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Clinical Cause & Effect – Putting your Functional Nutrition Certification into Practice - Blog Image

Clinical Cause & Effect – Putting your Functional Nutrition Certification into Practice

BY: Andrea Nakayama

DATE: 2022-02-21

In your practice, you’ll likely encounter clients who are taking prescription medications. We see it all the time in the Functional Nutrition Alliance Clinic. And while it’s not within our scope of practice to advise people on pharmaceuticals as Functional Nutritionists or Functional Nutrition Counselors, it is within our scope to help clients understand cause and effect.

A lesson from Full Body Systems, the leading Functional Nutrition certification and training course

Nothing that goes into the body goes without consequences – good, bad or both.

We talk extensively about the consequences of both functional and impaired digestion in our Functional Nutrition certification and training program, Full Body Systems

In Full Body Systems, we train practitioners to ask, “what’s going on in there?” We teach them to look for the physiological connections between different symptoms (even those seemingly unrelated to one another.) An example of how this systems biology comes into play is with the gut-brain or gut-immune connection. Understanding these connections reminds us to view conditions like depression, psoriasis, joint pain, fatigue, Hashimoto’s and more as linked to possible imbalances in the gut.)

Year after year, I see that one of the biggest revelations for students pursuing their Functional Nutrition Certification is the discovery of the importance of the role of the stomach in both digestion and overall health. The chemistry of the stomach’s secretions, it’s mucous lining, and the wicked strong muscles within the stomach all have important jobs in relation to processing the food we eat. There’s powerful stuff happening in there!

So what’s the cause and effect of taking a drug that affects the stomach?

Prilosec is a PPI (proton pump inhibitor). Omeprazole is its generic name. It’s used to decrease the production of stomach acid to help prevent heartburn or GERD (gastroesophageal reflux disease). Prilosec isn’t the only one.

There are a good number of PPIs including Prevacid, Nexium and at least 40 other brand name pharmaceuticals that are among the top 10 highest-selling class of drugs in the U.S. In fact, by 2017, Nexium was the best selling pharmaceutical drug in all history. It’s estimated that between 18 and 28% of North Americans use a PPI. You can see that it’s highly likely that you’ll encounter a client or patient on a PPI in your practice. But by taking a PPI we miss the opportunity to uncover “what’s going on in there.” Plus, we obstruct some key physiological functions that will impact digestion and so much more.

What’s the cause?

  • Why is there heartburn or GERD?

  • Is there really too much stomach acid being produced?

  • Why does the body produce stomach acid anyway?

  • Is stomach acid a bad thing that should be squelched?

These are the questions I encourage you to ask behind the scenes. Do you need to know the pathophysiology of every drug? No way! (Unless pharmacology is your scope of practice or your passion.) But when your client’s outcomes (and therefore your success), is being compromised by something other than their morning grande latte and Krispy Kreme doughnut, or their 2am bedtime, you might want to take note.

Let’s look at the simple pathophysiology of a PPI.

The pathophysiology of a proton pump inhibitor

Proton pump inhibitors suppress gastric acid secretion by inhibiting the hydrogen potassium ATP-ase enzyme system at the secretory surface of the gastric parietal cells.

Here’s the breakdown…

  • gastric acid is a digestive fluid naturally formed in the stomach

  • gastric acid is composed of hydrochloric acid (HCl), potassium chloride and sodium chloride

  • gastric acid is critical for the proper digestion of proteins; it stimulates digestive enzymes which break down the long chains of proteins into their building blocks, amino acids

  • secretion is a key function of digestion where different fluids are introduced at different phases to induce the chemical processing of the food we eat

  • hydrogen potassium ATP-ase is an enzyme that initiates the action of the protein that acts as a proton pump (to release gastric acid)

  • parietal cells are the cells within the stomach’s tissue lining

Cut-to-the-chase: There are constituents within the sheath of your stomach that are meant to help you break down your food. What are the consequences of inhibiting an essential digestive function?

What’s the effect?

  • risk of B12 deficiency (B12 utilization requires a healthy and not compromised stomach lining)

  • iron deficiency (ditto regarding the stomach, check those ferritin levels!)

  • additional nutrient depletion including folate, calcium and zinc, with longer term use

  • increased potential for food allergy or sensitivity (the poor body has to process food that hasn’t been fully broken down)

  • fatigue & low energy

Your Functional Nutrition certification and cause & effect in practice

Now, like I said, for those practitioners with a Functional Nutrition certification alone, it’s not our job to take our clients off their meds. Yet it is our job to help them understand how to welcome and initiate better health. That’s why they seek our help! 

Connecting the dots with client education around clinical cause and effect can be transformational and is in our hands.  Learn how our 10-month Functional Nutrition certification and training program can help you incorporate the principles of cause and effect into your practice today.

Read more from the Functional Nutrition Alliance

The biggest mistakes to practicing functionally

Functional Nutrition Matrix

What’s Functional and what’s not Part 1

What’s Functional and what’s not Part 2

What’s Functional and what’s not Part 3


Ahmed A, Clarke JO. Proton Pump Inhibitors (PPI) [Updated 2023 May 1]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK557385/

Shin JM, Sachs G. Pharmacology of proton pump inhibitors. Curr Gastroenterol Rep. 2008;10(6):528-534. doi:10.1007/s11894-008-0098-4

Ankar A, Kumar A. Vitamin B12 Deficiency. [Updated 2022 Oct 22]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2023 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK441923/

Annibale B, Capurso G, Delle Fave G. The stomach and iron deficiency anaemia: a forgotten link. Dig Liver Dis. 2003;35(4):288-295. doi:10.1016/s1590-8658(03)00067-7

Heidelbaugh JJ. Proton pump inhibitors and risk of vitamin and mineral deficiency: evidence and clinical implications. Ther Adv Drug Saf. 2013;4(3):125-133. doi:10.1177/2042098613482484

Robinson LB, Camargo CA Jr. Acid suppressant medications and the risk of allergic diseases. Expert Rev Clin Immunol. 2018;14(9):771-780. doi:10.1080/1744666X.2018.1512405Vinke P, Wesselink E, van Orten-Luiten W, van Norren K. The Use of Proton Pump Inhibitors May Increase Symptoms of Muscle Function Loss in Patients with Chronic Illnesses. Int J Mol Sci. 2020;21(1):323. Published 2020 Jan 3. doi:10.3390/ijms21010323

Andrea Nakayama

By: Andrea Nakayama, FxNA Founder & Functional Medicine Nutritionist

Functional Nutrition Alliance provides the comprehensive online Functional Nutrition training in the Science & Art of the Functional Nutrition practice. Learn to address the roots of your clients’ suffering with client education, diet & lifestyle modifications.


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