5 Steps to Heal Your Gut

by | May 27, 2019 | Digestive Health, Health Articles

From food triggers to uncomfortable digestive symptoms, here are 5 steps you can take to work towards healing your gut.

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I’m passionate about gut health. From a personal perspective, I’ve experienced first-hand the debilitating symptoms associated with a severe case of infectious gastroenteritis and the subsequent struggles with IBS. And as a result, you bet I’ve done a whole lot of work on healing my gut!

The digestive system is one of my favourite parts of the human body as it’s truly the basis for whole body health. It’s where we digest, absorb, and assimilate nutrients and it’s the major home of our immune system, protecting us from harmful pathogens, foreign particles and toxic substances entering our body. Our digestive tract is the primary barrier between us and the outside environment, and that my friends, is why gut health is so critical.

In a perfect world our gut would be happily metabolizing the food we eat, removing waste efficiently and fighting off illnesses effectively. And while many people go through most of their life without much complaint (#jealous), many aren’t experiencing the luxury of a robust digestive system and are instead experiencing food triggers, uncomfortable digestive symptoms, unusual bowel habits, and chronic inflammation.

Fortunately there are some steps we can take to mitigate these issues. And while it definitely involves patience, it’s absolutely possible to make improvements in your gut health. Each of the steps listed below were all things that I did when my digestion was an absolute disaster a few years ago, and some of them are still part of my life to this day.

5 Steps to Heal Your Gut

Healing your gut involves a few specific steps collectively known as the 5 R’s (remove, replace, reinoculate, repair and rebalance). Removing triggers, replacing your digestive system with factors that help it to function optimally, reinoculating your gut with the bacteria it needs to thrive, repairing tissues with specific types of healing nutraceuticals (supplements), and rebalancing the body with new lifestyle habits.

Before we dive in here, I want to point out that this process is best done alongside a qualified healthcare practitioner who has a thorough understanding of your unique situation.

1. Remove

This first step involves removing 3 main categories from your diet IF APPLICABLE.

*Please note that the removal of foods from your diet should be done carefully. This is a step that can lead to disordered eating behaviours if not done with proper guidance. The specific foods eliminated will depend on what’s contributing to your unique symptoms.

  • allergens/sensitivities
  • irritants
  • pathogens (if present)

This step involves removing triggers in the form of offending foods (food sensitivities, intolerances, allergies), items that promote inflammation or gastric irritation such as alcohol, and removing any existing pathogenic infections such as bacterial overgrowths or candida. Antimicrobials such as black walnut, oregano oil, grapefruit seed extract, olive leaf extract, berberine, caprylic acid, and garlic can help eradicate these infections.

An elimination diet may be helpful for determining your unique intolerances, such as the low FODMAP diet. This is a period of about 4-6 weeks where common food triggers are avoided and then re-introduced to determine tolerance. Foods are never intended to be avoided indefinitely in this process, unless absolutely required (such as allergy).

Reminder: It’s best to work with a qualified healthcare practitioner for any kind of elimination diet or when undergoing antimicrobial therapy.

2. Replace

Step two is to replace the factors that are lacking or not functioning optimally in our digestive system so that we can restore the proper function of our digestive organs such as our stomach, liver, gallbladder, or pancreas.

This can be achieved via supplements and may include stomach acid support (hydrochloric acid, apple cider vinegar), digestive enzymes, bile salts and/or digestive bitters. These types of supplements are very useful for easing the burden on a poorly functioning gut, enhancing our ability to break down and extract nutrients from food, and reducing symptoms.

Everybody’s requirements are different. Again, speak to your healthcare practitioner if you have questions about taking these kinds of supplements.

3. Reinoculate

Step three is to reinoculate! It’s a fancy word, but it simply means to reintroduce, and in this case, reintroduce friendly bacteria. If antimicrobial therapy (in step 1) was done, then this step would happen after.

Microbes play a critical role in what’s known as our microbiome and disruptions in this delicate bacterial balance from things like antibiotics, stress, food triggers, or a diet low in fibrous plant foods can lead to an array of symptoms and conditions (such as IBS).

Slowly increasing your consumption of prebiotic-rich foods (these are plant foods like vegetables, fruits, grains and legumes that stimulate the growth of our gut flora), probiotic-rich foods such as sauerkraut, kimchi and yogurt (coconut yogurt is my personal favourite!), as well as good quality probiotic supplementation is very important here.

4. Repair

The repair phase is where you really begin to put an emphasis on repairing the gut even further.

This is done through specific types of nutrients that have very therapeutic uses such as tissue-repairing glutamine (a favourite of mine), zinc, soothing deglycyrrhizinated licorice (DGL) and other mucilaginous herbs, and anti-inflammatories such as turmeric and omega-3 fatty acids from fish oil. Your healthcare provider can help shed some light on which ones may be best suitable for you and your unique case.

5. Rebalance

The fifth step is to rebalance the body with supportive lifestyle habits, such as reducing stress and getting proper sleep. These are often overlooked when we think about healing because it may not always feel like they make a big difference, but indeed they do. Maintaining a gut-friendly way of eating is also important, including the points mentioned in #3: Reinoculate phase.

Meditation, deep breathing exercises, and adaptogenic herbs are all things that can support this rebalance phase.

It’s important to remember that healing takes time. There’s no magic formula to improving your health nor is there a one-size-fits-all approach. It’s also important to remember that many of the lifestyle changes we make to better ourselves should be part of our lives long-term to continue to support our body (and to prevent us from slipping back to where we were before).

Once again, if you have any concerns, always speak to your healthcare provider.

If you’re looking for guidance on how to improve and support your digestive health, my 4-week Digestive Wellness Program is a great place for you to start. This program was created out of my own experiences overcoming chronic IBS symptoms.

Questions? Got an experience to share? Leave it below in the comments! I’d love to hear from you.

by Meghan Livingstone

Note: this post may contain affiliate links. Learn more here.

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  1. Marilena Bela

    Can you recommend a good probiotic, please?

  2. Jarn

    How about fasting? Do you think it could be one of method to to heal our gut?

    • Meghan

      I personally am a fan of intermittent fasting and it can be a great tool for gut health. I’ve written up a blog post on Intermittent Fasting, you can check it out for more info 🙂

  3. Suzette Horner

    If you were diagnosed with Sibo, what would your course of action be for yourself?

    • Meghan

      Hi Suzette! The best course of action for SIBO is antimicrobial therapy (including the herbs listed in this blog post under Remove) and a low sugar diet (similar to an anti-candida style diet) for up to 6 months. For some, antibiotic therapy may be necessary. Hope this helps 🙂

  4. Darlene Coleman

    I have very serious digest issues,My stomach is always burning inside

  5. Claire

    Do you have any advice for those suffering from gastroparesis?

  6. Jamie

    Hi Meghan – I’m also recovering from C. Difficile (diagnosed and treated in February) and have post infectious IBS with food intolerances. I’m still trying to determine all my food triggers and it’s been challenging to say the least. Is there any overlap with the steps you listed? And are there specific tests (other than a breath test for SIBO-which came back negative) to determine if there are pathogens in my system? Thanks so much! Your blog and YouTube videos have been so helpful and give me hope for the future!


    • Meghan

      Hi Jamie 🙂 Sorry to hear you’ve been dealing with C. diff! Not fun at all. I’d suggest getting a Comprehensive Stool Analysis done. Most Naturopaths can assist you with this. It’s a great way to get a detailed overview of the state of your gut (bacteria, parasites, microbe ratio, etc.) , more than just a breath test alone. Sending you lots of healthy healing vibes!

      • Valerie

        Hello Meghan, thank you so much for you interesting blog!! I am suffering from microbiota issues (candida and others) but antibiotics and antifungi don’t work anymore (both natural ones and the classical drugs). I am thus trying to recover by applying the four other steps of your recommendations. I am curious about the diet you followed while healing. Which food did you avoid for all this time in order to recover??

        • Meghan

          Hi Valerie! I am so sorry to hear you’ve been struggling. I’ve been there! There were a few foods I avoided such as gluten and dairy – if you want more info we cover all of this in my Digestive Reset Program. You can learn more here:


  7. Sophia

    how long did each step take you?

    • Meghan

      It’s hard to say exactly, but overall quite a few months in total! Everyone is very different x

  8. Adrienne Tabinga

    Hi Meghan – thanks so much for sharing this! I’m currently recovering from a number of mental and physical illnesses, with Generalized Anxiety Disorder being most prevalent. I’ve experienced extreme changes in my gut and digestion over the past few months because of my disorder, which led me to experience IBS. At the time I didn’t follow healthy steps to heal my gut when I had the symptoms, so my digestion and metabolism started to slow down and I now have irregular bowel movements. Just referencing your step to “Remove,” what if I am no longer intolerant to the foods that triggered my gut months ago because my system just slowed down/weakened instead? How do I know what foods trigger my digestion if it’s already depleted and kind of at a “burnout” stage? I’m just wondering on the next steps I should take in getting my gut healthy again – I know it’s gonna be a long journey for me. Thank you in advance!


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Hi, I’m Meghan. I’m a Certified Holistic Nutritionist, blogger, and YouTuber with a passion for healthy, simple living. I’m here to inspire you to listen to your body, eat mindfully and wholesomely, and create a fulfilling life that’s completely unique to you.