Issue 3, 2015

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

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?

Article information

Article type
Perspective
Submitted
21 Jan 2015
Accepted
24 Mar 2015
First published
25 Mar 2015
This article is Open Access
Creative Commons BY-NC license

Environ. Sci.: Water Res. Technol., 2015,1, 272-278

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. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements