New microbiome breakthrough from ZOE, thanks to community science

ZOE runs the largest study of nutrition in the world, and now, thanks to our community-based research, we’ve made a breakthrough discovery in gut microbiome science. 

By analyzing 35,000 stool samples, we’ve identified thousands of bacteria that are entirely new to science

We’ve always said that the more data we have, the more accurate our science becomes, so this is a real testament to the power that community science has in driving discoveries forward.

For our ZOE members, this means fresh details about associations between certain bacteria species and health. 

Now, rather than just 15 “good” and 15 “bad” bacteria, the ranks have swelled to 50 “good” and 50 “bad” bacteria.

And this is just the beginning.

How it started

In 2021, ZOE published a paper in the journal Nature Medicine outlining our PREDICT 1 study. In this research, we spotted links between specific gut bacteria and health outcomes.

Using almost 1,100 gut microbiome samples, we identified 15 “good” gut bacteria. These were linked to positive health measures, like healthy blood sugar responses after eating. 

We also identified 15 “bad” gut bacteria. These were associated with poorer health measures, like obesity and other risk factors for heart disease.

Dive deeper

Access to tens of thousands of samples helped us get a clearer picture of the microbes in your gut and their links to health. 

But this breakthrough wasn’t just a numbers game. It relied on the latest scientific techniques.

Most gut microbiome tests on the market use a technology called 16s, which isn’t good enough — it identifies bacteria by looking at the differences in just one gene. 

ZOE uses shotgun metagenomic sequencing and a computational tool called MetaPhlAn — pronounced “meta-flan” — to interpret the genetic information.

Prof. Nicola Segata, Ph.D., and Francesco Asnicar, Ph.D., from the University of Trento, headed up the research that helped us gather our new insights.

Francesco explains how the latest version of this technology, MetaPhlAn4, is “on average able to 'see' about twice the number of species,” compared with the previous version. 

Unlike 16s, which focuses on just one gene, MetaPhlAn4 looks at more than 5 million marker genes. 

This allows scientists to collect genetic information about bacteria that no one has seen before.

So, though some of the bacteria we’ve identified don’t have a name yet, we can still see how they’re linked to your health. 

In fact, Francesco explains that “The majority of the 50 new ‘good’ bacteria species were unknown to science.”

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Why it matters

ZOE’s new, deeper understanding of the connections between food, gut bacteria, and health means we can now provide more accurate information. 

This advance will benefit new and existing members: We’ll update everyone’s gut microbiome and food scores to reflect these new discoveries, helping us make our dietary advice even more personalized and accurate.

We’re also rolling out gut health retesting, so existing members can see how eating the ZOE way has changed their gut microbiome.

And we’re making waves in science circles, too. Francesco will be presenting our results at a human microbiome conference this week.

The take-home

  • ZOE just got smarter — our gut microbiome test is now better than ever, thanks to our members.

  • We now have 50 “good” and 50 “bad” gut bacteria to check for.

  • Your gut microbiome and food scores will automatically be updated.

  • And as members keep contributing to our data, our science will continue to improve.


Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology. (2023). 

MetaPhlAn 4.0. (n.d.). 

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nature Medicine. (2021).