Gut microbiome

What is a microbiome and how did I get it?

Published 17 Feb. 2021

Before you were born you had a digestive tract with no bacteria or fungi present. As you passed through the birth canal you were exposed to all of you mothers bacteria, this was your first dose of bacteria that would start to make up your microbiome. The bacteria started to multiply and take up residence in your eyes, nose, mouth, skin, stomach and intestinal tract. You created your own unique microbiome that was compatible with your immune system and this process was mostly complete by 3 to 5 years of age.[1] This means that as a young child the food that you ate, the activities you did and the environment you were in contributed to the make up of your gut flora.

The gut microbiome of your mother has a huge impact on you as a child and throughout your adult life. With the rise of a plentiful food supply that is high in sugars, gestational diabetes is becoming more common. Many women don't experience sever symptoms beyond weight gain, increased thirst and frequent urination, which are all just a common parts of pregnancy, so gestational diabetes can be easily left undiagnosed. This is a concern because if mom's gut flora is out of balance she will pass this to the baby which will then be predisposed to having a sugar craving gut flora. According to the Mayo Clinic, "Babies of mothers who have gestational diabetes have a higher risk of developing obesity and type 2 diabetes later in life." [2] We now know that obesity is linked to an unhealthy gut flora so if you get your mothers gut flora that is out of balance then you are more likely to have had weight issues and increased carb cravings all of your life.

Candida is considered an "opportunistic pathogen" which means that it only becomes an issue under specific conditions. The overgrowth of candida is typically moderated by your immune system and by other factors including intestinal flora, peristalsis and enzymes. If your immune system is unable to regulate candida then candida can spread rapidly.

Candida has a few methods to evade detection from your immune system.

One method is called virulence, where candida binds to a protein and effectively hides from your immune system. Candida is playing hide and seek with your immune system. If you hide behind floor length curtains its harder to find you than if you stand behind a lamp.

A second method of hiding from the immune system is when fungi and bacteria create a "biofilm", a coating made of proteins, lipids and sugars that acts as protection. An easy example of this is the biofilm that builds up on your teeth at night. This film sticks to you teeth and if we don't brush our teeth, the biofilm builds up forming plaque and the bacteria eventually can cause a cavity. This same type of mechanism can happen in your intestines with candida. When candida adheres to the intestines it can actually create holes in the intestinal membrane which is one way that leaky gut can develop.

A third method for evading immune system detection is when candida transforms from a yeast into their hypha form. [1] This is a very important mechanism that should be addressed when treating candida overgrowth because candida, a yeast, can choose to literally turn from a yeast into a fungus. This happens when the environment is no longer hospitable for yeast and to preserve its self it mutates into a fungus that can penetrate the intestine and move into other areas of the body. So it may appear that candida yeast cells are gone, but in fact they have only mutated into a fungal form.

How else does candida become overgrown?

Alterations to the gut microbiome can increase the chances of candida overgrowth. When researchers want to study candida in animals they create candida overgrowth by giving rats an antibiotic to kill off any beneficial bacteria that would typically out compete candida and then they introduce candida. [3] This means that if you have ever taken antibiotics you have altered your gut microbiome into a state that is easier for candida to proliferate.

A diet high is refined sugar and carbohydrates will feed the bad bacteria and fungi in your digestive system. You might wonder if sugar feeds the bad bacteria doesn't it feed the good bacteria too? Yes some good bacteria feed off of sugar but there are many good bacteria that actually feed off of fiber in your colon. If you are eating a diet low in fiber you are starving these good bacteria that produce anti-inflammatory compounds to keep you healthy.[4]

Is there any hope?

In a study done on mice who were given oral thrush, candida overgrowth in the mouth, the mice who were given oral probiotics, Lactobacillus Plantarum and rhamonsus, showed lower numbers of candida cells after 7 days. "In the group treated with L. rhamnosus, the reduction in yeast colonization was significantly higher compared with that of the group receiving nystatin." [3] This should give hope to those suffering from candida that it is possible that by changing your micobiome you could also see a reduction of candida without the use of pharmaceuticals. Unfortunately its not likely as simple of a case for most people because we were not just inoculated with a small amount of candida. Our hormones, lifestyle, genes, and food choices over the course of years has created a hospitable home for candida to live in and it takes a lot of dedication to keep candida flare ups from reoccurring.

If you want support during your health journey reach out for one on one guidance.


[1] Schulze, J., & Sonnenborn, U. (2009). Yeasts in the gut: from commensals to infectious agents. Deutsches Arzteblatt international, 106(51-52), 837–842.

[2] No author, "Gestational Diabetes." The Mayo Clinic, Aug. 26, 2020,

[3] VH Matsubara, Treatment with probiotics in experimental oral colonization by Candida albicans in murine model (DBA/2). Oral Diseases, Volume 18, Pages 260-264.

[4] Butler MJ, Perrini AA, Eckel LA. The Role of the Gut Microbiome, Immunity, and Neuroinflammation in the Pathophysiology of Eating Disorders. Nutrients. 2021; 13(2):500.

Take a few moments to watch this great video from a CalTech researcher who explains how the gut could influence mood!