TOPLINE:
A large-scale analysis suggested that the gut microbiome can be modulated by diet with both favorable and unfavorable effects on markers of health.
METHODOLOGY:
- Researchers used five large-scale microbiome cohorts from the ZOE PREDICT studies to assemble a microbiome dataset of 34,694 US and UK participants with detailed dietary records as well as anthropometric measures.
- The collected data included common health-risk factors such as BMI, triglycerides, blood glucose, and A1c, as well as several dietary indices and clinical markers that are intermediary measures of cardiometabolic health, such as the atherosclerotic cardiovascular risk and high-density lipoproteins.
TAKEAWAY:
- By analyzing metagenomic, diet, anthropometric, and host health data, the researchers identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors.
- They developed a ranking of species most favorably and unfavorably associated with human health markers, called the “ZOE Microbiome Health Ranking 2025.”
- The ranking system showed “strong and reproducible associations” between the ranking of microbial species and both BMI and host disease conditions in more than 7800 additional public samples.
- To validate the effect of dietary changes on the gut microbial species, the researchers analyzed two dietary intervention studies and found that favorably ranked species increased in abundance and prevalence, and unfavorably ranked species reduced over time.
IN PRACTICE:
“Causal inference is not possible without prospective cohort studies and interventional clinical trials,” the authors wrote. However, confirmation of the cross-sectional patterns in the longitudinal nutrition intervention trials “not only increases the intrinsic value of the rankings but confirms that the human gut microbiome can be modulated successfully by dietary intervention and that the effects on the microbiome of such interventions are both predictable and reproducible.”
Commenting on the findings, Lindsey Edwards, principal investigator, Centre Host Microbiome Interactions and research director for the Faecal Microbiota Transplant Programme, King’s College London, London, England, said: “Importantly, this study establishes that a change in dietary patterns can shift the species level composition of the microbiome, with knock-on effects on host health…In other words, modulating the microbiome to improve health is not just about adding microbes back in, but about understanding how we can support them to flourish in ways that enhance resilience and strengthen our health. This recognition marks a critical advance in how we understand and harness the microbiome for long-term wellbeing.”
SOURCE:
This study was led by Nicola Segata, PhD, Department CIBIO, University of Trento, Trento, Italy, and published online in Nature.
LIMITATIONS:
A key limitation of this study was that it did not allow the authors to directly disentangle the effect that diet exerted on the microbiome specifically to improve cardiometabolic health from the impact of diet only. To do so “would entail designing large-scale interventions in which both the introduction of single foods and alterations of specific microbiome characteristics…are tested,” the authors wrote.
DISCLOSURES:
Two coauthors reported being cofounders of ZOE Ltd and owning the ZOE PREDICT studies; several coauthors are or have been owners or consultants to the company. Segata and others reported receiving options with ZOE Ltd. Edwards declared serving as the research director for King’s College London’s PROMISE (Faecal Microbiota Transplant) FMT programme and founder of the R-BiOME Network; she also reported serving on advisory boards and committees (including EURFMT, PACT, and the British Society for Gastroenterology Gut Microbiota for Health Expert Panel), but has no industry funding or employment ties; her involvement is in academic, regulatory, and public engagement capacities.”
Marilynn Larkin, MA, is an award-winning medical writer and editor whose work has appeared in numerous publications, including Medscape Medical News and its sister publication MDedge, The Lancet (where she was a contributing editor), and Reuters Health.