Gut health glossary

Gut health glossary, understanding the language of gut health.
Gut health glossary, understanding the language of gut health.

At the time of writing (July 2019), the microbiome is emerging as an important new frontier in understanding and mediating health. From very tentative beginnings, a body of evidence is being established, that strongly suggests a relationship between gut bacteria and a wide range of physical and mental health concerns. However, despite the implications of managing gut health, there is a lack of simple and easily understandable information and advice. The goals of the Gut Well Soon website include the sharing of important information in this general subject area. We have started to collate a simple Gut Health Glossary that highlights and explains some of the terms currently being used to explain the science. Although our primary interest is in the gut microbiome, we also discuss the human microbiome in general terms and in its individual components (e.g. genitourinary microbiome, oral microbiome, skin microbiome, vaginal microbiome).

If you have anything to add or improvements to suggest feel free to drop us a line or add your comments in the field below. Please refer to our disclaimer.


Dysbiosis – Is the term used to describe an imbalance in a microbiota population. An imbalance could be an abnormally low or high level in a particular type or family of microbes or their maladaptation.

Gut-brain axis – Put simply there is a two-way communication system between the gut and the brain. A key element of this biochemical messaging is the interaction between the gut and central nervous system (CNS) mediated by gut flora.

Gut flora or gut microbiota, or gastrointestinal microbiota A term that is generally interchangeable with gut microbiota. It means the multifacted and complex community of microorganisms that reside in the digestive tract.

Human Microbiome Project – A leading research initiative, started in 2007, to develop our understanding of the relationship between the human microbiome and human health and disease.

Microbiome – The usual definition of the microbiome is the entire genetic collection of the microbes contained in a specific area. As such the human gut microbiome refers to the complete genetic profile of microbes in the human gut (see microbiota). The human microbiome can be sub divided into the distinct areas of human tissues and biofluids, such as genitourinary microbiome, oral microbiome, skin microbiome, and the vaginal microbiome.

Microbiota – The entire population of microbes contained within a specific area, typically includes bacteria, viruses and yeast. So the human gut microbiota refers to the entire population of microbes present in the human gut (see microbiome).

Microorganisms – An organism only visible at the microscopic level, typically a bacterium, virus, or fungus.

Pathogen – Is something that can be shown to have a causal relationship with an illness. A key issue to acknowledge is that while some microorganisms in humans are potential pathogens. The absence of other bacterium, individually or in combination, can also be linked to health problems.



1 If you’re looking for a general guide to the main terms you could start with Wikipedia.

2 For an overview of the current scientific thinking in this field, you might find the
NIH Human Microbiome Project a great jumping-off point.

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