What is the microbiome and microbiota?

Last modified: 07-29-2025

You hear it more and more often: the microbiome is important for your health. But what exactly is the microbiome? And what’s the difference between the microbiome and microbiota? These terms are often used interchangeably, but they don’t mean the same thing.

In this article, we’ll explain it step by step. That way, you’ll better understand what’s living in and on your body and why it matters for your health.

Microorganisms

To really understand what the microbiome is, we need to start at the beginning. All over and inside your body live millions of tiny, living creatures: microorganisms. They’re so small you can’t see them with the naked eye, only with a microscope.

There are different types of microorganisms: bacteria, fungi, yeasts, protozoa, and archaea. They live in every part of your body, like your mouth, skin, and gut. Each microorganism has its own job. Some protect you from getting sick, while others help you digest your food or go to the toilet regularly. Some types, if too many are present, can actually cause problems.

Another word for ‘microorganism’ is microbe, but they mean the same thing.

What is the microbiota?

As we mentioned, microorganisms live in almost every organ in your body. When you zoom in on one specific area — like your gut — the group of microbes living there is called the microbiota.

So for example, the microbes in your gut are called the gut microbiota.

In short: microbiota refers to all the microorganisms living in one specific part of your body.

So what is the microbiome?

The term microbiome sounds similar to microbiota, but it means something slightly different.

The microbiome includes the microbiota (all the microbes), the DNA of those microbes, the substances they produce (like enzymes), and the way they interact with each other and with your body

So in simple terms: the microbiome is the entire ‘world’ of microbes, including what they do and how they respond to each other and to you.

Take the gut as an example. The gut microbiome includes all the bacteria, fungi, and other microbes, their genetic material (DNA), and their influence on each other and on your health.

Read also: This is how gut bacteria influence your health

Why is your gut microbiome so important for your health?

Your gut is home to billions of microorganisms, most of which are bacteria. You get many of these during birth, and some stay with you for life.

They perform key functions, such as digesting food, supporting your immune system, producing vitamins, and even influencing how your brain works.

There are an estimated 4,000 types of gut bacteria. Most people have about 500 types, and about 40 types are found in nearly everyone.

But not all bacteria are helpful. Some can be unwanted, and if there are too many of them, they can cause problems like diarrhea, bloating, abdominal pain or excess gas. They can also cause issues elsewhere in the body, such as acne or other skin problems, eczema or rashes and unexplained fatigue.

Read also: Symptoms of gut microbiome imbalance: How it affects gut health

How is the microbiota formed?

You’re exposed to bacteria for the first time during birth. These microbes live on your mother’s vagina and skin, and they’re transferred to your body during delivery. Bacteria are also present in breast milk. When a baby drinks milk, those bacteria enter through the mouth and move into the gut. Eventually, they also reach the anus, and some are excreted through poop.

Toddlers explore the world by licking or chewing on just about everything. It may seem unhygienic, but this is how they’re exposed to more types of bacteria. When children start eating solid foods, the microbiome shifts again. Some bacteria thrive on certain foods, while others disappear.

Your genes also play a role. They influence which bacteria can survive and which ones don’t suit your body.

Usually, your gut microbiota is mostly developed by the time you’re 2 to 3 years old. After that, it can still change, due to food, illness, stress, or medication.

In older adults, the microbiome often becomes less diverse, which can affect overall health.

What bacteria live in my gut?

Your gut microbiome is completely unique. Some bacteria are very helpful, others are neutral, and some can cause problems if they grow too much.

If you’re experiencing gut issues and want to address them, it’s important to know which bacteria are living in your gut. That knowledge helps you look for targeted solutions.

A microbiome test can give you that insight. It doesn’t just show a few “good” or “bad” bacteria; it gives a full overview of all the microbes living in your gut.

Only with that information can you truly understand your gut health, and take meaningful steps to improve it through food and lifestyle.

Sources:

Shkoporov, A. N., & Hill, C. (2019). Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell host & microbe, 25(2), 195-209. doi: https://doi.org/10.1016/j.chom.2019.01.017

Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. The Biochemical journal, 474(11), 1823–1836. doi: https://doi.org/10.1042/BCJ20160510