ZOE study identifies 100 gut bacteria linked to health

ZOE, the company behind the world’s largest nutrition study, has announced a landmark discovery in gut microbiome science.

Published in Nature, the findings identify 100 species of gut bacteria – 50 associated with good health and 50 linked to poorer outcomes – providing the clearest picture yet of how microbes influence cardiometabolic health and body weight.

The study analysed more than 34,000 stool samples, making it one of the most extensive microbiome datasets ever assembled. Using advanced shotgun metagenomic sequencing and the MetaPhlAn4 computational tool, researchers were able to detect thousands of previously unknown bacterial species. Unlike older methods that examined just one gene, this technology assessed over 5 million genetic markers, allowing scientists to uncover microbes that had never been catalogued before.

The newly developed ZOE Microbiome Ranking categorises bacteria into “good” and “bad” groups based on their associations with health markers.

• Individuals with conditions such as type 2 diabetes or obesity were found to have higher levels of “bad” microbes and fewer “good” ones.
• Conversely, those with healthier weight and metabolic profiles had more “good” bacteria.Some of the newly identified beneficial microbes, such as Harryflintia acetispora, were shown to produce short-chain fatty acids (SCFAs) that reduce inflammation – even when consuming poor-quality foods.

This discovery provides the missing link scientists have sought for two decades: a reliable way to measure gut microbiome health. It offers reproducible associations between microbial composition and cardiometabolic conditions, paving the way for more precise dietary interventions. Importantly, ZOE’s ranking has been validated against other large public datasets, strengthening confidence in its findings.

The study builds on ZOE’s earlier PREDICT trials, which first identified 15 “good” and 15 “bad” bacteria. With the expanded dataset, researchers now have a far more comprehensive understanding of how diet influences gut health over time. Longitudinal data from ZOE’s nutrition programs showed that participants following tailored dietary advice experienced a drop in harmful microbes and an increase in beneficial ones, suggesting a causal link between nutrition and microbiome improvement.

ZOE has already integrated these findings into its Gut Health Tests in the UK, with plans to expand availability to the US. The company has also introduced Gut Bug Clusters, offering consumers new insights into their microbiome composition. By publishing the results in Nature, ZOE has made the data available to the wider scientific community, enabling further research into the role of gut bacteria in human health

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