May 14


The Secret to Good Health: Your Microbiome

By Cassie

May 14, 2019

microbiome, microbiome basics, what is the microbiome, why is the microbiome important

It seems like everyone is talking about the microbiome. It appears to be the health and science topic of the decade. Maybe of our lifetime! At this point it’s assumed that everyone knows the basics of the microbiome and new information is coming out every day. There is non-stop medical research proving that your “gut health” (aka microbiome) significantly impacts your over all health. In fact, every aspect of your health may be connected to your microbiome. Additionally, the advertising and constant discussion of pre-biotics and probiotics, including foods to eat, drinks to enjoy or supplements to take it can be overwhelming. If you’re feeling like you’re behind on all of this info this is a perfect opportunity to get up to speed!

What is the Microbiome

The term microbiome refers to all of the microorganisms that live in and on your body. This includes bacteria, fungi, protozoa and viruses. There are an estimated 100 trillion of them and they weigh approximately 3 – 5 lbs. However, when people use the term “microbiome” they are usually referring to the microorganisms that live in your digestive system especially your intestines.

Most of these microorganisms are beneficial and have a symbiotic relationship with you. They help break down your food and produce all sorts of hormones, vitamins, and neurotransmitters. They also regulate and stimulate body function and do a whole host of other stuff. In exchange you provide them with a place to live and nourishment. It’s a pretty awesome deal!

There are some strains of microorganisms that aren’t so beneficial. Some are more neutral as long as they aren’t over populated. But some are actually pathogens (disease causing). Interestingly the microorganisms you don’t have can also cause dysfunction or disease in your body. It is important to better understand the microbiome, how it works and how to take care of it. Anything you can do to keep a healthy balance of microorganisms is going to be worthwhile.

Where does your microbiome come from?

The microbiome isn’t part of your own DNA. It doesn’t come from your genes. Current theory is that humans don’t have a microbiome until birth. So, how is our microbiome established?


At the end of pregnancy the mother’s body begins to change in preparation for birth. The microbiome in her vagina changes substantially. During birth the baby is exposed to the microorganisms in the birth canal. This initial exposure is important to establishing the microbiome. There is a significant amount of research being done to address the best ways to expose babies born c-section because of this. It has been shown that people who were born via c-section have higher rates of disease, obesity and allergies. Lack of exposure to the mother’s microbiome during birth is believed to be the cause.

Breast feeding

It seems like we are constantly finding out new benefits of breast feeding. This is yet another recent discovery. It turns out that 30% of breast milk is not digestible. Seriously! Who would guess? The indigestible part of breast milk called oligosaccharides.  It serves as food for the microorganisms in the human gut. Oligosaccharides are very important to nourishing your microbiome.

Evnironmental exposure

Most of the microbiome is established prior to age 3. The most impactful factors are the humans, pets and bacteria a child is exposed to. Establishing a diversified microbiome is most beneficial to your health. Exposure to animals and other people helps children accumulate unique species of microorganisms. It is also very helpful to allow them to get dirty and play outside. And it is important to avoid sanitizing their environment or over exposing them to antibiotics or other medications.

Read my post How Clean is Too Clean for more information regarding the health consequences of disinfecting .

Why is a healthy microbiome important?

As mentioned earlier in this post, the microorganisms in your body serve a multitude of functions. They produce vitamins and help to break down your food. They also produce neurotransmitters, regulate and produce hormones, stimulate the immune system, and even send signals to your brain. Having a healthy microbiome is imperative to good health and disease prevention.

Digestion and vitamin production

The microorganisms in your digestive system aid in breaking down and digesting food. They help to make the nutrients in your food more easily absorbed in your body. They also ferment insoluble fiber in your large intestines.

Your digestive system isn’t able to break down food all on it’s own. It needs help. The microorganisms in your gut assist with this. This makes the nutrients in your food bioavailable (easily absorbed by your body). The bacteria in your microbiome also help to create B vitamins and vitamin K, which is necessary for clotting. B12 can only be formed by enzymes found in bacteria. So, your microbiome plays a key role in providing your body with this important vitamin.

The fermentation process helps to produce short chain fatty acids. Short chain fatty acids have many important rolls in the body. They prevent some chronic diseases, are used as a nutrient source and are important for muscle function. Short chain fatty acids also help protect your body from pathogens that can sometimes be found in food.

Without a healthy microbiome we would suffer from malnutrition, vitamin deficiency and gastrointestinal illness and distress.

Neurotransmitters and hormones


The microorganisms in the gut produce neurotransmitters such as dopamine, serotonin, and GABA. These are all associated with anxiety, depression and bi-polar disorder.

Researchers have also found differences in the microbiomes of people diagnosed with schizophrenia. They have even introduced samples of these microbiomes into mice and observed behaviors that appear to be symptoms of schizophrenia.

There is more seretonin produced in the gut than in the brain. This discovery has led to research into alternative treatment protocols for depression.

The microbiome plays an important role in neurotransmitter production and can have a significant impact on mental health.


Estrogen, cortisol, ghrelin and leptin are all effected by the microbiome.

The microbiome helps to regulate estrogen levels. There is emerging research indicating that estrogen related conditions such as PCOS and endometriosis might be able to be treated by addressing the microbiome.

Cortisol is the stress hormone that has been making headlines for it’s role in abdominal weight gain. High levels of cortisol causes sleep disturbances, anxiety, difficulty getting into a para sypathetic (rest and relax) state and can cause weight gain.

Ghrelin and leptin both control appetite. This is just one of the reasons that an unhealthy microbiome is associated with obesity. Obese people also have a less diverse microbiome.

Keeping the microbiome healthy is instrumental in keeping hormone levels optimal.

Your immune system

The microbiome helps to stimulate and regulate your immune system. Many chronic diseases are related to issues with the microbiome. The microbiome is likely to play a role in hearth disease, autoimmune disease, some cancers and even neurological diseases like Alzheimer disease and Parkinson’s. Interestingly, they have recently discovered that Parkinson’s patients consistently present with gastrointestinal complaints 5 – 10 years before the first neurological symptoms appear. Early diagnosis could drastically change outcomes for this debilitating disease. Furthermore, Auto-immune diseases appear to be passed through inherited microbiome not DNA. (Inherited microbiome refers to the inherited traits that effect your microbiome colonization).

Gut feelings

It turns out that “gut feelings” are real. The Vagus nerve connects your gut and brain. Until recently scientists believed that that nerve predominantly carried messages from your brain to your gut. Turns out that’s not the whole story. The vagus nerve carries more messages to the brain from the gut than the other way around. Not only that but there are microorganisms in your gut that can directly stimulate the vagus nerve. Clearly the brain relies on these communications from the gut so keeping it healthy is optimal.

Healthy microbiome = healthy you

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It’s pretty clear that all of the microbiome buzz is justified. The health of your microbiome is vitally important to your mental and physical health, your nourishment and even staving off chronic disease. It may be over simplifying to say a healthy microbiome = a healthy you. After all, there are many factors that go into creating a health. But, the truth is that everything you need to be healthy is imperative to the health of your microbiome. Now that you know the basics about the microbiome why not focus on how to take care of yours? Check out my post How to Heal Your Gut, today!

Share this post today to help someone you love who is suffering from gut related health issues!

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