Introduction
Gut health has become a major focus in nutrition, medicine, and consumer wellness, but the term is often used loosely. Claims about microbiome testing, probiotics, fermented foods, fibre, and “boosting” the gut microbiome are now common, yet the evidence behind these claims varies substantially.
In this episode, Dr. Emily Leeming examines what gut health actually refers to, why it cannot be reduced to the microbiome alone, and where current microbiome science is being applied before it is ready. The discussion covers the limits of commercial stool testing, the difficulty of defining a healthy microbiome, and the practical strategies most strongly supported by current evidence.
- [02:48] Interview start
- [04:17] Defining gut health
- [09:03] What is a "healthy microbiome"?
- [15:25] Microbiome testing - any clinical utility?
- [24:08] Interpreting microbiome studies
- [34:39] "30 plants a week" is not evidence-based
- [39:53] Serotonin and gut brain
- [45:34] Fiber research frontier
Episode Resources
- Join the Sigma newsletter for free
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- Enroll in the next cohort of our Applied Nutrition Literacy course
- Dr. Leeming’s website: emilyleeming.com
- Dr. Leeming’s newsletter: Second Brain
- Episode references:
- Marco et al., 2026 – The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health
- Joos et al., 2024 – Examining the healthy human microbiome concept
- Pocari et al., 2025 – International consensus statement on microbiome testing in clinical practice
- Servetas et al., 2026 – Evaluating the analytical performance of direct-to-consumer gut microbiome testing services
Guest Information
Emily Leeming, PhD is a scientist at King’s College London, dietitian, former chef, and author of two public-facing books. She has published and contributed to multiple academic publications in top peer-reviewed journals and is part of the PROSPECT Cancer Grand Challenges team, led by Harvard University, investigating early-onset colorectal cancer.
Dr. Leeming has a PhD in Diet and the Gut Microbiome from King’s College London. And previous to that she completed a Master of Science Degree in Nutrition and Dietetics at Monash University.
Study Notes
The episode explores why “gut health” should be understood as a broad concept involving gastrointestinal function, symptoms, disease activity, barrier integrity, immune signalling, and microbial activity, rather than being reduced to a stool test or a diversity score.
Particular attention is given to the current limits of direct-to-consumer microbiome testing, the uncertainty around defining a single “healthy microbiome,” and the practical foundations that remain best supported by evidence: fibre-rich plant foods, adequate fluids, and context-specific use of fermented foods or probiotics.
Useful Terminology
- Gut health: A broad construct referring to the health and function of the gastrointestinal tract, not only the gut microbiome. A state of normal gastrointestinal function without active gastrointestinal disease and without gut-related symptoms that affect quality of life.
- Gut microbiome: The community of microorganisms living in the gastrointestinal tract, especially the large intestine, together with their genes, metabolites, and “theatre of activity.”
- Microbial diversity: A measure of how many different microbial types are present and, depending on the metric, how evenly they are distributed.
- Microbial function: What gut microbes do metabolically and biologically, rather than simply which microbes are present. This includes production of molecules such as short-chain fatty acids, transformation of bile acids, effects on gut barrier integrity, immune signalling, and potentially gut–brain signalling.
- Short-chain fatty acids: Small fatty acids produced when gut microbes ferment dietary fibre and related substrates.
- Prebiotic: A substrate that is selectively used by host microorganisms and confers a health benefit.
- Gut barrier: The physical and functional boundary between the intestinal contents and the internal body environment. This includes the epithelial lining, the protective mucus layer, and permeability regulation.
- Commercial microbiome testing: Consumer-facing testing that typically analyses a stool sample and reports which microbes are detected and in what relative amounts.
Defining Gut Health: Broader Than the Microbiome
The ISAPP consensus statement provides a useful framework for clarifying what “gut health” should mean.
- Gut health is intended to encompass the full gastrointestinal tract, including the mouth, pharynx, oesophagus, stomach, small intestine, large intestine, rectum, and anus.
- It is closely related to “gastrointestinal health,” while “digestive health” can be viewed as a narrower term focused more specifically on digestion.
- The consensus definition explicitly includes gastrointestinal function and gut-related symptoms.
- It also recognises that a person with a gastrointestinal disease can still be in a state of gut health during clinical and pathological remission.
The concept is multidimensional rather than reducible to one marker.
- A person’s experience of symptoms matters, particularly when symptoms affect day-to-day function or quality of life.
- Objective function also matters, including motility, secretion, digestion, absorption, gut barrier function, immune activity, endocrine signalling, and microbial activity.
- The consensus statement also notes that poor gut health may sometimes exist without obvious
