5 Steps to Total Gut Healing

If you’ve been tapped in to the holistic health community for any period of time, you’re likely familiar with all of the new science about the gut microbiome—our 100 trillion organism-strong “mini ecosystem.”

It’s head-spinning, actually. And exciting. 

While addressing digestive function may not be the single solution for what ails us, it’s a huge (and often missing) piece of the puzzle for many.

Autoimmunity? Gut.

Depression? Gut. 

Anxiety? Gut. 

Skin issues? Gut. 

Fatigue? Gut. 

Joint pain? Gut. 

Headaches? Gut. 

ADHD? Gut. 

Asthma? Gut.

You may have heard of the 5R program—a highly therapeutic approach to healing the digestive lining that can result in remarkable improvement in nagging symptoms and often, total resolution. For real.

It helps to:

  1. Optimize digestion and nutrient assimilation
  2. Balance gut bacteria
  3. Promote detoxification
  4. Facilitate gastrointestinal healing

Let’s look closer:

1. Remove: Remove the stressors on your digestive system, including known or suspected food sensitivities. True digestive healing can never take place if we continue to eat foods—sometimes otherwise healthful, whole foods—that irritate the gut lining. 

Before you read any further, know that once these sensitivities are identified, that doesn’t mean you can never eat these foods again! They’re different than food allergies. In most cases, once the gut has healed, it’s fine to eat these prior troublemakers in moderation, although for most people, especially those with Hashimoto’s or other autoimmunity, I don’t recommend reintroducing gluten.

Food sensitivities can be a bit tricky to identify because the symptoms may show up hours or even a few days after exposure. This is why it’s so important to do an Elimination/Provocation (E/P) diet, which is considered “the gold standard” for identifying foods that don’t love you back. I give little credence to blood testing for food sensitivities—false negatives are too common.

(I provided an entire chapter in our Essential Thyroid Cookbook on how to do an E/P diet and sleuthing out dietary sensitivities, including suggested supplements that, in addition to the healing diet, help to turn over the epithelial cells of the gut for maximum healing (see #4 below). Many of our recipes, if not already E/P-friendly, offer easy (and delicious!) adaptations for making them work for an E/P diet.)

It’s also important to consider the “bad bugs”—bacteria, yeast, and/or parasites. Work with a qualified practitioner to determine if these might be an issue.

2. Replace: Replace what’s necessary for optimizing digestive secretions and enzymatic activity. This includes hydrochloric acid, digestive enzymes, and bile acids that can become depleted from poor diet, pharmaceutical use, and other factors.

Adequate fiber in the diet helps to support digestive transit time and motility (elimination of toxins). Fiber is easy to get from the diet—supplementation may not be necessary.

While some experts may suggest supplemental vitamins, minerals, and other nutrients, often times, the healing that takes place as a result of the 5R program optimizes nutrient assimilation from our foods such that supplementation isn’t needed. (That’s not to say that supplementation is never warranted.)

3. Repopulate / re-inoculate: It’s critical to restore the balance of friendly/beneficial bacteria and to allow these “good bugs” to flourish with probiotic-rich foods, fiber-rich foods, and probiotic supplementation.

Lisa just wrote a great post on PREbiotics—non-digestible fibers found in certain foods (many of which you’ll find in our Essential Thyroid Cookbook!) that enhance the microbiome by fertilizing and stimulating the colonization of healthy bacteria.

She says, “[Prebiotics] work synergistically with probiotics to promote healthy gut function. By feeding the colonies of healthy bacteria, prebiotics help to increase microbial diversity and improve the ratio of good to bad bacteria.”

As for probiotic supplementation, generally, it’s recommended to get a broad spectrum of bugs, especially the bifidobacteria and lactobacillus species. I also love soil-based organisms (SBO) like bacillis subtilis for those with autoimmune conditions.

But it’s important to know that some don’t do well with multi-strain probiotics—those who have histamine issues in the form of histamine overload and/or histamine intolerance.

I cannot cover this adequately in this post, but two strains that people with histamine issues often react negatively to are lactobacillus casei and lactobacillus bulgaricus. Often, they’re eating a low histamine diet and taking anti-histamine supplements, but are still symptomatic because of their probiotic.

Histamines are a significant consideration for many in the alopecia community—one of my primary areas of practice. Alopecia or not, if you have or suspect a histamine issue, you may be better off with a single strain probiotic.

4. Repair: While it may feel overwhelming to “repair” our complex digestive system, what’s amazing is that in a healthy human, our intestinal epithelial cells regenerate every four to five days—one of the fastest rates of reproduction of any tissue in the body. The primary reason that a lot of us don’t make this cellular regeneration is…food sensitivities. But the gut can also become compromised from inflammation, stress, “bad bugs,” and pharmaceutical use.

An Elimination/Provocation diet will get you far, but it doesn’t tell the whole story. It’s important to take supplements that help to fast track this cellular turnover—glutamine, collagen/gelatin, and an appropriate probiotic (see #3).

As for the collagen/gelatin, it’s preferred that you make your own bone broth. But supplementation is okay too. We provide a bone broth recipe in our Essential Thyroid Cookbook and you can also find one here (scroll down).

People with histamine issues will need to take the supplement, as broth is high histamine.

Other nutrients that help with gut repair include essential fatty acids, zinc, and vitamins A, D, C, and E.

5. Rebalance / restore: This is where we turn inward and assess our lifestyle. Quality sleep and proper circadian rhythm, restorative exercise, and stress management all positively affect digestion.

Here’s a great post on optimizing sleep > 

Here’s a great post on exercising when fatigue is an issue >

A high-stress lifestyle turns on our sympathetic (“fight or flight”) nervous system response, which causes our adrenals to pump out stress hormones, namely adrenaline and cortisol. High cortisol has been shown to irritate the gut lining.

Go here to get my Restore Your Adrenals guide >

Ideally, we’re spending much more time in the parasympathetic nervous system response—the “rest and…digest” (see?!) response. Some call it the “feed and breed” response.

In conclusion, altogether, the 5R approach isn’t too difficult. It just takes some time and focus. 

And it’s so worth it.


Hi !this is Ana, from Mallorca, Spain.I gave up eating gluten two years ago, though sometimes, when in restaurants , I know the food they serve is not 100% gluten free. Six months ago I gave up all dairies food. I recently got my labs with TSH being 0,008. In a few days I will be seeing my endocrinologist. Does anyone know what it means to have such a low TSH?

Thank you very much for your comments. Ana.

What type of single strain probiotic do you recommend? Also, you say if you have histamine issues that a collagen supplement is best, but what kind and where do you find a safe one?

I have hasimitios and I am gluten free.  I have recently started baking with Einkorn flour as the gluten is different and they say people who have gluten sensitivities can eat it.  how do you fell about Einkorn flour for patients that have thyroid disease?

I have mixed feelings about it. I haven’t done a lot of research on it. I still adhere to, “When in doubt, leave it out.”

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