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.
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.
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.
Interact With the Immune System
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.
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.
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.
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
Increase the number of beneficial bacteria
Support the beneficial bacteria through supporting diversity
Avoid supporting the problematic bacteria (lest they grow in numbers and crowd out diverse populations)
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.
7/22/2015 09:08:42 pm
Thanks, Dr. Snyder. This was a great introduction to the gut microbiome.
7/22/2015 09:54:33 pm
Thank you, Glenn. I appreciate the encouragement. If you think of it, let me know how you like Brain Maker - I haven't read it yet, but am always looking for good resources for people I work with. My introduction to the micro biome was through Dr. Natasha Campbell-McBride's book, "The Gut and Psychology Syndrome which includes perhaps the most comprehensive dietary interventions that address micro biome - the GAPS diet, but I suspect, Dr. Perlmutter's book, is better about citing research. I'm glad you found "Nutrient Power" useful.
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Courtney Snyder, MD
I'm a conventionally trained child, adolescent and adult psychiatrist. My current approach to health is both holistic (pertaining to the whole person) and functional (addressing the root causes of illness). I write this blog to share what I've learned.