How to achieve great digestion for improved energy, mood, mental clarity, disease prevention, and more!


Yesterday, I posted Part One of this mini series on How to Improve Your Digestion, where I provided some very basic tips on kicking your digestive steeze up a notch.

I wanted to dive deeper into the subject of digestion, because the process is magnificently complicated. In my first post, I discussed some basics which can give you some actionable tools to help achieve great digestion. For many of you, those tools will be enough to help superset your health and get you feeling energetic and well.

For those of you who have a compromised immune system or have battled with GI issues for a number of years, you may need additional testing and TLC in order to uncover the root cause of poor digestion.

Many people who have chronic gut issues live under the assumption that their food choices are solely to blame for improper digestion. This may or may not be true. It could be you have food sensitivities that are causing your immune system to short circuit, there is an underlying hormonal issue, and/or a bacterial or parasitic infection.

Many of us deal with a combination of the three, which can make troubleshooting poor digestion a challenge.

The good news is, there are many options for testing which can bring so much clarity to what is actually happening inside of you. There are also supplements we can take to improve digestion and heal from internal damage, as well as mindset shifts we can make to get a handle on our physical and mental wellness.

Let’s begin by discussing some of the tests you can take in order to put some science behind the state of your GI.

Crispy Salmon and Vegetable Stir Fry - an easy and delicious healthy dinner recipe that only takes 30 minutes to prepare


Feeling like you’ve tried everything and still don’t know which foods upset your GI? A food sensitivity test will eliminate much of the guesswork.

I recently did the ELISA/ACT test with the help of my RD, Dena Norton, which tests food and household products against your blood to see how your immune system reacts to them. The ELISA/ACT test is a blood test. You submit a blood sample and the lab uses it to observe which foods, drinks, additives, chemicals and household products to which you have an immune response.

They provide results that show which compounds illicit a strong immune reaction, a moderate immune reaction, and provide a list of compounds that cause no reaction. In this sense, you can know definitively which foods, chemicals, etc you need to avoid in order for your immune system to function properly.

Discovering which foods you digest poorly does not need to be a shot in the dark. On the flip side, uncovering which foods your body likes can be an incredibly healing experience! For years, I made assumptions about the foods I was reactive to, and it wasn’t until I took the food sensitivity test that the fog lifted and everything became clearer.

If you suspect you have food allergies, see an allergist. If you don’t have allergic reactions to food but you notice GI issues after eating, it may be worth taking a food sensitivity test with the help of a functional medicine doctor or registered dietitian. The main goal is to get your immune system to function properly so that you can thereby digest properly.

While food sensitivity tests are expensive, for me it was worth the peace of mind knowing which foods I can safely consume without having an immune reaction. Taking the guesswork out of your body by putting science behind it is absolutely worth the time and money!

One Skillet Ground Turkey Thai Curry Skillet with Rice - an easy one-pot meal of aromatic coconut milk sauce |



Bacterial and parasitic overgrowths are incredibly common. If you experience GI upset frequently, it could be that there is an overgrowth of some sort that needs to be dealt with. Addressing these underlying pathogens not only helps your body heal, but it brings life back to your immune system and helps regulate your digestive system.

The ultimate goal is to eliminate the bad bacteria and parasites so that your healthy bacteria can flourish, thus boosting your energy, ability to heal, and aids in healthy digestion. This may be easier said than done without knowing the exact type of overgrowth you’re experiencing.

In order to know which bacteria, yeast, fungus and/or parasites you have (spoiler alert: we all have something), a comprehensive stool test like the GI Map is incredibly powerful.

The GI Map looks for the DNA of a wide array of bacteria (both good and bad), parasites, and fungus. The problem with standard stool tests is they use what is in the stool sample to look for organisms, which may not always be present in the given sample, and many lab technicians don’t know what to actually look for. Creepy, right?

The GI Map gives an in-depth look at what is happening both inside and outside of your digestive system. It not only uncovers which pathogens are present, but it shows the amount and type of good bacteria (probiotics) present in your gut. If you’re low in good bacteria, but high in pathogens, it’s no wonder you’re experiencing symptoms.

One incredible facet of the GI Map is it tests for Zonulin, which is a protein found in your blood stream. High zonulin may be a sign of autoimmunity or food intolerance. High zonulin may be also be a sign of gut permeability, because zonulin would not be in your blood stream unless your gut were permeable. The more zonulin found, the greater the intestinal permeability. There isn’t enough science behind zonulin as it relates to leaky gut just yet; however, it may be an indicator something is happening in your gut that needs to be addressed.

In addition, the GI Map tests for how much secretory IgA you have. Simply put, Secretory IgA are little soldiers that live outside of your gut that peer in to be sure everything is okay. If they notice something is off, they send for help to destroy any invaders. Low secretory IgA can be the root cause of constant illness (whether you’re someone who always catches every cold or flu, or are battling with autoimmunity or chronic GI symptoms).

Working with a practitioner to boost your secretory IgA will make your immune system function properly and thereby provide support to every other system in your body, including digestion. I implement goat colostrum into my diet in order to boost my secretory IgA.

I highly suggest doing the GI Map instead of wasting time and money on a standard stool test ordered by your GI doctor. I’ve taken two standard stool tests, both of which turned up negative for everything.

Through the GI Map, I learned I had h. pylori overgrowth and blastoystis hominis, a parasitic infection. I also had low secretory IgA (low immune system function) and high zonulin (intestinal permeability). Without this information, I wouldn’t have been able to address the specific issues that my gut was facing and would have continued to guess. I work with Dena Norton remotely for my poo analysis (as well as hormone issues and depression). I highly, highly recommend her!


For years, I couldn’t figure out why my digestion moved so slowly. I also found it offensive that I could only eat around 1200 to 1500 calories a day (in addition to exercising daily) without gaining a weight quickly. That is, until I did blood work to test my thyroid function (TSH, T3 and T4) and found out I’m hypothyroid.

If you have hormonal imbalances or an overactive or under-active thyroid, the amount of food you eat and the way you digest it will most assuredly be affected. In addition, a recent study found that 30% of people who have hypothyroidism also have low stomach acid, and therefore struggle with Small Intestinal Bacterial Overgrowth (SIBO) due to improper digestion.

This is why some people can eat 2500 calories a day without moving a muscle and look like a Greek God or Goddess, while others must exercise regularly and watch what they eat.

Hormones, metabolism, and gut health work in tandem.

You can either do standard thyroid testing through a lab by having your blood drawn, do a saliva test get a snapshot of your estrogen, progesterone, testosterone, and cortisol, or do the Dutch test through a holistic practitioner.

The Dutch test reveals exactly what your hormones are doing from the top level down. It is a urine test that enables your practitioner to see how exactly your hormones are functioning throughout your cycle.  

My personal opinion is it is good practice to have your hormones tested at least once a year, particularly if you’re female.

Your genetics and your hormones play an enormous role in the way you digest food and the type of food that works best for you. If you feel like you just aren’t processing things the way you should, I suggest working with someone (your GP, functional medicine doctor, RD, etc) to determine which hormones are high or low.

Estrogen dominance is very common in our society, because many of the household products we put on our skin contain estrogen-mimicking compounds, which are metabolized as estrogen in our system. Too much estrogen can drive down progesterone, causing a hormonal imbalance.

High cortisol is also very common, as we often take on unnecessary stress through work, relationships, and lifestyle habits.

The food we eat and the way we conduct our lives play a significant role in our hormones every single day.  There are so many resources you can put to use to try to get your hormonal balance restored. Read Woman Code (in my opinion every woman should read this book), and check out 17 Ways You Can Balance Your Hormones Naturally.

You can also follow podcasts and websites that are geared for women struggling with hormone imbalances, such as

Once you have a handle on what is happening with your hormones, you can make diet, lifestyle and supplement changes to shift your hormones into balance. Remember, this too is a process and not only takes time to notice effects but is also something that needs to be monitored closely in the long-term (depending on the hormonal issue).

Similarly, doing regular blood work (testing iron, Vitamin D, cholesterol, etc) is bottom line something that should be a regular part of your life. I aim for testing everything every 6 months, but yearly works too.



If you experience mood and energy swings, feel constantly hungry, or you can’t go several hours without eating, you may have imbalanced blood sugar. Purchasing a blood glucose monitor is a very inexpensive way of figuring out if you have high/low fasted blood sugar, or if your blood sugar spikes after eating. I use Accu-Chek to monitor my blood glucose.

You can make dietary and lifestyle adjustments if necessary depending on the way your blood sugar reacts to eating in general or to specific foods. Through monitoring my own blood glucose levels, I observed my blood sugar shoots through the roof when I eat oats or nut flours/butters. While I am not allergic to oats and nuts, the fact that my body goes haywire after eating them could be an indication of intolerance.

I also learned unless I eat a diet that is low to moderate in carbohydrate, I have a high fasted blood sugar. In other words, my body does best on a low to moderate carb diet; therefore, I eat low carb on days I don’t get much exercise or moderate carb on days I get a lot of exercise. For me, this ranges between 50 to 200 grams of carbs, depending on my activity level.

For those of you who are interested in monitoring your blood sugar, I highly suggest you follow Robb Wolf’s website, podcast, Instagram, and read his books. The man knows blood better than anyone else I follow.



Taking regular blood tests can provide so much information as to what is happening inside your body. Monitoring your Iron, Vitamin D, cholesterol (pay attention to type of cholesterol, as high cholesterol is not necessarily a bad thing), and thyroid function (TSH, T3 and T4) at a minimum is a wise move.

Once you have these numbers, you can make minor (or if necessary, major) adjustments to diet, exercise, and/or supplements to nudge your body to normal ranges if your numbers are off.

Summary of Helpful Tests:

Eliminating guesswork is the move. To do so, take any or all of the following tests (using whichever method you and your practitioner decide are right for you):

  • Food sensitivity test (I recommend the ELISA/ACT)
  • Comprehensive stool test (I recommend the GI map)
  • Hormone test (I recommend the Dutch test and blood work to check thyroid function)
  • Blood panel testing cholesterol, thyroid function, Iron, Vitamin D, and more


There is no end to the amount of supplements you can take for any ailment. After getting your stool and hormones tested and completing standard blood work, your functional medicine doctor or RD can give you recommendations on supplements that will help nudge your body in the right direction.

I take quite a few supplements to support my hormones, digestion, and anxiety. Because I’m not a medical professional, I’m not going to divulge everything I take for fear you’ll do something crazy like mimic my own protocol.

What is generally accepted across the board by western and alternative practitioners alike for improving your digestion (and hormones) is these four: Omega-3 (either fish oil or flax oil), probiotics (the type and dose should be based off of your personal GI Map stool analysis), collagen, and L-Glutamine.

These four supplements help repair damaged intestines (in other words, help heal and seal your gut) and ensure the nutrients you’re taking in are properly absorbed. Not to mention, omega-3 is also super important for keeping your cholesterol levels hunky dory as well as your hormones balanced and brain functioning optimally.

I have also found marshmallow root and slippery elm to be very healing on the gut. My favorite supplement I take daily is GI-Revive. It is a combination of natural herbs that all help heal and seal the gut lining.

Because the supplement industry isn’t regulated, I suggest you speak with a professional before choosing a brand on your own so you aren’t wasting your money with no results. Supplements are not created equally so be sure you’re sourcing your pills wisely.

Did you know most probiotics die within 20 minutes of entering your gut? This is why you need to take probiotics regularly in order to notice a difference. The best probiotic is a soil-based probiotic (aka spore based or diatomaceous earth), as it is more effective than other forms of probiotics in forming colonies (i.e. the good bugs live longer).

It is also wise to change up the type of probiotic you use in order to maximize the amount of strains in your gut. I take both a soil-based probiotic and a lactobacillus (which contains multiple types of lacto strains) every single day.

If you can eat fermented food without experiencing GI symptoms (bloating, gas, diarrhea), go for it! I can’t, so I get my probiotics in supplement form. It’s expensive, but in my opinion, worth it.

To Summarize:

Supplements for Digestion and Gut Health:

  • Omega-3 capsules, consuming fish or flax oil
  • Probiotics (discuss which ones are right for you with your healthcare professional)
  • L-Glutamine
  • Collagen
  • Bonus: marshmallow root, slippery elm


If you tell yourself your digestion is broken and you’ve done everything you can and you may as well throw yourself on the ground like a rag doll, don’t give up. The stress we feel around food is more harmful to our bodies than the food itself. If you need to take a break from thinking about food, do so knowing that when you’re ready to focus on good digestion again, you’re confidant you can find your true north.

The fake it until you make it mantra can absolutely be applied to your health. Telling yourself you are healthy, worthy, and loveable daily is extremely healing. In my opinion, the single most important step I’ve taken in healing my gut has been keeping my mind in check.

Manage Stress

Ask yourself what really matters and who you want to be. When you’re in alignment with your true self, everything in life falls effortlessly into place. If you are out of alignment due to work, relationships, health issues, self-judgment, etc, you experience chronic stress, which takes a heavy toll on your body.

Some stress is unavoidable, but most stress is completely avoidable. If something is off in your life, take action. Making changes can be scary, but doing nothing will keep you stuck in the same physical and mental state.

Having a solid community of friends and family is crucial to our overall well-being. There are studies that show social isolation and loneliness kill us faster than any disease can. Ask yourself what you need from your friendships and relationships in order to feel loved and supported.

I manage my own stress in a number of ways. I use CBD and THC, and I take a high dose of B Vitamins to ensure my brain chemistry is right. I get monthly massages, do yoga at least once a week, spend quality time in nature, and exercise daily. I also make food and lifestyle decisions that support my hormones to ensure I’m not placing any unnecessary stress on my body. I have gone to therapy and read all the self-help books, which I find to be very useful and healing. I can’t recommend seeking help enough.

Depending on where you are in life, reducing stress may just be your step 1 to great health.

Baby Steps

What “they” say is true – consistency is key, and Rome wasn’t built in a day.  Make one change at a time and wait. Start with figuring out your fiber tolerance, wait a week for your body to adjust, then go down the line from there. If you feel like you’ve tried everything under the sun, don’t wait a second longer – take a food sensitivity test.

We U.S. dwellers tend to want everything right now. Your body doesn’t work like that. Go slow and pay attention. If you make more than one change at a time, it will be difficult to figure out which change is the one that is effective or ineffective. So exercise your patience muscle. It will benefit you in the long-run.

When to Take a Break:

If you become overwhelmed by running tests, troubleshooting and reading endless articles and books about health, stop and take a breather. Managing stress is a huge component to your overall health, so if you feel stressed about improving your health, don’t act until the stress dissipates.

Go easy on yourself and love on yourself. Mediate, read things that take literally no brain power and illicit only positive emotions. Watch movies and shows that make you laugh. Take a hiatus from the news, social media, and/or relationships that make you feel crappy. Do more you and less other people.


Putting science behind your health through various forms of testing can be nerve-wracking and expensive. Not to mention, the process to fix any issues that are uncovered can take quite some time! It has taken me a full year to both uncover and heal from my underlying digestive issues, but I can’t stress enough how valuable the process has been for me. I have never in my life felt so well as I do now!

Uncovering the root cause of digestive issues is powerfully healing. Life is hard enough as it is, and there is no reason to treat GI symptoms as something you just have to live with. You don’t! You can absolutely take control of your health and feel your personal best.

Hit me up if you have any questions. Similarly, if you have feedback on what has helped your own digestion, feel free to leave it in the comments below!

I wish you all the best of luck on your health journey. We walk this path together!

Remember always: you are loved, valuable and impactful!


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Julia Mueller
Meet the Author

Julia Mueller

Julia Mueller is a recipe developer, cookbook author, and founder of The Roasted Root. She has authored three bestselling cookbooks, – Paleo Power Powers, Delicious Probiotic Drinks, and The Quintessential Kale Cookbook. Her recipes have been featured in several national publications such as BuzzFeed, Self, Tasty, Country Living,, etc.

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Questions and Reviews

  1. Thank you for sharing! The information and direction provided gives me much needed encouragement in dealing with this chronic condition.

    1. I’m so happy it’s helpful, Holly! I think the most important thing to remember is there are professionals out there who are true healers and know so much more than we do. Taking charge of gut health is an ever-evolving process and the way your body operates is often vastly different from everyone we know. It takes strength to stick to the protocol we know is right for us. My warmest wishes go out to you on your journey! xoxo

  2. Great read!!!
    Thanks, Julia… for sharing such an informative blog post about the factors which should be taken into consideration to stabilize the digestion process. Gut microbes play an important role in the process of digestion and assimilation. Any signs which indicate that the microbial population in the gut declining should not be ignored and suitable precautionary measures should be taken into consideration to enhance the growth of the gut microbes.

    1. Thank you, Gary!! That was very well-articulated – I couldn’t have said it better, myself! Thanks for the the well-informed input and for your support! xoxo 😀

  3. Hey Julie, I appreciate you sharing this post. I’m struggling with some sort of disgestive disorder (I won’t quite know what it is until I have my endoscopy done). I’ve always struggled with eating healthy, but I never had any problems until recently when I woke up one morning with nausea and a lot of chest pain and indigestion. My GI believes it could be a stomach ulcer (im crossing my fingers its not). I’m only 20 years old, I would love to have my life back but I don’t know where to start or what to do. I don’t wanna rely on medicine for the rest of my life to “bandage” whatever my problem is. How did you first start and who helped you get back on track to healing your body? I suffer from a lot of anxiety and depression as well, so obviously it isn’t making my problem any better. I don’t know what could help me feel better or what I should do.