5 Steps to Restore Gut Health

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Following these 5 steps can resolve your digestive issues and get you feeling great!

If you have bloating, gas, diarrhea, constipation, or any combination of these, you’re probably frustrated. Maybe angry. You just want to get better. To feel better. The “5 R” Program can help.

What is the 5 R program?


Woman bent over holding her stomach.

In the functional nutrition world, the 5 R program is widely used to fix the root causes of gut issues and to restore gut health. The 5 R program was developed by the Institute of Functional Medicine. My program is based on the Institute of Functional Medicine’s program.

Understanding how your digestive tract works can help.

To understand why the 5 Rs are important, having an understanding of what your digestive tract does and what can go wrong helps. Your digestive tract (also called your GI tract or your gut) is about 30 feet long. Its primary role is the digestion (breaking down) and absorption of food.

Your digestive tract starts with your mouth, continues to your esophagus, stomach, small intestine, large intestine, then anus. Each part has a specific role in digesting and absorbing the things that you eat and drink. Given its length, the different parts, and the multiple roles of your digestive tract, that’s a lot of areas and ways things can go wrong. (If you want to understand more about your digestive tract, this article that starts in the mouth and continues to the stomach and this one that starts in the small intestine and continues through the anus explain the parts in more detail.)

Digestive problems are typically caused by three things.

  1. Imbalance of the microbes (also called dysbiosis)
  2. Increased intestinal permeability (also called “leaky gut”)
  3. Inflammation

What’s the goal of the 5 R program?

The 5 R program is to address the root causes of the common digestive symptoms you’re having (and even some of the uncommon ones). Addressing the root causes, the three things above, means the symptoms go away.

The real goal – to help you feel better!

What are the 5 R’s?

The 5 Rs are:

  1. Remove – remove things that cause irritation, damage, and inflammation
  2. Replace – add or restore what your body needs to digest the food you eat
  3. Repair – repair damage to the intestinal wall
  4. Reinoculate – introduce beneficial bacteria and restore balance to your microbiome
  5. Relax – focus on managing and reducing stress

Many protocols have “Rebalance” as the 5th R. However, I’ve found, along with some of my colleagues, that stress reduction and stress management aren’t addressed the full benefits of the program aren’t realized. If we work on fixing everything except stress, you don’t end up feeling as good as you could and should.

What are the details of each of the 5 R’s?

#1 – Remove – remove things that cause irritation, damage, and inflammation

Removing focuses on taking things out that are causing irritation, damage, and inflammation. This includes foods, toxins, fake foods, chemicals, bad microbes, and other bad bugs.

Some items that should be removed include:

  • NSAIDS
  • Alcohol
  • Caffeine
  • Foods with added sugar
  • Additives and preservatives
  • Artificial sweeteners

You will also want to remove foods that cause your immune system to react. These aren’t just foods that you have an allergic reaction to. It includes foods that you have an intolerance or sensitivity to. (Here’s more information about the difference between allergies, intolerances, and sensitivities.) Just because we are removing a food doesn’t mean you can never have it again. For a lot of people, they find once their digestive system is healed they can start eating those foods again.

A basic list of foods I recommend removing include:

  • Gluten
  • Dairy
  • Soy
  • Corn
  • Eggs
  • Nuts
  • FODMAPs
  • Nightshade vegetables (depending on your symptoms)
  • Cruciferous vegetables (depending on your symptoms)
  • Yeast
  • Histamine-containing foods (depending on your symptoms)

If you want to zero-in on foods that set your immune system on fire, there is also food sensitivity testing.  

Many people have an overgrowth of harmful microbes or have bacteria, yeasts, viruses, or parasites that are causing problems. You want to get these removed as quickly as possible. In my practice, I use an advanced functional medicine stool test that identifies any bad bugs that may have set up shop in your digestive system. Once you understand what bad microbes and other bad bugs are in your digestive tract, you can work on evicting them.

This step also includes reducing inflammation in the gut. Removing all of the items above will help reduce inflammation. In order to reduce it further, I work with clients to add in supplements that are targeted to soothe and reduce inflammation.

#2 – Replace – add or restore what your body needs to digest the food you eat

When your digestive system isn’t working properly, it often isn’t producing the substances that help break your food down. Two key substances are stomach acid and digestive enzymes. (Actually, there are a bunch of digestive enzymes specific for each type of food. I’m lumping them together because I use supplements that contain a variety of enzymes with my clients.)

If you’re low on stomach acid and/or digestive enzymes, your body isn’t breaking the food down enough for it to absorb the nutrients it needs (in addition to causing digestive problems).  (Learn more about stomach acid and digestive enzymes.)

Replace also includes using vitamin and mineral supplements to ensure that you’re getting enough of those to restore your health (and for a lot of people, energy).

#3 – Repair – repair damage to the intestinal wall

Repair is all about repairing any damage that has been done to the intestinal lining.

The wall of your intestinal tract is thin. Think of it like a brick wall made from thin bricks and mortar. When it is damaged, the mortar can get chipped, cracked, or removed. This allows things from the digestive tract to get absorbed into your body – where they don’t belong!

The Repair step provides your body the nutrients it needs to heal and repair the cracks in the wall. This usually involves supplements targeted to repair the lining of your digestive tract.

#4 – Reinoculate – introduce beneficial bacteria and restore balance to your microbiome

Reinoculation involves getting plenty of good bacteria back into your digestive tract. These bacteria help with digesting the food that you eat, and producing things that your body needs including some vitamins.

The microbes in your gut (also called your microbiome) communicate with your brain through the nervous, endocrine, and hormonal systems. We are constantly uncovering more about how the microbiome helps us stay healthy both mentally and physically. (Here’s more information on the microbiome.)

If we don’t have enough of the good bacteria, then the bad bacteria can take over. In the Remove step, you worked on removing things that cause you not to feel well. One of those things are the bad microbes. In this step, we’re putting back the good bacteria.

Reinoculation can be done with foods, prebiotics, probiotics, and polyphenols. A combination of foods and supplements works well in the reinoculation step.

#5 – Relax

Stress negatively affects your digestive tract and it can be more than just feeling “stressed.”

Stress can result from:

  • Not enough quality sleep
  • Illness
  • Poor diet or not eating on your body’s schedule
  • Pain
  • Injury
  • Over-exercise
  • Surgery

Stress actually feeds the bad microbes that we were removed in the first phase of the program. If you continue to be stressed while you’re trying to kill them off they can put up a fierce battle making the process more difficult than it could be.

Another reason to reduce stress is that cortisol and adrenaline, the stress hormones, interfere with the body’s ability to digest food and for your body to get the nutrition it needs from the food you’re eating.

While eliminating stress isn’t possible, you can work on ways to manage it better. Relaxing, meditating, getting some gentle exercise, eating good foods on a schedule, and more can all help.

If you don’t take steps to manage your stress levels, you won’t receive the full benefits of the program.

Can the R’s be done together?

Absolutely!  I usually focus on phases 1, 2, 3 and 5 and then start phase 4 (reinoculate) a couple of months later. This allows all of the bad microbes and bad bugs to be eliminated and new microbes to be re-introduced.

How soon will I feel better?

That’s a hard question to answer. My clients usually start feeling better within a couple to a few weeks and continue to improve over the next few months.

Will it relieve my symptoms?

Without talking to you, I can’t make any guarantees. I find that this program helps my clients and their symptoms. Depending on the underlying cause for their symptoms they are either symptom-free or able to manage their symptoms so they feel better and live a normal life.

How should I get started?

Starting with the first R – Remove – you should get on the path to feeling better. You can use the list of foods and substances mentioned in the #1 Remove section of this article to get started.

A better way to get started is to get my guide which will help you understand why going gluten free and dairy free matters for restoring your gut health. The guide also includes easy meal ideas that are gluten free and dairy free.

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Dr. Penny



My goal is help you take control of your triggers so you can lead a normal life. I’ve had Irritable Bowel Syndrome for over 14 years. I’ve been told, “It’s all in your head.” And, “You just need to figure out what’s causing your symptoms” without being provided any help to figure it out. I’ve finally gotten my symptoms under control. I want to help you do the same thing. I want to help you get your life back.


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