Use of direct gradient analysis to uncover biological hypotheses in 16s survey data and beyond

Sci Rep. 2012;2:774. doi: 10.1038/srep00774. Epub 2012 Oct 26.


This study investigated the use of direct gradient analysis of bacterial 16S pyrosequencing surveys to identify relevant bacterial community signals in the midst of a "noisy" background, and to facilitate hypothesis-testing both within and beyond the realm of ecological surveys. The results, utilizing 3 different real world data sets, demonstrate the utility of adding direct gradient analysis to any analysis that draws conclusions from indirect methods such as Principal Component Analysis (PCA) and Principal Coordinates Analysis (PCoA). Direct gradient analysis produces testable models, and can identify significant patterns in the midst of noisy data. Additionally, we demonstrate that direct gradient analysis can be used with other kinds of multivariate data sets, such as flow cytometric data, to identify differentially expressed populations. The results of this study demonstrate the utility of direct gradient analysis in microbial ecology and in other areas of research where large multivariate data sets are involved.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Bacteria / genetics
  • Cecum / microbiology
  • Humans
  • Lung / microbiology
  • Metagenome
  • Mice
  • Principal Component Analysis
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / metabolism*


  • RNA, Ribosomal, 16S