Jump to main content
Jump to site search

Issue 3, 2015
Previous Article Next Article

Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?

Author affiliations

Abstract

There is increasing interest in using meta-omics association studies to investigate contaminant biotransformations. The general strategy is to characterize the complete set of genes, transcripts, or enzymes from in situ environmental communities and use the abundances of particular genes, transcripts, or enzymes to establish associations with the communities' potential to biotransform one or more contaminants. The associations can then be used to generate hypotheses about the underlying biological causes of particular biotransformations. While meta-omics association studies are undoubtedly powerful, they have a tendency to generate large numbers of non-causal associations, making it potentially difficult to identify the genes, transcripts, or enzymes that cause or promote a particular biotransformation. In this perspective, we describe general scenarios that could lead to pervasive non-causal associations or conceal causal associations. We next explore our own published data for evidence of pervasive non-causal associations. Finally, we evaluate whether causal associations could be identified despite the discussed limitations. Analysis of our own published data suggests that, despite their limitations, meta-omics association studies might still be useful for improving our understanding and predicting the contaminant biotransformation capacities of microbial communities.

Graphical abstract: Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?

Back to tab navigation

Publication details

The article was received on 21 Jan 2015, accepted on 24 Mar 2015 and first published on 25 Mar 2015


Article type: Perspective
DOI: 10.1039/C5EW00016E
Citation: Environ. Sci.: Water Res. Technol., 2015,1, 272-278
  • Open access: Creative Commons BY-NC license
  •   Request permissions

    Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?

    D. R. Johnson, D. E. Helbling, Y. Men and K. Fenner, Environ. Sci.: Water Res. Technol., 2015, 1, 272
    DOI: 10.1039/C5EW00016E

    This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material and it is not used for commercial purposes.

    Reproduced material should be attributed as follows:

    • For reproduction of material from NJC:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
    • For reproduction of material from PCCP:
      [Original citation] - Published by the PCCP Owner Societies.
    • For reproduction of material from PPS:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
    • For reproduction of material from all other RSC journals:
      [Original citation] - Published by The Royal Society of Chemistry.

    Information about reproducing material from RSC articles with different licences is available on our Permission Requests page.

Search articles by author

Spotlight

Advertisements