although I go over these basics in all my courses, in this article, I cover what I call “Functional Fundamentals”—basics you must implement regardless of your symptoms or conditions.

These fundamentals are so unglamorous that they are easily overlooked. People who become well-versed in managing chronic health conditions can become exceptionally well-educated. I have learned much from my patients over the years and see that they can sometimes get lost in the weeds of the latest study or supplement. Even in my most educated and empowered patients, I often see these simple foundations go ignored.

I’m not saying these basics will fix everything in everyone, however, they are essential to the chronic health puzzle.

1. Do You Eat Enough Protein?

One of the biggest mistakes I see people make is not eating enough protein. It is common for patients with food sensitivities and autoimmunity on limited diets to under-consume protein.

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Insufficient protein can make it impossible to rebuild intestinal cells to heal leaky gut or to recover tissue damaged by autoimmunity. Protein insufficiency is also linked to immune dysfunction, making it impossible to control autoimmunity over the long haul.
Adequate protein intake is essential to provide the building blocks to help rebuild a leaky gut and recover from autoimmune damage to tissues (joints, nerves, endocrine glands, etc.).
In more than 25 years of working with patients who suffer from leaky gut and autoimmunity, I can’t begin to describe how futile efforts to recover were until they consumed adequate protein.

How Much Protein Is Enough?

Your ideal intake should be .36–1 gram of protein per pound of body weight. Typically, it is suggested to use “ideal” body weight if you are overweight, but it may be appropriate for you to go higher than that, particularly if you’ve been under-eating protein.

There are roughly 7 grams of protein per ounce of meat.

Here are some examples of protein content:

  • 4.6 ounces of salmon ~28 grams.
  • 5 ounces of strip sirloin steak ~35 grams.
  • 4 ounces of cooked, skinless chicken breast ~28 grams.

Sources of Protein

Protein from meat is more bioavailable and complete than protein from plants. Meat proteins are also more complete in terms of amino acids. Vegans and vegetarians need to consume more protein and pay attention to amino acid profiles, including leucine.

I generally don’t recommend plant proteins because they are immune reactive for many people with autoimmunity and leaky gut. Eggs and dairy are also commonly immune reactive. As with most diet-related issues, protein tolerance depends on the individual.

If you significantly undereat protein, increase consumption gradually. You may need the aid of hydrochloric (HCl) acid, digestive enzymes, and gallbladder support if you feel protein is difficult to digest. You may also need to be screened for an H. pylori infection, which is a common cause of low HCl or indigestion. See my gut health videos for more explanation.

I don’t recommend protein powders that contain whey, milk, soy, egg white, or pea because they are immune-reactive ingredients for many people with chronic health issues. Protein powders made from beef, collagen, or chicken may be more suitable. Again, this depends on the individual.

While periodic fasting can help reduce inflammation in some people, I do not recommend it for those who have long been protein-deficient until they rebuild their protein sufficiency and general resilience.

Simply put, it is physiologically impossible to recover and restore proper immune function if you do not have the protein building blocks necessary for tissue and cell recovery and development.

2. Essential Fatty Acid Diversity

Essential fatty acid (EFA) balance is one of the most overlooked areas in managing autoimmunity, chronic health conditions, and repairing leaky gut. EFAs are converted to prostaglandins, which profoundly affect immune modulation. Industrialized vegetable oils and trans fatty acids promote the synthesis of pro-inflammatory prostaglandins and should be avoided.

It is estimated that up to 80 percent of the U.S. population fails to get enough EFAs daily, which promotes chronic inflammation and immune dysregulation. EFAs are “essential” because the body cannot make them, and must come from the diet.
To promote healing of tissues, reduce inflammation, and modulate autoimmunity, you must ingest a balance of omega-3, omega-6, omega-9, and arachidonic acid fats.

Fish Oil Is Best if You Have High Blood Sugar and Insulin Resistance

It’s important to mention that insulin resistance plays a role in which omega-3 fatty acid sources are best for you, as many Americans are insulin resistant. You likely have insulin resistance if your fasting blood sugar is over 100 or your HbA1c is 5.6 or higher. In these cases, fish is the best source as insulin resistance can hinder the body’s ability to convert alpha-linolenic acid (ALA), a type of omega-3 fatty acid found in plant sources like flaxseed, chia, walnut, and hemp seed into a more usable form.

Eating a diet high in omega-6 fats may also hinder this conversion of ALA to omega-3s. Our hunter-gatherer ancestors ate about a 1-to-1 ratio of omega-6 fats to omega-3. Today, the average American eats a ratio of as high as 25 to 1—way too many omega-6 fats compared to omega-3 fats. This is due largely to sunflower, cottonseed, soybean, sesame, and canola oils in processed foods.

This extreme imbalance between omega-6 and omega-3 creates a highly inflammatory environment that plays a role in many chronic conditions, including heart disease, diabetes, autoimmune disease, leaky gut, and brain degeneration.

The best way to prevent or reverse this inflammatory environment is to increase your omega-3 fats and lower your consumption of omega-6.

How Much Fish Oil Should You Take?

Since most people do not consume enough EFAs, I recommend supplementing with a high-quality fish oil. However, people who take fish oil commonly do not take enough.

A healthy intake of omega-3 is 3500 mg for a person eating 2000 calories per day. If you eat 3000 calories, you should take at least 5250 mg of omega-3 oils daily. The average EFA capsule is 1000 mg. That means if you eat 2000 calories, you should take about four a day; if you eat 3000 calories a day, you should take 5 to 6 capsules of fish oil daily.

Algal oil supplements derived from algae are a good plant-based source of EPA and DHA (omega-3 fatty acids also found in cold-water, fatty fish). Of course, you can also eat fatty fish regularly, and raw nuts and seeds if you tolerate them.

EPA and DHA Serve Different Functions

Most fish oil supplements have a 1:1 ratio of DHA to EPA. Both are important, but each has different functions in the body.

EPA has more of an anti-inflammatory focus, while DHA has the greatest effect on brain health. If your goal is mainly to dampen inflammation, then regular fish oil or fish oil with concentrated EPA is appropriate.

If your goal is to impact your brain health, then consider fish oil with a high concentration of DHA. Individuals with neurological imbalances derive more benefit when ratios of DHA to EPA are greater than 1:1. I like to use ratios greater than 10:1 or 20:1 of DHA to EPA.

Omega-6 and Omega-9 Fatty Acids

Omega 6 and 9 fatty acids are necessary for good immune health—though caution should be taken as overconsumption of omega 6 is pro-inflammatory.

Cold-processed rapeseed oil (not to be confused with standard canola oil) and flaxseed oil are good sources of omega 6. Omega-9 fatty acids are commonly found in olive and avocado oil.

Arachidonic Acid

Arachidonic acid (AA) is commonly vilified as pro-inflammatory, but we need it for healthy immune function. AA’s reputation for being pro-inflammatory comes from the overconsumption of omega-6 fatty acids in the general population.

Sources of arachidonic acid include fatty meats, shellfish, butter, and ghee. Many people with an intolerance to the dairy protein casein may nevertheless tolerate butter and ghee.

Including diverse sources of these healthy fatty acids in your diet is critical to modulating inflammation and autoimmunity.

3. Blood Sugar Imbalances Are a Powerful Trigger of Inflammation

High and low blood sugar spikes can lead to systemic inflammation, immune flares, hormonal imbalances, and compromised brain function. Supporting balanced blood sugar is critical for recovery from any inflammatory condition.

Many people with chronic health conditions have blood sugar that is too high, too low or swings wildly between the two.

Blood Sugar That Drops too Low Triggers Inflammation

The biggest sign of a blood sugar imbalance is energy changes throughout the day—it should remain stable. One of the most common mistakes I’ve seen



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