Huge 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. 

Our findings were published today in Nature, the world's most influential scientific journal.

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.

This study is the culmination of our first 8 years of ZOE. 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.

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Dive deeper

Our latest study builds on these findings. Thanks to Members who chose to be part of our research, we had access to more than 34,000 samples. This provided an even clearer picture of the microbes in our gut and their links to health.

Although we've known there are links between the gut microbiome and a range of health markers, pinning down what makes a "healthy" gut microbiome has been incredibly challenging. The ZOE Microbiome Ranking finally provides this missing link.

Using this ranking of bacteria, we found reproducible associations between gut microbiome composition and a range of cardiometabolic health conditions and body mass index (BMI).

In other words, if an individual had a cardiometabolic health condition, such as type 2 diabetes, they were more likely to have higher numbers of "bad" microbes and lower levels of "good" bacteria than someone without a cardiometabolic condition. They were also more likely to have a higher BMI.

Conversely, individuals with a healthy weight or without a health condition had more of the "good" bacteria.

Importantly, we double-checked these associations with other public datasets that included data from thousands of people to ensure they're water-tight.

The ZOE Microbiome Ranking is incredibly exciting for us, but it will also help drive scientific research into the gut microbiome more broadly.

By choosing to publish this in Nature, this information is being shared with the research community. We are releasing what we call the "ZOE Microbiome Ranking 2024" which is this list of microbes based on the data set collected in 2024, which forms the basis for this paper.

This kind of longitudinal data in gut microbiome science is extremely rare in such large numbers. It really helps us to better understand if there is a causal link between our diet, gut microbiome, and health outcomes.

Shotgun technology

These breakthroughs weren't just a numbers game. They 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 examining differences in just one gene. 

Prof. Nicola Segata, Ph.D., and Francesco Asnicar, Ph.D., from the University of Trento, worked closely with us on  the research that helped 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 means that, although some of the bacteria we’ve identified don’t have a name yet, we can still see how they’re linked to health. 

While most of the "bad" species were familiar to scientists, according to Francesco, “The majority of the 50 new 'good’ bacteria species were unknown to science.”

This makes sense. Understanding which microbes are harmful is important. However, knowing which species can support health has long been the missing part of the puzzle.

Interestingly, we also found that some of these "good" microbes, like Harryflintia acetispora, are particularly useful.

Amazingly, they can eat poor-quality foods, containing simple sugars, and still produce health-promoting compounds called short-chain fatty acids (SCFAs). Among a range of benefits, SCFAs help reduce inflammation.

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Why it matters

It’s hugely exciting that our research has been published in Nature, a journal that is consistently ranked number one in the world for influence, meaning it only publishes the highest-quality research.

More importantly, our new, deeper understanding of the connections between food, gut bacteria, and health means we can now provide even more accurate information to our Members. 

This new science is already available in ZOE’s Gut Health Tests in the UK, and it will be coming soon to the US.

Based on the results of this study, we have introduced Gut Bug Clusters. This innovation provides fresh insights that aren’t available anywhere else. Read more about how they work here.

We’ve also made this science available for other scientists to use, allowing the scientific community to continue building an ever-more precise global microbiome score.

If you'd like to learn about the microbes that call your gut home, become a ZOE Member and order your gut health test today.