December 10, 2025

expert reaction to study looking at the gut microbiome and associations with markers of health

A study published in Nature looks at the gut microorganisms associated with markers of health. 

Dr Fred Warren, Group Leader, starch breakdown in the digestive tract, Quadram Institute, said:

“This large scale study represents one of the largest gut microbiome studies published to date, and is an impressive piece of work.  The authors exploit their large dataset to characterise the “microbial dark matter”, previously unknown and uncultured bacteria which form a significant part of our gut microbiome and which may have a significant bearing on health and disease.  However, their interpretation of “good vs. bad” bacteria on the basis of association with health markers is an oversimplification.  All of these bacterial species are part of a normal, healthy gut microbiome and their association with disease is complex and context dependent.  There is much more research to be done before this work can be applied to making real world decisions about health and dietary choices.”

Dr Lindsey Edwards, Principal Investigator, Centre Host Microbiome Interactions; Research Director for The Faecal Microbiota Transplant Programme; and Lecturer in Microbiology, King’s College London, said:

“For some years now, scientists and clinicians have spoken about the importance of the microbiome, but we have had no real measures of what a healthy microbiome actually looks like.  This study is a landmark because, for the first time, we have an evidence-based idea of health.  It provides a foundation for understanding microbial balance in ways that could transform both research and clinical practice.

“The implications are profound: by defining health rather than just disease, this work opens the door to more precise diagnostics, improved regulation, and innovative therapies.  It is a timely and constructive contribution to global debates on microbiome science and public health.

“The field has lacked large‑scale, comprehensive studies exploring these links in diverse populations.  Here, over 34,000 US and UK participants were investigated with metagenomic, diet, anthropometric and host health data.  The study identifies both known and yet to be cultured (unknown to us) gut microbiome species significantly associated with health outcomes, different diets, and risk factors.  This is the largest dataset of its kind to date and marks an important contribution to the field.  In time, however, it will need to be expanded to cover more globally diverse populations.

“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.  It is not simply about restoring microbial species but about restoring their functional and metabolic capability.  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.

“The authors themselves emphasize that causal inference is not possible without prospective cohort studies and interventional clinical trials.  The study shows correlations among microbiome species, health outcomes, dietary patterns, and risk factors.  In other words, it establishes associations — which species tend to appear more often in healthier individuals or alongside certain diets.  The study cannot prove causality.  We cannot say that the presence (or absence) of a particular species causes better health, nor that changing diet will directly lead to improved outcomes via the microbiome.  To prove that, you need prospective cohort studies and interventional clinical trials where you deliberately change diet or microbiome composition and then measure health effects.  While the study does not prove cause, it provides the evidence base needed to design trials that can test causality.

“What is needed now are those interventional randomised controlled trials, and this study provides an excellent scientific underpinning for them.  By moving from association to intervention, we can begin to test how supporting beneficial microbes and their functions translates into measurable improvements in our resilience and long‑term wellbeing.

“This study gives us a robust place to start interventional trials that could transform microbiome health.”

‘Gut micro-organisms associated with health, nutrition and dietary interventions’ by Francesco Asnicar et al. was published in Nature at 16:00 UK time on Wednesday 10 December 2025. 

DOI: 10.1038/s41586-025-09854-7

Declared interests

Dr Fred Warren: “I currently receive research funding through the BBSRC CASE program from PepsiCo and Campden BRI.  I also hold Innovate UK funding with FibreUP drinks, although I do not directly receive research funding from this company.”

Dr Lindsey Edwards: “I am the Research Director for King’s College London’s PROMISE (Faecal Microbiota Transplant) FMT programme and founder of the R-BiOME Network.  I serve on advisory boards and committees (including EURFMT, PACT, and the British Society for Gastroenterology Gut Microbiota for Health Expert Panel).  I have no industry funding or employment ties; my involvement is in academic, regulatory, and public engagement capacities.”

For all other experts, no reply to our request for DOIs was received.