Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle
Abstract/Contents
- Abstract
We analyzed the combined microbiome data from five previous studies with samples across five continents. We clearly demonstrate that there are no consistent bacterial taxa associated with either Bacteroides- or Prevotella-dominated communities across the studies. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the “enterotypes” hypothesis. The apparent segregation of the samples seen in many ordination plots is due to the differences in the samples’ Prevotella and Bacteroides abundances and does not represent consistent microbial communities within the “enterotypes” and is not associated to other taxa across studies. The projections we see are consistent with a continuum of values created from a simple mixture of Bacteroides and Prevotella; these two biomarkers are significantly correlated to the projection axes. We suggest that previous findings citing Bacteroides- and Prevotella-dominated clusters are the result of an artifact caused by the greater relative abundance of these two taxa over other taxa in the human gut and the sparsity of Prevotella abundant samples. Conclusions: We believe that the term “enterotypes” is misleading because it implies both an underlying consistency of community taxa and a clear separation of sets of human gut samples, neither of which is supported by the broader data. We propose the use of “biomarker” as a more accurate description of these and other taxa that correlate with diet, lifestyle, and disease state.
This paper was published in the journal Microbiome, this repository contains all the supplementary code and data necessary to replicate the analysis presented in that article.
Description
Type of resource | software, multimedia |
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Date created | November 2015 |
Creators/Contributors
Author | Gorvitovskaia, Anastasia | |
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Author | Holmes, Susan P. | |
Author | Huse, Susan M. |
Subjects
Subject | R markdown |
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Subject | microbiome |
Subject | ordination |
Subject | PCoA |
Subject | NMDS |
Subject | biomarkers |
Subject | Statistics Department Stanford |
Genre | Dataset |
Bibliographic information
Related Publication |
Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle,
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Related item | |
Location | https://purl.stanford.edu/fs506ff9976 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
Preferred citation
- Preferred Citation
- Gorvitovskaia, Anastasia and Holmes, Susan P. and Huse, Susan M.. (2015). Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Stanford Digital Repository. Available at: http://purl.stanford.edu/fs506ff9976
Collection
Reproducible Research Support for Statistics of the Microbiome
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- Contact
- susan@stat.stanford.edu
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