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Microbiome: how your gut affects your health.

Updated: Mar 29, 2023

The amazing ecosystem of your gut and it's role in better health, immune, and mood.

By now everyone has heard about the microbiome.

Essentially it is defined as a complex organization of bacteria, viruses, fungi and their DNA living mostly symbiotically in our bodies; specifically the gut.

The "GUT" is another name for our gastro-intestinal (GI) tract. The GI tract is the tube from your mouth to your anus. Interestingly, the gut is technically considered OUTSIDE our bodies. That's right, the entire gut is separate and apart from our "INSIDE" body.

Fun facts about our gut and microbiome:

  • the protective barrier between the "outside" gut and the "inside" of our body is only ONE cell layer thick!

  • Your microbiome composition is more specific to you than your fingerprint.

  • There are always "pathogens" in our gut microbiome. It's not about having only "good" organisms, it's all about balance.

  • There are more organisms in your microbiome (10 to the 14th power) than you have cells in your body!

  • Your microbiome communicates with your brain via the enteric nervous system. Your enteric nervous system has more neurons (200-600 million) than your spinal cord!

Establishing a healthy microbiome- it all starts with mommy

Babies born via natural delivery begin colonization of their microbiome from a transfer from their mother as they pass the birth canal. (Bacteriodes, Bifidobacteria, and Lactobacillus).

Unfortunately, babies born via C-section begin their microbiome colonization via bacteria from the hospital or surrounding environment consisting mostly of Staphylococcus, Streptococcus, and Clostridium.

You may recognize some of the names on these bacteria and notice that the ones from mom are more of the beneficial species and the ones from the outside environment tend to be more of the non-beneficial species.

So yes, if you were born with via natural delivery, you were born with an advantage.

However, we know now that how you live you life (lifestyle habits) play a significant role in how that advantage plays out.

So fear not those who were born via C-section!

Just because some of us were born without a certain advantage doesn't mean that we can't create a very healthy microbiome. More information on that below.

Anatomy of your gut lining

A normal intestinal lining is only ONE cell thick. Yes, only ONE.

That single layer of tissue is all that prevents you from getting unwanted food particles, pathogens, or irritating enzymes from entering your blood stream.

Between those cells there are what are called tight junctions (see image).

Tight junctions are the filter that essentially allows nutrients into the blood stream but blocks all the "bad" stuff from entering the body.

The good news is that layer is renewed basically EVERY DAY.

Nice, right?

You can see from the image above that the cells are mucosal cells. The mucus produced from those cells trap and block pathogens from getting near the tight junctions. The mucus membrane also has proteins that will digest pathogens.

It is important to keep that mucus lining healthy.

Leaky gut

The technical term is increased intestinal permeability.

I like the colloquial term "leaky gut" because it clearly illustrates what is happening. When the intestinal lining cells are compromised and the tight junctions lose their integrity, things that normally are blocked from entering your blood stream suddenly can enter and wreak havoc.

That havoc comes in the form of a significant immune response (because everything that gets in is a foreign entity to your immune system) leading to SYSTEMIC INFLAMMATION!

That means the whole body is now inflamed. And an inflamed body is a very unhappy body;.

Reasons the gut lining can be compromised:

  1. STRESS- suppresses the activity of the healthy bacteria and decreases mucus cell activity

  2. ANTIBIOTICS- leads to an imbalance of the microbiome. Antibiotics kill ALL organisms; both good and bad.


  4. UNHEALTHY DIET- too much sugar can lead to an overgrowth of bad bacteria, fungus, yeast

  5. LOW STOMACH ACID (hypochlorhydria)- poorly digested foods as a result of low stomach acidity can lead to damage of the gut lining. (low stomach pH is a whole other topic).


  7. NSAIDs- ibuprofen, aspirin and other "pain relievers" cause damage to the gut lining to the point of bleeding. (basically they poke holes in the lining). That means the cell layer protecting the gut lining has been destroyed=tight junctions are destroyed.

  8. BIOLOGIC DRUGS- (Humira, Enbrel, Rituxan)- suppress the immune system so your body has no defense.

Common symptoms associated with leaky gut/ dysbiosis

  1. PAIN- joints, back, neck, anywhere




  5. DEPRESSION/ANXIETY- a host of mood disorders are associated with gut dysbiosis

  6. SKIN RASH- ezcema, psoriasis, vitiligo

  7. OSTEOPENIA/ OSTEOPOROSIS- the gut lining has vitamin D receptors that are impacted with stress and dysbiosis, leading to poor vitamin D utilization, poor calcium utilization and then thyroid/parathyroid dysfunction. This is the mechanism of osteoporosis. (again, a topic in itself).

Basically almost every health complaint you can think of can be connected in one way or other to the microbiome!

What to do to improve your microbiome or keep it healthy

1. EAT MORE PLANTS- having 30 varieties of plants and spices per week can significantly support your microbiome. This includes herbs, nuts, seeds, spices.

Example: making a salad with 5 vegetables and 2 fruits, salt, pepper, sesame seeds, walnuts= 11 variety. And remember this is for a WEEK so pretty easy to do.


  • kimchi

  • miso

  • sauerkraut

  • kombucha

  • kefir

  • yogurt (unsweetened)

  • real pickles

3. HIGH FIBER FOODS- these foods act as a prebiotic. This means high fiber foods is what feeds the good bacteria or probiotic.

Can I test my microbiome health?

Standard Process has a test to measure composition and overall health of your microbiome.

For more information click on the photo to read more about the test.

In a nutshell it takes a stool sample, measures the composition of your microbiome, and makes supplement and lifestyle recommendations.

I wish you could order it directly but as it is, it requires that the practitioner order the test for you.

Supplements to help support and improve microbiome health

If you want a more comprehensive solution, it probably makes sense to do the microbiome test and get a comprehensive support report.

However, a good overall support of your microbiome includes the following: (all these are in the Standard Process/Mediherb line).

  1. Prosynbiotic- this supplement has both prebiotic and probiotic support

  2. Black Cumin Seed- acts as a biofilm enzyme to break up biofilm that protects bad bacteria

  3. Zypan- betaine hydrochloride and enzymes to ensure proper stomach acidity and enzyme support for healthy digestion of food.

  4. Gastrofiber- my favorite choice for a complete fiber suppor

The microbiome has just recently made a wide spread appearance in the knowledge base of many people. It's significance in the clinical world however, has been known by holistic practitioners for decades. Our symbiotic relationship with a vast array of micro-organisms is fascinating and that knowledge continues to evolve. I guess the future of our health and ability to thrive is not just on us as individuals but also depends on our relationship and balance with the outside world.

Even if those relationships are microscopic in nature.

Do yourself a favor and invest in promoting a healthy gut and helping your microbiome to thrive.


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