Table 1

Glossary of common terms related to the gut microbiome

TermFurther details
Gut microbiotaThe total assemblage of microorganisms present within the gut mucosal environment.1
Gut microbiomeThe entire gut ecological habitat, including the microorganisms themselves, as well as their genomes, and the surrounding environmental conditions.1
DysbiosisA term still used commonly to describe perturbation of the composition of the gut microbiome compared with what might be expected in the healthy host. However, in reality, often a poorly descriptive term without a specific biological definition.
PathobiontMicroorganisms that usually interact with the host symbiotically, but have the potential to act as pathogens and cause disease under certain conditions.
Faecal microbiota transplant (FMT)Typically, a liquidised suspension of microbes (and their associated environmental milieu) derived from manipulated whole stool, administered to the gut of affected patients. Stool is obtained from healthy screened donors, and prepared using homogenisation, mixing with a diluent (eg, normal saline) and filtration. However, lyophilised FMT preparations are now also increasingly being used.