Gut health: what does it mean, can we measure it, and, if so, how?

In celebration of the World Microbiome Day, we reflect on our experience discussing and developing a consensus definition for gut health, published in February 2026 in Nature Reviews Gastroenterology and Hepatology.

The gastrointestinal tract, or alimentary canal, refers to the conduit from the mouth to the anus and is the primary site in the body responsible for food digestion, nutrient absorption, and waste removal. It is lined by mucosa containing epithelial cells and other cell types, such as immune and hormone-producing enteroendocrine cells, which are integrated into systemic responses affecting digestion, immunity, and neural activity, among other functions. The gastrointestinal tract also houses the gut microbiome, encompassing thousands of different microbial species from all domains of life and whose composition and functions differ between compartments (for example, the mouth, stomach, small and large intestine) and between individuals according to their age, diet, genetic background, and health status.

 The phrase ‘gut health’ was introduced into the scientific literature in the early 2000s as a useful way to convey health benefits of prebiotics, such as inulin and oligofructose. The term has since gained popularity as a catch-all phrase to describe a state of health localized to the gastrointestinal tract that is disturbed in those with symptoms but that can be restored by the consumption of various substances. Implicit in this concept is an understanding of what exactly we mean by “gut health”. While thousands of papers across the disciplines of medicine, veterinary sciences, nutrition, and microbiology use the term, its definition has not received the attention that it obviously merits. Indeed, prior to the publication of our paper, the most recent definition of gut health was attributed to a 2011 commentary written by one of our coauthors, Dr. Stephan Bischoff, University of Hohenheim. Since that time, the concept of gut health gained particular traction in studies associating diet, the gut microbiome, and gastrointestinal and systemic diseases.

 To bring clarity to this field, the International Scientific Association for Probiotics and Prebiotics (ISAPP), a non-profit scientific organization for advancement of biotics research, gathered an international group of 13 scientists and clinicians to discuss what constitutes gut health and how we can measure it. As co-chairs of the meeting, we included leading experts in various relevant fields, including but not limited to gastroenterology, pediatrics, nutrition, immunology and microbiology. Researchers and clinicians were invited to the panel based on their areas of expertise, ensuring that all aspects of gut health were represented. To explore what gut health could mean, our initial discussions took place over one and a half days in London, UK. Although we entered the meeting skeptical of whether it would be possible to reach a definition, by the end of the day, we found there was much agreement and enthusiasm to develop a definition. After the in-person discussion, the paper took shape through 6 months of writing, correspondence and online meetings between the authors to further debate and align on the definition and associated framework.

 The panel defined gut health as a state of normal gastrointestinal function without active gastrointestinal disease and gut-related symptoms that affect quality of life. The definition takes into account both physiological function and an individual’s experience of symptoms – with the latter deemed essential from a clinical perspective. Within the framework of gut health, the experts agreed that the scientific basis of gut health could be addressed through the investigation of six domains: digestive physiology, microbiome, gut barrier, immunity, metabolism, and gut-brain axis. The gut microbiome is centrally placed and interacts with all other domains. However, the panel also concluded that, despite considerable progress in describing what might constitute a “healthy microbiome” metrics defining a health-associated gut microbiome have yet to be delineated.

 We believe the paper provides a much-needed framework to facilitate a comprehensive approach to health. It is intended to be applied by researchers designing studies where gut health is an endpoint, as well as in the clinical management of digestive health and disease. We hope the concepts presented lead to a more structured approach in clinical studies and in fundamental research delineating which aspect of gut health is being examined. Progress will be greatly facilitated by the development of validated biomarkers for each functional domain, including what defines a health-associated gut microbiome. By defining gut health, we provide a framework that promotes the use of the term in a more thoughtful and coordinated way between researchers, clinicians, and the broader public alike.