The DOI matches its Crossref record.
The vocabulary of microbiome research: a proposal
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Microbiome definition re-visited: old concepts and new challenges
Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00875-0 · Cited by 2,275
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
Eisenhofer, R., Minich, J. J., Marotz, C., Cooper, A., Knight, R., & Weyrich, L. S. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.11.003 · Cited by 1,146
The evolution of the host microbiome as an ecosystem on a leash
Foster, K. R., Schluter, J., Coyte, K. Z., & Rakoff-Nahoum, S. (2017) · Nature · doi:10.1038/nature23292 · Cited by 935
The Vaginal Microenvironment: The Physiologic Role of Lactobacilli
Amabebe, E., & Anumba, D. O. C. (2018) · Frontiers in Medicine · doi:10.3389/fmed.2018.00181 · Cited by 785
Fassarella, M., Blaak, E. E., Penders, J., Nauta, A., Smidt, H., & Zoetendal, E. G. (2021) · Gut · doi:10.1136/gutjnl-2020-321747 · Cited by 772
Metadata
- Authors
- Marchesi, J. R., & Ravel, J.
- Venue
- Microbiome
- Published
- 2015-07-30
- Volume
- 3
- Issue
- 1
- Pages
- 31-31
- ISSN
- 2049-2618 (ISSN-L)
- OpenAlex
- W2151277589
- Cited by
- 1,220
- References
- 0
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The vocabulary of microbiome research: a proposal. https://app.cochat.ai/papers/10.1186/s40168-015-0094-5
- The paper
- Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome. https://doi.org/10.1186/s40168-015-0094-5
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
