The Microbiome - A Universe Unto Ourselves

Courtney Snyder, MD

What is the microbiome and why are so many researchers studying it's impact on human health including mental health?  How can we take care of it?  And, what can it teach us about fear, the importance of diversity and our relationship with the natural world?

The microbiome is the collection of microbes that live in and on our bodies.  There are estimated to be 100 trillion in our gastrointestinal tract - about ten times the number of cells in our body. Spread out, it is believed the microbiome could cover a football field.  Though there are an estimated 500 -1000 different species, only one third seem to be common to most people.  The other two thirds are specific to each one of us.  So, along with our unique experiences and genomes, we have unique microbiomes.
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Where do all these microbes come from?  It's generally thought that at the time of birth, when the babies mouth is exposed to the mother’s vaginal fluid (which has some fecal microbes) that the microbiome is "seeded."  More bacteria is acquired from the mother’s skin during breast feeding and then more when babies explore their environment (often with their mouth).  Nature’s intent, as you can see, is a healthy level of "contamination" - not a germ free existence.  By the age of three the microbiota has become pretty stable and similar to that of an adult. It will continue to evolve  into adulthood and change in response to our diet and our environment.  

Until our recent history, people didn’t think about the microbiome, nor did they need to.  The microbes quietly got their own needs met while doing their part to maintain our health.  After discovering bacteria and infection, we began to fear microbes - all of them - and we went on to successfully wipe many of them out without making any distinctions. Now scientists are trying to figure out which bacteria are helpful, which are harmful, and which are just hanging out. They're also trying to understand how cesarean sections, antibiotics (and other medications), hand sanitizers, dishwashers, a Westernized diet and less time getting dirty in the outdoors relates to the explosion of chronic health conditions from allergies, eczema, asthma, other autoimmune, gastrointestinal, cardiovascular, neurologic and psychiatric conditions as well as cancer. While the microbiome isn’t the only factor at play, it seems to be up there with genetics and environmental factors when it comes to human health and illness.  There is still much to be learned.

These three are constantly interacting with one another.

So, what are those beneficial bacteria doing for us as we’re giving them room and board? It turns out a lot.

Protective Barrier - between our bodies and the rest of the world.

• Neutralize a number of toxic substances including carcinogens and metals from the environment
• Absorbs toxins produced by pathogenic/bad microbes
• Reduce ph - the acidic environment makes it difficult for pathogenic microbes to thrive
• Inactivate histamine - which is important not only for allergy symptoms, but also brain related symptoms.

Interact With the Immune System

• Helps the immune system respond appropriately to invaders through a number of cascading events. Without a healthy microbiome a person is immunocompromised, ie. more susceptible to infection, which sadly can mean more antibiotics and further disruption to the microbiome.  The result is a vicious cycle many are unknowingly living out
• Prevent opportunistic/bad bacteria (which may be harmless in small numbers) from getting out of control
• Helps the immune system distinguish between friend and foe so that the immune system isn’t inadvertently going after the body, as in autoimmune conditions

Integrity of the Gut Lining
Lack of healthy microbes can result in a permeable gut lining  - a “leaky gut”  - whereby infection, undigested food, toxins, or metals can get into the blood and travel to other parts of the body. The result can be a wide range of inflammatory conditions.

Absorption of Nutrients 
such as magnesium, zinc, selenium, copper, calcium, manganese, sulphur, phosphorus, iron, potassium, sodium, B vitamins, folic acid, fatty acids, and glutathione, to name just a few.

Synthesis of Nutrients
including many B vitamins, K and various amino acids.

Digestion
Without beneficial flora, we would be unable to digest carbohydrates.  Microbes help us to digest certain proteins - ie. casomorphines (from milk) and glutomorphines (from gluten).  If these proteins remain undigested and make it through a "leaky gut" they can interfere with brain and immune function and contribute to autoimmunity.  In psychiatry, this has been studied in autism, depression, schizophrenia and explains why many with these conditions benefit from a gluten free and casein free diet.  

Interacts With the Endocrine System 
The microbiome impacts how we respond to stress.

Interacts With the Nervous System
This occurs in a number of ways.  One is by making certain neurotransmitters.  Less friendly bacteria can also make toxins/byproducts and inflammatory molecules that can negatively affect brain. This is why constipation or not having regular bowel movements is especially problematic for brain health.

Influences Metabolism  
Metabolism relates to how our bodies acquire energy for cells which allows us to grow, reproduce, survive and respond to our environment. Just one example - obesity is increasingly being understood as a result of gut flora imbalances.

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In short, an unhealthy microbiome can leave the brain (or any other part of the body) vulnerable to infection, toxins, metals and even undigested food particles that make it through the permeable gut lining and cause inflammation. Add to this an exaggerated stress response - ie. elevated stress hormones. Then add deficiencies of nutrients that play a role in the synthesis of neurotransmitters and deficiencies in antioxidants that protect the brain and things can get pretty complicated.

If within each of us is a world of microbes, what can we do to support the good guys who promote health and peace in that world and how can we prevent the problematic microbes from gaining too much power?  

Like many, I unknowingly killed off many healthy microbes when I took antibiotics for recurrent sinus infections a few year ago.  For me, a range of neurologic symptoms followed.  I believe the damage to my microbiome and the secondary nutrient deficiencies unmasked a genetic vulnerability.   Had I known then what I know now, I would've put my energy into improving my gut flora (and replacing specific nutrients) rather than further harming beneficial microbes.

Here's what I try to do now:

Take care of beneficial bacteria

• Avoid unnecessary use of antibiotics, acid blockers and anti-inflammatory medication
• Try to choose organic unprocessed foods free of pesticides, other chemicals and antibiotics, etc.

Increase the number of beneficial bacteria

• Probiotic food
• Probiotics
• Prebiotics or prebiotic foods (ie. food for beneficial bacteria).
• Get outside in the dirt - ie. gardening

Support the beneficial bacteria through supporting diversity

• Instead of eating a typical Westernized diet which has been shown to lower diversity (and increase inflammation),  choose foods that are high in various types of fiber (ie. a range of vegetables, fruit, nuts, beans, seeds).  Fiber gives the healthy microbes something to do.  Choose whole foods , ie. foods with the least amount of processing.  The more a food is processed the more rapidly that food will be absorbed high up in the gastrointestinal tract.  This translates to less work for gut microbes and they want something to do.
• Exercise has been shown to increase diversity of microbes.

Avoid supporting the problematic bacteria (lest they grow in numbers and crowd out diverse populations)

• Avoid sugar and refined carbohydrates (Many of us functional medicine would go as far as to say avoid grains all together).
• Don’t use artificial sweeteners which are being shown to impact the microbiome and seem to contribute to obesity. 

The microbiome is quite amazing and our growing understanding is changing the way we understand most chronic health conditions.  Separately this understanding challenges us to  honor diversity in ourselves and in our world.  Lastly the microbiome is an ever present and humbling reminder that we are part of a miraculous natural world  - one we live in and that lives within us.