How Your Gut Flora Impacts Health

Flora is the scientific term for a group of plant or bacteria life, typically particular to a certain area. It is often contrasted with the term "fauna," which is used to describe the animal life of the same particular area. In the area of health and medicine, flora is the term used to describe the microorganisms that exist on or within the human body, such as the gut flora or the skin flora. When talking about flora in the context of the human body, the term refers to bacteria, yeast, and other fungi.

3D view of Gut Bacteria
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Gut flora refers to the world of microorganisms, predominantly bacteria, that populate our intestines. Research has been increasingly focused on trying to understand the role that the gut flora play in terms of human health. A variety of names are used to refer to this inner population of microorganisms:

  • Gut bacteria
  • Intestinal flora
  • Microbiota
  • Microbiome
  • Microflora

It has become exceedingly apparent that the gut flora plays an important role in both our health and our vulnerability to disease.


Babies are born with intestines that are believed to be either completely or mostly sterile. As they go through their mother's birth canal, they are exposed to the microorganisms of her vagina, which is the origin of the population of the microbiome. The microbiome is further populated by environmental exposure and intake of breast milk, formula, and ultimately food. These are the factors that populate the microbiome of babies that are born via cesarean section and don't travel through the birth canal. The makeup of the gut flora then continues to evolve throughout our lifespan.


The substances secreted through the process of digestion have an effect as to where gut bacteria proliferate. Stomach acid, bile acid, and pancreatic enzymes typically prevent the colonization of bacteria in the stomach or the beginning section of the small intestine. (Small intestinal bacterial overgrowth is a health problem in which excess bacteria are found in the small intestine.)

Therefore, gut bacteria are found to some extent in the last part of your small intestine, but overwhelmingly so in your large intestine. It is estimated that there are more than a thousand types of microbes in your body. (A 2015 study reported that these microbes make up anywhere from 25% to 54% of your stool.) This world of microorganisms is separated internally from your body through a single layer of cells on your large intestine—cells known as epithelial cells.


As stated above, your gut flora are key players in your health. Two of the most important roles have to do with immune system protection and metabolism. For these important functions, there needs to be an optimal preponderance of "friendly" bacteria. Let's take a look at each of these functions in turn:

Support for the Immune System

There appear to be two ways in which our gut bacteria support our immune system. The first is that helpful bacteria provide direct protection for the lining of our large intestines, keeping out substances that would be harmful to us. When this system is compromised, a state of increased intestinal permeability (leaky gut syndrome) may be present. The second is that favorable gut bacteria work with the immune system at the level of the lining of our intestines to fight against disease-causing bacteria or other substances.

Helpful Metabolic Effects

Our gut flora plays an important role in providing us with vitamins and other nutrients essential to our health. The microbiome also interacts with carbohydrates that were not digested in the small intestine (such as resistant starch and FODMAPs). This interaction provides further nutrients, encourages epithelial cell growth, and modulates fat storage.

Associated Health Problems

It is now recognized that a less than optimal composition of gut flora can contribute to health problems, both digestive and non-digestive. The health problems that for now appear to have direct links to an unhealthy balance of the gut flora, a state known as dysbiosis, include:

Caring for Your Gut Flora

Keeping your stress down, minimizing antibiotic use, and eating a well-rounded nutritious diet (including foods that are considered as prebiotics) all hold the potential for optimizing your gut flora. In addition, although the benefits are far from proven, probiotics may be of help and don't typically seem to make things worse. A procedure known as fecal microbiota transplantation appears to hold some promise in extreme cases for enhancing the health of the gut flora.

3 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Bull MJ, Plummer NT. Part 1: The human gut microbiome in health and disease. Integr Med (Encinitas). 2014;13(6):17-22. 

  2. Peterson LW, Artis D. Intestinal epithelial cells: regulators of barrier function and immune homeostasis. Nat Rev Immunol. 2014;14(3):141-53. doi:10.1038/nri3608

  3. Bull MJ, Plummer NT. Part 2: Treatments for chronic gastrointestinal disease and gut dysbiosis. Integr Med (Encinitas). 2015;14(1):25-33.

Additional Reading

By Barbara Bolen, PhD
Barbara Bolen, PhD, is a licensed clinical psychologist and health coach. She has written multiple books focused on living with irritable bowel syndrome.