Woman prepares greens in a blender

So you’ve started the journey to optimize your health! You’ve been cutting back on the processed foods and started incorporating more whole foods into your diet. But yet, you feel as though you still aren’t reaping the full benefits.

Some reasons why you may be feeling this way is because the foods you are consuming aren’t as nutritious as you thought. You might be thinking, “They are fruits and vegetables! How aren’t they nutritious?” 

Well, they are still nutritious but depending on how it was grown and the health of the soil that it was produced in, the nutrient density and nutrient value of the food can have a wide range. Read our previous article, , to find out how you can obtain the highest quality foods to optimize your health. 

Another issue that you should keep in mind is that even when you do eat the cleanest, nutrient-rich diet, you may not be absorbing as many nutrients as you think. 

How Gut Health Affects Nutrient Absorption 

Having good gut health is crucial to overall well being. When your gut is happy and healthy, it is effective and efficient in its vital role of absorbing nutrients. Not only do we need to be mindful of what kinds of nutrition we are putting into our bodies, but we need to ensure our body is actually able to take in those nutrients. 

A significant factor that determines good gut health is the makeup of your microbiome environment. Your gut microbiome contains good kinds of bacteria and harmful types. It’s when the bad bacteria starts overtaking the gut that we begin to see issues all throughout the body. We also need a diverse environment that is made up of a variety of bacteria. This diverse environment makes the gut both more resilient and more capable of absorbing different vital nutrients.

How does this happen? Well, your gut microbiome plays a role in gastric development and function, micronutrient synthesis, and drug metabolism. The good diverse bacteria play a role in absorbing the nutrients that you consume. When your gut is filled with harmful bacteria, they interfere with these natural processes. They can cause inflammation and irritation that hinders absorption- especially in the small intestine where the majority of your nutrients are absorbed. If your small intestine (where most of our nutrients are absorbed) doesn’t absorb the nutrients, then the nutrients travel to the colon and are expelled through the stool without being absorbed or used by the body.

The gut has a semi-permeable membrane that allows tiny micronutrients to go to other parts of the body while keeping larger molecules inside. Harmful bacteria, toxins, and food sensitivities can cause damage to your gut membrane and increase the permeability. This allows those larger molecules (gluten molecules, for example) that are supposed to stay inside the gastrointestinal tract to enter into the bloodstream. 

Not only does that halt your body from breaking down and using the consumed nutrients correctly, but these bigger molecules can travel to places they don’t belong and cause damage to other organs.

Reasons for Low Nutrient Absorption


If you are taking antibiotics, you may not be absorbing as many nutrients from your diet, as you think. Not only is your gut affected when you take antibiotics for medical reasons, but if your food sources contain traces of antibiotics, it could affect your gut absorption as well. Many larger factory farms give their livestock antibiotics as a precaution so they don’t get sick. However, those antibiotics get into the meat that we later consume. Your gut’s microbial function decreases, which reduces the digestibility and usage of certain nutrients. It’s important to eat properly raised animal meat so be sure to choose meat that states that it’s antibiotic-free, or even better, from a local farmer that you trust.

Food Sensitivities

Many people may have food sensitivities without having clear cut symptoms. Foods that most commonly cause harmful effects include gluten, lactose, peanuts, soy, fish, and shellfish. However, a person may also have a food sensitivity to a specific food like a particular type of fruit or vegetable. These sensitivities can be caused by an absence of a specific enzyme that usually breaks down that type of food, therefore not allowing it to be digested (i.e. lactose intolerant individuals don’t have enough of the lactase enzyme). Another way a food sensitivity can come about is when your body recognizes one of these foods as foreign or harmful, which sets off your immune system response. This can then cause a reaction on the barrier of the small intestine, which can then cause malabsorption.

Sensitivities are usually a delayed response vs an allergy. This makes it difficult to really pinpoint the offending food or food items that are contributing to this. This is where food sensitivity testing becomes very helpful in your clinical assessment.  

Excessive Stress

When you are experiencing stress on an ongoing basis, it sets off your fight or flight response. This increases your adrenal function and your digestion is slowed or put on pause. In order to properly digest the foods we consume, we must “rest to digest”. Eating in a parasympathetic state helps to absorb the nutrients you are consuming, when digestion is halted, so are the nutrients going to your cells. 

Mold Toxicity (Mycotoxins)

Mycotoxins are the toxic byproducts of fungi like Fusarium, Aspergillus, Stachybotrys, and black mold. You may come in contact with these through food contamination, inhalation, or absorption. These toxins can change the microbiota of your gut, increase your gut membrane permeability, and decrease nutrient absorption. It can promote harmful bacteria like Bacteroides (increasing inflammation) and reduce the beneficial bacteria like Lactobacillus reuteri

Infections in the Gut

Whether you are dealing with an infection in the gut due to a virus, bacteria, or parasite, they can all affect your gut health. These infections cause increased inflammation, which impacts the gut membrane and the ability to absorb nutrients. SIBO (small intestinal bacterial overgrowth), for example, can increase malabsorption because of damage caused to the cells that line the gut (mucosa). 

Low Stomach Acid

Stomach acid allows your body to break down minerals and protein so they are easily digested and absorbed. When your stomach acid is low, it hinders this process leading to lower nutrient absorption. If you are concerned you are dealing with this issue, you can read more about it on a previous blog of ours, “A Functional Medicine Approach to Low Stomach Acid”.

Is Your Gut Working Optimally?

You might be wondering, “how do I know if my gut is working as it should?” Some people may show signs and symptoms that concern them enough to reach out for help. These could include anything from gas, bloating, diarrhea, fatigue, and many others. Other times, individuals may not show symptoms or know that they aren’t absorbing nutrients effectively. 

A great way to determine if your gut health is being compromised is by taking some simple lab tests. In2GREAT offers a number of tests that can suggest if gut health needs to be a priority of yours. Some of our tests include: 

  • GI Map and Zonulin: this test accurately and reliably allows us to create personalized treatment protocols to address gut dysfunction based on which infections are urgent, which areas of the gut are already optimized, and which areas should be addressed after an infection is resolved.
  • Wheat Zoomer: this test provides: 
    • The most comprehensive and sensitive assessment of gluten and wheat sensitivity
    • The earliest and most sensitive detection of celiac available
    • The most thorough assessment of intestinal barrier stability
  • Vibrant 3Dense: this test is the only highly sensitive peptide-based array able to test for reactivity to over 33,000 peptides in wheat and gluten
  • Gut Zoomer: this test measures over 170 species of bacteria, aiding us in detecting the root causes of acute or chronic illness that stem from the gastrointestinal tract, with correlations to disease states and health risks 
  • SIBO: this test uses a non-invasive breath test to detect the presence of elevated levels of hydrogen or methane gas, or both. This excessive buildup of bacteria is often diagnosed as SIBO.
  • IBSSure: this test is a quick and reliable tool for determining IBS-D, which is associated with Small Intestinal Bacterial Overgrowth (SIBO)
  • Adrenal testing (CAR): this test uses three saliva samples, collected several hours apart, to determine if the HPA axis is not responding appropriately, which can be an indicator of a stressor.
  • Food sensitivity (ELISA): these tests are the most comprehensive and specific tests in determining and addressing the hidden causes of many common health concerns.They offer the gold standard in delayed food, food additives, and chemicals hypersensitivity testing
  • Micronutrient: this test measures direct levels of extra and intracellular micronutrients, giving the most complete and accurate picture of your micronutrient status.This holistic view of nutrient status can aid in differentiating between dietary, genetic, and other factors that may be impairing your nutrient metabolism or absorption. 

How to Boost Nutrient Absorption

If you have a suspicion that your gut health could use a little love, here are some things you can do to boost gut health and aid nutrient absorption. 

  • Get labs drawn. This way you will know exactly what kinds of issues you are dealing with so you can focus on ways to minimize those specific root causes.
  • Pairing certain foods together can increase absorption. Some examples include vitamin C and plant-based iron, turmeric and black pepper, tomatoes and olive oil, complementary proteins, and vitamin A, D, E, and K with dietary fats. 
  • Eat a wide array of fruits and vegetables. This can increase the diversity of good bacteria in your gut microbiome. This can help restore your gut so that it can work optimally again.
  • Avoid processed foods and alcohol. These can both reduce gut health by increasing harmful bacteria and damaging the gut lining. 
  • Manage Stress. When you are in a more relaxed state, your body can focus its energy on digestion, and therefore be able to actually absorb more nutrients.

If you are interested in making your health a priority, in2GREAT, a Functional Medicine Practice in Kansas City, can help you achieve this. Contact us via our online form or give us a call at (913) 906-7787.

Dr Corey Priest, DC - Functional medicine practitioner

About the author

Dr. Corey Priest has been practicing functional medicine since 2001. in2GREAT was founded in 2014 by Dr Priest after 13 years of experience with his other practices. Over his career, Dr. Priest has worked with and helped well over 10,000 patients under a functional medicine model.

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