An editorial by Marchesi & Ravel proposed some definitions in microbiome research to harmonize and clarify the vocabulary used in scientific literature, according to the rapid evolution of the field towards genomic and metabolic analyses. The misuse of terms such as microbiome, microbiota, metabolomic, metagenome or metagenomics, among others, could contribute to the misunderstanding of some studies by the scientific community and the general public.


Then, for example, the authors proposed ‘microbiota’ to refer to the microorganisms present in a defined environment. ‘Microbiome’ is used for two concepts: one to refer to the entire habitat, including the microorganisms and their genomes, and another one limited to the collection of genes and genomes of members of a microbiota. This second concept (more European usage) also fits the definition of ‘metagenome’. Regarding the analytical approaches, the ‘Metabolome’ is the census of all metabolites present in a given strain or tissue. In particular, when it refers to all metabolites from a microbiota, Nicholson suggests calling it ‘metabonome’. Finally, Marchesi & Ravel agreed to limit the use of the words ‘flora’ and ‘microflora’ to the popular literature.


For a more extensive definition of these and other terms, read the full article.



Marchesi JR & Ravel J. (2015) The vocabulary of microbiome research: a proposal. Microbiome 3:31 doi:10.1186/s40168-015-0094-5