The Microbiome

The microbiota is the term that refers to all of the microorganisms exposed to outside surfaces. The microbiome, on the other hand, is the entire set up genes of a given organism. This includes the gastro-intestinal organs (mouth to anus), skin, nose, ears and genitals and includes all of the bacteria, protozoa, fungi and even viruses that inhabit our bodies. It is estimated that 90% of cells (approximated 100 trillion cells) found in our bodies are not human, but come from 40,000 bacterial strains. Imagine then, that we are only 10% human and the remainder is microbial. Each of these bacteria in our body carries genetic material. The term microbiome, then, is defined as the entire set up genes of a given organism and includes all of the genetic material from the bacteria. Some people call this microbiome, our “second genome” or our second brain. Not only are the “human” genes outnumbered by the genetic material from our microbiota, it is likely that the microbiome has more influence on our overall health.

Our Health Monitor

Hippocrates said that “all diseases begin in the gut”-460 BC. The gut appears to be a main regulator of immunity, our health monitor. It is responsible for monitoring bacteria and viruses that come into the mouth with everything that we eat and prevents those infections from getting into our blood stream and becoming systemic diseases. Many of us believe that this second genome plays a crucial role in deciding how healthy, or how sick, we will be. The proliferation of the wrong kind of microbiota may predispose us to cancer, heart disease, obesity and infection and puts us at risk for inflammatory bowel disease and other autoimmune disease such as type I diabetes, rheumatoid arthritis, multiple sclerosis and lupus. It also likely impacts our risk for getting allergies. These microbial communities change as we age and shift based on our diets and exposures, which can lead to an over or under production of certain microbes.

Cells in Your Body

90% of the cells in your body are bacteria.

The Gut Bugs are Mood Regulators

The gut is responsible for production of many neurotransmitters (such as tryptophan, histamine and serotonin) that are used in the brain as mood regulators. Many antidepressants (such as SSRIs) are based on the concept of increasing serotonin to improve mood.

The Leaky Gut

Another method where we see the immune system affected is in the concept of intestinal permeability, also known as the “leaky gut.” The gut is made up our stomach, small intestine, large intestine and rectum. It is a made up of 3000 square feet of surface area. The more surface area that is present allows for better ability to absorb and digest. The gut is made up of an abundance of intestinal villi which are outpouchings in the colon and are responsible for absorption and are first exposed to whatever comes into the GI tract. The outer layer of those villi are the intestinal epithelial cell and can be considered the first line of attack on the battlefield. These cells are followed by the intestinal dendritic cells which are often considered the first responders. Beyond that, we see the immune cells (the T and B cells) which are actively immune fighters. These cells are the snipers and our navy seals. They are the best of the best and ready to attack any foreign material that invades our body. As Harvard professor and pediatric gastroenterologist, Dr. Alessio Fasano says, the intestinal mucosa [gut] is the battlefield on which friends and foes need to be recognized and properly managed to find the ideal balance between tolerance and immune response.

The thought that comes to mind is that what makes one person have a leaky gut for hours and another person has a leaky gut for just minutes. This leads to our understanding that a person must have a genetic predisposition to a disease. We can’t fix predisposition because that it what we get from our parents. But it is only with the environmental trigger, however, that a person actually becomes sick. Fasano and others believe that many autoimmune diseases are affected by food sensitivities and changes in the microbiome at an early age. The leaky gut has been associated with other autoimmune diseases such as type I diabetes.[i] Type I diabetes is one such autoimmune disease which a patient’s own immune system attacks the insulin producing beta cells. Without insulin, our bodies are unable to process sugars and convert them to a storage form, fat. The link between how the leaky gut triggers immune reactions that attack the pancreas in some people and cause type I diabetes and in others creates lupus, rheumatoid arthritis or multiple sclerosis is not clear. Each person has different genetic predispositions and environmental triggers. Importantly, there are other environmental triggers for inflammation beside diet and gut permeability. We can’t ignore the role of stress and trauma, obesity and smoking as important causes of total body inflammation.[ii]


[i] Vaarala O, Leaking gut in type 1 diabetes. Curr Opin Gastroenterol, 2008; 24(6): 701-6

[ii] Berk M, Williams LJ et al. So depression is an inflammatory disease, but where does the inflammation come from? BMC Medicine, 2013; 11:200