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The Marvelous Microbiome

March 1, 2020

The Marvelous MicrobiomeIt seems that the microbiome is a term that has been on many health professional’s lips in the past few years. This is not without good reason. The microbiome is composed of bacteria, fungi, and viruses that live within our digestive tract. The gut hosts over 100 trillion microbes in the microbiota. That’s about 10 times as many cells as there are in our entire bodies! We are basically under the control of what lives within us, though we do have the power to make choices about how we feed our microbiome and this, in turn, alters the composition of it. The microbiome needs to eat, it makes waste products, as well neurotransmitters (chemical signals that act on our nervous system), vitamins, and hormones. So, the microbiome eats what we eat, it excretes waste, and also interacts with our waste. The microbiome can even transform the waste ready to leave our body into waste that is absorbed all over again, sometimes in a more toxic form. The microbiota, in releasing neurotransmitters, can cause our moods to change, make us anxious, or depressed. And maybe most importantly of all, our microbiome trains our immune system.

The Microbiome and What We Ingest
The microbiome and a nice thick layer of mucus are what protect the one-cell-thick lining of our intestines from damage and foreign invasion (viruses, bacteria, large proteins and antigens). Changes in the microbiome occur quickly and are always changing based on what we ingest and what hormones are released in response to stress, sleep, and exercise. Perhaps the most direct control we have over our microbiome is what we ingest. The microbiota that make up the microbiome will turn dietary fiber, for example, into short chain fatty acids that are ideal food for maintaining the health of our intestinal cells. The composition of our diets, how much and what kind of fat, fiber, protein, and carbohydrates all impact the composition of our microbiome.

Medications also have the ability to change the microbiome. The most well understood is antibiotics. Antibiotics are fairly non-specific and kill many of the bacteria that they come in contact with, and therefore are implicated in decimating the amount and diversity of the bacteria in the gut and the microbiome, often permanently. When the microbiome composition changes and becomes unbalanced it can lead to changes in the lining of the gut, the immune system, and the neurotransmitters in our bodies. We can exert a fair amount of control over our microbiome by regulating our response to stress, choosing mindfulness, and getting adequate amounts of sleep and exercise. For each individual this looks different, working with a microbiome-literate doctor can help tailor sleep and exercise goals.

Leaky Gut
A little background is necessary to understand why the gut lining is so important. The lining of the gut is one cell layer thick and separates the contents of the intestines from the lymphoid tissue (where 60-70% of your immune system resides) or the GALT (gut associated lymphoid tissue). Bacteria from the microbiome are constantly sampling the contents of the intestines and sending signals to the GALT to be interpreted and to learn what is happening in the “outside” world. If the single layer of cells that makes up the lining of our gut is damaged from toxic materials secreted by unbalanced bacterial populations or pathogenic bacteria, our gut becomes “leaky” and this can lead to a very confused, very upregulated, and very unbalanced immune system. When the gut lining is exposed, or becomes inflamed or irritated, it cannot keep out foreign substances like bacteria, viruses, or proteins. Immune dysregulation and food sensitivities can crop up when the leaky gut is allowing proteins into the GALT. The immune system uses protein signaling to identify familiar proteins that are part of the self. When proteins are present that are unfamiliar, the immune system is triggered into responding to these proteins as if they were invaders. The cascade of events usually begins with inflammation, and if the leaking is not fixed, it can turn into a food sensitivity, autoimmunity, or chronic illness.

Identifying a Problem With Our Microbiome
It may seem obvious; if you have a stomachache after eating a certain food, then you have a problem with your intestines. But it’s not always that simple. Gas, bloating, flatulence, burping, nausea, reflux, and changes in your bowel movements can all indicate changes in the health of the gut and usually the root of these changes is related to the health of the microbiome. For some it’s a feeling of foggy headedness after eating a specific food. For others it’s sneezing and itching after eating offending foods. Still others may notice mood swings related to meals or the onset of anxiety or depression. Alternatively, someone may have always eaten a certain food, but after a course of oral antibiotics, cannot tolerate their favorite foods. Still others may experience a change in health after taking ibuprofen long-term. Medications have the ability to change the health of the gut lining and the microbiome. It may feel as if we are no longer in control of our lives, and as if our health and wellbeing have been hijacked suddenly. After learning about the importance of the microbiome and the influence it has over the many biological systems in our bodies, we may wonder, what can we do about it?

Ways To Improve Our Microbial Balance
The good news is that there are ways to improve our microbial balance and health that are accessible and simple. The first is altering what you ingest. Food can be healing or food can be detrimental to healing. When considering the health of the microbiota, we want to consider the importance of fiber, plant-based antioxidants, and fats. It is also important to mention eating whole foods, preferably organic (as glyphosate, a popular weed-killer often sprayed on non-organic and GMO products has the effect of opening up the lining of our gut). Microbes from the soil that organic whole foods were grown in interface with and build up the microbiome, improve the balance, and seed the microbiome with diverse microbes. In addition, since our neurotransmitters are made in the gut and they interact with the brain (and because it’s a two-way street), learning a healthy response to stress can have a direct impact on the composition of the microbiome.

So far, no probiotics have been mentioned in this article. That is because not all probiotics are created equal nor are all probiotics right for all people all the time. How do you know what kind of probiotic is right for you? See a doctor familiar with functional stool testing to get a baseline for your particular microbiome. You can re-test periodically to see if the interventions you are using are working. If you suspect that you have an illness related to a damaged gut or an unbalanced microbiome, find a doctor who can test this for you. Then follow up with a protocol that removes the cause of the damage, repairs damage done, and restores balance to the microbiome. When in doubt, see the checklist below for finding the right doctor.

Work with a doctor:

  • Who understands the interconnectedness of the body’s systems.
  • Who can order the appropriate testing to identify the root cause of your symptoms.
  • Who can prescribe the right diet for your symptoms based on lab results.
  • Who has knowledge of probiotics to use.
  • Who can put you on a regimen of herbs to repair the gut.
  • Who can help guide you through stress reduction techniques.

Sarah Buck, ND practices in Yarmouth, ME. Her clinical interests and specialties lie in finding the root cause of autoimmune conditions and gastrointestinal disturbances. Sarah enjoys spending time outdoors, gardening, wildcrafting herbs, and just playing. She lives in Portland with her husband, young daughter, and dog.