The role of the digestive tract is to breakdown and absorb nutrients, help regulate the excretion of water and electrolytes, and eliminate waste and toxins through the stool. To accomplish this goal, the digestive tract must maintain proper acidity in the stomach, have adequate amounts of digestive enzymes, and make sure the barrier that separates the inside of the intestines from the blood stream is permeable only to nutrients needed for life. Increased gut permeability (“leaky gut”) is one of the most important concepts in functional medicine and is the basis for most chronic disease. Critical to this process is the gut’s own immune system and the population of microscopic organisms that inhabit the gut known as the “microbiome.” Finally, we also recognize the connection between the gut and the brain. The gut-brain connection is a two-way street in which imbalances in the gut affects the brain and the brain’s activity affects the gut. This occurs by way of a long nerve, called the Vagus nerve which connects the base of the brain to organs in the thoracic and abdominal cavity, and the inappropriate leakage of material across a compromised gut barrier, such as lipopolysaccharides (LPS). Lipopolysaccharides have been associated with a variety of neurological diseases, including Alzheimer’s, Amyotrophic Lateral Sclerosis, Migraine, and Fibromyalgia, among others. This is because an LPS-triggered inflammation appears to disrupt the barrier between the blood and the brain which leads to inflammation within the brain, and damage to the energy-producing engines of the cells known as the mitochondria.

Defense & Repair

This system is generally thought of as your immune system and its interaction with your body’s general tissue repair systems. Your immune system has the task of identifying enemies from within and without and then facilitating cellular repair when the inflammatory assault on the invader is finished. Every cell in your body has an immune system tag that tells it not to destroy that particular cell. Then, when a cell dies the immune system recognizes the changes in the tags of the dead or dying cells and goes in and cleans them up. Your cells are also preprogrammed with an ‘auto destruct’ program call apoptosis. If the cell becomes diseased or sick it will die and again your immune system will clean it up, and then assist in tissue repair. If this system becomes dysregulated, chronic inflammation becomes rampant; this can result in autoimmune diseases or immune system and repair dysfunction and chronic inflammation. These symptoms are diffuse and range from chronic fatigue, to aches/pains, joint inflammation and in some patients chronic relapsing and remitting fevers and illness.


This is mitochondrial science. The mitochondria are the nuclear power house of every cell in your body. Single cell organisms, like bacteria, won’t have a fully developed mitochondrial system and so can only exist as single cells. Humans however have a complex biochemical system that acts like an atomic reactor, breaking down nutritional compounds and capturing the energy released from the breakdown. If the system works correctly, you can have a high-performance athlete; if it doesn’t, you can have someone debilitated from Chronic Fatigue Syndrome. Because energy is the basis for life, this system’s interactions with all other systems is legend. Without an understanding of bioenergetics (the science of energy production in biologic systems) it is impossible to appreciate the interconnected web of mitochondrial energy affecting any particular disease.

Biotransformation & Elimination

These processes account for the way your body interacts with your nutritional inputs and then converts the waste products of metabolism into non-threatening inert compounds that can then be excreted from your body. If these don’t perform correctly toxic compounds and metabolites can slowly build up in your system over time. Your biochemical systems have to convert solid food, liquid drink, and gaseous air into the most basic elements that can nourish each cell in your body. Your body has multiple redundant biochemical systems to facilitate this. However, in some individuals—due to nutritional deficiencies, toxin exposures, genetic mutations, chronic stressors or chronic inflammation the cellular systems won’t function property resulting in a slow breakdown in function.


The transport system involves the transport of nutrition, hormones, enzymatic factors within the context of the Functional Medicine Matrix. It is difficult to discuss this matrix node without the context of all others. Hormones are transported either paracrine (cells in close proximity to other cells like in GI tract) or endocrine (across multiple domains like thyroid hormones). Energy itself can be transported intracellularly via ATP or within the body via glucose and fatty acid molecules. The immune systems can function via transcellular migration (across cells walls) or through the blood to different parts of the body. Transport attempts to uncover disconnections in the body’s natural transport systems and then to either address these issues or enhance them based on the interactions within the web of all other interconnections in the body.


Communication can be understood as your whole-body hormone system. It includes your thyroid system, the male or female hormone system, the hormone organs of origin (ie-adrenal and thyroid) and their connections with the nervous system. This also includes the hormones communication with cells at their cell walls and the nucleus of each cell. We are discovering the neuroendocrine system (the integrated nervous system with endocrine hormone system), neurohormonal system (the integrated nervous system with sex hormones like estrogen and testosterone) and also the neuroimmunological system (the integrated nervous system with its interactions with the immune system). This all falls under Communication.

Structural Integrity

The structural integrity category is a little more complicated and diffuse but can best be thought of as cellular integrity. Things need to stick together in order to function. If the bricks in your house fall out of place one by one, eventually the whole house collapses. Cellular integrity includes that of your arteries and veins as well as that of your tissues. However, tissue breakdown starts at the cellular and arteriolar level. We typically view cardiovascular disease as its own specialty and in Functional Medicine it is given a whole study module yet the same processes that cause heart attacks and strokes also decrease kidney function, brain perfusion and blood flow to the entire body. The break down in vascular integrity that starts in the teen age years doesn’t result in heart disease for decades yet the same process in ongoing in the entire body, not just the heart. It’s best to view vascular disease as a whole-body process and not merely limited to the heart and brain.


This area is related to Cognitive function and Perceptual patterns. While biochemistry can inform your mental state, it is also true your mental state can inform your biochemistry. Our thoughts can have profound influence on our hormone, immune and digestive states. If we are carrying toxic or limiting thoughts and beliefs, these can have adverse effects on our physiology.


Our ability to regulate our emotional state can have deep impact on our health.


Meaning, Purpose and connection are critical to wellbeing. In fact Social connection and a sense of being a part of “something bigger than ourselves” has emerged as an important health factor.