The Human Microbiome: Defining What It Is and What It Does

June 6, 2023

The human microbiome is a largely misunderstood yet crucial part of our health. The microbiome is made up of bacteria and other microbial material that live on and inside of us. We contain trillions of these microbes, in fact we contain more microbial DNA than human DNA.

Don’t know much about the microbiome? Fear not, we going to tell you everything you need to know about the microbiome in the following sections:

  • Microbiome definition
  • Types of microbiomes
  • Types of bacteria and microbes
  • What does the microbiome do?
  • What conditions are associated with the microbiome?
  • Microbiome intervention: FMT and bacterial therapies
  • Learn more about the microbiome

Let’s start by better defining what the microbiome is.

Microbiome definition

The microbiome consists of all of the bacteria, fungi, protozoa and viruses that live in and on the human body. The microbiome exists within certain niches in the body; for example, there is the gut microbiome, skin microbiome and vaginal microbiome. Each are structurally distinct and play a different role within their niche.

Microbiome composition and health is affected by factors that include diet, stress, geography, and ancestral background. And these different microbiomes play an important role in key bodily functions like digestion, immune response and brain health(gut-brain axis).

Different microbiomes and their functions

The microbiome exists within different niches in the body. Each microbiome niche has a unique microbial composition and a specific function within the body. The gut microbiota for example plays a large role in digestion, while the skin microbiome can protect against skin infections.

Gut microbiome

The gut microbiome is the densest of our microbiomes. There are trillions of bacteria living in our gut alone. Because it is such a robust microbial community, it is incredibly important to our health and affects many areas of the body beyond just our gut.

The gut microbiome has responsibilities in food digestion, immune regulation and mental health (90% of serotonin is created in the gut). And imbalances in the gut microbiome have been connected to many conditions including IBD, Obesity and Autism.

Skin microbiome

The skin microbiome or the skin flora, lives on us, rather than inside of us and it may be the most diverse of the microbial sites. When healthy, the skin microbiome can act as a protective barrier to skin infections and other skin ailments. Its imbalance can cause everything from eczema and dandruff to acne.

Oral microbiome

The oral microbiome is made up of about 700 microbial species. It plays an important role in the digestion of food. A healthy oral microbiome is associated with good dental health and a lower risk for cavities and gingivitis.

As it is the initial point of entry into the digestive tract and respiratory system, an unhealthy oral microbiome can have effects beyond the mouth. The oral microbiome can be negatively impacted by poor oral hygiene practices, smoking and tobacco use,  and consumption of acidic and sugar rich foods.

Other microbiomes

Microbiomes also exist in the vagina, ear canal, nose - basically every area of the human body. Each of these microbiomes has a specific population of bacteria and assist with functions specific to their niche.

The full breadth of the microbiome is not yet fully understood. The effects of the bacteria and other microbes that live within us still need to be studied, but early research is showing the enormous impact these communities have and their potential to aid in or impair our health.

Types of bacteria and other microbes

Each microbiome has a unique makeup and the combination of microbes in the body can hugely impact someones health. Certain bacteria in the body can make the difference between getting sick or not. Though the exact relationship between certain bacteria and illnesses not yet fully understood, there remains an appreciation for their roles in some human illness.

Types of intestinal bacteria

There are four main types of intestinal bacteria that live within the human gut. They are the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. Bacteroides make up 30% of the human gut flora, suggestion they are particularly important to host health.The relationship between these bacteria and host is symbiotic.

While people can survive without gut flora, they provide many useful functions to human health. And the imbalance of any the above mentioned groups of bacteria can have a great impact on the well being of the host.

What does the microbiome do?

The microbiome plays a key role is some very important bodily functions. It assists with immune system regulation, mental health and digestion. Though we are only at the beginning of understanding what other roles the microbiome plays in the body, scientists are clear that it does affect the following systems.  

Immune system regulation

The microbiome plays a role in developing and maintaining the immune system.Gut flora assists in maintaining homeostasis in the immune system by fighting off harmful pathogens, put simply good bacteria fights off bad bacteria. It has also been noted that dysbiosis of the gut microbiota can affect the functionality of the immune system and lead to autoimmune diseases.

Gut-brain axis

The bidirectional relationship between the GI tract and the brain is undeniable. There are clear ways in which the gut and brain are connected, for example the vagus nerve runs signal from the gut to brain and vise-versa to signal hunger. Research into the gut-brain axis is moving quickly and might help us better understand brain function.

Though there are some clear get-brain connections, there are also many others that are less understood. Pathways that might be key to understanding the functions of conditions such as Autism, Parkinson's and depression.

Digestion and food breakdown

Until recently scientists believed that the human body was fully responsible for digestion of food but it turns out the bacteria in our gut plays a large role in what we are able to eat and digest. Bacterial enzymes in our gut can break down complex sugar other food molecules into fuel. These bacteria can also produce vitamins in the body, making them more essential than previously realized.

What conditions are associated with the microbiome?

There are a number of conditions that have known associations with microbiome. These conditions seem to be related to dysbiosis of the microbiome. Dysbiosis is defined as an imbalance of microbial material in the body. Those who suffer from the following conditions are more often affected by such microbial imbalances.

  • Arthritis

The exact microbes that are associated with each of the proceeding conditions are not yet known. More study of the microbiome must be done to understand what roles specific bacteria play in certain conditions. As of now only the association of microbiome and disease is fairly inexact.

Microbiome intervention: FMT and bacterial therapies

With an increase focus of the microbiomes role in health comes an increase focus on treating the microbiome. One of the most intriguing and promising treatments for dysbiosis is a practice called Fecal Microbiota Transplantation (FMT). The treatment uses healthy stool to restore a sick microbiome to health.

What is FMT?

Fecal transplants are a therapy involving the implantation of stool from a healthy donor into the gut of a person with a microbiome in dysbiosis. The therapy has been around for some two thousand years, but has only recently come into common practice for the treatment of Clostridium Difficile Colitis.

Though most widely used for the treatment of C-Diff (for which it has a 90% cure rate), FMT is also being explored as a treatment for many different microbiome related conditions. Studies are underway for Ulcerative Colitis, Crohn’s, Autism, Obesity, Parkinson’s, etc.

How does FMT treat the microbiome?

FMT treats the microbiome by re-establishing balance of bacteria within the gut. It works by transferring healthy microbes from the donor to the recipient. In some cases the good bacterium is used to stave off the bad bacteria and in other cases the good bacteria simply helps repopulated lost bacteria.

Learn more about the microbiome

How to Improve Gut Microbiome Health: Development from Infant to Adult

The microbiome is nearly fully developed by the age of three. Learn more about how the microbiome is developed and what you can do to keep it healthy from birth to beyond.

No Guts, No Glory: How Microbiome Research is Changing Medicine

Learn more about how scientist are harnessing the power of the microbiome to treat and prevent illness.

What is Dysbiosis: How Bacteria in Your Body Disrupts Your Health

Dysbiosis can develop from poor diet or after a round of antibiotics. Learn more about its causes and consequences in this article.