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Paleo 101 Part 2: 3 Major Roadblocks When Going Paleo

by Dr. Justin Marchegiani
Home/Blog/Protect Your Mental Wellbeing During the COVID-19 Pandemic

In part 1 of our Paleo Template series, we discussed inflammation, blood sugar lipid lab markers, and what to look for on these tests as you begin a Paleo plan. Briefly: we want to see your lipids improve, whether it’s triglyceride to HDL ratio of cholesterol to HDL ratio, and we want to see improvement in inflammation and blood sugar. These would be the nice benefits of an anti-inflammatory, nutrient-dense, low-toxin eating plan.

Let’s say you’re one to two months in, and you’re seeing some improvement. You’re on the right track, but you’re hitting some roadblocks. Maybe you’re fatigued or have energy issues, your fingernail quality doesn’t look good, you still have some digestive issues (bloating, gas, constipation, or diarrhea), and maybe they’ve even gotten worse since you you’ve increased your protein content.

Anti-inflammatory, nutrient-dense, low-toxin food should not make you feel worse unless your digestive system is impaired in some way, so now it’s time to dig a bit deeper and address those roadblocks.

What Are the Paleo Roadblocks?

The three main roadblocks we’re going to address are anemia, infections, and thyroid issues. Like last time, we’ll cover the lab markers we would look at when considering each.


In people whose hydrochloric acid (HCl, stomach acid) levels are low, anemia can be an issue. Interestingly this happens in people who eat a lot of easy-to-digest food. Because of their anemia, their stomach acid and their digestive secretions weaken because they aren’t being tuned up with the proper proteins. This is commonly seen in people who have a strictly vegetarian or vegan diet. There may even be some gastrointestinal inflammation preventing us from binding minerals, and the low HCL may be preventing us from ionizing so the minerals, such as iron and calcium and selenium and magnesium, can get into our bloodstream.

Lab Tests for Anemia

When we see anemia issues, the first pattern we’ll look for is a decrease in red blood cells, hematocrit, and hemoglobin. It may not necessarily be low, but it may just be in that bottom 20% of the range. This will tell us if there’s a broad-spectrum anemia.

The next anemia pattern we’ll look for is through the iron panel. TIBC and UIBC are different iron-binding proteins, and they actually tend to go high when iron is low. So, the more binding proteins we have, the more iron our body needs. We will also typically see iron saturation and ferritin levels drop. If we see these markers in our anemia patterns, then we know we probably have an iron-based anemia.

We’ll also look for anemia patterns through B vitamin markers: MCHC, MCV, and MCH. These markers just tell us how big the red blood cells/hemoglobin are. The bigger our red blood cells are, the more immature they are. Red blood cells get smaller as they mature. So this will be an indicator of two kinds of anemia—B vitamin and iron.


A chronic infection, such as a parasite infection, bacterial infection, viral infection, or even a fungal infection, may be present and preventing you from optimizing your nutrition. These infections affect our immune system. About 70–80% of our immune system lives in the gastric associated lymphoid tissue (GALT) of our stomach and in the mucosal associated lymphoid tissue (MALT) of our intestinal tract. With so much of our immune system living in our stomach and intestinal tract, it’s easy to see why an infection could be affecting our ability to properly absorb nutrients.

We have two branches to our nervous system: Our sympathetic nervous system is our flight-or-flight nervous system, and our parasympathetic nervous system is our rest-and-digest system. When we have digestive immune stress, it signals the sympathetic nervous system (i.e., our fight-or-flight system).

When our sympathetic nervous system is fired up, it’s going to drive more of our fight-or-flight response. This will decrease hydrochloric acid and enzymes, and it will increase blood flow to the extremities—arms, hands, and feet—to allow us to fight and flee. This is one of the major issues when we’re under chronic stress, and those stressors could stem from infections without you even knowing.

Lab Tests for Infections

One lab test we would look at for infections would be a stool panel, and not just the conventional hospital or Lab Corps tests; I run many of those and they sometimes miss the infection. We would run a specialty DNA, PCR-based testing, giving us a higher level of specificity.

We can also draw conclusions from a CBC with differential panel. This looks at our white blood cells—our neutrophils, lymphocytes, monocytes, eosinophils, and basophils (an easy pneumonic device to remember these: never let monkeys eat bananas). We might consider the following based on an increase in these cells:

Thyroid Issues

Next we have thyroid issues. Cold hands, cold feet, constipation, mood issues, and energy issues are all signs the thyroid is not functioning appropriately, so we’ll want to run a complete thyroid panel.

Lab Tests for the Thyroid

We typically test our TSH, which is a brain hormone. This gives us a peek inside the window to what’s happening with our brain and how it’s communicating with our thyroid. We’ll also look at thyroid hormones: free T4/T3 and total T4/T3. T4 tells us what is coming out of the thyroid tissue, and T3 gets converted by the liver and intestines, by healthy stress levels, and at the thyroid (about 20% gets converted at the thyroid).

We’ll also test antibodies, giving us a look at our immune system. Our immune system could actually be attacking our thyroid gland and making various antibodies called TPO, TB antibodies, thyro-binding globulin antibodies, and even TSH receptor site antibodies. This would tell us if we are dealing with an autoimmune thyroid condition, such as Hashimoto’s thyroiditis.


Transitioning to an anti-inflammatory, nutrient-dense, low-toxin diet takes time. The Paleo template will get you on the right path, but you will likely encounter a few roadblocks along the way. Don’t let them dissuade you—address them one by one, and before you know it, those roadblocks will be far behind you.

To schedule a FREE consult with a functional medicine doctor to help with lab markers as you prepare to begin Paleo template, click here.

Roadblock photo licensed under the Creative Commons.


The Paleo movement incorporates several different optimizing perspectives for helping you improve your health, all based on the latest science. Everyone is different. We want to support you in understanding your unique genetic makeup, symptoms and health goals so you can choose the path that is right for you.

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Dr. Justin Marchegiani

Dr. Justin witnessed chronic disease like diabetes, heart disease, and obesity first hand while working in a surgical center at the University of Massachusetts. This experience shifted his focus from conventional medicine to a more holistic or natural approach to healing, where the underlying cause of his patient’s health issues are addressed and not just medicated and surgically removed.