Updated 17th April 2024

The gut microbiome: Why is it important for your health?

Share this article

  • Share on Facebook
  • Share on Twitter
  • Print this page
  • Email this page

Trillions of bacteria and other microbes live in your gut and make up your individual gut microbiome. These microbes influence many aspects of your health, including your immune system, and they help digest the food you eat.

Your diet is key to making sure that your gut microbiome is in good shape to support your health. Knowing which microbes are in your gut can help you pick the best foods to eat that feed your microbes.

In this article, you can find out what the microbiome is and what it does, why it’s important for your health, and how the foods you eat shape your unique microbiome.

Fast facts on the gut microbiome:

  • Your gut microbiome is the collection of all the genetic material from the microbes in your gut.

  • It contains around 3 million genes.

  • Gut microbes digest fiber from your food, shape your immune system, and help protect you from pathogens.

  • Your diet is a key factor in determining which microbes are in your gut.

  • Fiber-rich, minimally processed foods support a healthy microbiome.

  • Ultra-processed foods promote the growth of harmful microbes.

What is the gut microbiome?

There are trillions of microbes that live in your gut. Bacteria are the most common type. But there are also viruses, fungi, and protozoa, which are small organisms made up of single cells.

Together these make the gut microbiota, the collection of all the organisms that live in the gut.

The term gut microbiome actually refers to all of the genetic material from each of the microbes added together, but the terms microbiota and microbiome are often used interchangeably.

Everyone’s microbiome is different. Diet, drugs, genetics, the way you were born, and your age all play a role in determining which microbes live in your gut.

Research from the world’s largest, in-depth nutritional study, called the PREDICT program, found that identical twins have around 34% of their gut microbes in common. People who are unrelated, meanwhile, share around 30% of their gut microbes.

Discover your unique biology

Understand how your body responds to food with ZOE

Take the first step
ZOE Test Kit

Just like no two fingerprints are the same, each person’s gut microbiome is totally unique. 

In total, scientists estimate that there are around 3 million genes in the gut microbiome. By contrast, the human genome has about 23,000 genes.

Your microbes are more than just passengers. Their vast set of genes carry the code for many functions that are vital for your health. But some microbes are foes, rather than friends. And the foods you eat can help tip the balance in your favor.

What does the gut microbiome do?

The gut microbiome has a number of jobs, including:

•   extracting nutrients from food

•   digesting fiber and proteins from food

•   making vitamins B and K

•   shaping the immune system

•   protecting the body from pathogens

One key job the gut microbiome performs is to digest fiber from the food you eat, as your body can’t digest fiber on its own.

Your microbes turn fiber into molecules, or metabolites, such as short-chain fatty acids (SCFAs).

These metabolites are important for a range of things, including gut health, blood sugar and blood fat control, appetite control, and the immune system.

Gut microbes can also digest protein and make B vitamins and vitamin K.

Researchers estimate that your gut microbiome can produce thousands of different metabolites.

Studies in mice have shown that animals lacking a microbiome don’t develop a normal immune system, highlighting how crucial your gut microbes are.

They work together with your immune cells to protect you from infection and disease.

Your microbes also stop the growth of pathogens in your gut. They do this by competing for the space, maintaining the health of the intestinal barrier, and by producing molecules that kill invading pathogens.

Why is the gut microbiome important for your health?

Scientists have found over 1,000 different species of bacteria in gut microbiome samples, although each individual only has around 160 of these species in their gut.

Three phyla or groups of bacteria make up the most abundant members of the gut microbiome.

They are:

•   Firmicutes, including Lactobacillus

•   Bacteroidetes, including Prevotella

•   Actinobacteria, including Bifidobacterium

The precise mix of microbes in your gut directly influences your health. This is because some microbes are beneficial and others harmful.

Tipping the balance in favor of harmful species can contribute to a number of health conditions, including obesity and autoimmune diseases.

Join our mailing list

Get occasional updates on our latest developments and scientific discoveries. No spam. We promise.

Scientists also believe that having a lower diversity of microbes in the gut, meaning fewer different species, can put you at risk of disease.

People with a lower gut microbiome diversity are more likely to develop inflammatory bowel disease, celiac disease, type 2 diabetes, eczema, and psoriatic arthritis.

That’s why having a diverse microbiome with many beneficial microbes is important for your health.

In the podcast below, ZOE cofounders Prof. Tim Spector and Jonathan Wolf talk with gastroenterologist Dr. Will Bulsiewicz about how your gut microbiome shapes your health.

How does food impact your gut microbiome?

Research has shown that the foods you eat have a major influence on your gut microbiome.

A typical Western diet — which is high in sugar, fats, and ultra-processed foods and low in fiber — can be detrimental to the microbial diversity in the gut.

One study found that mice that received a diet low in fiber for 4 weeks saw a reduction in the levels of 60% of the microbial species in their gut. When the scientists kept feeding the mice this diet, the loss of microbial diversity became permanent within four generations.

Data from the PREDICT Program has found clear links between participants’ diets and their gut microbiome profile.

Eating ultra-processed foods — which are typically high in chemical additives, sugar, fat, and salt and low in fiber — was associated with higher levels of potentially harmful, or “bad,” microbes.

On the other hand, the scientists saw more beneficial, or “good,” microbes in the guts of volunteers who ate a diet that heavily featured plant-based and minimally processed foods.

How to look after your gut microbiome

You can support your gut microbiome by feeding it the foods that your “good” microbes like.

Prof. Tim Spector, a leading microbiome researcher at King’s College London in the U.K. and co-founder at ZOE, goes into more detail in this article on his five top tips for a healthier gut microbiome.

Based on his advice, here are some things to try:

•   Eat more plant-based foods.

•   Include foods in all different colors.

•   Try fermented foods like kimchi or yogurt.

•   Leave gaps between eating.

•   Cut down on ultra-processed foods.

However, there really is no one-size-fits-all approach to nurturing the beneficial microbes in the gut because we all have unique gut microbiomes.

Understanding which microbes live in your gut can help you understand what foods can help them thrive. The ZOE program identifies the best foods for you by analyzing your gut microbiome in combination with your blood sugar and fat responses.

Using the most advanced tests — based on those used in the PREDICT studies — and cutting-edge science available, ZOE helps you pick foods to improve your gut health naturally.


The trillions of microbes in your gut make up the gut microbiome. They are important for your health, and the exact contents of your gut microbiome is unique to you. 

A microbiome that lacks diversity and features potentially harmful microbes can increase your risk of developing a range of health conditions. On the other hand, a healthy diet that is rich in fiber and low in ultra-processed foods can support a diverse microbiome.


A human gut microbial gene catalog established by metagenomic sequencing. Nature. (2010).


Diet-induced extinction in the gut microbiota compounds over generations. Nature. (2016).


Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. (2018).


Interaction between microbiota and immunity in health and disease. Cell Research. (2020).


Role of the gut microbiota in nutrition and health. The BMJ. (2018).


What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. (2019).


Share this article

  • Share on Facebook
  • Share on Twitter
  • Print this page
  • Email this page