This is the first in a series of articles explaining some of the foundations of Functional Medicine. Functional Medicine is a medical practice concerned with the optimal functioning of the body and its organs, focused on finding the root cause of dis-ease rather than merely relieving symptoms.
Microbiome - the ecological community of commensal (one benefiting from another),symbiotic (both benefiting from each other), and pathogenic (one harming another)organisms that literally share our body space. Scientists have found these organisms in our stomach, intestines, nasal cavities, mouth, genitals and skin. The focus in microbiome research involves the digestive tract.
It is safe to say that most of us have heard about the importance of having ‘good’ bacteria in our bodies and that taking ‘probiotics’ is an important health strategy. These ideas are becoming more wide spread due to the completion of the Human Microbiome Project (2008-2014+). This project was initiated shortly after the Human Genome Project (the study of human DNA) was not able to provide answers to many of our health problems.
The Microbiome Project found that the number of bacteria in our body far outnumber our actual body cells (by at least 10Xs) and have far greater genetic material than we do (by at least 150Xs!). As of 2014, scientists have identified over 1500 different strains of bacteria performing specific functions, and are expecting to discover over 1000 more. There remains speculation as to how and why we have far greater bacteria DNA than our own but we do know that they play very important roles in the functioning of our bodies. Some of these roles are described below.
Digestion - It has long been known that the bacteria in our gut help with digestion. An important function is to convert some of the starches we eat into short chain fatty acids (SCFAs). SCFAs provide energy to our gut, liver and muscles cells, reduce inflammation, increase fat metabolism, and improve cholesterol and triglycerides. Good bacteria also produce many enzymes needed to break down other things that our bodies have a hard time doing. They even produce nutrients (Vitamin K, B vitamins, etc.) and help us to absorb nutrients.
Infection - The microbiome can produce specific antibiotics to control the growth of various species. Good bacteria can out-compete bad bacteria for binding sites, space and nutrients, thus keeping pathogens at bay. Too many pathogens in the gut can result in fatigue, ‘foggy brain’, diarrhea, bloating, cramping and even ulcers (ulcers usually involve an overgrowth of H. pylori in the stomach). Other pathogenic over-growths lead to UTIs, yeast infections, sinus infections, sore throats, staph infections, etc.
Body weight and Insulin Resistance – Fascinating experiments were done demonstrating the effect on body weight. If the entire contents of the colon of a skinny person are emptied and the contents of the colon of an overweight person are transplanted into the skinny person, the skinny person will rapidly become overweight. We now know some of the mechanisms for this. We also notice that people with diabetes, pre-diabetes and metabolic syndrome have imbalances in their gut microbiome.
Inflammation, Autoimmune Diseases and Immune Modulation – People who deal with chronic inflammation and autoimmune diseases often have problems with their gut microbiome. The formation of our Gut Immune System (GALT) is dependent on and ‘learns’ how to react or not react based on the microbiome. The microbiome also produces immune cytokines like IL-1, IL-5, IL-6, IFN-g, TNF-a and interacts with Toll-like Receptors (TLR2&4). Many medications target these cytokines.
Mental Health – Numerous studies show symptoms of depression, anxiety and other disorders often correlate to a lack certain gut bacteria. Psycho-biology is a new field created to study this link and improve treatment options.
Knowing this, how do we maintain a healthy and diverse microbiome?
Helpful things you can do:
Regularly consume cultured and fermented foods and beverages
Do not be afraid of germs (play in the dirt, garden, be around a variety of people) and don’t use hand sanitizer or antibacterial soaps
Use Probiotics intelligently (see my next article ‘Forget what you thought you knew about probiotics’)
Eat a whole food, plant based diet that is mostly organic
Try intermittent fasting
Avoid C-section births and breast feed for at least 6 months.
Harmful things you should avoid:
Using antibiotics more than once every 2-3 years
Excessive alcohol or coffee
Medications such as steroids (Prednisone), opiates/pain pills, NSAIDs (Advil, Aleve, Celebrex, etc.), proton pump inhibitors (Nexium, Prilosec, Prevacid, etc.), and long term use of birth control pills
Excessive mental/emotional stress
Excessive physical stress (extreme athletes, etc.)
You should get your microbiome tested if:
You are not doing things from the helpful list regularly
You are exposed to several of the things from the harmful list
You have digestive complaints
You have a chronic, recurring, and/or difficult to treat illness
Microbiome testing is easily done through my office using a stool sample.