What is the Microbiome and Why Should You Care?

The incidence of autoimmune disease is skyrocketing and we don’t understand why. The incidence of type 1 diabetes is doubling every 20 years and that’s too fast for “genetic drift” to be the cause. The answer lies with something in the environment, but what? And how would that environmental trigger cause autoimmune disease, anyway? The key to understanding the connection between our genes, our environment and our immune system may be the microbiome.

What is the microbiome?

You are not alone. Ever. Because trillions of microbes (bacteria, viruses, fungi and yeast) call you home. They live on your skin and in your mouth. They’re hanging out in your nostrils and in your genitals, but most of them live in your large intestine. Say hello to your microbiome – trillions of microscopic creatures that live on and inside of you.

Although science has known about the microbiome for decades, it’s only recently that we’ve focused on how the microbiome impacts on our health. When I was in medical school in the 1990s, we were taught that these “commensal” bacteria in our intestines were usually just innocent bystanders. Other than when bacterial overgrowth caused diarrhea after antibiotics, this microbiome was largely ignored. But lately, medical researchers have started wondering if there is more to the microbiome story.

Turns out, these trillions of microbes living within us are actually a complex, organized community. Our initial microbiome is passed onto us at birth by our mother and constantly evolves over our lifetime based on factors such as diet, infections, environmental exposures and hygiene. We have a give-and-take relationship – our microbiome is fed and housed in our intestinal tract and, in return, it helps us digest food, extract vitamins and minerals, and even helps train our immune system. But that’s really only the beginning. There’s some fascinating on-going research studying how the microbiome actually communicates with our immune, endocrine and nervous systems, raising the question of whether our microbiome has more control over us than we think.

So, Why Should We Care About the Microbiome?

The vast majority of our microbiome is in the GI tract. You know what else lives there? The majority of our immune system. In fact, not only are these microbes living on the lining of our intestines, but bacteria are found actually inside the immune cells (called lymphoid tissue) of our gut. During the first 2-3 years of life, as our microbiome grows when exposed to new bacteria, our immune system is also developing. Early research reveals the microbiome may have a role of training our immune system to recognize friendly bacteria so that the immune system doesn’t attack its own host. The importance of this intimate relationship between the microbiome and the immune system during our early years is being further studied in specific autoimmune diseases such as celiac, Crohns, multiple sclerosis and rheumatoid arthritis. Again, these are early days for this research, and at this time we don’t understand if changes in the microbiome seen in these diseases are a cause, an effect, or a correlation without causation.

Can we improve our health by changing our microbiome?

This is an essential question and one without an answer for now. We know that the populations with higher incidences of autoimmune disease also have less diversity in their microbiomes. So the people of Finland, who have the highest incidence of type 1 diabetes in the world, also have the least diverse microbiomes. And we know some of the factors that impact on the diversity of our microbiomes:

The Western diet, which is high in refined sugars and processed foods and low in fruits and vegetables, is associated with a less diverse microbiome.
The composition of the microbiome is affected by the amount and types of bacteria to which we are exposed. And we are exposed to bacteria not just when we have infections, but also in daily life starting with mode of birth (vaginal vs. Caesarean birth, hospital vs. home delivery), as well as the overall hygiene of our environment (the cleanliness of our drinking water, the number of people living in our homes, our exposure to animals, farms and dirt, etc).
Antibiotic use decreases microbiome diversity. Environmental exposures such as pesticides, heavy metals, toxins and chemicals that make their way into our bodies via food supply, skin and cleaning products, occupational and home exposures also have an impact on the composition of the microbiome.

So, where does all this information leave us? One thing I’ve been struck by when hearing people’s stories over the past few years is that some people improve their autoimmune disease with lifestyle changes such as changes in diet and limited environmental exposures. If we are what we eat, then our microbiome is what we feed it. I find this to be a promising area for autoimmune sufferers; one day in the not-so-distant future, I hope that our understanding will grow as research answers more questions on the relationship between the microbiome and autoimmune disease.

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