Updated 19th August 2026
Why ZOE's gut health test outperforms others
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ZOE has one of the largest microbiome databases on the planet and has also developed the best analytical tools to help our scientists understand this data. I want to take this opportunity to explain why our gut microbiome test, analysis, and score are way ahead of the competition.
I’ll also explain what we’ve already learned about the gut microbiome’s links to health and, importantly, what we’re yet to discover.
Thanks to ZOE’s PREDICT studies and our ZOE members, we have now analysed tens of thousands of stool samples.
This unparalleled dataset has helped us identify links between dietary patterns and the gut microbiome. It has also helped us spot links between certain species of bacteria and markers of poorer health.
Before getting into the details, I need to outline some caveats about language. It might seem subtle, but it’s essential to get it right:
Currently, we can say that X gut bacteria is associated or linked with markers of poorer health. But we can’t say that X gut bacteria cause poorer health We’re working on unpicking the causal relationship, but that will take more research.
However, our data shows strong, reproducible relationships between our diet, gut microbiome, and health markers. We believe there is a causal relationship, but we haven’t demonstrated that. Yet.
This is because a single species of microbe, like a single gene, is unlikely to be responsible on its own. Plus, some of the changes in the gut microbiome may be caused by disease rather than causing the disease themselves.
ZOE’s advanced gut microbiome test
Most companies that offer gut microbiome tests use a technology called 16s. This technique identifies bacteria by looking at the differences in just one gene. ZOE, however, uses something called shotgun metagenomic sequencing.
Rather than looking at a single gene, this technique allows us to “see” every single gene in every single microbe in the sample.
We analyse this genetic information with a tool called MetaPhlAn — pronounced “meta-flan.”
The latest version of MetaPhlAn, called MetaPhlAn4, can “see” about twice the number of species than the previous version. Unlike 16s, which focuses on just one gene, MetaPhlAn4 can look at more than 5 million marker genes.
A quick analogy will help you visualise the gulf between these two techniques: 16s is like trying to identify a species of mammal from a single hair — misidentification is very likely.
MetaPhlAn4, on the other hand, is like identifying a mammal from its hair, bones, teeth, internal organs, and a high-resolution photo of the whole animal — it’s much more reliable.
Here’s a real-world example: 16s can identify that a bacterium falls into the Firmicutes category.
But this won’t necessarily provide helpful information — there are hundreds of Firmicutes species; some are linked to markers of good health, and some are linked to markers of poor health. So, 16s provides severely limited information.
Unlike 16s, the detail provided by our techniques allows us to collect genetic information about bacteria that no one has seen before. It’s already helped us identify hundreds of gut bacteria that are entirely new to science.
Can you trust the results?
Some microbiome testing companies have been criticised because stool samples from the same individual can generate very different results. In other words, the tests are not reproducible. This is because most companies use 16s technology.
The fact that 16s tests are rarely reproducible explains why most companies don’t offer gut retests. Thanks to our cutting-edge technology, ZOE is different.
As part of our PREDICT1 study, we conducted two gut microbiome tests on around 100 individuals 2 weeks apart. We found that the tests were reproducible — the results were much more similar when conducted on the same person twice than between two individuals.
Combining threads
Understanding the precise relationships between gut bacteria and health is challenging work. ZOE’s scientists are weaving multiple threads of evidence together to steadily build a clearer picture.
Our research has identified the top 100 gut bacteria associated with important health measures.
Fifty of these were associated with poorer health markers and 50 species were associated with positive health markers.
Again, this doesn’t mean “bad” bacteria cause poorer health. Instead, it shows that people with X bacteria are more likely to have X risk factors for health conditions.
Thanks to ZOE’s recent METHOD study and gut retests, we have shown that following ZOE closely leads to significant, positive changes in the gut microbiome.
Specifically, we found that following a healthy diet that includes a diversity of plants and whole foods is associated with decreased levels of “bad” species and increased levels of “good” species.
Advancing microbiome science
ZOE is dedicated to helping expand our collective knowledge about the gut microbiome. Our scientists and collaborators recently published a paper on coffee and the microbiome. Our results appear in the high-impact scientific journal Nature Microbiology.
This study showed that it is possible to identify who drinks coffee by analysing their gut microbiome, partly thanks to a coffee-loving bacteria called Lawsonibacter asaccharolyticus.
In recent years, ZOE has also focused on menopause, an understudied topic that affects almost half of us. We developed a new tool, MenoScale, to help women make sense of their symptoms.
And we have more research in motion: In the near future, we will publish a paper that outlines how vegan and vegetarian diets alter the gut microbiome and another on the complex world of bile salts.
ZOE is focused on chipping away at these complex but vital topics. With each study, we glean fresh insights into how the gut microbiome shapes human health and disease.
The health of your gut microbiome plays a vital role in your overall health. To learn what your gut needs, join ZOE to receive your at-home test kit and personalised nutrition program.
