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How to Use Functional Nutrition In Your Clinic: Including Top Specialty Labs Commonly Used

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How to Use Functional Nutrition In Your Clinic: Including Top Specialty Labs Commonly Used

Tired of hearing that "calories in, calories out" is the only way to think about your diet? A functional nutrition approach to diet and lifestyle offers a much more personalized, holistic approach to nutrition's role in health and disease.

As chronic disease rates continue to rise in the US, the demand for nutrition professionals as part of a multidisciplinary approach to promoting good health is becoming increasingly important. Functional nutrition, a branch of functional medicine, can serve as a highly personalized approach to helping individuals understand the connection between their nutrition, lifestyle, and state of health and well-being.  


What is Nutrition?

At its core, nutrition is about eating a regular, balanced diet that fuels your body to get through your day-to-day activities, exercise, and meet your metabolic needs. What we eat is considered an important environmental factor that influences our health positively or negatively. Adequate nutrition ensures you take in enough vitamins, minerals, and macronutrients (like protein, fats, and carbohydrates) to maintain your brain function, muscle activity, bone health, nervous system, blood circulation, and more.

What is Functional Nutrition?

Functional nutrition is a subcategory of functional medicine based on a holistic perspective of the body - physical, spiritual, and emotional - and using healthy, whole-food approaches to nutrition to address the root causes of illness and support optimal gut health. Instead of just looking at calories and the micronutrient content of food, functional nutrition also emphasizes an individual's environment, lifestyle, cultural background, genomics, stress levels, and more to tailor nutritional recommendations for a specific goal. The field of functional nutrition embraces the concept of bio-individuality, meaning that each patient has specific needs when it comes to nutrition and overall care.

Functional nutrition provides a way to help people understand how their nutritional choices, as well as their lifestyle, impact their overall health and well-being. This fits in well in the bigger picture of personalized lifestyle medicine, which continues to thrive in today's healthcare landscape as more and more people look for health advice tailored to their unique needs.  

Who Can Use Functional Nutrition in Their Wellness Practice?

As functional nutrition is a major pillar of functional medicine, a variety of providers incorporate functional nutrition into their wellness practices. These include Functional Dietician Nutritionists, certified Functional Medicine practitioners (these may be MDs, DOs, DCs, NMDs/NDs, NPs), Doctors of Acupuncture and Chinese Medicine, Functional Medicine Health Coaches, Functional Diagnostic Nutrition Practitioners (FDN-Ps), and certified nutritionists.  

Common Labs Used By Functional Nutritionists

Functional Nutritionists may use various functional medicine labs to help evaluate a given case and provide a highly personalized nutrition and lifestyle plan for optimal results. Regulations for ordering labs vary by state, and the ability to order labs directly will depend on the practitioner's licensure.  

Comprehensive Stool Test

Because gut health and supporting a diverse gut microbiome is central to the practice of functional nutrition, evaluating the health of the gut microbiome is an important part of nutritional advice. Ensuring an individual can properly digest and absorb their food and address any infections or inflammation is important for any nutritional protocol to achieve optimal results. Tests like the GI MAP can help evaluate markers of digestion, inflammation, and potential infections so that any nutritional protocol can address underlying gut issues.  

Micronutrient Panel

Testing levels of important micronutrients, like zinc or magnesium, is an important starting point when designing a personalized nutrition plan. It helps guide supplementation if necessary and highlights certain vitamins and minerals that must be emphasized in a functional nutrition protocol.  

Evaluating micronutrients can be especially important for certain populations, including those with chronic inflammatory illnesses or poor gut health, which can impact nutrient absorption.   Athletes, who may require more than the minimum recommendations for certain vitamins and minerals to achieve optimal performance, can also benefit from micronutrient testing. Individuals with high-stress levels or restrictive diets would also be good candidates for micronutrient testing to ensure the body can meet metabolic demands.  

Genomics Testing

Functional nutrition practitioners may also use nutrigenetic and nutrigenomic testing, which evaluate the potential genetic factors that can impact a person's response to certain diets, and how different nutritional protocols may impact gene expression, respectively. A panel such as DNA Diet is an example of nutrigenomic testing to help guide more personalized nutrition protocols, giving insight into different nutrition protocols often used by functional nutritionists (like a Mediterranean-type diet or a low-carbohydrate or low-fat diet) and which may be ideal for your genetics.

Food Intolerance Testing

Sometimes, functional nutritionists may use food intolerance testing initially to help identify foods that may be problematic for an individual. The food intolerance testing results can then be used to create a personalized elimination diet while the gut heals, versus following a cookie-cutter elimination diet that may not include all the offending foods for that person.  


Common Functional Nutrition Protocols Used In Functional Nutrition

While functional nutrition emphasizes a highly personalized approach to nutrition recommendations, there are some common functional nutrition protocols that are used to support optimal health and well-being.

Anti-Inflammatory/Mediterranean-Type Diet

The Mediterranean diet emphasizes nutrient-dense foods traditionally consumed by populations living near the Mediterranean Sea. Its main principles include consuming seasonal produce, fish and lean meats, healthy fats like olives and olive oil, and unrefined whole grains. Alongside the nutritional component are common lifestyle themes found in these populations, such as plenty of walking and physical activity, the importance of community and social relationships, and a balanced life overall. The Mediterranean diet is linked to lower inflammation levels, and has plenty of research behind its benefits.  

Paleo-type Diet

In a Paleo-type diet, nutrition recommendations are centered around what our Paleolithic ancestors likely ate many years ago - grass-fed meats, wild-caught fish, healthy fats, free-range eggs, seasonal produce, and nuts and seeds. This nutritional approach typically suggests avoiding refined sugar, processed foods, legumes, and refined grains, none of which would have been available to our ancestors. Some followers of the Paleo diet also avoid dairy, while others include grass-fed dairy - this is where personalization can be helpful based on an individual's needs and tolerances.  

Autoimmune Protocol Diet

The autoimmune protocol, or AIP, is an offshoot of the Paleo diet created with the needs of those with autoimmune conditions in mind. While the AIP follows many of the same principles of the Paleo-type diet, it eliminates eggs, dairy, nuts, and seeds, all of which can initially be common food sensitivities or intolerances for those with autoimmune illnesses. The AIP has been shown to reduce systemic inflammation and modulate the immune system in those with autoimmune conditions like Hashimoto's thyroiditis. It is a helpful option for functional nutritionists to use when working with clients with these conditions.  

Elimination Diet

The elimination diet is considered to be the gold standard in functional nutrition and functional medicine for identifying food reactions. It can be challenging to identify or detect problematic foods just from a history and diet diary due to the large variety of symptoms that can stem from food sensitivities and potential delayed reactions to foods. In a traditional elimination diet, suspect foods are removed for 3-4 weeks, then reintroduced one food at a time under the direction of a knowledgeable practitioner to help determine what foods may be causing symptoms. Food intolerance testing can help further personalize this approach.


A low FODMAP diet may be used by functional nutritionists initially when working with cases of IBS (irritable bowel syndrome) or SIBO (small intestine bacterial overgrowth), having been shown to be effective at reducing symptoms in these populations in 75% of cases. FODMAPs is an acronym standing for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols, which are short-chain carbohydrates that easily ferment in the intestine, leading to symptoms like gas, bloating, pain, and more. This particular diet plan should be used short-term, as it is very restrictive and is typically reserved for those with a confirmed diagnosis of SIBO or IBS.

Gluten-Free Diet

A gluten-free diet may be recommended not only for those with confirmed celiac disease but also for individuals with leaky gut syndrome and IBS, non-Celiac gluten sensitivities (NCGS), or those with autoimmune thyroid disease. While a gluten-free diet is lifelong for an individual with a confirmed diagnosis of Celiac disease, the diet may be used temporarily by functional nutritionists as a therapeutic healing approach for these other conditions.



Functional nutrition is a subcategory of functional medicine focusing on highly personalized nutritional approaches to supporting optimal health and well-being. A functional nutritionist will also incorporate lifestyle recommendations as part of a holistic approach for each case, using functional medicine labs to help customize their recommendations where applicable.  

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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