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Microbiome vs. Metagenome: How Do They Differ?

With respect to microbiome science, there's a lot of confusion surrounding the difference between the microbiome and the metagenome (or microbial genome). Although these terms are used within the same context, they differ. Let's examine the meanings of these terms and how they differ from one another scientifically.

Microbiome vs. Metagenome: What is the Microbiome?

When you hear the word microbiome, you might think of the bacteria that live in your gut. That's partly correct! Your gut microbiome is a collection of bacteria and other microorganisms that reside in your digestive tract.

But did you know every part of your body has a microbiome?

Microbes exist in body parts and organs including inside your mouth, under your nails, and even on top of your eyelids. For example, your gut has a microbiome that’s unique from the microbiome in your lungs, saliva, biliary tract, mammary glands, and other organs.

Whether your microbiome is beneficial or harmful from a health standpoint depends on what kind of microbes live in each habitat. While some microorganisms that make up the gut microbiome might cause disease, others have beneficial roles.

For example, some bacteria in the gut microbiome boost nutrient absorption and are beneficial for immune health. Surprisingly, almost 80% of your immune system lies in your gut and the gut bugs, or microorganisms, that live there influence how your immune system functions.

What is the Metagenome?

Now that you know what microbiome refers to, what does the term metagenome mean? The metagenome is the total of the genetic material present in a microbiome.

Thus, the microbiome is the population of microorganisms that make up a habitat, like your gut microbiome, while the metagenome is the set of genes found in that population of microorganisms.

As you know, genes are the DNA, or genetic material within the cells of each organism. DNA codes for the proteins that control how cells function and how the human body functions as a whole.

The proteins that genes encode after different behaviors and physiological states within in a cell and affect the function of the human body as a whole.

So, a microbiome is a population of microorganisms, while the metagenome is the complete set of genes within that population.

The metagenome represents all the combined genetic information within a microbiome. This includes all the DNA from resident microbes, including bacteria, fungi, and viruses.

Microbiomes Change Over Time

The microbes, or bacteria, fungi, and viruses, which make up the microbiome are living organisms and they change over time and in response to environmental factors.

The composition of your gut microbiome, for example, varies with factors like age and gender, but also lifestyle factors, such as diet, exercise habits, and stress levels. These factors can alter the microbiome in a way that promotes disease, which is why maintaining a healthy microbiome is so important.

Lifestyle and Age Affect Your Microbiomes

Microbiome changes begin early in life. An infant’s microbiome is mostly made up of bacteria found in breast milk. (such as Bifidobacterium). This changes to more stable communities by around three years old.

Changes again occur around the time of preschool. Exposure to a variety of microbial sources such as pets and other children at school or daycare shapes these changes.

The composition of an individual’s gut microbiome also impacts digestive and immune system function. That’s why it’s important to maintain a healthy gut microbiome.

Although research into what an optimal gut microbiome health looks like is still in its infancy, scientists believe that a diverse microbiome, consisting of many types of bacterial species, is healthier than a gut microbiome composed of a limited number of species.

Feed Your Gut Microbiome Well

Scientists point out that feeding your gut microbiome a variety of fiber-rich, plant-based foods helps support the healthy bacterial inhabitants that live there.

Some types of fiber are “prebiotic,” meaning they feed healthy gut bacteria and help maintain a diversity of beneficial bacteria.

Also, antibiotics can disrupt a healthy gut microbiome, sometimes for many months. So, it’s not a smart idea to take antibiotics unless you need them.

The Bottom Line

Now you know what the terms microbiome and metagenome mean and how they differ. The microbiome refers to the microorganisms that make up a particular part of the body, like the gut, while metagenome refers to the collective information (in the form of DNA) they carry.

Hopefully, you can now use these terms with confidence.


This content is for informational purposes only and does not substitute for formal and individualized diagnosis, prognosis, treatment, prescription, and/or dietary advice from a licensed medical professional. Do not stop or alter your current course of treatment. If pregnant or nursing, consult with a qualified provider on an individual basis. Seek immediate help if you are experiencing a medical emergency.