Julian Marchesi and myself have written an editorial that attempt at stimulating discussions on harmonizing the use and definition of terms in microbiome research. We believe it is important as so many misnomers are found in the literature. We hope that this editorial will stimulate discussions and further refinements of these terms. You can comment on NCBI or on the Microbiome website The editorial was published in Microbiome, which I am the Editor in Chief.
Here is the abstract:
The advancement of DNA/RNA, proteins, and metabolite analytical platforms, combined with increased computing technologies, has transformed the field of microbial community analysis. This transformation is evident by the exponential increase in the number of publications describing the composition and structure, and sometimes function, of the microbial communities inhabiting the human body. This rapid evolution of the field has been accompanied by confusion in the vocabulary used to describe different aspects of these communities and their environments. The misuse of terms such as microbiome, microbiota, metabolomic, and metagenome and metagenomics among others has contributed to misunderstanding of many study results by the scientific community and the general public alike. A few review articles have previously defined those terms, but mainly as sidebars, and no clear definitions or use cases have been published. In this editorial, we aim to propose clear definitions of each of these terms, which we would implore scientists in the field to adopt and perfect.
Full citation: Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome. 2015 Jul 30;3:31. doi: 10.1186/s40168-015-0094-5. eCollection 2015. PubMed PMID: 26229597; PubMed Central PMCID: PMC4520061.