Published in the journal Nature, researchers from Zoe, the University of Trento, Italy and Kings College London analyzed more than 34,000 microbiomes (Zoe platform users from the UK and US) to create a measure of gut microbiome health they have named the ZOE Microbiome Health Ranking 2025.
The ranking has been made available for research scientists across the world as “a reliable and repeatable measure of microbiome health.”
“It is a huge breakthrough discovery moment for us and a true milestone in microbiome science,” Dr. Federica Amati, Zoe’s head nutritionist and study co-author, told NutraIngredients. “We can now map the beneficial side of the microbiome with greater clarity than ever before, and it’s already evolving how we think about gut health.”
She explained the ranking has been validated against multiple independent global datasets, and it appears to hold up across different populations and environments.
“By making the ranking publicly available, we’re giving scientists a common standard that they can use to benchmark microbiome health in any cohort,” Dr. Amati said. “That means better reproducibility, better comparison across studies and a much clearer understanding of how the microbiome relates to metabolic health.
“That said, continued validation in even more diverse global groups is essential and we’re very committed to that,” she added.
While the rhetoric has always been that we do not know what a healthy microbiome looks like, the Zoe team believes this research provides that long awaited answer.
“I think that this study gives us a scientifically robust answer for the first time,” Dr. Amati said.
“We now have a clear, evidence-based microbial signature that defines what a healthier microbiome looks like. It’s not the final word. The microbiome is complex and ever-evolving, but this takes us to a deeper level of understanding and measurement—which will in turn give us the knowledge to improve gut health at a global scale.”
Professor Sarah Berry, ZOE’s chief scientist, added: “We call it a ‘gut health revolution’ because the gut is central to overall health—and, for the first time, we have a reliable, repeatable way to measure gut health and track improvements.”
New strains discovered
The ranking reveals that of the top 50 microbial species most strongly associated with better health, 22 are entirely new to microbiologists. Among the 28 species for which at least the name of a close microbe is known, 24 have never been characterized in vitro.
“For me, the most surprising finding is just how much of the healthy microbiome has been invisible to science until now,” Dr. Amati said. “So we’ve effectively uncovered a missing fraction of the microbiome—the beneficial species that help to drive key areas of metabolic health.”
She explained the species rankings were defined using cross-sectional independent cohorts which “were strongly and consistently predictive” of the bugs most associated with dietary interventions.
Across case-control studies of several diseases, healthy individuals carried, on average, 3.6 more “good” microbes than those with a diagnosed condition.
People who have a healthy weight had an average of 5.2 more good bugs compared to people living with obesity.
Despite the overall agreement, a set of 65 bugs were differently linked with diet and health. The researchers suggest some of these species may be health-promoting, even in challenging dietary environments. One example consistent with what has been reported in literature is Harryflintia acetispora, which might be able to digest simple sugars such as fructose and convert them into short-chain fatty acids.
“These unusual microbes remind us that biology always has outliers that challenge our assumptions and that there is still so much to discover about the powerful world of the gut microbiome,” Dr. Amati said.
During a recent Zoe podcast focused on the new research, Professor Tim Spector, co-founder of ZOE, revealed the team is working to cultivate the newly discovered microbes to potentially create new probiotics.
Discussing probiotic supplements on the market, Spector said these products “really haven’t changed much” in the last 100 years, with companies tending to use the same 10 or 20 strains over and over.
Claim criticism
William DePaolo, biomedical consultant at The Healing Scholar, argues Zoe did not discover a universal healthy microbiome but took data from affluent app-using adults in the United States and United Kingdom and “ran a giant correlation exercise to see which microbes tend to show up with ‘better’ numbers in that specific group.”
“The Zoe paper already shows that what they call ‘good’ or ‘bad’ taxa do not behave consistently between the UK and U.S. cohorts,” he said. “If the same company cannot get stable signals across two high income, English speaking populations that already share a lot of diet and lifestyle patterns, it is hard to argue this framework will work globally. That is the first big red flag.”
He noted that what constitutes a healthy gut microbiome will vary according to a multitude of factors, such as age, immune function, medications, mobility, diet and social context. He suggested any attempt to define ‘healthy’ should, at minimum, stratify by those factors.
“A single score that ignores all of that will mostly reflect the people who dominated the dataset, not some universal truth about gut health,” he told NI.
What’s more, he pointed out that the same taxa can play very different roles in different hosts. Again, a number of factors will impact this, including; diet, background microbiome, host genetics, immune tone, metabolic status and drugs like PPIs, metformin or antibiotics.
“If you are going to rank bugs, you should be very explicit that these are statistical associations with modest effect sizes in a specific population, not universal villains and heroes,” DePaolo added, emphasizing the need for publicly funded, diverse cohorts instead of company-owned datasets, “that are heavily skewed toward affluent users”.
Source: Nature, doi: 10.1038/s41586-025-09854-7. “Gut micro-organisms associated with health, nutrition and dietary interventions”. Authors: Asnicar, F. et al.
