Find part 1 of this post here.

In part 1, I considered the Autoimmune Protocol, The Wahls Protocols and the Bulletproof Diet.

This post offers an overview of 6 more healing protocols:

  • Jacob's Gut Healing protocol;
  • The Brainmaker Diet;
  • Your Personal Paleo Code;
  • Paleo;
  • Primal; &
  • the Whole 30.

Jacob's Gut Healing Protocol

Jacob does a beautiful job of explaining how the gut works in Digestive Health with REAL Food (2013).

This is the most restrictive protocol of the dozen, with only 4 vegetables included during the elimination phase. If you are simultaneously on the Autoimmune Protocol (AIP), you'll be down to 3, as one of those (green beans) is not AIP-friendly.

created this diet specifically for people suffering from gut dysbiosis and significant digestive issues and therefore it removes all the usual foods that can cause leaky gut and systemic inflammation, as well as carbohydrates that are difficult to digest.

Compatibility: Jacob's Gut Healing Protocol

If you omit the green beans, this protocol is compatible with the AIP and with most of the other protocols on this list, simply because it is so restrictive.

Unlike some of the others, it is not intended for long term use.

Our experience: Jacob's Gut Healing Protocol

This is the protocol that gave Matthew some relief after 1½ years of unexplained, increasingly severe and debilitating nausea. The nausea was not autoimmune in origin, so it was not reversing on the AIP.

Though Jacob's protocol did not cure his nausea, it reduced it enough that he could think straight, get some of his life back, work with his Functional Medicine Doctor to develop a hypothesis and begin a new treatment. Which pretty much makes

I highly recommend book for anyone who is still experiencing digestive issues after trying one of the other healing protocols.

The Brain Maker Diet

Dr David Perlmutter clearly explains how the origin of most illness, including mental illness, is directly connected to gut health, and offers his 'Brain Maker Diet' in the 2015 book Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain for Life.

In keeping with most other protocols on this list, David highlights foods that nourish a healthy microbiome as a key to well-being. Like other protocols, the Brain Maker diet advocates fermented foods, but unlike some others, it includes fermented dairy and even tempeh, a fermented soy product.

It is a low-carbohydrate diet that recommends 72-hour fasts 4 times a year (but offers no cautions about fasting for women).

Compatibility: The Brain Maker Diet

The Brain Maker Diet has many elements in common with other protocols, but is less restrictive. Its emphasis on fermented dairy products (the meal plan includes dairy daily) makes this diet generally less compatible with others on this list.

Our experience: The Brain Maker Diet

I haven't tried the Brain Maker diet because it contains foods that I already know are not optimal for me. However, I did try elements of the protocol  in David's 2011 book Power Up Your Brain: The Neuroscience of Enlightenment, co-written with Alberto Villoldo, including regular multi-day fasting. I found that, as for many woman, prolonged fasting caused negative effects.

As both Matthew and I were already committed to a more rigorous protocol when I read Brain Maker, the primary benefit of this book was the clear explanation of the biological systems involved in brain health.

Your Personal Paleo Diet

Chris Kresser published what is now called Your Personal Paleo Diet in 2013.

The dietary component is aligned with the other protocols on this list, and includes variations for people with autoimmune conditions and blood sugar and/or weight regulation issues.

Chris emphasizes that no one protocol will work for everyone, and advocates starting with his 30-day elimination diet and then customizing to meet individual circumstances

Compatibility: Your Personal Paleo Diet

Because Your Personal Paleo Diet encourages an individualized approach, it is potentially compatible with all the other protocols on this list.

Like most of the others, it emphasizes lifestyle practices as an integral part of the protocol, and though Chris has a somewhat unique interpretation, these are aligned with the lifestyle elements of the AIP and the Primal Blueprint.

Your Personal Paleo Diet is unique in the way it calculates carbohydrate levels. Like the AIP, it is not a low-carb protocol. In fact, Chris recommends not counting low-carb vegetables toward daily carbohydrate consumption at all, and only including high-carb vegetables and fruits in these calculations.

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Our experience: Your Personal Paleo Diet

Our experience has been that modification of any protocol has been necessary to achieve results, which supports the central premise of Your Personal Paleo Diet.

Both Matthew and I have been working to implement the lifestyle recommendations from this protocol, including cultivating pleasure and getting outside~.


Paleo can be viewed as the overarching category into which all of the other protocols on this list fall, including those that allow for some gluten-free grains and occasional legumes.

For people without serious chronic health issues, it might be enough.

My favorite Paleo cookbooks are Nom Nom Paleo by Michelle Tam and Well Fed by Melissa Joulwan.

Compatibility: Paleo

Paleo is somewhat open to interpretation, but it is generally agreed that it excludes grains, legumes, junk food, sugar, vegetable oils and most dairy products (except, perhaps, ghee).

Paleo people vary in how closely they adhere to an ancestral eating plan, but all agree that it's an excellent idea to avoid gluten entirely.

Our experience: Paleo

I started with paleo four years ago and experienced significant health benefits, but Matthew, as a person with multiple autoimmune conditions and significantly impaired gut health, found that a regular paleo diet made him feel worse.

The conclusion? The more complex your health issues, the more pure and anti-inflammatory your protocol will probably have to be.

Primal Blueprint

Mark Sisson is the force behind the Primal movement.

Though from a dietary perspective Primal might seem just like a slightly more relaxed version of paleo (it allows full-fat dairy & suggests that 80% fidelity to the diet is sufficient) it is a rigorous and evidence-based optimization protocol that is quite specific about lifestyle elements like movement, sleep, play, sun exposure, and stress management.

You can find everything you need to know on Mark's blog, starting with the Definitive guide to the Primal Blueprint.

Compatibility: Primal Blueprint

Primal, like the Bulletproof Diet, is an optimization protocol. It is designed to help generally healthy people to optimize their performance and experience.

Healing Optimization

On the continuum of healing protocols, the Primal eating plan is more relaxed, but the lifestyle elements are entirely aligned with the stricter healing approaches.

Our experience: Primal Blueprint

Mark's 2009 book The Primal Blueprint was the first healing protocol book published and the first one I read.

I started with Primal eating but soon found that I did better without the dairy. It took a couple of years to understand the importance of the lifestyle elements of the protocol and I am still working to incorporate these fully.

Whole 30

Dallas and Melissa Hartwig's Whole 30 elimination diet advocates paleo purity for 30 days as a healing reset.

It Starts With Food came out in 2012, but you can find all the Whole 30 details online.

Compatibility: Whole 30

The Whole 30 requires fidelity to the diet for 30 days.

The AIP and Jacob's Gut Healing Protocol are also elimination diets, but they specify that food reintroductions begin only when problematic symptoms have reversed (which in the case of the AIP can take years). The Whole 30 is substantially less restrictive than the AIP or the Wahls Paleo Plus.

Our experience: Whole 30

I started doing Whole 30s during the first year I was paleo and Matthew sometimes joined me.

This was well before either of us contemplated following a rigorous healing protocol full-time, and so doing a whole 30 felt like a quite a big deal.

Now that we've been on a stricter-than-whole-30 dietary regime for almost 2 years, I can see that these early forays into pure eating for a month at a time was an important step in the process of committing to a healing protocol lifestyle.

This post is part 2 of 3

Part 3 will outline the N=1 Protocol, so you can begin to create a healing pattern of living specific to you.

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Paleo on the Go delivers for free anywhere in the US and has a diverse menu of Paleo (including Autoimmune Protocol) ready-prepared foods.

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