The sequencing of the human genome in 2003 placed genomics in the spotlight in our search for disease cures but in the past decade a “second genome” has been uncovered. The microbiota, all the bacteria, viruses, fungi, protozoa and other forms of microbial life that live on and in us, is being considered a “forgotten organ” a “second genome.”

Microbes have been around for more than 3.5 billion years making them the oldest form of life on earth. For the past six million years, they have been evolving together with humans. As they have changed over time, microbes and humans have formed complex relationships with each other and form a crucial ecosystem. Imbalances in this ecosystem have been linked to a host of chronic, non-communicable diseases, including obesity, autoimmune and allergic disorders, vascular disease, depression and other mental disorders.

Research is clearly showing that our microbiome is crucial to human health.  While we have been educated to think of microorganisms as carriers of disease they do more good than harm. We live, and have evolved, as a part of nature with our microbes performing numerous beneficial functions relevant to supporting our life. They help us digest food, prevent disease-causing pathogens from invading the body, synthesize essential nutrients and vitamins and tutor the immune system to attack pathogens without overreacting and damaging the body itself.

We receive the clear majority of our critical gut microbiome, mainly bacteria, from our mothers during birth and breastfeeding. The method of delivery impacts the baby’s microbiome, with vaginal delivery having a strong beneficial effect and cesarean delivery reducing the number and diversity of beneficial bacteria. There is a strong correlation between the global rise of cesarean delivery, our abuse of antibiotics and the incidence of numerous chronic, non-communicable diseases.

The greatest concentration of microbes is in our gut which contains as many or quite possibly more cells than we think of as “us” and that is about 30 trillion. Approximately 500 – to 1500 bacterial species, comprising from 2 to 20 million genes – the microbiome – interact with “our” genome creating a complex ecosystem. During the past couple of decades studying microbes, researchers have come to realize that microbes constitute part of who we are biologically, not just life forms that live within us.

The gastrointestinal tract’s trillions of bacteria train the body’s immune system.  The most important function of the immune system is to distinguish what cells and substances belong to your body and are health enabling, and which aren’t! What belongs to the body is referred to as “self,” and something that doesn’t belong as “non-self.”  Through millions of years of evolution, our immune system has acquired the ability to learn and recognize the billions of different cells and substances it encounters every day. Researchers have found that certain immune cells are educated in the gut to not attack beneficial bacteria but when this education is disrupted it can lead to inflammatory bowel diseases like Crohn’s and ulcerative colitis.

Changes in the microbiome can trigger changes in human cellular activities, resulting in disease or contribute to disease progression. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy the gut. Much of this diversity remains unexplained, although diet, environment, antibiotic use, host genetics and early microbial exposure have all been implicated

Why is it that the body’s immune system knows to ignore these beneficial bacteria that are so important for our ability to live a healthy life and attack those that are causing disease? The key question I’m always asking myself is where do I begin and end. In other words, since the microbes are essential to our health can we exclude them and call them non-self?

The diversity of genes among the microbiome of individuals is immense compared to genomic variation. Individual humans are about 99.9% identical to one another in terms of their host genome yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the microbiome is quite a bit more variable, with only a third of its constituent genes found in most healthy individuals. A better understanding of the microbiome will broaden our understanding of human health and likely lead to more effective ways to deploy traditional treatments and contribute to new treatments as well.

Nurturing your gut bacteria is one of the most important practices you can do to get and stay healthy. Gut bacteria thrive on what you feed them. Our industrial food supply has changed what we feed those microbes dramatically over the past half-century leading to many of our health problems including obesity. Give them whole, fresh, real foods and good gut bacteria thrive. Feed them junk, and bad bugs flourish, resulting in leaky gut, toxic overload, and inflammation.

We have changed our internal ecosystem more rapidly and extensively during the past century than in any comparable time in human history. This society-wide shift, driven by what we eat and the quantity and type of microbes we’re exposed to in our daily lives, looks to be increasing our vulnerability to chronic disease. This imbalance is a major area of research and along with genetic predispositions may be one of the underlying causes challenging our sick care system. A thought I’d like to leave you with is that maybe we need to start thinking of ourselves as ecosystems and that a major aspect of disease is that system being out of balance.

Written by Bill Schaser, Director of Education