How to Heal Your Gut 101

So many of my patients struggle with underlying gut issues, whether they know it or not. Gut health is an obvious goal when someone is struggling with chronic digestive symptoms. But sometimes ‘healing the gut’ isn’t even on the radar. Many patients come to me for much more pressing concerns like hypothyroidism and Hashimoto’s, fertility concerns, hormonal imbalances, food sensitivities, fatigue, etc.

And therein lies the rather ironic kicker: nearly all of these conditions (and most types of chronic disease) are in some way often rooted in gut health issues.

This comes as a shock to many people because either:

  1. They have never made the connection between common digestive issues—like bloating, constipation, or acid reflux for example—and their other symptoms,
  2. They’ve lived with digestive issues for so long that they’ve just accepted them as normal,
  3. Nobody has ever mentioned gut health as a possible root cause

However, new research has shone a fascinating light on the deep interconnectedness of our gut microbiome (a world unto itself which consists of trillions of intelligent microbiota) and our physical, mental, and emotional health.

Which is why I believe it’s everyone’s right to learn as much as they can about how to care for their gut microbiome proactively, and how to spot and begin to heal common gut infections.

Why gut health is so darn important today (even if you don’t have digestive complaints)

In Western medicine, we tend to view the body’s organs and systems as compartmentalized lone-rangers so to speak.

Having heart problems? It’s probably a circulatory system issue. Having trouble with depression? That’s a serotonin imbalance. Overweight? You’re obviously eating too many calories.

However, new research is rapidly changing our understanding of how interconnected the body is (something Eastern systems of medicine, like Traditional Chinese Medicine and Ayurveda have known for centuries).

And much of that research points to gut health as ground-zero for nearly all types of chronic disease, especially autoimmunity, mood issues, chronic skin conditions, blood sugar problems, sleep problems, and (of course) digestive complaints.

What do all these conditions have in common?

They’re inflammatory conditions, meaning they’re caused and/or exacerbated by chronic inflammation,1 and inflammation begins in the gut (more on this to come!).2
Now, you’ve probably heard the term “you are what you eat.” In Functional Medicine, we take it a step further. As my dear friend Jill Carhahan MD says: “you are what you eat, and then absorb, and then what you do or do not detoxify.”

And your ability to digest and absorb essential nutrients and detoxify the slew of chemicals we get exposed to everyday relies heavily on the integrity of your gut lining.

But what’s really incredible is all the things your gut is responsible for—beyond digestion— including:

  • Hormonal health and estrogen metabolism3
  • Stress response (the gut has its own nervous system called the “enteric nervous system which influences how we respond to stress)4
  • Immune health (up to 80% of it is in your gut)5
  • Allergen response 6
  • Diabetes7
  • Inflammation modulation8
  • Brain health and cognitive function9
  • Mental and emotional health via the gut-brain connection10

And this is by no means an exhaustive list of the gut’s functions or co-functions, which is why understanding gut health is so darn important to our overall well-being.

Why does the gut become unhealthy?

First, let’s picture what a healthy gut should look like: a long, hollow tube that’s sealed up tight enough to keep out pathogens and toxins while allowing microscopic nutrients, fluids, etc. to flow through. It’s a pretty amazing thing, really…
This is well summarized in a peer-reviewed gastroenterology journal:

“This barrier represents a huge mucosal surface, where billions of bacteria face the largest immune system of our body. On the one hand, an intact intestinal barrier protects the human organism against invasion of microorganisms and toxins, on the other hand, this barrier must be open to absorb essential fluids and nutrients. Such opposing goals are achieved by a complex anatomical and functional structure the intestinal barrier consists of, the functional status of which is described by ‘intestinal permeability’.”11

Now, let’s consider what happens when the functional status of the gut, or intestinal permeability, is compromised. This is sometimes referred to as “Leaky Gut” although I prefer the term intestinal permeability.

When one or more factors damage the intestinal barrier and thereby increase intestinal permeability, larger substances like partially digested food proteins, pathogens, toxins etc can essentially cross over into the bloodstream and activate the immune system.12

This can unsettle the balance in the immune system between tolerance and immunity to non-self antigens, and if not corrected quickly, can create a state of chronic inflammation that impacts immunity, mood, digestion, and all those other things I mentioned above.

Our modern day world is full of the factors which potentially damage the intestinal barrier. 12 of the most notable negative inputs include:

  1. Antibiotic use—antibiotics can be necessary at times, but they come with a cost, having been shown to cause changes in the intestinal flora in a way that favors the proliferation and virulence of pathogens.13
  2. Acid blocking medications (aka Proton Pump Inhibitors)—again, sometimes necessary, but often overused, and shown to cause dysbiosis of gut microbiota.14,15
  3. Birth control pills16
  4. NSAIDs17
  5. Chlorinated drinking water18
  6. A variety of household chemicals—found in cleaners, pesticides, personal care products, etc19
  7. Mold and mycotoxins20
  8.  Pesticides and GMOs—glyphosate has very real implications for gut health that we’re just beginning to understand.21
  9. Processed foods, toxic fats (fast foods, fried foods, vegetable oils, etc), and a high sugar diet.22
  10. Alcohol—has been shown to deplete certain bacteria with anti-inflammatory activity, and over time cause damage and increased intestinal permeability.23,24
  11. Artificial Sweeteners—studies have shown they can negatively affect the gut microbiome (and increase blood sugar!)25,26
  12.  Chronic stress27

It’s also important to understand the role that gluten plays in intestinal permeability.

Doctor and researcher Alessio Fasano, MD first identified a protein called zonulin,28 which is released in the presence of small intestinal exposure to bacteria and gluten, among others. Zonulin has been shown to influence the tight junctions in the gut—thus causing an increase in intestinal permeability and autoimmune disease in genetically susceptible individuals.

This discovery was important because it explains the vicious cycle that occurs once the intestinal lining becomes damaged…and why I recommend a gluten-free diet for anyone dealing with intestinal permeability issues.

How do you know if you have a leaky gut?

In my practice, I’m constantly preaching the necessity of understanding the root cause (aka: the “why”) of how disease and imbalances develop.

For it’s only when we understand the “why” that we can retrace our steps and make effective changes to treat the problem and prevent future flare ups.

So, how do you know if you have a leaky gut in the first place? I’d argue that any of the following suggest that intestinal permeability could be an issue:

  • You don’t tolerate probiotics or fermented foods
  • You have to follow a low-FODMAP diet
  • You’ve been diagnosed with Irritable Bowel Syndrome (IBS)
  • You have other chronic digestive issues, like bloating, heartburn, diarrhea or constipation
  • You have multiple food sensitivities
  • You have an autoimmune disease like Hashimoto’s
  • You have skin rashes or rosacea

These are some of the most obvious issues. But as I mentioned above, any number of chronic issues may be rooted in gut health problems.

Can you repair your gut? How to heal your gut with the 5-Rs

This 5-R process is the strategy I use with patients who present with symptoms of intestinal permeability and autoimmunity.

By following the 5-Rs we can identify the causes of leaky gut, heal specific gut infections (there’s usually more than one), and take steps to prevent future digestive health ailments. Here’s how this process works.

1. Remove

Step one is to remove any underlying stressors that negatively affect gut health. For many people these include:

  • Gut infections like bacterial overgrowth (SIBO), candida/fungal overgrowth, parasites and/or problematic bacteria.
  • Food sensitivities that we identify using an “elimination diet” and/or lab work. Different people will have different food sensitivities, but most people with issues here need to remove gluten (because it triggers that release of zonulin we discussed earlier).

2. Replace

Next we work on replacing digestive secretions, which are critical to normal digestive function and often compromised by diet, medications, diseases, aging, stress or other factors. This depends on the person, but includes:

  • Addressing low digestive enzyme function and pancreatic insufficiency
  • Restoring low stomach acid/ and hypochlorhydria
  • Enhancing gallbladder and liver function
  • Replacing bile acids, especially for people who have had their gallbladder removed
  • Addressing motility issues which can be affected by thyroid disorders, chronic stress and/or HPA axis dysfunction

3. Reinoculate

Remove and replace can take time and effort. When ready, people should be able to reintroduce probiotic foods or supplements, and consume prebiotic foods that are high in soluble fibers. Note that if these are reintroduced too soon, or not well tolerated, we may have to readdress #1 and #2 above.

When working with patients I often use a spore-forming probiotic early on, since it is usually well tolerated in people with bacterial overgrowth and other gut infections.

4. Repair

In this step, our goal is to help the lining of the GI tract repair itself by supplying key nutrients that can often be in short supply in a compromised gut.

Key nutrients for gut repair include:

  • Essential fatty acids—Anti-inflammatory omega-3 fatty acids have been shown to favorably influence gut microbiota through short-chain fatty acids, and also likely play a role in helping to maintain intestinal permeability.29 Essential fatty acids are found in fatty fish, grass fed beef, flax or chia seed. EFA supplements such as a high-quality fish oil or plant-based EFA are also helpful.
  • Serum derived Immunoglobulins—the mechanism isn’t exactly clear, but this is a well tolerated, low risk intervention that has been shown to improve symptoms of IBS and may play a role in improving intestinal permeability and modulating immune activation.30
  • Polyphenols—Phenolic compounds have been shown to favorably influence the gut microbiota mostly through the inhibition of pathogenic bacteria and the stimulation of beneficial bacteria.31 One of my favorite ways to incorporate more polyphenols is with a daily cup (or two) of my favorite toxin-free tea. Polyphenols are also abundant in dark chocolate (yay!), red wine, blueberries, and other superfruits.
  • Antioxidants—these are your vitamins A, C, and E which fight cell-damaging free radicals and may help restore gut-liver function.32 Preformed vitamin A is abundant in cod liver oil, organ meats and pastured egg yolks; while it’s provitamin beta-carotene is abundant in orange fruits and vegetables. Vitamin C is found in citrus, kiwi, mango, berries, and brassica vegetables. Vitamin E is found in leafy greens, sunflower seeds, and nuts.
  • Zinc—Suboptimal zinc levels (which are pretty common) have been shown to negatively impact gut microbiome diversity and immunity.33. Zinc is found in oysters, beef, and pumpkin seeds.
  • Glutamine—This amino acid plays a role in repairing the gut lining and reducing inflammation.34 Glutamine is found in bone broth, meat cooked on the bone, collagen, or gelatin. L-glutamine supplements can also be beneficial.
  • Vitamin D—Vitamin D may help reduce gut-associated inflammation while enhancing intestinal barrier integrity and boosting immunity.35,36 Since many people are deficient in vitamin D, I usually recommend a Vitamin D3/K2 supplement. But pure, unfiltered sunshine is an excellent source as well! Healthy food sources include eggs, fish, cod liver oil, and shiitake mushrooms.37

5. Rebalance

Here, we put our focus on how to create a balanced lifestyle that nurtures a healthy stress response which supports long-term gut health.

Lifestyle factors include:

  • Sleep—which dramatically impacts your digestive health.
  • Exercise—including a balance of high-intensity and restorative exercises to nurture body, mind, and spirit.
  • Our response to stress—chronic stress can quite literally punch holes in your gut38 (a topic for another time), thus finding ways to respond to life’s inevitable stressors more creatively and learning ways to de-stress is essential. Things like mindfulness meditation, spending time in nature, listening to music, socializing, and deep breathing are all helpful practices.

My favorite supplements for gut health

I really don’t have a one-size-fits-all protocol for healing gut infections. It’s important to work with your doctor to find the root cause.

A few of the supplements I commonly recommend for patients with digestive complaints include:

  • a spore forming probiotic
  • serum derived immunoglobulins
  • a combination of herbs (used short term for 8-12 weeks)
  • and digestive enzymes

Sometimes I also utilize pharmacologic interventions, and I’m always sure to test and treat thyroid issues when indicated since thyroid dysfunction can profoundly influence the gut.

In closing

It is truly amazing how far we’ve come in our understanding of how gut health affects our entire bodies, from digestion to hormonal imbalance and even our mood. But, there’s still a long way to go when it comes to patient education…which is why I’m so happy you’re here!

If you’re suffering from digestive issues, autoimmunity, thyroid issues, hormonal imbalance, food sensitivities…or any of the symptoms we discussed today, I’d encourage you to find a functional medicine physician (like me!) to help you work through the 5 Rs to treat and heal your gut. It really is incredible how a process like this can open the floodgates to helping you overcome a variety of seemingly “unrelated” health problems…even if your digestion seems fine.

Want to work together on this?

Reach out to me and let’s get started on the road to heal your gut for good.

During your functional medicine consultation, we’ll figure out:

  • If your gut is really the issue…and what other issues may be at play
  • What root causes, such as gut infections or thyroid issues, are present
  • Any food sensitivities or nutrient deficiencies at play
  • How to address your unique case through a customized 5R approach to diet, lifestyle, and supplement recommendations
  • And more!

Contact my office to learn more!



About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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