Episode 027: Using the Tools of Functional Nutrition to Uncover Root Causes

Using Functional Nutrition to Address IBS

In this episode, I share what the four main tools are that we use in Functional Nutrition, and I use myself as a case study on how these tools helped me uncover the root causes in my own health struggles with fatigue, thyroid dysfunction, unexplained weight, SIBO, heavy metal toxins and more. I pull back the curtains and share all the details of my health struggles in hopes of:

  • Demonstrating what Functional Nutrition is and how it can be used for just about any health problems

  • Showing you how understanding where food meets physiology can not only teach you about the basic functions of your body, but can also be powerful in reframing how you think about your health, and even weight loss, since that’s something so many of us struggle with, but also, reframe your relationship with food.

  • Getting you thinking about health beyond just “health and fitness”, “diet and exercise” and all those catchphrases and buzzwords that seem to embody what “health” is. While they are true, they’re only a partial part of our health stories.


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Hi guys, welcome back to the Live FAB Life podcast.

Before we dive in to today’s episode, here’s a quick recap for you of the last two episodes, because it sets up this one.

In Episode 025 I shared a client case study, using Functional Nutrition to address Irritable Bowel Syndrome, and in Episode 026, I introduced you to what Functional Nutrition is, and the three tiers that we use in it. So if you haven’t listened to those episodes yet, please go back and listen to them before you listen to Episode 027.

Because today I’m walking through the tools that we use in Functional Nutrition - and I’m presenting myself as a case study in how I used those tools to help me.

I’m about to pull back the curtains and share all the details of my health struggles, and my goal for doing this is to:

  • Demonstrate what Functional Nutrition is and how it can be used for just about any health problems
  • Show you how understanding where food meets physiology can not only teach you about the basic functions of your body, but can also be powerful in reframing how you think about your health, and even weight loss, since that’s something so many of us struggle with, but also, reframe your relationship with food.
  • Get you thinking about health beyond just “health and fitness”, “diet and exercise” and all those catch phrases and buzzwords that seem to embody what “health” is. While they are true, they’re only a partial part of our health stories.

So today I’m sharing what the four main tools are that we use in Functional Nutrition and how I’ve used them to help me uncover exactly what are the root causes in my own health struggles.

  • The health history and intake form
  • The Food Mood Poop Journal
  • The Functional Timeline
  • The Functional Nutrition Matrix

Tool #1: The health history and intake form So you know when you visit the doctor and you have to complete a form listing what your current concerns are? Well, we do the same in Functional Nutrition, but it is way more extensive than a two pager. In fact, my client intake form that I use is 14 pages long. Yes, 14 pages.

Because I’m not only asking you about your current concerns, but I’m looking to understand:

your health history - what have you experienced, since - birth, what have others in your family struggled with - your parents, siblings, grandparents, extended family. Are there patterns there?

  • What are your current health concerns
  • What’s your current nutritional status
  • What’s your digestion like
  • What’s your medical status
  • What health hazards have you been potentially exposed to
  • What’s your dental history
  • What’s your lifestyle, mental health, sleep history and more

Because taking a functional approach means taking all of these areas into consideration as potential factors in the health concerns that you have today, especially when your concerns are multi-factorial, meaning, there’s lots of different things going on, like I do.

You didn’t get to this place overnight - in fact, what you’re experiencing now, especially if it’s chronic, probably took years to develop. And it may take a long time to undo and repair the damage.

So, I said I was going to present myself as a case study, so let me share with you a brief glimpse of what my client intake and health history looks like. This episode would be way too long if I went into everything in depth so I’m going to cover the main portions of it which will hopefully give you a good idea the type of data I collect in my first session with a new client, or what we call the Functional Nutrition Intake session.

Okay, so my name is Naomi Nakamura, I live in the San Francisco Bay Area. I’m 43 years old, 5 feet tall and I weigh 150 lbs. A year ago I weighed 124 lbs. My ideal weight is 124 lbs, a weight I maintained for well over 12 years.

I was 5 lb 15 ounces when I was born, I’m the oldest child in my family. I work as a Program Manager in high tech, I’m also a health coach.

For exercise, I used to do long-distance running, but I suffered severe adrenal burnout, and now I do mostly strength training, weight lifting, walking, light running, and during warm weather I like to swim. I’ll occasionally do yoga, but admittedly, the Type A in me doesn’t love it - it’s too slow paced. I do love reformer Pilates, but I’m not currently practicing it at the moment.

I have travelled outside of the United States, to Europe, Asia and Canada, but that was 10 years ago. I haven’t really experienced any major life changes, although I had some recent changes in my 9-5 that were rather stressful. I haven’t experienced any major life losses in my family, other than some extended family members passing a while ago.

My current main health concerns are:

  • Low thyroid function
  • Recurring SIBO
  • Unexplained weight gain (gained 30 lbs last year)
  • And now heavy metal toxins.

I have a history of taking antibiotics as a child for ear infections, and I began taking them daily when I was about 13 or 14 years old when my dermatologist prescribed Erythromycin for acne. I took this every day until I was 30 years old when they were no longer effective for my cystic acne. Then I switched for birth control pills which I took for 10 years.

Today the only medication I take is Armor for my thyroid, although I take a number of nutritional supplements to support my digestive and immune systems. Specifically I take a multi-vitamin, digestive enzymes, Vitamin D, Prothera for liver support, Fermented Fish Oil, CoQ10, Zinc since it’s cold and flu season, Chlorella, and a probiotic.

I also eat superfoods like camu camu for vitamin C, cacao for magnesium, fresh ginger, turmeric, parsley, dandelion greens, lemon water and more, for nutrient support and detoxification.

I do have family history of poor thyroid function, autoimmune disease, high blood pressure, diabetes, strokes and kidney disease.

I do not eat refined sugar, gluten and dairy and also avoid most nightshades, grains, processed foods and hydrogenated oils as much as possible because they cause me painful gas and bloating, as well as loose stools. I also don’t drink soda, alcohol or coffee. I loosely follow a Paleo diet, but will modify to suit my individual needs. I would guesstimate that 85% of my meals are home-cooked.

I poop 2-3 times a day. The consistency of my poop varies, although it is much better than what it used to be. Following the Bristol Stool Chart, I’d say it varies between a 3 to 5.

I’ve never had food poisoning, but do experience gas, sometimes painfully, depending on what I eat.

I’m very sensitive to odors, and have been exposed to heavy metals, primarily lead, mercury, cadmium and other heavy metals to lesser degrees.

Upon further testing, we learned that my mercury exposure is mostly inorganic and my detoxification pathways aren’t functioning optimally. So my dentist has recommended removing my 11 dental amalgam fillings.

I have always been a poor sleeper, in fact, since childhood. Though I have identified a routine that helps me have better sleep, but I am not always disciplined about following it and if I don’t follow it, I am guaranteed not to sleep well.

I did not have a period for 10 years while I was doing intense exercise, long-distance running and taking birth control pills, but once I stopped doing those things, I now have a normal cycle again.

I was always called “moody” when I was a kid and have struggled with anxiety and bouts of depression in the past. I’ve been seeing a psychologist for the past 9 years which has helped tremendously in dealing with these concerns.

I have a strong support system who will help me sustain any changes I need to make.

My goals are to get off thyroid medication, return to my normal weight, to have consistent restful sleep and to no longer have a fatty liver. I want this for myself because I want to feel energized, vibrant and fit into my clothes again.

Okay, believe it or not, that was an abbreviated version of the client intake and health history data that we in Functional Nutrition collect. Going through all of it would take at least a full hour, and that’s what I do in my Functional Case Review, otherwise known as the first session with my clients.

Tool #2 - Food Mood Poop Journal After I collect all of this data, I then ask my client to do some data collection for me, through the Food Mood Poop Journal.

I know it has a funny name, but its a powerful tool. I like to have my clients keep a Food Mood Poop Journal for about 5 days, with at least one day being the weekend - because we tend to eat a little differently on the weekends, than we do during the week.

So what’s in a Food Mood Poop Journal?

Well, first we record how much sleep they got the previous night. So I like write down how many hours I slept, what time I went to bed, what time I woke up, how many times I woke up during the night, and on a scale of 1 to 10 with 10 being the best and 1 being the worst, rate the quality of my sleep.

Then, we record what we ate, and at what times. We don’t count calories or or measure macros or weigh our food. But we do want to know all of the ingredients in it. So if you’ve seen my Instagram stories of me making a smoothie, then you know how much stuff I pack into it. So on my Food Mood Poop Journal, I list all of it.

Then throughout the day I’ll record when I poop, and use the Bristol Stool Chart, which I’ll link to in the show notes, to rate the consistency of my poop.

And I’ll also record my mood - which is no not necessarily emotional, but rather, everything that I’m feeling of significance throughout the day.

For example, I couldn’t keep my eyes open and was falling asleep at 3 pm. Or, I had a headache all day. Or I was feeling jittery and irritable.

So I have my clients track this for 5 days, with one day being a weekend. As a bonus, I have them take a bunch of colored markers, and then make a dot at the bottom of the food column for every day indicating the color of the foods they ate.

So have you heard about “eating the colors of the rainbow?” That refers to eating as many different colored foods as possible. So using colored markers or pencils to see what colors they ate every day is a good exercise to track that.

Then after five days, I have my clients send me their Food Mood Poop Journal, before our next session.

What many find is that what they think they’re eating is not how they’re actually eating. And typically we always find some things to clean up there.

So for me, if I were to look at the past week of my Food Mood Poop Journal, we’d find that:

I could have eaten more orange and yellow foods. Some suggestions there would have been yellow squashes like delicata, butternut or spaghetti squash. Or even things like mangoes, pineapple, oranges or bananas - but I try to steer clear of too much sugary fruits. On occasion, yes, but too much, especially at one time - not. It’s too sweet for my palate.

I also could have used more hearty lunches. I’d eat a big breakfast so not hungry at lunch, but not quite enough to make it to dinner. Also, I was going to sleep waayy too late. Knowing that I my natural alarm clock gets me up at the same time every day, it’s super important for me to go to bed early, and well, the Olympics just didn’t help for that to happen.

So it’s no wonder that my moods were a little off last week - I was tired!, probably a little dehydrated and perhaps could have affected some unusual bowel movements that sided on the constipated side - which is very unusual for me.

See how powerful a Food Mood Poop Journal is? It a great framework for making correlations and connecting the dots between what we’re eating, how we’re feeling, and how our body is functioning. It’s helped my clients to discover food sensitivities and intolerances, and other things going on in their daily lives that they just didn’t correlate their health.

Now the best part about the Food Mood Poop Journal is that it’s free! We all know how expensive lab testing can be, so this is a great diagnostic tool to start out with before doing down that Tier 3 route! Any notebook can make a Food Mood Poop Journal, but if you want a little help in getting started with keeping one, I have a free download for you of a PDF that you can use. And when you sign up for it, I’ll teach you how to use it through some follow-up instructional emails.

You can get your Food Mood Poop Journal at www.livefablife.com/fmpj or go to the show notes for this episode at www.livefablife.com/027.

Okay so I referred to the Tier 3 route, which, in Functional Nutrition is lab testing. But The Food Mood Poop journal does the Tier 1 - where we address the non-negotiables of cleaning up our diet by removing the most common inflammatory food, of sugar, gluten and dairy, plus any other personalized non-negotiables like getting more sleep, fostering a supportive community or even avoiding further disruptive foods like grains and nightshades.

So how does this reflect in my case study?

Well, I already avoid sugar, gluten and dairy - and I have for years. I’ve done many basic, advanced and specialty elimination diets, like a Low FODMAP diet, to further explore what foods I may be intolerant of. I know I struggle with poor sleep - so that is an going issue but one that I’ve actively been working on, and I can check yes for the other areas of a supportive community, regular exercise, etc. So I can confidently say I’ve addressed Tier 1.

But I’m still struggling with gas and bloating, unexplained weight gain, and occasional fatigue, so we shift our focus to Tier 2, which still practicing Tier 1.

Tier 2 is where we address deficiencies - like nutritional deficiencies.

Again, this is where the colored markers exercise that we do with the Food Mood Poop Journal come into play. We can see if we’re eating a diet with sufficient vitamins and minerals and other nutrients. And if we’re not, we address how we can make shifts in our diet to add these nutrients.

And if what we’re eating has all of the nutrients we need, but we still aren’t feeling great, perhaps there’s some gut issues that need to be addressed. I’ll address what is a gut issue in next week’s episode, but Tier 2 is where we address in gut healing modalities like drinking bone broth, probiotics or even meditation to support gut healing.

And the reason gut healing is so important when it comes to addressing nutritional deficiencies is because of absorption. One of the main steps of the digestive process is the ability for the body to absorb nutrients from food, and that happens in the gut. And if your gut - any part of it is damaged - that may not be happening, no matter how healthy of a diet you’re eating.

So how does our gut get damaged? Through stress - emotional stress, eating inflammatory foods, overexercising, exposure to toxic chemicals, prolonged use of antibiotics and more.

So bringing it back to my case study I can put a check through all of those sources of stress:

  • I struggled with anxiety and depression - check
  • I used to eat an inflammatory diet of sugar, hydrogenated oils, gluten and dairy - check
  • I definitely overexercised - check
  • I have high levels of lead, mercury, cadmium and more - check
  • I took antibiotics and birth control pills for 30 years - check

So its no wonder I have gut issues. But I’ve been focusing on healing my gut for a few years now.

I even took things a step further by detoxing my kitchen - by swapping out my non-stick cookware for cast iron and stainless steel, got rid of plastic by switching to glass; I switched out all of my personal care products to ones that had a safety ranking of #1 or #2 in the Environmental Working Group’s Skin Deep database, and even started doing body detox activities like castor oil packs, saunas, dry skin brushing, contrast showering and even epsom salt baths.

But not all of my issues are resolved. For maybe 80% of people, addressing Tiers 1 and 2 will resolve their problems. But for someone who is multi-factorial, like me, this is where we move to Tier 3 - where we bring in a functional or integrative medicine doctor. And this is where lab tests come in.

So I shared how my initial health concerns were leg pain and adrenal burnout. I cleaned up my diet a long time ago, and I’ve been working on gut healing for about four or five years now. But since not all my health concerns are resolved, we turned to lab tests to tell us what else is going on in there.

This is where we learned that my thyroid isn’t functioning properly, not that much of a surprise because where there’s adrenal or cortisol dysfunction, you’ll also find thyroid dysfunction. And Dr. Aviva Romm talks about this in depth in her book, “The Adrenal Thyroid Connection” that I’ll link to in the show notes.

Being that the thyroid is intricately tied to metabolism, it’s not that much of a surprise that I have unexplained weight gain.

So is my thyroid dysfunction the root cause of my issues?

I’ve been on thyroid medication for two years now and while it’s helped increase my energy levels to some degree, but it hasn’t completely been resolved. Eating a thyroid-supportive diet hasn’t made that much of a difference either, so that tells us that there’s something else going on there.

Also, lab tests also showed that despite quitting sugar years ago, I still have a fatty liver.

And after cleaning up my diet, cutting back from over-exercising but still regularly exercising has only resulted in a 30 lb weight gain in the past year

So what the heck is going on?

Both my doctor and I were confused. We explored different things like leptin-resistance (if you don’t know what leptin is, it’s a hormone that regulates your appetite) and other possibilities based on my family history like autoimmune diseases, thankfully, those things checked out okay.

That’s when we finally came to heavy metal toxins. We did a heavy metals test and that’s where I tested off the charts for lead and mercury with cadmium right behind it and number of other heavy metals in lower levels.

Now your first instinct might be, “well, take out your dental fillings!” But here’s the thing - the chelation process of removing dental fillings can be very hard on the body because you could be further exposed to those toxins. And it’s also a very expensive process.

So, after consulting with Dr. Alderson, my dentist and naturopath who I interviewed in Episode 004, we decided to take a conversative approach and first address the toxins issue by avoidance.

I changed my drinking water to only drinking reverse osmosis water. I get it from Whole Foods - it’s not the best option because it’s still dispensed in a plastic gallon. And although that plastic gallon is BPA-free, that doesn’t mean its free of other harmful ingredients play bisphenol-f and others. Reverse osmosis water also strips out the good minerals that we do need, so I’ve attempted to remineralize it by adding himalayan salt to my water. Not the best approach but better than drinking tap water, bottled water - which is usually just tap water anyway, or even using a Brita filter - which is what I was using but learned that it doesn’t filter out heavy metals.

I also avoided seafood for six months, which, if you know me, you know how much I looooooooove my seafood. So that was difficult, but not impossible.

Now after 6 months, there really wasn’t any change, so this is where the other two tools of Functional Nutrition came into play. I should mention, that I build these tools shortly after the client’s Food Mood Poop Journal analysis, but they are documents that are always updated.

So Tool #3 is the Functional Timeline, where I take their intake data and create a timeline, plotting out their health concerns, with their medications and supplements, significant triggers or triggering life events, into a comprehensive timeline, starting from birth to present day.

This gives a really, really insightful visual to see what things happened in a person’s lifetime that lead them to the things they’re battling today.

And Tool #4 takes this same data and organizes it into the Functional Nutrition Matrix where we can see what were the antecedents, or historical factors, triggering events, what categories of symptoms a person has - whether it be gastrointestinal, immune and inflammatory, environmental input, oxidative stress and energy production, detoxification, hormones, mind and spirit or even structural challenges. We plot out their data into this visual, and then round it out with what are their habits: what’s their sleep and diet like, how are they exercising, are they sufficiently hydrated, what’s their stress level like?

These visuals give us a complete picture of just what is going on. Not only is it powerful to the client, but also to the rest of their healthcare team.

So coming back to my case study, after seeing my functional timeline and matrix, and knowing what has and hasn’t work with regard to my attempts to detox heavy metals, we took things a step further and to test what kind of mercury is in my body.

I did another lab test, testing my blood, urine and hair to see where the source of my mercury exposure was coming from. By far, it showed inorganic mercury, which are things like dental fillings (of which I have 11), and that it was affecting my kidneys, so no surprise that my detoxification pathways are clouded.

So no surprise that there’s so much dysfunction going on in my body because there’s chemicals in there that’s disrupting my detoxification and metabolism. So its no wonder that I have unexplained weight gain, stubborn weight loss, poor sleep, imbalanced hormones and even recurring SIBO!

So are heavy metals the root cause of my health concerns?

Possibly! We won’t know for sure until we remove the source of heavy metals. But until that happens, all the supplements and efforts I make to detox, won’t be nearly as effective because the source of the toxins are still there.

Once we remove the source, which starts in April, we’ll then be able to see how my body responds, to give us an idea of what happens next.

So I’ve taken you through my experience of going through Tiers 1, 2 and 3 of the Functional Nutrition Framework, and I’ve introduced the four tools of Functional Nutrition:

  • The Client Intake and Health History Form
  • The Food Mood Poop Journal, which you can get on the show notes
  • The Functional Timeline
  • And the Functional Nutrition Framework so you can see how bring our stories into a powerful visual of what’s happened and provides a comprehensive and complete story is of what’s going on in one’s health.

So hopefully, I’ve demonstrated what Functional Nutrition is and how it can be used for just about any health problems.

Hopefully I’ve show you how understanding where food meets physiology can teach you about the basic functions of the human body, and also help you reframe how you think about your health and reframe your relationship with food.

Gaining 30 lbs in one year is difficult to deal with. If I didn’t have the understanding of how what our thyroid is and how it’s supposed to function, how digestion is the foundation of health and how heavy metals causes dysfunction, I probably would be killing myself in the gym trying to burn calories, starving myself thinking I was eating too much - and unknowingly causing further damage to myself. Mentally I’d probably be beating myself up thinking I wasn’t good enough, or thinking I was a lesser person, a lesser athlete. But knowing how the body is supposed to function, how my body is functioning and what’s causing the gaps, helps me to have a lot of grace and acceptance for where I am and know what I need to do to reach my goals of getting off thyroid medication, returning to my normal weight, getting consistent restful sleep and no longer having a fatty liver, and ultimately feeling energized, vibrant and able fit into my clothes again.

I hope I’ve got you thinking about how all these things might apply to you, no matter what your health struggles are. Are you approaching it from a “let’s treat the symptoms” or “a treat the root cause” approach? In the long run, which one would be better for you?

Now after listening to this episode, it might be worth your while, to go back and listen to Episode 025 with Kristen, and listening it with new “eyes” and seeing if there’s anything new you can draw from it.

Taking this approach, this Functional Nutrition approach has helped me know what to do to feel better, but has also helped me address some of my emotional issues with weight gain, emotional eating and I know that it can to.

If you’d like to get started with a Functional Nutrition approach, go to the show notes, download your Food Mood Poop Journal, follow the instructions that I’ll send you on how to use it and see what you can learn from it. The clues are there, right in front of you, waiting to be found.

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Naomi Nakamura is a certified Holistic Health Coach who takes a holistic approach through functional nutrition. Through her weekly show, The Live FAB Live Podcast, coaching programs, and safer skincare solutions, she helps people with acne and other chronic skin issues clear up their skin by teaching them where food meets physiology and how food, gut health, stress, and toxins are intricately connected to the health and appearance of our skin. Naomi resides in the San Francisco Bay Area and can often be found romping around the city with her puppy girl, Coco Pop! Connect with Naomi at: Facebook | Twitter | Instagram | Pinterest.