What is a gut microbiome test and how can it help you?

A gut microbiome test can tell you what types of microbes live in your gut and their links with better or worse health outcomes. Your gut microbiome affects many parts of the body, including digestion, immunity, and your nervous system.

Your gut is also home to trillions of bacteria and about 3 million genes — and this genetic material is unique to you.

Everyone has a unique microbiome, even identical twins. This uniqueness can, in part, explain why a diet that is “healthy” for one person can sometimes be harmful (or at least not ideal) for another.

In fact, ZOE’s research shows that everyone has their own unique responses to different foods.

We know that having good gut bacteria is key for our overall health. The links between an unbalanced microbiome and conditions like inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity, and diabetes are well-established

ZOE’s PREDICT program, which is the largest nutritional study of its kind, identified which microbes are “good” — associated with positive health indicators — and which are “bad” — associated with poor health indicators.

Researchers also know that you can alter your gut microbiome by changing what you eat.

Knowing the composition of your microbiome can help you take steps in the right direction to limit harmful bacteria and encourage overall gut health.

What is gut microbiome testing?

Simply put, gut microbiome testing uses a stool (poop) sample to find out which microbes live in your gut. This includes bacteria, fungi, and viruses.

With information from this test, experts can also recommend personalized dietary advice. 

If you are taking an at-home gut microbiome test, you will receive detailed instructions on how to collect the stool sample. You will likely receive a special container to put the sample in, which you’ll then send to the lab for testing. 

Scientists in a lab will then extract DNA from your stool sample and sequence (i.e., “read”) it, using advanced equipment.

After they analyze the data, they will be able to tell you the estimated composition of your gut microbiome.

How knowing your gut composition can help

The microbes in your gut help to digest your food and use food components for their own metabolism. This means the foods you eat help determine what types of microbes live in this system. 

Fiber-rich foods, for example, are vital for fiber-eating bacteria that are associated with a healthy gut microbiome. 

On the other hand, ultra-processed foods can encourage harmful bacteria to grow and upset the gut’s delicate balance.

In the short term, eating processed foods like ice cream or potato chips might cause a temporary lift in blood sugar or even a mild upset stomach, but it is usually nothing to worry about. 

In the long term, however, an ultra-processed diet provides the ideal conditions for “bad” microbes to thrive.

These bad microbes likely increase the risk of poor health outcomes, such as obesity, type 2 diabetes, or even mental health conditions like depression.

Authors of a 2019 article in the journal Nature Reviews Microbiology summarized the recent progress in the scientific community: We now know that an individual’s diet is a “key determinant” in their microbiome, which, in turn, impacts on how they respond to the food they eat.

‘Good’ and ‘bad’ bugs

To help you understand your individual profile, ZOE’s research identified 15 “good” and 15 “bad” types of microbes through the largest study of its kind, combining nutrition, microbiome testing, and cardiometabolic health assessment. 

These “good” and “bad” microbes are each linked to “good” and “bad” health markers. The research also identified the food most associated with high or low levels of these microbes.

Once you know which microbes you have and what they like to eat, you can change your diet to feed the good microbes and encourage their growth while preventing the bad ones from taking over. 

You can take a free quiz to learn how you can change your diet in line with your unique microbiome.

While gut microbiome testing is not a diagnostic test, it can be very useful if you are interested in knowing more about your gut health. 

However, researchers do see the potential for gut microbiome testing to reduce the time and effort it takes to diagnose gastrointestinal issues and to shed light on better treatment options in the future.

How do gut microbiome tests work?

Gut microbiome tests have come a long way since doctors began using them. ZOE uses the latest in sequencing technology — a process called deep shotgun sequencing.

In deep shotgun sequencing, the DNA is first cut into tiny fragments. These are then sequenced or "read," and the "readings" are pieced together to form a completed puzzle of your microbiome.

The aim is to have a complete list of all the microbes in your gut (including bacteria, archaea, fungi, and viruses), which microbial genes (“functions”) these microbes possess, and to know how many of each microbe or gene there are.

Older-style 16S rRNA tests are useful in some cases, but they can’t tell you which individual species of bacteria are living in your gut, and they can’t see all of the individual genes and functions present in the microbiome. 

These gene sequencing tests completely miss viruses, and they need to be applied twice with a different variant to identify fungi.

In 2019, researchers argued that the benefits of deep shotgun sequencing mean it is quickly replacing the older style tests.

They also noted that it comes with more technological challenges, which makes it essential to only use tests from reputable organizations.

What does a microbiome test tell you?

There are many types of gut health tests available, and not all of them provide the same results. 

Some tests can tell you the overall diversity of the gut bacteria, since a more diverse microbiome is often — but not always — a sign of good gut health.

Other types will look for specific bacteria, viruses, or fungi if a doctor is trying to diagnose a particular illness.

ZOE’s at-home gut microbiome test kit looks for the 15 “good” and 15 “bad” types of bacteria to provide you with your unique score. The ZOE test also provides a list of the many other microbes that exist in your gut.

Some microbiome tests offer additional information. The ZOE test, for example, will also provide:

  • a profile of your body’s response to fat and sugar

  • personalized dietary advice, so you know how to act on the new information about your gut microbiome and food responses

The ZOE program can provide this advice because it draws on data from over 10,000 people and uses artificial intelligence to suggest the best food swaps for your body. 

A gut microbiome test can tell you a lot about your digestion and gut health, but it will not be able to diagnose diseases. Your microbiome is just one piece of the complex puzzle that makes up your body and overall health. 

If you are experiencing any digestive problems or other symptoms, it is best to speak to a doctor before doing an at-home microbiome test.


Gut microbiome tests can tell you what types of bacteria, archaea, viruses, and fungi are in your gut and how they might be affecting your health. 

In most cases, you can do the test from the comfort of your home by simply collecting a stool sample and sending it to a specialized lab. Scientists will analyze the sample in the lab and send you the results.

At ZOE, we use the latest in gut microbiome testing to give you a full profile of the “good” and “bad” microbes living in your gut. With these insights, we also provide comprehensive advice on how to change or maintain your diet.

Simple dietary changes can improve the composition of your gut microbiome by providing the right conditions for those “good” gut bacteria to thrive.

If you’re still curious and want to discover more about how your gut microbiome supports your overall health, check out our Health Academy.

If you’re ready to find out which microbes are affecting your health and how you can modify your diet, try ZOE’s at-home test kit.


Diet–microbiota interactions as moderators of human metabolism. Nature. (2016).


Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. (2016).


Microbiome 101: Studying, analyzing, and interpreting gut microbiome data for clinicians. Clinical gastroenterology and hepatology (2019). 


Part 1: The Human Gut Microbiome in Health and Disease. Integrative Medicine: A Clinician’s Journal. (2014). 


Revisit gut microbiota and its impact on human health and disease. Journal of Food and Drug Analysis. (2019). https://www.sciencedirect.com/science/article/pii/S1021949819300122

Shotgun metagenomics, from sampling to analysis. Nature Biotechnology. (2017).


The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology. (2019).