Essential Lab Tests for a Complete Immune System Work Up Using Functional Medicine

Functional Medicine has a long and rich history of innovation in the laboratory science field going back to the 1960’s. Thanks to generations of researchers, lab directors and clinicians, our collective understanding of the origins of many common health complaints continues to advance exponentially every year. I am deeply grateful to my teachers, Dr. Richard S. Lord, PhD and Dr. William Timmins, ND, two of the most respected lab directors in the field, for their contributions.

In my current practice, I use a series of labs to understand how a patient’s body systems are working. We do Salivary Cortisol testing for assessing the stress hormones, GI testing to look at the microbiome and digestive functions, and Organic Acids and the ION Panel to look at metabolism, brain health, detox systems and nutrient levels. These tests also provide important information on the genetic underpinnings of many common health complaints. Most of our patients do all three types of tests for a comprehensive understanding of their health. 

To begin with the “functional” in “functional medicine” means that we are assessing patients for the early beginnings of disease processes when there are clear signs of cellular or organ “dysfunction” but (hopefully) prior to the onset of a serious illness. So we strive to find problems with cell replication based on oxidative stress PRIOR to the development of a tumor and a diagnosis of cancer. We strive to find imbalances in neurotransmitters prior to the development of ADD/ADHD, severe depression or chronic anxiety.

The lab testing done within the speciality area of functional medicine attempts to uncover root causes of common health concerns prior to their development into a full blown critical situation. Conventional medical labs are designed for other purposes. They are mostly focused on uncovering a disease once it has progressed fully from a “dysfunction” of a body system to a “pathology” or life threatening problem. Of course we need both systems in place to handle the range of human suffering in the world. One doesn’t replace the other.

The basics of human physiology dictate that any health issue starts at the deepest level, the atomic level. We are made up of these tiny particles, and from them, we build molecules. Molecules are big structures that constitute our body chemistry as they react and do their thing.  From molecules we build cells – muscle cells, brain cells, heart cells – all extremely important structures which combine in fascinating ways to create organs like your digestive tract, your lungs and so on.

Functional medicine MEASURES all of these biological realities. We measure oxidative stress, which is a direct analysis of what the electrons in your body are doing. We measure many molecules to ascertain if normal energy production and hormone production can take place. We measure the health and function  of portions of cells like cell membranes which create the structure of each cell, we can even measure DNA inside the cells to see if there is damage taking place to your DNA.  We measure liver function through seeing how well detoxification pathways can work. These detox pathways will have major problems long before liver enzymes on a conventional medical test will elevate. Similarly we can measure L-Lactate and Pyruvate which will elevate long before insulin will, again being able to see into the body when the origins of blood sugar problems are starting, long before diabetes would occur. 

Functional medicine is a deep dive into the science of the body and how your biochemistry and physiological systems work. In the late 1960’s at the University of Texas, Austin, a group of dedicated biochemists were unraveling the details of the human body and discovering for the first time many of the B vitamins and other key nutrients that allow the body to work properly. Into this intense scientific whirlwind Richard Lord showed up to begin his PhD working under Roger Williams and other greats in the field of human nutrition research. 

From the outset, Dr. Lord wanted to figure out a way to test for nutrient levels and to this end he devoted his long career. After getting his PhD he settled into working for the premier lab company in the field and began to run tests that were in keeping with the scientific discoveries of the day.

From these beginnings, amino acid testing was born. Amino acids are the tiny little bits that make up every protein in the human body. From amino acids, our DNA produces the essentials required for life from bone cells to heart cells from brain chemicals to muscle tissue. If any of the key amino acids are missing production of proteins comes to a  halt and this leads to untold human suffering. Fatigue, depression, anxiety, chronic pain all these can result from a lack of ability to construct protein which again can come about from a lack of the right amino acids. Testing your amino acids is akin to testing your body’s ability to make all the essential components of every organ, tissue and cell.

Dr. Lord went on to also develop highly accurate tests for essential fatty acids, the omega 3 and omega 6 fats are critical to brain health, immune regulation and the inflammatory response. These fats are even required for fat burning which seems strange but is true. Low levels of omega 3 or 6’s leads to inflammation, depression, joint pain, hormone imbalances and immune system weakness. The “essential” in “essential fatty acids” is a real thing. The ability to read fatty acid profiles is quite something and takes most clinicians years to learn but is well worth the time invested.

Organic acid testing looks at metabolism in depth to analyze your fat burning capacity, poor fat burning leads to unsightly body fat build up and also results in poor energy production leaving you tired and making it harder to get motivated to exercise. These tests also examine carbohydrate and protein metabolism so you can create an ideal diet with just the right balance of protein and carbs for your body. By testing carbohydrate markers we can also determine how stable your blood sugar is and if you are at risk of developing a problem with the hormone insulin. Poor insulin handling leads to a whole host of serious health problems from increasing your risk of heart disease and diabetes to having that classic deep drop in energy in the late afternoon or sleeping poorly.

Organic acids also reveal nutrient levels for the B vitamins which are involved in breaking down your food for cellular energy. Low B vitamins can lead to poor quality skin, hair and nails as well as triggering sugar cravings and poor utilization of oxygen, meaning you get overweight and tired. These B vitamin markers are often out of range with hormone imbalances and detoxification issues as well. Of course there is a large amount of interest these days in the process called “methylation” and B6, B12 and folate are very accurately measured on organic acids to give you an exact understanding of your methylation capacity and the overall functioning of the genes related to MTHFR. 

Detoxification is critical for the removal of environmental toxins, both chemicals and heavy metals. Your liver and kidneys act like the air filter and water purifier for your body and brain and if you are not successful at removing all the environmental poisons we are all exposed to daily then they build up and damage your tissues.  From car exhaust to the many additives put into the food we eat most people end up with several hundred toxins in their bodies and your detox pathways are challenged to say the least by this constant onslaught. We can accurately measure all the major detox pathways and create a personalized detox program that will clean up your body quickly. The tests also measure brain health in a wide variety of ways. They look at the production of the key brain chemicals that dictate our very thoughts and feelings from dopamine to serotonin.

Also included is an analysis of inflammation in the brain for those with memory or focus problems or “brain fog”. Mitochondrial energy production is examined in detail for those suffering from fatigue. Antioxidant levels are examined in a variety of ways, poor antioxidant protection leads to greater risk of heart disease, cancer and diabetes. 

The Organix Profile test goes on to also examine digestive health and analyzes bacterial growth patterns that represent the health of your microbiome, you can figure out if you are eating enough fruits and vegetables or falling short at that task and it reveals the presence of yeast or fungal overgrowth often referred to as candida. You can figure out so much regarding your body from these tests as a patient of mine said this week “why doesn’t everyone do these?”

The Kalish Method has it’s roots in naturopathic medical philosophy which, for thousands of years, has expounded on the importance of the gut in all health conditions. The latest scientific research now supports these concepts and each year, thousands of studies show the connection of the GI tract, through the microbiome, to almost every chronic health condition. 

Neurological diseases, obesity and metabolic imbalances, sugar cravings, diabetes, heart disease and every “-itis” you can imagine from gastritis to colitis to arthritis and sinusitis can now be directly linked back to the gut microbiome. We now know there is a profound gut/brain connection, meaning much anxiety, depression and brain fog stems from chronic GI issues and the status of the GI tract can even impact your hormones. 

My current teacher, Dr. Richard Lord is the scientific genius responsible for the leading functional medicine test that examines the health status of the microbiome. 

The microbiome, or community of bacteria that are good for you in your gut makes up an entire organ system. These bacteria collectively regulate everything from your immune system to your metabolism which translates into meaning if you have an immune problem or are overweight chances are your GI tract is not super healthy. In addition to the essential contribution to human health from the microbiome, your gut health is also dependent on the various GI organs being in good shape and on you not having any chronic, low grade GI system infections. The testing we do examines all three of these areas: microbiome, GI organ function and GI pathogens.

Accurate reading of the health status of your microbiome allows practitioners to make very specific diet and supplement recommendations that can help you make significant improvements in everything from your mood to your immune system. The various GI testing I use in my clinic also reveals the status of your key digestive organs including the gallbladder, pancreas and stomach, all of which are designed to secrete substances that unlock the power of the nutrients in your food. The gallbladder’s production of bile acts as a powerful anti-bacterial that knocks out bad organisms as it helps you break down and emulsify dietary fat. The pancreas produces enzymes that help break down your food and prepare it for absorption in the small intestine and the stomach’s production of hydrochloric acid is a foundation for the release of stored energy in your food. 

If you have digestive symptoms like bloating, heartburn, constipation or loose stool, it is very likely that one or more of these digestive organs is not working well. Through lab testing we can easily see the early warning signs of GI organ dysfunction and make specific supplement and lifestyle recommendations to turn things around. These GI panels also examine fiber consumption to see if you are getting enough of the right kind of foods such as beans, grains, fruits and vegetables as part of your diet.

The third component to GI testing is a look at GI pathogens. These are the bad gut bugs that can cause so many chronic health problems such as fatigue, depression and weight loss resistance (where you eat properly but your body “resists” losing weight). The most dramatic healing responses I’ve seen have often been when we properly identify and then eliminate these types of GI bugs. There are at least three major groups including protozoans (tiny parasites), bad bacteria and yeast or fungal organisms that need to be checked. Conventional medicine sees these GI infections as a big fat “whatever” and has ignored their diagnosis and treatment since before I was born which has left us in a situation where many people suffering from these low grade infections are in the general population, unwittingly passing these bugs along to friends and neighbors.

My career started off with a focus on hormone testing and hormones and neurotransmitters have always been a strong interest of mine. I spent a decade working with some of the top hormone experts in the country including John R. Lee, MD and William Timmins, ND learning the ins and outs of hormone testing and treatment options. After that decade I spent twelve years studying neurotransmitters with a leading expert and tested thousands of patients and taught classes to physicians in the use of neurotransmitter analysis. Now, I combine these two knowledge-sets and have the great good fortune to be able to synthesize all I’ve learned into patient programs and physician education programs. 

Hormone symptoms such as low sex drive, hot flashes, night sweats, PMS, PCOS and infertility lend themselves well to a functional medicine approach. They often have their roots in a lifestyle issue, i.e. stress, poor diet, lack of exercise, and so the combination of functional medicine labs and guided supplement programs along with lifestyle changes almost always helps improve these types of problems. 

Neurotransmitter imbalances can stem from three major areas: nutrient deficits, injury to the brain cells through physical trauma or chemical trauma or genetic variables. Functional medicine testing can reveal which of these three issues is occurring and allow us to create a supplement and lifestyle program to improve brain health. This relates to symptoms like depression, anxiety, brain fog, ADD/ADHD, fatigue and sleep disturbances. Nutrient deficits related to brain activity revolve around imbalances in several amino acids such as tryptophan and tyrosine and significant B vitamin deficits. All of these variables can be measured. 

Sometimes it’s as simple as a folate, thiamin and tyrosine deficiency and once resolved, symptoms fade. Nutrient deficits can come about because of poor diet choices, or because of poor digestive function leading to an inability of your body to absorb nutrients from your food or supplements. Digestive problems are so common that we often see nutrient deficits as a direct result of GI tract dysfunction. 

Trauma to the brain is an odd one. Head trauma from a car accident, fall or concussion damages and can kill brain cells. If enough brain cells are destroyed head trauma can lead to long term issues like depression and memory loss. What’s less well known is that chemical trauma destroys brain cells also. Chemical trauma to the brain occurs with our exposure to chemicals and heavy metals that specifically target the brain. These are called neurotoxins. Once inside your body and attracted to the brain they cause damage through a process called oxidative stress. Chemicals and heavy metals can strip an electron off of an otherwise healthy molecule and turn that molecule into a brain cell killing machine. Many of the chemicals and metals we are exposed to through daily life in the modern world are “lipophilic” meaning they love fat and your brain is made up of 60% fat so these types of environmental poisons have an affinity for accumulating in the brain. 

The third area of neurotransmitter dysfunction is based on our genes. With the extensive lab testing I now use on all new patients I find most of us have at least a few faulty genes that can contribute to poor brain function. It could be as simple as a B6 problem that just taking a multivitamin would resolve or it can be as complex as an accelerated neuroinflammatory response that is depleting a brain chemical like serotonin. Some genetic defects do not end up leading to symptomatic expression so we live and diet with them not aware of their presence. However, at this point in human history we have dumped over 80,000 various chemical compounds into our natural environment and we are all saturated with chemical or heavy metal residues that are challenging to flush out of the body and so what were once minor genetic defects that didn’t add up to causing any problems can now lead to total catastrophe. 

Any genetically based problems with detoxification systems, amino acids, fatty acids or vitamins and antioxidants can lead to depletion of vital brain chemicals. Low levels of these compounds create fatigue, depression and anxiety, sleep problems and focus or memory deficits. We live in interesting times. Never before experienced levels of environmental toxins combined with the scientific advances with lab testing to find and fix the problems the toxins create. An epidemic of processed foods destroying any hope of normal digestion combined with advanced microbiome analysis to see the problem in real time. High pressure work environments, endless hours in traffic, raising kids while working full time – all driving us nuts with stress combined with stress hormone test based programs to reset the hormonal system. 

Functional medicine offers so many prime solutions for the health problems we currently face. My goal in the next decade is to test as many patients and teach as many doctors as possible to reveal to a larger audience how profound this little known obscure area of advanced functional medicine lab testing truly is.

Dr. Dan Kalish

Dr. Daniel Kalish is dedicated to teaching doctors Functional Medicine philosophy and practices. Through The Kalish Institute’s educational programs he has trained over 1,000 practitioners worldwide in The Kalish Method which solves patient challenges through a proven lab based approach.

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