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The Paleo Nurse ✚ Presents: The Role of Gut Flora in Health Part 1


All disease begins in the gut.” – Hippocrates.

Over 2,400 years after the father of modern medicine made this claim, we are now re-discovering the role of gut flora, and just how true that statement was.  The digestive tract is home to 100 trillion microorganisms, known as the gut flora.  The majority of these microorganisms are bacteria, with a small percentage consisting of fungi and protozoa.  The functions of the gut flora are complex enough to resemble those of an organ, leading some researchers to refer to the gut flora as a “forgotten organ”.  Indeed, the gut flora plays a number of roles so vital to the human body that if the gut were to be sterilized, long-term survival would be unlikely.

Types of Gut Flora

There are three main categories of microorganisms found in the gut:

1.) Essential Flora:  This is the “friendly” bacteria that is found in the gut.  In the healthy individual, essential flora dominates and controls other types of less desirable microorganisms.  When functioning normally, this type of flora is responsible for conducting numerous roles that keep the body healthy.

2.) Opportunistic Flora:  This group of microbes is found in the gut in limited numbers that are strictly controlled by the essential flora in the healthy individual.  This type of flora is capable of causing disease if the essential flora becomes compromised and is unable to control the growth and numbers of opportunistic flora.

3.) Transitional Flora:  These are various microorganisms that are introduced into the body through eating and drinking.  When the essential flora is healthy and functioning normally, this type of flora will pass through the digestive track without causing harm.  However, if the essential flora is damaged, this group of microbes can cause disease.

Role of Essential Gut Flora

Beyond controlling the population of opportunistic and transitional flora, essential gut flora plays an active role in the normal digestion and absorption of food by producing enzymes that aid in the process of breaking down proteins, carbohydrates, and fats.  It also aids in the transportation of minerals, vitamins, water, and other nutrients through the gut wall into the bloodstream for use by the body.  Certain types of essential flora are capable of manufacturing nutrients such as vitamins K2, B1, B2, B3 B6, B12, folic acid, pantothenic acid, and various amino acids.  In addition to producing these nutrients to be used directly by the body, the essential flora provides nourishment to the cells of the intestinal wall that have primary responsibility for digesting and absorbing food.  When the essential gut flora is compromised and not functioning normally, it is common for the individual to become malnourished and have multiple nutrient deficiencies and food intolerances.  In other words, in order to remain healthy or restore health, healthy essential flora is necessary.

In the last decade or so, the importance of the gut flora to immune function, overall health, and disease has become an emerging area of focus.  Although there is still much to be learned about the role of gut flora in immune function, it is becoming increasingly clear that disease (and health) really does begin in the gut!  Studies have shown that the gut flora has a profound influence on the development and maturation of the immune system after birth (Bouskra et al., 2008; Macpherson & Harris, 2004).  In addition, it has been estimated that approximately 80-85% of the immune system is located in the gut.

In the next post in this series, we will continue to explore the role of the essential gut flora in immune system function.  We will also discuss how to maintain healthy gut flora.  Stay tuned



Bouskra D. et al. (2008). Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 456(7221), 507–510.

Macpherson, A.J. & Harris, N.L. (2004). Interactions between commensal intestinal bacteria and the immune system. Nature Reviews: Immunology, 4(6), 478 – 485.

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