Gut Health 101: Building a Strong Gut

Good health starts with great gut health

I don’t remember when I started to have stomach aches every day. My digestive symptoms started gradually and then became daily, and then turned into seasonal allergies and later into “allergies” all-year-round. Only later did I realize that what I was eating (and how I was eating) was causing my gut symptoms. And only after a lot of studying did I connect my gut health to my immune symptoms. My hope is to help you connect your symptoms to gut health and give you the roadmap to rebuilding a healthy gut.

Here are the 4 steps on the roadmap to a healthy gut:

  1. Clear – If you think about the gut like a garden, this is where we remove the “weeds”: food triggers and microbial overgrowths

  2. Spark – Here we strengthen the “digestive fire” that helps us break down food properly and stimulate the coordinated movement of the gut tract

  3. Reboot – Once we’ve cleared out the weeds, and “amped up” digestion, we can feed and reseed the garden! Here we repair the gut lining, replenish and feed the good gut bugs

  4. Rebalance – Even the most balanced gut, requires daily habits to retrain and reinforce healthy gut function – this is the phase we build resilience in the gut.

Unsure if you even have digestive issues? Sometimes it’s obvious and often, it’s not. Here are a few questions to help you find out if you need to build your gut health:

  1. Do you experience indigestion? Reflux, heartburn, abdominal pain, diarrhea, constipation, gas/bloating, a bitter taste in the mouth after eating, bad breath? Have been diagnosed with esophageal spasms or IBS? These issues are certainly common but they are also signs of a struggling digestive system.

  2. Do you have an autoimmune condition like rheumatoid arthritis or Hashimotos? Reucrrent issues like fatigue, migraines, chronic pain, anxiety/depression and insomnia? Difficulty concentrating, skin rashes, sinus congestion? Almost every chronic condition has been linked to gut issues, whether we feel indigestion or not.

  3. Have you been working on improving your gut health for some time already but noticed that taking probiotics or removing certain foods didn’t help very much? These therapies can be very helpful when applied strategically.

  4. Have you found removing foods to be helpful but found the restricted diet to be unsustainable for the long term? Eliminating major gut triggers can be a powerful tool. Many people with indigestion find removing wheat, dairy or fermentable carbohydrates (ie. low FODMAP diet or Specific Carbohydrate Diet) very helpful. But it’s only one part of a gut repair program. Our goal is always to reintroduce as much variety into our diet as possible. A healthy gut flora depends on a diet with lots of variety.

  5. Have you had lab tests come back “normal” (even though you still have symptoms)? When H pylori tests, and parasite stool tests – even abdominal imaging – all come back “normal” it can be frustrating to be left with no new information. The problem is, many of these tests are designed to help us identify disease, not changes in function. In naturopathic medicine the development of disease is a progression: from health to dysfunction to further dysfunction and finally disease. The digestive function along this spectrum varies widely and many of us are somewhere in that spectrum of dysfunction right now. Taking very detailed health history and using functional testing can be invaluable for assessing our function.

  6. Do you eat a whole foods diet with lots of fruit and vegetables but still feel out of balance and deficient? Have a tendency to low iron or vitamin B12?

If you answered Yes to one or more of these questions, your gut could benefit from some support. Well, you’re in the right place! The 4 steps for building a strong gut are for those of you who have had chronic indigestion, for those who seem “stuck” even with treatments, and for those of you who want to improve gut health in order to unlock more energy, better mood and less pain.

Keep in mind that chronic gut issues have often developed over weeks, months or years. Addressing these accumulating dysfunctions need to be done layer by layer, so order matters!


CLEAR: Remove the “weeds” from the gut terrain

  • Do you get yeast infections as soon as you take antibiotics?

  • Do you feel worse after eating (and feel best with an empty stomach)?

  • Do you seem to have sensitivities to a lot of foods, including “healthy foods”?

  • Have you found taking probiotics didn’t help? Or actually made symptoms worse?

This first phase in rebuilding the gut is important and often missed. We often start with taking probiotics. But like throwing grass seed on a lawn that’s overgrown with weeds, probiotics have very little effect on improving the gut terrain – until we clear the overgrowth. Addressing the overgrowth of pathogenic microbes, or “bad bugs” can not only reduce digestive symptoms but also pave the way for new beneficial microbes to “seed” and survive.

Most are familiar with the “bad bugs” we get with food poisoning or traveler’s diarrhea. But “bad bugs” can stick around and cause long term gut issues too. In one study, over 80% of patients with IBS had bacterial overgrowth in their small intestine (SIBO) upon testing. Chronic microbial overgrowths in the gut are not rare. Tests like the Lactulose SIBO Breath Test can be helpful to confirm this bacterial overgrowth. In addition, fungal overgrowths in the gut are also possible and have similar symptoms to SIBO and IBS.

The underlying causes of IBS aren’t fully understood but dysbiosis, too many “bad bugs” vs “good bugs” in the gut, appears to be an important factor.

How do we get “bad bugs” in our gut?
The gut flora refers to all the microbes, bacteria, fungi, viruses and parasites, in our entire digestive tract. The term “microbiome” refers to the whole community of microbes in an ecosystem, like that of our human body so this includes the microbes on our skin, scalp and in our sinuses and vaginal tract, everywhere. Our human cells are outnumbered 10 to 1 by microbial cells! It’s no surprise then that we are not only affected by the microbiome, we rely on it. The microbiome is linked to heart health, immune system, digestion, metabolism, circadian rhythms and even blood sugar! Overgrowth of “bad bugs” in the gut can even affect insulin resistance! We are learning more about the microbiome, or “the invisible organ” every day. So far it appears there is no “one ideal” microbiome. But researchers agree diversity is key to a healthy microbiome. Just like ecosystems on our planet, a lack of biodiversity in our own microbiome, makes us more prone to disease.

So back to our question, how do we end up with dysbiosis? In addition to taking antibiotics, there are multiple common factors that shift our microbiome:

  • Pesticides are common in our food industry. For example, the commonly used glyphosate is known to reduce beneficial gut flora and allow harmful gut flora to survive

  • Our gut bugs eat what we eat

    • When we have a lack of variety in our foods, we lose diversity in our gut flora.

    • Lack of fiber in the diet leads to the loss of “good gut bugs”

  • Weak stomach acid caused by chronic stress, reflux medications and thyroid dysfunction can allow more “bad bugs” to get into our gut and survive there

  • Acute infections (travellers diarrhea, food poisoning) can lead to long term dysbiosis

A patient had developed abdominal pain, heartburn and joint pain that was worse with wheat products and beer. He took probiotics but it didn’t help. He took beer and wheat out of his diet and that improved his symptoms somewhat. When we finally addressed a yeast overgrowth and repaired this gut, all his symptoms improved and he was comfortably able to reintroduce wheat and moderate alcohol.

Take action in the CLEAR phase:

  • Remove the weeds in the terrain: Identify microbial overgrowths

  • Remove suspected triggers of foods like alcohol, wheat, dairy, fermentable carbohydrates

  • Choose organic foods when possible (start with the “Dirty Dozen”)

SPARK: “Stoke the fire” for better digestion and gut movement

  • Do you have undigested food in your stool?

  • Do you feel full quickly or for a long time after eating?

  • Do you have bloating or burping after eating?

  • Do you tend to have chronic low iron or other mineral deficiencies?

  • Do you have a thick white or even black coat on your tongue?

  • Do you feel tired or get loose stools after eating foods like salads or smoothies?

If you answered yes to any of the above, your “Digestive Fire” needs strengthening. In Traditional Chinese Medicine, our digestion is thought of as a fire. When the fire is strong, the food enters and is broken down completely. When the fire is weak, the food is only partially digested and we get the symptoms above

Take action in the CLEAR phase:

  • Timing: Our gut relies on a strong day and night rhythm. Maximize on timing by eating meals at the same time every day (ideally during daylight hours). This helps to strengthen digestion and regular consistent gut movement.

  • Taste: Adding bitter foods can help “stoke” that Digestive Fire:

    • Add bitter foods like arugula, bittermelon and ginger to meals

    • Herbal digestive bitters that include the herb gentian or apple cider vinegar with a little water taken with a meal may be helpful

  • Temperature: If you have a weak Digestive Fire, avoid foods that could “snuff out” the fire. Avoid cold, raw foods including salads, veggie sticks, sushi and ice cold water. Instead choose warm cooked foods and room temperature or warm beverages.

  • Digest food or thoughts, not both at the same time. In Traditional Chinese Medicine, the digestive system processes both food and thoughts. If we’re worrying or overthinking, we have less resources available for digesting food. Consider going for a short walk or journaling before eating.

REBOOT: Fertilize & Reseed the Gut Terrain

At this phase our gut is usually feeling comfortable with only occasional or mild symptoms. This is the stage where we can really improve the symptoms outside of our gut. Other issues that can benefit from this phase:

  • Autoimmune joint or skin issues

  • Blood sugar issues

  • Hayfever/allergies

  • Mood issues

Normally our gut is selectively permeable: letting nutrients into our bloodstream and keeping bad bugs and their toxins out. But chronic gut inflammation due to alcohol, food sensitivities, microbial overgrowth, some medications, chronic stress, etc. can lead to a “leaky gut” where undigested food particles “leak” into the bloodstream and trigger an immune response that can affect joints, skin, scalp, thyroid and brain function. This process in the gut is a “tipping point” in the development of many chronic conditions.

Repairing the Gut Lining
Look for things that may be contributing to gut inflammation (alcohol, wheat, etc.) or preventing you from repairing your gut naturally (over-the-counter pain medications or chronic stress). Glutamine, an amino acid found in some foods can help to repair the cells in the gut lining. Thankfully the gut lining regenerates itself every 5 days! Huge potential for healing exists here.

Fertilize and Reseed the Gut Terrain
Feed the good bugs with prebiotics like lots of fruit and vegetables fibers – the more variety the better! Fermented foods also help to feed beneficial flora and help introduce some probiotics as well.

My patient with rheumatoid arthritis had seen the strong link between her indigestion and joint pain by doing an elimination diet. But she found the diet to be unsustainable for the long term. Identifying the worst triggers for her and repairing the gut lining helped her find a long term solution that increases variety in her diet while reducing body pain.

Take action in the REBOOT Phase:

  • Repair the gut lining: talk to your practitioner about alternatives to anti-inflammatory medications that may be affecting your gut lining; reduce wheat and alcohol

  • Include glutamine: Glutamine-rich foods include cabbage and bone broth

  • Include plenty of fiber (for example, aim for 1 more cup of vegetables daily) and fermented foods (a couple tablespoons with a meal daily)

  • This is when probiotics can shine!

  • Review oral health and hygiene practices as a the oral cavity can be a source of some of the “bad bugs” getting into your gut and blood stream

REBALANCE: Robust Daily Rhythms for Gut Health

This is the phase we build resilience in the gut. Our habits help to retrain and reinforce good gut function daily and automatically so we can quickly rebalance after the occasional rich holiday meal or change in eating patterns with travel or shift work.

Good daily habits for gut support also helps with detoxification functions, microbial balance in the scalp, skin, vaginal tract, healthy immune system and more. We think of “brain chemical messengers” like serotonin and melatonin as coming from the brain, but the gut produces 90% of serotonin in the body and 400x more melatonin than the brain! Our mood, PMS, and insomnia are often related to gut health.

Take action in the REBALANCE Phase:

  • Optimize day and night patterns

    • Wake and sleep times: consistent from day to day; and in sync with nature’s day and night cycle

    • Eating and fasting: If you’re spending more hours of the day eating than fasting, shift your eating times (ie. eat dinner earlier) so that your overnight fast is at least 12 hours long most nights

  • Digestion and healing happen when we’re in a resting state:

    • Daily “yin” or quiet activities to help shift you body to the “rest and digest” state: Journaling, reading, connecting with others and “alone time”

  • (Many of the above action steps can be started, and be beneficial, right away.)

  • Aim for variety: every time you shop, try one new fruit, vegetable or spice that you haven’t tried before. Introducing more variety of foods can be an exciting part of this phase! However, the ability to tolerate greater variety usually requires addressing the previous three steps (Clear, Spark and Reboot) first.

The gut has such a huge potential to heal! I hope you’ve gained some insight into how to address the different “layers” of gut function so you can feel more comfortable, get more out of what you eat and improve your overall health. If something in today’s presentation resonated with you, I encourage you to put it into action.

To a healthy, happy gut,
Dr. Carin

We use cookies to improve your experience and to help us understand how you use our site. Please refer to our cookie notice and privacy policy for more information regarding cookies and other third-party tracking that may be enabled.