What are the microbiome and microbiota?

Last updated: 10-09-2025

You hear it more and more often: “healthy guts are the foundation of your health” or “your gut is your second brain.” But what do people actually mean by that? And why are scientists constantly talking about the microbiome or microbiota? It may sound complicated, but it’s really about the millions of tiny residents living in your gut: bacteria.

In this blog, we explain what gut bacteria are, what the microbiome (or microbiota) actually is, how it forms from birth, and why this invisible world is more important than you might think.

Gut bacteria: your hidden co-residents

A gigantic community lives in your intestines: trillions of bacteria, fungi, yeasts, and other microorganisms (also called microbes). You can’t see them with the naked eye (but you can with a microscope), yet together they weigh about one and a half kilos — about as much as your brain!

These gut residents work hard. They help digest your food, produce vitamins, train your immune system, and protect you from intruders. Think of them as a bustling city: some bacteria are the construction workers, others the sanitation crew, and still others the police keeping order. Without these ‘citizens,’ your body simply wouldn’t function properly.

What is the microbiome? And what is the microbiota?

The terms microbiome and microbiota are often used interchangeably, but they don’t mean exactly the same thing.

Microbiota: all the microorganisms (such as bacteria, yeasts, and other microbes) living in a specific place in or on your body. For example, the gut microbiota (all microbes in your intestines) or the skin microbiota (the microbes living on your skin).

Microbiome: this goes a step further. It refers not only to the collection of microbes themselves, but also their DNA, the substances they produce (such as enzymes and metabolites), and the ways they cooperate and communicate.

In short: the microbiota are the residents, and the microbiome is the entire habitat including everything those residents do and produce.

In everyday language, people often say gut flora, but that’s not actually correct. Plants don’t grow in your intestines — microbes do.

How does your microbiome develop?

Your microbiome doesn’t form later in life; it starts developing at birth. During a vaginal delivery, a baby receives a substantial dose of the mother’s bacteria. With a C-section, that transfer is different: the starting point is often skin and environmental bacteria, which sets a different baseline for your microbiota.

In the first months, breastfeeding plays a big role. It contains special sugars that the baby can’t digest but are intended to feed certain beneficial bacteria – such as Bifidobacteria –. And let’s be honest: babies who put everything in their mouths, from toys to sand, may seem messy, but that actually helps make their microbiome more diverse.

Your genes (genetic material) also have a say: they partly determine which bacteria can more easily settle in your gut. Once solid foods are introduced, the microbiome shifts again and different species become more important. Around age three your microbiome is fairly stable, but it remains influenced throughout life by diet, stress, medication, and lifestyle.

Why is your microbiome important?

More and more research shows that your microbiome does more than just assist with digestion. Here are some of the most important functions:

• Digestion: gut bacteria help break down food and make nutrients available.
• Energy: they produce short-chain fatty acids that fuel your intestines.
• Vitamins: certain bacteria produce vitamins such as vitamin K and some B vitamins.
• Protection: they keep pathogens at bay by occupying the best spots in your gut.
• Communication: they interact with your immune system and your brain – the so-called gut-brain axis.

In short: your microbiome isn’t a side note, but a key player in your health.

Also read: How gut bacteria influence your health

Also read: Symptoms of a disrupted gut microbiome: how it affects gut health

How do you keep your microbiome in balance?

Your microbiome is sensitive to how you live. Things that influence it include:

• Diet: fiber-rich foods (vegetables, fruit, whole grains) feed beneficial bacteria. Lots of sugar and ultra-processed foods mainly fuel the undesirable ones.
• Variety: the more diverse your diet, the more diverse your gut residents become. And variety roughly equals resilience.
• Exercise: regular movement supports a healthier gut.
• Stress: chronic stress can throw your microbiome out of balance.

But… everyone’s microbiome is unique. And that’s important to know! What works well for one person might do nothing for another. One person may respond well to certain foods, while another experiences bloating or gas. That’s why there’s no universal ‘perfect diet’.

Read more: What does a healthy microbiome look like?
 

What can you do yourself?

No two microbiomes are the same; it’s as unique as your fingerprint. That’s why scientists and doctors increasingly look at personal analyses.

A microbiome test shows which bacteria live in your gut, who plays the leading role, and who might be taking up too much space. With that knowledge, you better understand why your gut sometimes protests (rumbling, bloating), or why you’re symptom-free. It gives you a behind-the-scenes look at your own gut city and tools to better nourish and care for those residents.

So we won’t hand you a superficial list of only ‘good’ or ‘bad’ bacteria, but a complete overview of all bacteria living in your gut, including tailor-made tips & tricks on how to influence them. Only with this information can you truly say something meaningful about your gut health — and take targeted action with diet or lifestyle.

In summary

Gut bacteria aren’t an invisible side issue, but a complete community working around the clock for your health. Your microbiome helps with digestion, protects against intruders (pathogens), and even communicates with your brain.

What’s special is that your microbiome is shaped from birth, yet you can influence it throughout life via diet, stress, exercise, and lifestyle. Because every microbiome is unique, there’s no one-size-fits-all “how to keep my gut healthy” approach. That’s exactly why it’s interesting to discover how your personal microbiome works and which habits make the difference for you.

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