The 4R Protocol 101

Welcome. If you’ve ended up here, then either you’ve been incredibly lucky with google, or you have some kind of gut related issue.


Assuming it’s the latter, you’ll probably have been told about, or advised to follow, the 4R program/protocol.


And with good reason. The 4R protocol is one of the most tried, tested and effective dietary strategies for improving gut health.


Our digestive system is a highly complex, yet incredibly efficient blend of structural, functional, hormonal, enzymatic and excretory processes. Not only that, it’s incredibly resilient and has multiple fail safes and back up strategies for when things go wrong.


Unfortunately, modern nutrition can, over time, overwhelm all of those fail safes. It’s usually at this point that small cracks start to appear, (figuratively, not literally).


Most of the symptoms of gut disfunction are often regarded as the simple effects of modern living, rather than signs of anything untoward. Consider the following:

  • Indigestion
  • Athletes foot
  • Stomach cramps
  • Constipation
  • Diarrhoea
  • Cravings
  • Restlessness
  • Insomnia
  • Cracked nails
  • Rashes

These are just some of the issues that can have their roots in the digestive process.


So, the 4R protocol?


The 4 R’s stand for:

  • Remove: Anything that’s contributing to the problem
  • Replace: Nutrients or enzymes the body needs to improve digestion
  • Re-inoculate/Restore: Bring levels of healthy bacteria in the intestines back up to optimal
  • Repair: Provide the body with the nutrients necessary to rebuild the lining and mucosal layer of the gut.

Each of the 4 phases normally lasts a minimum of 2-4 weeks, with 4 being optimal.


What follows is a broad overview of the strategy we recommend for each.

There are two branches to the removal phase. The first is to remove or kill off any problematic bacteria, parasites or yeast overgrowth. This is where we typically recommend getting a stool analysis done if you haven’t already, as this can identify the specific microbial. Certain microbials are more or less resistant to certain strategies, which means a problem specific approach tends to be easier and more effective at getting rid of the problem.


In most cases though, it’s a case of taking a course of anti-microbials. The most commonly recommended are oregano, berberine, plant tannins, garlic and uva ursi (please note that Uva Ursi should only be taken under the supervision of a qualified health professional and typically for no longer than 5 days). Depending on which one is best for a specific bacteria or parasite, you’d typically take these either as a supplement or a tincture.


We’ll advise you specifically what we think is the best option for you regarding supplement use in phase 1.


The second component of the remove phase is to avoid any trigger or feeding foods.


If you’ve read anything elsewhere about the 4R protocol, you may note that opinion varies significantly on this aspect. Some practitioners recommend removing only trigger foods, (foods that elicit a fairly quick onset of symptoms). Others recommend removing all refined foods and others recommend removing any and all sugars.


Based on our experience, we’ve found that the most effective strategy is hands down, to get rid of the lot. It’s a pain in the arse, it’s restrictive and it’s not a lot of fun. Over the years though, out of all the clients that have followed the protocol, the difference in results and efficiency is night and day. One client went the whole 16 weeks and despite feeling significantly better at the end, found that bacteria still hadn’t been killed off completely due to a fondness for a beer or two at the weekend, (and had to start the whole thing again as a result).


Bottom line, suck it up and get it done. Do it once, but do it well. You’ll be glad you did after it’s over.

Here’s a list of things to cut out or ideally avoid:

  • Wheat
  • Gluten
  • Dairy
  • Eggs
  • Nuts
  • Yeast
  • Shellfish
  • Citrus fruits
  • Fructose, lactose and sucrose
  • Spicy foods
  • Refined foods
  • Alcohol

Ideally, you’ll avoid these foods for the duration of the 16 weeks, but at an absolute minimum the first 4 weeks.


So, what can you eat?


All vegetables are fine, as are meat and fish, although limit or avoid shellfish for the first 4 weeks. Any non-wheat grains are also ok, such as brown rice, quinoa and millet.


Fruit is best limited to berries only and in small amounts. It’s likely that it won’t impact progress significantly for most people, but we’ve seen a very small number of past clients either slow, or even halt their progress as a result of their fruit consumption. Our advice as a result is to just avoid it if you can for the first 4 weeks.


Use herbs as much as you like for seasoning, but be a little cautious with spices, particularly the hotter ones. The following list is a fairly complete, but not exhaustive list of what we’d recommend:



  • Coriander
  • Parsley
  • Tarragon
  • Garlic
  • Ginger
  • Turmeric
  • Asafoetida
  • Fenugreek
  • Oregano
  • Basil
  • Mustard
  • Cumin
  • Fennel
  • Salt

Use sparingly

  • Cayenne
  • Chilli
  • Paprika
  • Pepper


In phase 2, we’re looking to improve how your body actually digests or processes food. The goal is to make sure that food is broken down properly in the stomach and then further in the intestine.


To do this, it may be worth supplementing with digestive enzymes and/or HCl (hydrochloric acid).


Please note, supplemental HCl is not actually neat acid, but rather Betaine HCL. Betaine hydrochloride (HCl) is a dietary supplement made from a combination of betaine and hydrochloric acid. It is however a very short-lived supplement and should therefore only be taken with high protein meals (20g or higher of solid fish or meat protein) and not at any other time. The goal in using it is to aid digestion and absorption in the short term, whilst any underlying causes are addressed.


We’ll advise you specifically what we think is the best option for you regarding phase 2.

This phase is about making sure you have a good balance of healthy/helpful bacteria in the gut. Historic or frequent use of anti-biotics can significantly compromise the quality, quantity and type of gut bacteria.


You have a couple of options in this phase.


The first is to start consuming healthy bacteria rich foods such as yoghurt, sauerkraut and tofu/tempeh.


The second is to take a pre/probiotic supplement.


Of the two options, we recommend the latter for efficiency and effectiveness reasons.


The two strains of probiotics that have the most research behind them are the Lactobacillus acidophilus NCFM strain and Bifidobacterium lactis Bi-07 strain. Taking these in supplement form ensures you get a meaningful dose of the strains that are most likely to have a beneficial effect.


Once your gut health is optimal, fermented foods are fine, but for the program, supplemental forms are better and as always, we’ll advise you specifically what we think is the best option for you regarding phase 3.

In this last phase, the goal is to make sure that the lining of the gut is restored structurally and inflammation free.


There are three nutrients that have been shown to help with this phase.


L-Glutamine, which is used to repair the layer of mucus lining the gut.

De-glycyrrhizinized liquorice (DGL) root, which is used to repair the cells in the large intestine.

Aloe-vera, which can help to reduce inflammation and soothe any areas of irritation in the gut.


As with previous phases, we’ll advise you specifically what we think is the best option for you regarding phase 4.

In closing, we’d make one final observation and suggestion. Of all the clients we’ve coached through this process, we’ve noticed that those who adhere most strictly to the plan, see the most dramatic results. Their energy levels skyrocket, their mood improves, and their symptoms disappear. Their body composition also improves significantly. For that reason, we’d encourage anyone who chooses to follow a 4R protocol to do so as diligently as possible. Sometimes, although not often, small changes that according to the research, shouldn’t have an impact, have drastically reduced the effectiveness of the program. Because of that, in our opinion, it’s not worth half-arseing it, unless you genuinely have no other option.


Be strict, accept that it’ll be a pain in the backside for the first few weeks whilst you adjust to it. Then prepare yourself to start reaping the rewards and experiencing levels of energy and health you’d forgotten were possible.