5 steps to restore gut health

Does Disease Begin in the Gut? – 5 Steps to Restore Gut Health

5-Steps to Restore Gut Health_ Tales of a Scrunchy Mom

5 Steps to Restore Your Gut Health

Your Mighty Microbiome

Have you heard the phrase, “It’s all about the microbiome”? Chances are you have and there are several important reasons for this.

Below we’ll explore how the gut-brain connection works, why you need to understand this important process, 3 effective ways you can optimize your gut function, and how to put together a healing protocol with the 5 R’s.

** This post may contain affiliate links which means I may make a small commission at no additional cost to you when you click through and make a purchase. Thanks for your support! **

When I suffered from a parasite infestation several years ago, I found myself constantly in an irritable mood, bloated no matter what I ate, waking up in the middle of the night (around 3 am) and craving foods I had long before phased out of my diet (give me all the sugar!).

Before finally see my naturopathic doctor about this, I didn’t understand why I suddenly felt “crazy.” Now that I have a better understanding of the role a balanced gut plays in our overall well-being, it makes total sense why they call the gut our “second brain.”

What is gut health?

Hidden within the walls of your digestive system is what is known as “your second brain” and this “brain in your gut” is changing the way that we look at the links between mood, digestion, health and even the way that you think.

Does disease begin with gut health?

The technical answer is “NO,” not all diseases start in the gut. For example, it doesn’t apply to genetic or inherited diseases. But, there is evidence that many chronic metabolic diseases do begin in the gut. We can prevent these diseases by following a few simple steps.

restore gut health

Understanding the “Second Brain” and Why the Microbiome Matters

This “little brain” is called the ‘enteric nervous system’ or ENS and it comprises two thin layers of over 100 million nerve cells that line your GI tract from your esophagus to your rectum.

The role of the ENS is to control digestion, including swallowing to releasing the enzymes that help break down food, and to control blood flow, which aids with both nutrient absorption and elimination.

The ENS communicates with our brain with significant implications. When you have an unhealthy gut, symptoms of imbalance can manifest themselves in other parts of your body. This is your body’s way of telling you that something is wrong or out of balance.

Studies have found that increasing your gut-health can lead to improvements in:

  • Immune function – 80% of our immune system is located in our guts
  • Brain function
  • Symptoms of anger, sadness, and depression
  • Obesity and weight management
  • Toxin levels in the body
  • Irritable Bowel Syndrome (IBS)
  • Allergies
  • Chronic Fatigue Syndrome

How does the microbiome work?

The ENS may sense things that our cerebral brain can’t. Evidence has been found that when the GI tract is irritated it sends signals to the central nervous system, which can trigger our mood and ultimately affect it. When you consider that between 30%-40% of the population has bowel problems of some kind and that a higher percentage of these individuals develop depression and/or anxiety it’s easy to see how there could be a connection.

reduce stress to restore gut health

Our bodies are filled with bacteria – good and bad. There are more bacteria in a human body than there are cells. In fact, there are an estimated 100 trillion microorganisms living in our bowels alone (yup, we’re basically more bacteria than human). The key to optimal gut-health is to have more good than bad bacteria in your gut. 

The fancy name for the good microorganisms is probiotics. Probiotics help us do things like:

  • Digest food;
  • Absorb nutrients;
  • Break down medications; and
  • Kill some of the bad bacteria that lead to infection.

3 Simple Ways to Start to Heal Your Gut

Probiotics and Gut Healing Foods

There are quite a few ways to get probiotics, but one of the easiest is to take a supplement. You will find many different kinds under different brand names. Talk to your physician or natural health practitioner for a brand recommendation.

There are also foods that are naturally high in probiotics. These foods include:

  • Unpasteurized Cheese – Gouda, Cheddar, Provolone, and Gruyere are some examples
  • Buttermilk
  • Kefir
  • Miso
  • Sauerkraut
  • Apple Cider Vinegar – mix into water with raw honey (or stevia) and cinnamon if you don’t like to take it straight
  • Kombucha
  • Yogurt – be sure and read the labels and avoid brands high in sugar (plain Greek yogurt is a good place to start)
  • Asparagus, onions, garlic, leeks, and artichoke

gut healing foods to restore gut health

Other gut healing foods and supplements:

Getting more probiotics and other gut healing foods into your system is one of the best steps to improve poor digestion and restore gut health.

Manage Your Stress Levels

So much easier said than done! But imperative if we want a healthy gut, mind, and body.

Stress, especially long-term stress, affects our gut bacteria by slowing down digestion (transit time) which can lead to an overgrowth of harmful bacteria. In addition, stress also affects the production of hormones and neurochemicals that communicate with our brain.

Prolonged stress can cause these chemicals and hormones to change permanently (unless you specifically work to change them back). Long-term stress may also lead to gastroesophageal reflux disease (GERD), stomach ulcers, IBD, IBS, poor digestion, and potential food allergies.

reduce stress to restore your gut health

Laughter really is the best medicine! It helps to reduce stress and floods our body with “happy hormones.” 

There was even a study conducted where researchers looked at healthy people as well as those with atopic dermatitis – a disease that is often associated with imbalances in gut bacteria. The researchers had the participants watch funny movies daily for one week. In only one week, the patient’s gut flora had changed and resembled the healthy participants.

The gut-brain connection acts in a loop: the brain affects the gut and the gut affects the brain. When you improve one the other will naturally improve too.

Play in The Dirt!

Mudpies, anyone? Maybe our little ones are on to something here.

As adults, gardening is a good way for us to “play” in the dirt. Not only will it get you outside, give you exercise, vitamin D exposure from sunlight, and fresh air, but putting your bare hands into the soil introduces your body to the microorganisms that are found on the plants and in the ground

We have to stop viewing all bacteria as the enemy! Our obsession with over sterilization and anti-bacterial everything can actually be quite detrimental. The result of our aversion to “bacteria” is that many types of bad bacteria are getting stronger while the good bacteria are dying.

play in the dirt to restore gut health

Studies have shown that kids who grow up with a dog have both a lower risk of allergies and a healthier immune system.

Dogs are associated with a type of house dust that actually exposes us to important strains of bacteria (L. johnsonii is one) which is essential within the digestive tract.

Dogs also work somewhat like a probiotic, helping develop healthy bacteria that boosts your immune system, stopping you from getting ill, and possibly reducing allergies. Dogs also help you, or in some cases force you, to exercise more and help relieve stress in your life.

5 Steps to Heal Your Gut

When you’re unsure where to start, follow this 5-step system to begin restoring your gut health.


Remove any food or activity contributing to the imbalance of your gut as much as possible: stress, unhealthy and allergenic foods, environmental toxins, etc. Problematic foods and drinks may include dairy, gluten, corn, caffeine, alcohol, and refined sugars – remove these for 2-3 weeks. You can reintroduce these things slowly to note how your body responds.


If you have an imbalanced gut you’re probably also experiencing symptoms of poor digestion (heartburn, burping, bloating, gas, etc). Assist your digestive system with digestive enzymes and gut healing foods.


Add beneficial bacteria back into your system by taking quality probiotic and prebiotic supplements and foods.


Help your gut to heal by eating a nutritious diet that reduces inflammation, including antioxidants, healthy fats, amino acids, vitamins, and minerals.


Take inventory of your lifestyle to ensure you’re caring for your wellbeing on a holistic level. Address your sleep habits, emotional and mental support systems, rest and relaxation.

Restore your gut with the 5 R's

While the state of your gut health may not be the only determining factor in your susceptibility to disease, it IS a big part of the equation and has implications that extend into your mental health as well. Don’t ignore it!

Once I was able to rid my body of parasites and restore the balance of my microbiome, my moods naturally improved, I slept soundly through the night and my cravings subsided. I felt like ME again!

But parasites aren’t the only way our gut can become imbalanced. A lack of probiotics, prebiotics, rest, and exercise along with a diet high in empty carbs and sugar (which feed bad bacteria) can be contributing factors.

Start with the 3 strategies above, put it together with the 5 R system and you’ll be on your way to a healthier gut!

For more healthy gut tips, read my post: “12 Simple Daily Habits That Balance Your Gut”

What are your favorite ways to nourish your gut?






6 thoughts on “Does Disease Begin in the Gut? – 5 Steps to Restore Gut Health”

  1. Great article! I have some of the symptoms you’ve mentioned and have been looking into ways to heal my gut. I already do several of the things you recommend and am currently researching a good probiotic to take. Thanks for the tips!

  2. Hello I was just reading and wanted to known more about finding which food intorlances my son might have I am doing a food elimination diet for now him but it’s super hard and not even sure if it is helping him. Thank you for writing me back

  3. I usually drink 16 ounces of homemade kombucha every day. Sometimes I fill several bottles and infuse them with a variety of different combinations. My favorites are peach/ginger, blueberry/lavender, and strawberry/orange. I have a few questions: When you remove foods that may be causing inflammation, how long should you remove them from your diet before starting to re-introduce them back one at a time? How long is enough time to clear your system? And when it comes to certain bad foods like refined white sugar and refined white flour (particularly GMO flour), why re-introduce them at all?

    1. Good questions! After removing possible problematic foods and drinks (like wheat, corn, citrus, nightshade vegetables, nuts, coffee, alcohol, sugar or dairy) for 2-3 weeks, you can begin to add them back in one at a time. The purpose is simply to identify trigger foods and the cause of symptoms (joint pain, headaches, bloating, bowel changes, etc.). Of course with “foods” like refined sugar and GMO flour, there really isn’t a need to reintroduce them (or at least not long-term) unless you simply want to confirm that it was indeed causing digestive disturbances. This is just one method. Personally, I’d rather save myself the time and see a health kinesiologist who can quickly test for food sensitivities with nutrition response testing (that would be a good topic for another post!). But if you can’t afford that route, an elimination diet is an option 😉

Leave a Comment

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.