Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Dec;8(12):2357-9.
doi: 10.1038/ismej.2014.157. Epub 2014 Aug 29.

Which is more important for classifying microbial communities: who's there or what they can do?

Zhenjiang Xu  1 , Daniel Malmer  1 , Morgan G I Langille  2 , Samuel F Way  3 , Rob Knight  4
Affiliations

Which is more important for classifying microbial communities: who's there or what they can do?

Zhenjiang Xu et al. ISME J. 2014 Dec.
No abstract available

PubMed Disclaimer

Figures

Figure 1
Figure 1
Accuracy of supervised classification. Random Forest classification model was performed, using caret (Kuhn, 2008) R package, with 5 repeats of 10-fold cross validation on CBH, CS, CSS, FSH, FS (from Knights et al., 2011a and following the same naming) and HMP (from Langille et al., 2013; other data sets with paired shotgun and 16S sequences are too small in sample size for classification) data sets. Kappa statistic is used here as measure of accuracy to assess the agreement between predicted classification and reality. (a) The average accuracies using as input the OTUs clustered at 97% sequence similarity, the functional profile predicted from the OTUs using PICRUSt or the annotation from shotgun metagenomic sequences (for HMP data set only). (b) The pairwise comparisons between the accuracies using those three inputs as predictive features. The error bars indicate 95% confidence interval.
See this image and copyright information in PMC

References

    1. Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–214. - PMC - PubMed
    1. Knights D, Costello EK, Knight R. Supervised classification of human microbiota. FEMS Microbiol Rev. 2011;35:343–359. - PubMed
    1. Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe. 2011;10:292–296. - PMC - PubMed
    1. Kuhn M. Building predictive models in R using the caret package. J Stat Softw. 2008;28:1–26.
    1. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814–821. - PMC - PubMed

Publication types