Gut Health Penelope McDonnell

Gut Health: Getting to the Root of the Issue

“Imagine you have a tree you love. One day you notice its leaves have turned brown. They will, you understand, soon wither and fall off. Imagine now that you call an expert who, after close examination of the leaves, recommends that you paint them green and attach them back to their branches so the tree at least can appear to be healthy.  Everyone would agree that’s crazy. If you want to get your tree truly healthy, you can’t just cover up the problem. You need to get to the root of it… [and] the problem is most likely in the roots.”

— Alejandro Junger, MD and author of “Clean Gut”

The digestive tract is a complex and magical mechanism that serves as the foundation for your overall health. It breaks down food, absorbs nutrients, houses important immune supportive bacteria and has close communication with your brain. Actually, it has more receptors for “feel good” neurotransmitters (like serotonin and dopamine) than your brain does!

Your gut is a highly sophisticated and resilient system that is designed to manage itself.  But sometimes it can’t, and we struggle to understand the problem.

Here are some of the patient concerns I hear most often:

“I get so bloated after meals and I can’t figure out why!”

“I have SIBO (Small intestinal Bowel Overgrowth)– and it won’t go away. Can you help me?”

“I have the worst heartburn. Medication helps, but when I don’t use them, it comes back!”

“My gastroenterologist tells me my pain is related to my gall bladder. What can I do?”

“My stomach sometimes hurts for no reason and it’s getting worse.”

“I think I have food allergies that are causing me to bloat and have gas. Can you help?”

“I go back and forth between having diarrhea and constipation. It just won’t go away.”

And since diet and digestion affect mood and cognition, behavioral-based concerns are usually close behind.

“I feel so depressed.”

“I just can’t focus anymore, and I don’t know why.”

“I have trouble sleeping, but I haven’t changed anything in my routine.”

Fixing hard-to-solve gut problems is an area where naturopathic medicine really shines.


We have lots of wonderful protocols that target a solution strategy called the 4R’s:

Remove (inflammatory foods, unwanted bacteria, and parasites)

Replace (with nutrient-dense foods and digestive enzymes/Betaine HCL to help break down food, if needed)

Repair (soothe and nurture the gut with herbs, supplements, and nutrient-dense foods)

Reinoculate (with pre and probiotics)

When tailored to your specific concern, this four phased plan can have some pretty miraculous results. Pain subsides, energy returns, bloating/gas/heartburn symptoms reduce and slowly disappear. And your mood improves.

So how do we start to personalize and implement the 4R strategy?


A good stool test can tell you if you have: unwanted bacteria or parasites, inflammation, low levels of digestive enzymes, enough good bacteria, or signs of small intestinal overgrowth (SIBO). Food sensitivity testing may also be warranted and can show which foods cause the strongest inflammatory reaction when you eat them. In some cases, we might even do some heavy metal testing, but only depending on your exposure through food or environment.

Food Diary:

We take close look at your diet using a four-day diet diary, which is filled out prior to your appointment. A food diary tells us a lot about what you might be doing or eating that is upsetting your system.

How much sugar and simple carbs are you eating?

How nutrient dense is your food?

What portion of your diet contains veggies, protein, good fats, nuts, and seeds?

Are you skipping meals and/or having too many late-night snacks? Do you have carb/sugar cravings that just won’t go away?

Do you crave carbonated beverages?

Do you eat lots of acidic foods?

The answers to these questions can make all the difference in understanding the concern or issue.


Various components of your lifestyle may be playing a role in your gut discomfort.

How is your stress level?

Are you getting good quality sleep?

What portion of your meals is green and leafy?

Do you find yourself socializing over wine and rich food most nights out of the week?

Have you been on repetitive doses of antibiotics?

Do you spend most of your day sitting at a desk?

How much water to you drink?

Your lifestyle and habits can reveal to us what it is that is irritating your gut and making it act out. And it could take just a simple lifestyle tweak to fix it!

After completing these three steps, we take all the information and data to create a personalized protocol just for you.


Your personalized protocol includes:

Food Plan (a detailed food plan with suggestions on what to eat and when)

Supplement Plan (effective supplements or tinctures to fast-track healing)

Lifestyle Modifications (they can be as simple as taking some deep breathes before a meal)

Overall time to wellness varies, but some patients feel better immediately, especially if the issue was bacteria related. If there was lots of inflammation or the problem has gone on for a long time, recovery could take a few weeks to months, depending on the severity of the issue.


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